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loadScript ../../jsmol/j2s/core/corejmol.z.js

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../../jsmol/j2s/core/corejmol.z.js

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4289774814,4294967264,4278255360,4281519410,4294635750,4294902015,4286578688,4284927402,4278190285,4290401747,4287852763,4282168177,4286277870,4278254234,4282962380,4291237253,4279834992,4294311930,4294960353,4294960309,4294958765,4278190208,4294833638,4286611456,4285238819,4294944E3,4294919424,4292505814,4293847210,4288215960,4289720046,4292571283,4294963157,4294957753,4291659071,4294951115,4292714717,4289781990,4286578816,4294901760,4290547599,4282477025,4287317267,4294606962,4294222944,4281240407,

4294964718,4288696877,4290822336,4287090411,4285160141,4285563024,4294966010,4278255487,4282811060,4291998860,4278222976,4292394968,4294927175,4282441936,4293821166,4294303411,4294967295,4294309365,4294967040,4288335154,4289714175,4281240407,4288217011,4286611584,4286611584,4294945723,4294919424,4294375029]);b.mapJavaScriptColors=new java.util.Hashtable;for(b=JU.CU.colorNames.length;0<=--b;)JU.CU.mapJavaScriptColors.put(JU.CU.colorNames[b],Integer.$valueOf(JU.CU.colorArgbs[b]))});u("JU");C(null,"JU.DF",

["JU.PT","$.SB"],function(){var b=H(JU,"DF",null);b.setUseNumberLocalization=c(b,"setUseNumberLocalization",function(a){JU.DF.useNumberLocalization[0]=a?Boolean.TRUE:Boolean.FALSE},"~B");b.formatDecimalDbl=c(b,"formatDecimalDbl",function(a,d){return 2147483647==d||-Infinity==a||Infinity==a||Double.isNaN(a)?""+a:JU.DF.formatDecimal(a,d)},"~N,~N");b.formatDecimal=c(b,"formatDecimal",function(a,d){if(-Infinity==a||(Infinity==a||Double.isNaN(a))||2147483647==d)return""+a;var g=0>a;g&&(a=-a);var b;if(0>

d){d=-d;d>JU.DF.formattingStrings.length&&(d=JU.DF.formattingStrings.length);if(0==a)return JU.DF.formattingStrings[d-1]+"E+0";var c;1>Math.abs(a)?(b=100,c=1E-100*a):(b=-100,c=1E100*a);c=(""+c).toUpperCase();var e=c.indexOf("E");0>e?c=""+a:(b=JU.PT.parseInt(c.substring(e+(c.indexOf("E+")==e?2:1)))+b,c=JU.PT.parseFloat(c.substring(0,e)),c=JU.DF.formatDecimal(c,d-1),c.startsWith("10.")&&(c=JU.DF.formatDecimal(1,d-1),b++));return(g?"-":"")+c+"E"+(0<=b?"+":"")+b}d>=JU.DF.formattingStrings.length&&(d=

JU.DF.formattingStrings.length-1);c=(""+a).toUpperCase();b=c.indexOf(".");if(0>b)return(g?"-":"")+c+JU.DF.formattingStrings[d].substring(1);e=c.indexOf("E-");0<e&&(b=JU.PT.parseInt(c.substring(e+1)),c="0."+"0000000000000000000000000000000000000000".substring(0,-b-1)+c.substring(0,1)+c.substring(2,e),b=1);e=c.indexOf("E");0<e&&(b=JU.PT.parseInt(c.substring(e+1)),c=c.substring(0,1)+c.substring(2,e)+"0000000000000000000000000000000000000000",c=c.substring(0,b+1)+"."+c.substring(b+1),b=c.indexOf("."));

var e=c.length,h=d+b+1;if(h<e&&"5"<=c.charAt(h))return JU.DF.formatDecimal((g?-1:1)*(a+JU.DF.formatAdds[d]),d);var k=c.substring(0,0==d?b:++b),h=JU.SB.newS(k);g&&(k.equals("0.")&&d+2<=e&&c.substring(2,2+d).equals("0000000000000000000000000000000000000000".substring(0,d)))&&(g=!1);for(k=0;k<d;k++,b++)b<e?h.appendC(c.charAt(b)):h.appendC("0");c=(g?"-":"")+h;return Boolean.TRUE.equals(JU.DF.useNumberLocalization[0])?c:c.$replace(",",".")},"~N,~N");b.formatDecimalTrimmed=c(b,"formatDecimalTrimmed",function(a,

d){for(var g=JU.DF.formatDecimalDbl(a,d),b=g.length-1;0<=b&&"0"==g.charAt(b);)b--;return g.substring(0,b+1)},"~N,~N");b.formatDecimalTrimmed0=c(b,"formatDecimalTrimmed0",function(a,d){for(var g=JU.DF.formatDecimalDbl(a,d),b=g.length-1,c=g.indexOf(".")+1;b>c&&"0"==g.charAt(b);)b--;return g.substring(0,b+1)},"~N,~N");b.formattingStrings=w(-1,"0 0.0 0.00 0.000 0.0000 0.00000 0.000000 0.0000000 0.00000000 0.000000000 0.0000000000 0.00000000000 0.000000000000".split(" "));b.formatAdds=R(-1,[0.5,0.05,0.005,

5E-4,5E-5,5E-6,5E-7,5E-8,5E-9,5E-10,5E-11,5E-12,5E-13]);b.useNumberLocalization=w(-1,[Boolean.TRUE])});u("JU");C(["java.lang.Enum"],"JU.Encoding",null,function(){var b=H(JU,"Encoding",Enum);I(b,"NONE",0,[]);I(b,"UTF8",1,[]);I(b,"UTF_16BE",2,[]);I(b,"UTF_16LE",3,[]);I(b,"UTF_32BE",4,[]);I(b,"UTF_32LE",5,[])});u("JU");C(["java.util.ArrayList"],"JU.Lst",null,function(){var b=H(JU,"Lst",java.util.ArrayList);c(b,"addLast",function(a){return this.add1(a)},"~O");j(b,"add",function(a,d){return this.add2(a,

d)},"~N,~O");c(b,"removeItemAt",function(a){return this._removeItemAt(a)},"~N");c(b,"removeObj",function(a){return this._removeObject(a)},"~O")});u("JU");n=v(function(){this.m22=this.m21=this.m20=this.m12=this.m11=this.m10=this.m02=this.m01=this.m00=0;r(this,arguments)},JU,"M34",null);c(n,"setAA33",function(b){var a=b.x,d=b.y,g=b.z;b=b.angle;var l=Math.sqrt(a*a+d*d+g*g),l=1/l,a=a*l,d=d*l,g=g*l,c=Math.cos(b);b=Math.sin(b);l=1-c;this.m00=c+a*a*l;this.m11=c+d*d*l;this.m22=c+g*g*l;var c=a*d*l,e=g*b;this.m01=

c-e;this.m10=c+e;c=a*g*l;e=d*b;this.m02=c+e;this.m20=c-e;c=d*g*l;e=a*b;this.m12=c-e;this.m21=c+e},"JU.A4");c(n,"rotate",function(b){this.rotate2(b,b)},"JU.T3");c(n,"rotate2",function(b,a){a.set(this.m00*b.x+this.m01*b.y+this.m02*b.z,this.m10*b.x+this.m11*b.y+this.m12*b.z,this.m20*b.x+this.m21*b.y+this.m22*b.z)},"JU.T3,JU.T3");c(n,"setM33",function(b){this.m00=b.m00;this.m01=b.m01;this.m02=b.m02;this.m10=b.m10;this.m11=b.m11;this.m12=b.m12;this.m20=b.m20;this.m21=b.m21;this.m22=b.m22},"JU.M34");c(n,

"clear33",function(){this.m00=this.m01=this.m02=this.m10=this.m11=this.m12=this.m20=this.m21=this.m22=0});c(n,"set33",function(b,a,d){switch(b){case 0:switch(a){case 0:this.m00=d;return;case 1:this.m01=d;return;case 2:this.m02=d;return}break;case 1:switch(a){case 0:this.m10=d;return;case 1:this.m11=d;return;case 2:this.m12=d;return}break;case 2:switch(a){case 0:this.m20=d;return;case 1:this.m21=d;return;case 2:this.m22=d;return}}this.err()},"~N,~N,~N");c(n,"get33",function(b,a){switch(b){case 0:switch(a){case 0:return this.m00;

case 1:return this.m01;case 2:return this.m02}break;case 1:switch(a){case 0:return this.m10;case 1:return this.m11;case 2:return this.m12}break;case 2:switch(a){case 0:return this.m20;case 1:return this.m21;case 2:return this.m22}}this.err();return 0},"~N,~N");c(n,"setRow33",function(b,a){switch(b){case 0:this.m00=a[0];this.m01=a[1];this.m02=a[2];break;case 1:this.m10=a[0];this.m11=a[1];this.m12=a[2];break;case 2:this.m20=a[0];this.m21=a[1];this.m22=a[2];break;default:this.err()}},"~N,~A");c(n,"getRow33",

function(b,a){switch(b){case 0:a[0]=this.m00;a[1]=this.m01;a[2]=this.m02;return;case 1:a[0]=this.m10;a[1]=this.m11;a[2]=this.m12;return;case 2:a[0]=this.m20;a[1]=this.m21;a[2]=this.m22;return}this.err()},"~N,~A");c(n,"setColumn33",function(b,a){switch(b){case 0:this.m00=a[0];this.m10=a[1];this.m20=a[2];break;case 1:this.m01=a[0];this.m11=a[1];this.m21=a[2];break;case 2:this.m02=a[0];this.m12=a[1];this.m22=a[2];break;default:this.err()}},"~N,~A");c(n,"getColumn33",function(b,a){switch(b){case 0:a[0]=

this.m00;a[1]=this.m10;a[2]=this.m20;break;case 1:a[0]=this.m01;a[1]=this.m11;a[2]=this.m21;break;case 2:a[0]=this.m02;a[1]=this.m12;a[2]=this.m22;break;default:this.err()}},"~N,~A");c(n,"add33",function(b){this.m00+=b.m00;this.m01+=b.m01;this.m02+=b.m02;this.m10+=b.m10;this.m11+=b.m11;this.m12+=b.m12;this.m20+=b.m20;this.m21+=b.m21;this.m22+=b.m22},"JU.M34");c(n,"sub33",function(b){this.m00-=b.m00;this.m01-=b.m01;this.m02-=b.m02;this.m10-=b.m10;this.m11-=b.m11;this.m12-=b.m12;this.m20-=b.m20;this.m21-=

b.m21;this.m22-=b.m22},"JU.M34");c(n,"mul33",function(b){this.m00*=b;this.m01*=b;this.m02*=b;this.m10*=b;this.m11*=b;this.m12*=b;this.m20*=b;this.m21*=b;this.m22*=b},"~N");c(n,"transpose33",function(){var b=this.m01;this.m01=this.m10;this.m10=b;b=this.m02;this.m02=this.m20;this.m20=b;b=this.m12;this.m12=this.m21;this.m21=b});c(n,"setXRot",function(b){var a=Math.cos(b);b=Math.sin(b);this.m00=1;this.m10=this.m02=this.m01=0;this.m11=a;this.m12=-b;this.m20=0;this.m21=b;this.m22=a},"~N");c(n,"setYRot",

function(b){var a=Math.cos(b);b=Math.sin(b);this.m00=a;this.m01=0;this.m02=b;this.m10=0;this.m11=1;this.m12=0;this.m20=-b;this.m21=0;this.m22=a},"~N");c(n,"setZRot",function(b){var a=Math.cos(b);b=Math.sin(b);this.m00=a;this.m01=-b;this.m02=0;this.m10=b;this.m11=a;this.m21=this.m20=this.m12=0;this.m22=1},"~N");c(n,"determinant3",function(){return this.m00*(this.m11*this.m22-this.m21*this.m12)-this.m01*(this.m10*this.m22-this.m20*this.m12)+this.m02*(this.m10*this.m21-this.m20*this.m11)});c(n,"err",

function(){throw new ArrayIndexOutOfBoundsException("matrix column/row out of bounds");});u("JU");C(["JU.M34"],"JU.M3",["JU.T3"],function(){var b=H(JU,"M3",JU.M34,java.io.Serializable);b.newA9=c(b,"newA9",function(a){var d=new JU.M3;d.setA(a);return d},"~A");b.newM3=c(b,"newM3",function(a){var d=new JU.M3;if(null==a)return d.setScale(1),d;d.m00=a.m00;d.m01=a.m01;d.m02=a.m02;d.m10=a.m10;d.m11=a.m11;d.m12=a.m12;d.m20=a.m20;d.m21=a.m21;d.m22=a.m22;return d},"JU.M3");c(b,"setScale",function(a){this.clear33();

this.m00=this.m11=this.m22=a},"~N");c(b,"setM3",function(a){this.setM33(a)},"JU.M34");c(b,"setA",function(a){this.m00=a[0];this.m01=a[1];this.m02=a[2];this.m10=a[3];this.m11=a[4];this.m12=a[5];this.m20=a[6];this.m21=a[7];this.m22=a[8]},"~A");c(b,"setElement",function(a,d,g){this.set33(a,d,g)},"~N,~N,~N");c(b,"getElement",function(a,d){return this.get33(a,d)},"~N,~N");c(b,"setRow",function(a,d,g,b){switch(a){case 0:this.m00=d;this.m01=g;this.m02=b;break;case 1:this.m10=d;this.m11=g;this.m12=b;break;

case 2:this.m20=d;this.m21=g;this.m22=b;break;default:this.err()}},"~N,~N,~N,~N");c(b,"setRowV",function(a,d){switch(a){case 0:this.m00=d.x;this.m01=d.y;this.m02=d.z;break;case 1:this.m10=d.x;this.m11=d.y;this.m12=d.z;break;case 2:this.m20=d.x;this.m21=d.y;this.m22=d.z;break;default:this.err()}},"~N,JU.T3");c(b,"setRowA",function(a,d){this.setRow33(a,d)},"~N,~A");j(b,"getRow",function(a,d){this.getRow33(a,d)},"~N,~A");c(b,"setColumn3",function(a,d,g,b){switch(a){case 0:this.m00=d;this.m10=g;this.m20=

b;break;case 1:this.m01=d;this.m11=g;this.m21=b;break;case 2:this.m02=d;this.m12=g;this.m22=b;break;default:this.err()}},"~N,~N,~N,~N");c(b,"setColumnV",function(a,d){switch(a){case 0:this.m00=d.x;this.m10=d.y;this.m20=d.z;break;case 1:this.m01=d.x;this.m11=d.y;this.m21=d.z;break;case 2:this.m02=d.x;this.m12=d.y;this.m22=d.z;break;default:this.err()}},"~N,JU.T3");c(b,"getColumnV",function(a,d){switch(a){case 0:d.x=this.m00;d.y=this.m10;d.z=this.m20;break;case 1:d.x=this.m01;d.y=this.m11;d.z=this.m21;

break;case 2:d.x=this.m02;d.y=this.m12;d.z=this.m22;break;default:this.err()}},"~N,JU.T3");c(b,"setColumnA",function(a,d){this.setColumn33(a,d)},"~N,~A");c(b,"getColumn",function(a,d){this.getColumn33(a,d)},"~N,~A");c(b,"add",function(a){this.add33(a)},"JU.M3");c(b,"sub",function(a){this.sub33(a)},"JU.M3");c(b,"transpose",function(){this.transpose33()});c(b,"transposeM",function(a){this.setM33(a);this.transpose33()},"JU.M3");c(b,"invertM",function(a){this.setM33(a);this.invert()},"JU.M3");c(b,"invert",

function(){var a=this.determinant3();0!=a&&(a=1/a,this.set9(this.m11*this.m22-this.m12*this.m21,this.m02*this.m21-this.m01*this.m22,this.m01*this.m12-this.m02*this.m11,this.m12*this.m20-this.m10*this.m22,this.m00*this.m22-this.m02*this.m20,this.m02*this.m10-this.m00*this.m12,this.m10*this.m21-this.m11*this.m20,this.m01*this.m20-this.m00*this.m21,this.m00*this.m11-this.m01*this.m10),this.scale(a))});c(b,"setAsXRotation",function(a){this.setXRot(a);return this},"~N");c(b,"setAsYRotation",function(a){this.setYRot(a);

return this},"~N");c(b,"setAsZRotation",function(a){this.setZRot(a);return this},"~N");c(b,"scale",function(a){this.mul33(a)},"~N");c(b,"mul",function(a){this.mul2(this,a)},"JU.M3");c(b,"mul2",function(a,d){this.set9(a.m00*d.m00+a.m01*d.m10+a.m02*d.m20,a.m00*d.m01+a.m01*d.m11+a.m02*d.m21,a.m00*d.m02+a.m01*d.m12+a.m02*d.m22,a.m10*d.m00+a.m11*d.m10+a.m12*d.m20,a.m10*d.m01+a.m11*d.m11+a.m12*d.m21,a.m10*d.m02+a.m11*d.m12+a.m12*d.m22,a.m20*d.m00+a.m21*d.m10+a.m22*d.m20,a.m20*d.m01+a.m21*d.m11+a.m22*d.m21,

a.m20*d.m02+a.m21*d.m12+a.m22*d.m22)},"JU.M3,JU.M3");j(b,"equals",function(a){return!y(a,"JU.M3")?!1:this.m00==a.m00&&this.m01==a.m01&&this.m02==a.m02&&this.m10==a.m10&&this.m11==a.m11&&this.m12==a.m12&&this.m20==a.m20&&this.m21==a.m21&&this.m22==a.m22},"~O");j(b,"hashCode",function(){return JU.T3.floatToIntBits(this.m00)^JU.T3.floatToIntBits(this.m01)^JU.T3.floatToIntBits(this.m02)^JU.T3.floatToIntBits(this.m10)^JU.T3.floatToIntBits(this.m11)^JU.T3.floatToIntBits(this.m12)^JU.T3.floatToIntBits(this.m20)^

JU.T3.floatToIntBits(this.m21)^JU.T3.floatToIntBits(this.m22)});c(b,"setZero",function(){this.clear33()});c(b,"set9",function(a,d,g,b,c,e,h,k,m){this.m00=a;this.m01=d;this.m02=g;this.m10=b;this.m11=c;this.m12=e;this.m20=h;this.m21=k;this.m22=m},"~N,~N,~N,~N,~N,~N,~N,~N,~N");j(b,"toString",function(){return"[\n ["+this.m00+"\t"+this.m01+"\t"+this.m02+"]\n ["+this.m10+"\t"+this.m11+"\t"+this.m12+"]\n ["+this.m20+"\t"+this.m21+"\t"+this.m22+"] ]"});c(b,"setAA",function(a){this.setAA33(a);return this},

"JU.A4");c(b,"setAsBallRotation",function(a,d,g){var b=Math.sqrt(d*d+g*g),c=b*a;if(0==c)return this.setScale(1),!1;a=Math.cos(c);c=Math.sin(c);g=-g/b;d/=b;b=a-1;this.m00=1+b*g*g;this.m01=this.m10=b*g*d;this.m20=-(this.m02=c*g);this.m11=1+b*d*d;this.m21=-(this.m12=c*d);this.m22=a;return!0},"~N,~N,~N");c(b,"isRotation",function(){return 0.001>Math.abs(this.determinant3()-1)})});u("JU");C(["JU.M34"],"JU.M4",["JU.T3"],function(){var b=v(function(){this.m33=this.m32=this.m31=this.m30=this.m23=this.m13=

this.m03=0;r(this,arguments)},JU,"M4",JU.M34);b.newA16=c(b,"newA16",function(a){var d=new JU.M4;d.m00=a[0];d.m01=a[1];d.m02=a[2];d.m03=a[3];d.m10=a[4];d.m11=a[5];d.m12=a[6];d.m13=a[7];d.m20=a[8];d.m21=a[9];d.m22=a[10];d.m23=a[11];d.m30=a[12];d.m31=a[13];d.m32=a[14];d.m33=a[15];return d},"~A");b.newM4=c(b,"newM4",function(a){var d=new JU.M4;if(null==a)return d.setIdentity(),d;d.setToM3(a);d.m03=a.m03;d.m13=a.m13;d.m23=a.m23;d.m30=a.m30;d.m31=a.m31;d.m32=a.m32;d.m33=a.m33;return d},"JU.M4");b.newMV=

c(b,"newMV",function(a,d){var g=new JU.M4;g.setMV(a,d);return g},"JU.M3,JU.T3");c(b,"setZero",function(){this.clear33();this.m03=this.m13=this.m23=this.m30=this.m31=this.m32=this.m33=0});c(b,"setIdentity",function(){this.setZero();this.m00=this.m11=this.m22=this.m33=1});c(b,"setM4",function(a){this.setM33(a);this.m03=a.m03;this.m13=a.m13;this.m23=a.m23;this.m30=a.m30;this.m31=a.m31;this.m32=a.m32;this.m33=a.m33;return this},"JU.M4");c(b,"setMV",function(a,d){this.setM33(a);this.setTranslation(d);

this.m33=1},"JU.M3,JU.T3");c(b,"setToM3",function(a){this.setM33(a);this.m03=this.m13=this.m23=this.m30=this.m31=this.m32=0;this.m33=1},"JU.M34");c(b,"setToAA",function(a){this.setIdentity();this.setAA33(a)},"JU.A4");c(b,"setA",function(a){this.m00=a[0];this.m01=a[1];this.m02=a[2];this.m03=a[3];this.m10=a[4];this.m11=a[5];this.m12=a[6];this.m13=a[7];this.m20=a[8];this.m21=a[9];this.m22=a[10];this.m23=a[11];this.m30=a[12];this.m31=a[13];this.m32=a[14];this.m33=a[15]},"~A");c(b,"setTranslation",function(a){this.m03=

a.x;this.m13=a.y;this.m23=a.z},"JU.T3");c(b,"setElement",function(a,d,g){if(3>a&&3>d)this.set33(a,d,g);else{(3<a||3<d)&&this.err();switch(a){case 0:this.m03=g;return;case 1:this.m13=g;return;case 2:this.m23=g;return}switch(d){case 0:this.m30=g;break;case 1:this.m31=g;break;case 2:this.m32=g;break;case 3:this.m33=g}}},"~N,~N,~N");c(b,"getElement",function(a,d){if(3>a&&3>d)return this.get33(a,d);if(3<a||3<d)return this.err(),0;switch(a){case 0:return this.m03;case 1:return this.m13;case 2:return this.m23;

default:switch(d){case 0:return this.m30;case 1:return this.m31;case 2:return this.m32;default:return this.m33}}},"~N,~N");c(b,"getTranslation",function(a){a.x=this.m03;a.y=this.m13;a.z=this.m23},"JU.T3");c(b,"getRotationScale",function(a){a.m00=this.m00;a.m01=this.m01;a.m02=this.m02;a.m10=this.m10;a.m11=this.m11;a.m12=this.m12;a.m20=this.m20;a.m21=this.m21;a.m22=this.m22},"JU.M3");c(b,"setRotationScale",function(a){this.m00=a.m00;this.m01=a.m01;this.m02=a.m02;this.m10=a.m10;this.m11=a.m11;this.m12=

a.m12;this.m20=a.m20;this.m21=a.m21;this.m22=a.m22},"JU.M3");c(b,"setRowA",function(a,d){3>a&&this.setRow33(a,d);switch(a){case 0:this.m03=d[3];return;case 1:this.m13=d[3];return;case 2:this.m23=d[3];return;case 3:this.m30=d[0];this.m31=d[1];this.m32=d[2];this.m33=d[3];return}this.err()},"~N,~A");j(b,"getRow",function(a,d){3>a&&this.getRow33(a,d);switch(a){case 0:d[3]=this.m03;return;case 1:d[3]=this.m13;return;case 2:d[3]=this.m23;return;case 3:d[0]=this.m30;d[1]=this.m31;d[2]=this.m32;d[3]=this.m33;

return}this.err()},"~N,~A");c(b,"setColumn4",function(a,d,g,b,c){0==a?(this.m00=d,this.m10=g,this.m20=b,this.m30=c):1==a?(this.m01=d,this.m11=g,this.m21=b,this.m31=c):2==a?(this.m02=d,this.m12=g,this.m22=b,this.m32=c):3==a?(this.m03=d,this.m13=g,this.m23=b,this.m33=c):this.err()},"~N,~N,~N,~N,~N");c(b,"setColumnA",function(a,d){3>a&&this.setColumn33(a,d);switch(a){case 0:this.m30=d[3];break;case 1:this.m31=d[3];break;case 2:this.m32=d[3];break;case 3:this.m03=d[0];this.m13=d[1];this.m23=d[2];this.m33=

d[3];break;default:this.err()}},"~N,~A");c(b,"getColumn",function(a,d){3>a&&this.getColumn33(a,d);switch(a){case 0:d[3]=this.m30;break;case 1:d[3]=this.m31;break;case 2:d[3]=this.m32;break;case 3:d[0]=this.m03;d[1]=this.m13;d[2]=this.m23;d[3]=this.m33;break;default:this.err()}},"~N,~A");c(b,"sub",function(a){this.sub33(a);this.m03-=a.m03;this.m13-=a.m13;this.m23-=a.m23;this.m30-=a.m30;this.m31-=a.m31;this.m32-=a.m32;this.m33-=a.m33},"JU.M4");c(b,"add",function(a){this.m03+=a.x;this.m13+=a.y;this.m23+=

a.z},"JU.T3");c(b,"transpose",function(){this.transpose33();var a=this.m03;this.m03=this.m30;this.m30=a;a=this.m13;this.m13=this.m31;this.m31=a;a=this.m23;this.m23=this.m32;this.m32=a});c(b,"invert",function(){var a=this.determinant4();if(0==a)return this;a=1/a;this.set(this.m11*(this.m22*this.m33-this.m23*this.m32)+this.m12*(this.m23*this.m31-this.m21*this.m33)+this.m13*(this.m21*this.m32-this.m22*this.m31),this.m21*(this.m02*this.m33-this.m03*this.m32)+this.m22*(this.m03*this.m31-this.m01*this.m33)+

this.m23*(this.m01*this.m32-this.m02*this.m31),this.m31*(this.m02*this.m13-this.m03*this.m12)+this.m32*(this.m03*this.m11-this.m01*this.m13)+this.m33*(this.m01*this.m12-this.m02*this.m11),this.m01*(this.m13*this.m22-this.m12*this.m23)+this.m02*(this.m11*this.m23-this.m13*this.m21)+this.m03*(this.m12*this.m21-this.m11*this.m22),this.m12*(this.m20*this.m33-this.m23*this.m30)+this.m13*(this.m22*this.m30-this.m20*this.m32)+this.m10*(this.m23*this.m32-this.m22*this.m33),this.m22*(this.m00*this.m33-this.m03*

this.m30)+this.m23*(this.m02*this.m30-this.m00*this.m32)+this.m20*(this.m03*this.m32-this.m02*this.m33),this.m32*(this.m00*this.m13-this.m03*this.m10)+this.m33*(this.m02*this.m10-this.m00*this.m12)+this.m30*(this.m03*this.m12-this.m02*this.m13),this.m02*(this.m13*this.m20-this.m10*this.m23)+this.m03*(this.m10*this.m22-this.m12*this.m20)+this.m00*(this.m12*this.m23-this.m13*this.m22),this.m13*(this.m20*this.m31-this.m21*this.m30)+this.m10*(this.m21*this.m33-this.m23*this.m31)+this.m11*(this.m23*this.m30-

this.m20*this.m33),this.m23*(this.m00*this.m31-this.m01*this.m30)+this.m20*(this.m01*this.m33-this.m03*this.m31)+this.m21*(this.m03*this.m30-this.m00*this.m33),this.m33*(this.m00*this.m11-this.m01*this.m10)+this.m30*(this.m01*this.m13-this.m03*this.m11)+this.m31*(this.m03*this.m10-this.m00*this.m13),this.m03*(this.m11*this.m20-this.m10*this.m21)+this.m00*(this.m13*this.m21-this.m11*this.m23)+this.m01*(this.m10*this.m23-this.m13*this.m20),this.m10*(this.m22*this.m31-this.m21*this.m32)+this.m11*(this.m20*

this.m32-this.m22*this.m30)+this.m12*(this.m21*this.m30-this.m20*this.m31),this.m20*(this.m02*this.m31-this.m01*this.m32)+this.m21*(this.m00*this.m32-this.m02*this.m30)+this.m22*(this.m01*this.m30-this.m00*this.m31),this.m30*(this.m02*this.m11-this.m01*this.m12)+this.m31*(this.m00*this.m12-this.m02*this.m10)+this.m32*(this.m01*this.m10-this.m00*this.m11),this.m00*(this.m11*this.m22-this.m12*this.m21)+this.m01*(this.m12*this.m20-this.m10*this.m22)+this.m02*(this.m10*this.m21-this.m11*this.m20));this.scale(a);

return this});c(b,"set",function(a,d,g,b,c,e,h,k,m,A,j,q,x,s,G,M){this.m00=a;this.m01=d;this.m02=g;this.m03=b;this.m10=c;this.m11=e;this.m12=h;this.m13=k;this.m20=m;this.m21=A;this.m22=j;this.m23=q;this.m30=x;this.m31=s;this.m32=G;this.m33=M},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");c(b,"determinant4",function(){return(this.m00*this.m11-this.m01*this.m10)*(this.m22*this.m33-this.m23*this.m32)-(this.m00*this.m12-this.m02*this.m10)*(this.m21*this.m33-this.m23*this.m31)+(this.m00*this.m13-

this.m03*this.m10)*(this.m21*this.m32-this.m22*this.m31)+(this.m01*this.m12-this.m02*this.m11)*(this.m20*this.m33-this.m23*this.m30)-(this.m01*this.m13-this.m03*this.m11)*(this.m20*this.m32-this.m22*this.m30)+(this.m02*this.m13-this.m03*this.m12)*(this.m20*this.m31-this.m21*this.m30)});c(b,"scale",function(a){this.mul33(a);this.m03*=a;this.m13*=a;this.m23*=a;this.m30*=a;this.m31*=a;this.m32*=a;this.m33*=a},"~N");c(b,"mul",function(a){this.mul2(this,a)},"JU.M4");c(b,"mul2",function(a,d){this.set(a.m00*

d.m00+a.m01*d.m10+a.m02*d.m20+a.m03*d.m30,a.m00*d.m01+a.m01*d.m11+a.m02*d.m21+a.m03*d.m31,a.m00*d.m02+a.m01*d.m12+a.m02*d.m22+a.m03*d.m32,a.m00*d.m03+a.m01*d.m13+a.m02*d.m23+a.m03*d.m33,a.m10*d.m00+a.m11*d.m10+a.m12*d.m20+a.m13*d.m30,a.m10*d.m01+a.m11*d.m11+a.m12*d.m21+a.m13*d.m31,a.m10*d.m02+a.m11*d.m12+a.m12*d.m22+a.m13*d.m32,a.m10*d.m03+a.m11*d.m13+a.m12*d.m23+a.m13*d.m33,a.m20*d.m00+a.m21*d.m10+a.m22*d.m20+a.m23*d.m30,a.m20*d.m01+a.m21*d.m11+a.m22*d.m21+a.m23*d.m31,a.m20*d.m02+a.m21*d.m12+a.m22*

d.m22+a.m23*d.m32,a.m20*d.m03+a.m21*d.m13+a.m22*d.m23+a.m23*d.m33,a.m30*d.m00+a.m31*d.m10+a.m32*d.m20+a.m33*d.m30,a.m30*d.m01+a.m31*d.m11+a.m32*d.m21+a.m33*d.m31,a.m30*d.m02+a.m31*d.m12+a.m32*d.m22+a.m33*d.m32,a.m30*d.m03+a.m31*d.m13+a.m32*d.m23+a.m33*d.m33)},"JU.M4,JU.M4");c(b,"transform",function(a){this.transform2(a,a)},"JU.T4");c(b,"transform2",function(a,d){d.set4(this.m00*a.x+this.m01*a.y+this.m02*a.z+this.m03*a.w,this.m10*a.x+this.m11*a.y+this.m12*a.z+this.m13*a.w,this.m20*a.x+this.m21*a.y+

this.m22*a.z+this.m23*a.w,this.m30*a.x+this.m31*a.y+this.m32*a.z+this.m33*a.w)},"JU.T4,JU.T4");c(b,"rotTrans",function(a){this.rotTrans2(a,a)},"JU.T3");c(b,"rotTrans2",function(a,d){d.set(this.m00*a.x+this.m01*a.y+this.m02*a.z+this.m03,this.m10*a.x+this.m11*a.y+this.m12*a.z+this.m13,this.m20*a.x+this.m21*a.y+this.m22*a.z+this.m23);return d},"JU.T3,JU.T3");c(b,"setAsXYRotation",function(a){this.setIdentity();var d=Math.cos(a);a=Math.sin(a);this.m22=d;this.m23=-a;this.m32=a;this.m33=d;return this},

"~N");c(b,"setAsYZRotation",function(a){this.setIdentity();var d=Math.cos(a);a=Math.sin(a);this.m00=d;this.m03=-a;this.m30=a;this.m33=d;return this},"~N");c(b,"setAsXZRotation",function(a){this.setIdentity();var d=Math.cos(a);a=Math.sin(a);this.m11=d;this.m13=-a;this.m31=a;this.m33=d;return this},"~N");j(b,"equals",function(a){return!y(a,"JU.M4")?!1:this.m00==a.m00&&this.m01==a.m01&&this.m02==a.m02&&this.m03==a.m03&&this.m10==a.m10&&this.m11==a.m11&&this.m12==a.m12&&this.m13==a.m13&&this.m20==a.m20&&

this.m21==a.m21&&this.m22==a.m22&&this.m23==a.m23&&this.m30==a.m30&&this.m31==a.m31&&this.m32==a.m32&&this.m33==a.m33},"~O");j(b,"hashCode",function(){return JU.T3.floatToIntBits(this.m00)^JU.T3.floatToIntBits(this.m01)^JU.T3.floatToIntBits(this.m02)^JU.T3.floatToIntBits(this.m03)^JU.T3.floatToIntBits(this.m10)^JU.T3.floatToIntBits(this.m11)^JU.T3.floatToIntBits(this.m12)^JU.T3.floatToIntBits(this.m13)^JU.T3.floatToIntBits(this.m20)^JU.T3.floatToIntBits(this.m21)^JU.T3.floatToIntBits(this.m22)^JU.T3.floatToIntBits(this.m23)^

JU.T3.floatToIntBits(this.m30)^JU.T3.floatToIntBits(this.m31)^JU.T3.floatToIntBits(this.m32)^JU.T3.floatToIntBits(this.m33)});j(b,"toString",function(){return"[\n ["+this.m00+"\t"+this.m01+"\t"+this.m02+"\t"+this.m03+"]\n ["+this.m10+"\t"+this.m11+"\t"+this.m12+"\t"+this.m13+"]\n ["+this.m20+"\t"+this.m21+"\t"+this.m22+"\t"+this.m23+"]\n ["+this.m30+"\t"+this.m31+"\t"+this.m32+"\t"+this.m33+"] ]"});c(b,"round",function(a){this.m00=this.rnd(this.m00,a);this.m01=this.rnd(this.m01,a);this.m02=this.rnd(this.m02,

a);this.m03=this.rnd(this.m03,a);this.m10=this.rnd(this.m10,a);this.m11=this.rnd(this.m11,a);this.m12=this.rnd(this.m12,a);this.m13=this.rnd(this.m13,a);this.m20=this.rnd(this.m20,a);this.m21=this.rnd(this.m21,a);this.m22=this.rnd(this.m22,a);this.m23=this.rnd(this.m23,a);this.m30=this.rnd(this.m30,a);this.m31=this.rnd(this.m31,a);this.m32=this.rnd(this.m32,a);this.m33=this.rnd(this.m33,a);return this},"~N");c(b,"rnd",function(a,d){return Math.abs(a)<d?0:a},"~N,~N")});u("JU");C(["java.io.OutputStream",

"javajs.api.GenericOutputChannel"],"JU.OC",["java.io.BufferedWriter","$.ByteArrayOutputStream","$.OutputStreamWriter","JU.Base64","$.SB"],function(){var b=v(function(){this.bw=this.fileName=this.bytePoster=null;this.isLocalFile=!1;this.byteCount=0;this.closed=this.isCanceled=!1;this.type=this.sb=this.os=null;this.$isBase64=!1;this.bytes=this.os0=null;this.bigEndian=!0;r(this,arguments)},JU,"OC",java.io.OutputStream,javajs.api.GenericOutputChannel);z(b,function(){L(this,JU.OC,[])});z(b,function(a){L(this,

JU.OC,[]);this.setParams(null,a,!1,null)},"~S");c(b,"setParams",function(a,d,g,b){this.bytePoster=a;if(this.$isBase64=";base64,".equals(d))d=null,this.os0=b,b=null;this.fileName=d;this.os=b;this.isLocalFile=null!=d&&!JU.OC.isRemote(d);g&&(!this.$isBase64&&null!=b)&&(this.bw=new java.io.BufferedWriter(new java.io.OutputStreamWriter(b)));return this},"javajs.api.BytePoster,~S,~B,java.io.OutputStream");j(b,"isBigEndian",function(){return this.bigEndian});c(b,"setBigEndian",function(a){this.bigEndian=

a},"~B");c(b,"setBytes",function(a){this.bytes=a;return this},"~A");c(b,"getFileName",function(){return this.fileName});c(b,"getName",function(){return null==this.fileName?null:this.fileName.substring(this.fileName.lastIndexOf("/")+1)});c(b,"getByteCount",function(){return this.byteCount});c(b,"setType",function(a){this.type=a},"~S");c(b,"getType",function(){return this.type});c(b,"append",function(a){try{if(null!=this.bw)this.bw.write(a);else if(null==this.os)null==this.sb&&(this.sb=new JU.SB),this.sb.append(a);

else{var d=a.getBytes();this.os.write(d,0,d.length);this.byteCount+=d.length;return this}}catch(g){if(!F(g,"java.io.IOException"))throw g;}this.byteCount+=a.length;return this},"~S");j(b,"reset",function(){this.sb=null;this.initOS()});c(b,"initOS",function(){if(null!=this.sb){var a=this.sb.toString();this.reset();this.append(a)}else{try{this.os=null,null==this.os&&(this.os=new java.io.ByteArrayOutputStream),null!=this.bw&&(this.bw.close(),this.bw=new java.io.BufferedWriter(new java.io.OutputStreamWriter(this.os)))}catch(d){if(F(d,

Exception))System.out.println(d.toString());else throw d;}this.byteCount=0}});j(b,"writeByteAsInt",function(a){null==this.os&&this.initOS();this.os.writeByteAsInt(a);this.byteCount++},"~N");j(b,"write",function(a,d,g){null==this.os&&this.initOS();0>g&&(g=a.length-d);try{this.os.write(a,d,g)}catch(b){if(!F(b,"java.io.IOException"))throw b;}this.byteCount+=g},"~A,~N,~N");j(b,"writeShort",function(a){this.isBigEndian()?(this.writeByteAsInt(a>>8),this.writeByteAsInt(a)):(this.writeByteAsInt(a),this.writeByteAsInt(a>>

8))},"~N");j(b,"writeLong",function(a){this.isBigEndian()?(this.writeInt(a>>32&4294967295),this.writeInt(a&4294967295)):(this.writeByteAsInt(a>>56),this.writeByteAsInt(a>>48),this.writeByteAsInt(a>>40),this.writeByteAsInt(a>>32),this.writeByteAsInt(a>>24),this.writeByteAsInt(a>>16),this.writeByteAsInt(a>>8),this.writeByteAsInt(a))},"~N");c(b,"cancel",function(){this.isCanceled=!0;this.closeChannel()});j(b,"closeChannel",function(){if(this.closed)return null;try{null!=this.bw?(this.bw.flush(),this.bw.close()):

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c(b,"isBase64",function(a){return 0==a.indexOf(";base64,")},"JU.SB");b.isCompoundDocumentS=c(b,"isCompoundDocumentS",function(a){return JU.Rdr.isCompoundDocumentB(JU.Rdr.getMagic(a,8))},"java.io.InputStream");b.isCompoundDocumentB=c(b,"isCompoundDocumentB",function(a){return 8<=a.length&&208==(a[0]&255)&&207==(a[1]&255)&&17==(a[2]&255)&&224==(a[3]&255)&&161==(a[4]&255)&&177==(a[5]&255)&&26==(a[6]&255)&&225==(a[7]&255)},"~A");b.isBZip2S=c(b,"isBZip2S",function(a){return JU.Rdr.isBZip2B(JU.Rdr.getMagic(a,

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a&&2<=a.length&&125==(a[0]&255)&&113==(a[1]&255)},"~A");b.isMessagePackS=c(b,"isMessagePackS",function(a){return JU.Rdr.isMessagePackB(JU.Rdr.getMagic(a,2))},"java.io.InputStream");b.isMessagePackB=c(b,"isMessagePackB",function(a){var g;return null!=a&&1<=a.length&&(222==(g=a[0]&255)||128==(g&224)&&80!=a[1])},"~A");b.isPngZipStream=c(b,"isPngZipStream",function(a){return JU.Rdr.isPngZipB(JU.Rdr.getMagic(a,55))},"java.io.InputStream");b.isPngZipB=c(b,"isPngZipB",function(a){return 0==a[50]&&80==a[51]&&

78==a[52]&&71==a[53]&&74==a[54]},"~A");b.isZipS=c(b,"isZipS",function(a){return JU.Rdr.isZipB(JU.Rdr.getMagic(a,4))},"java.io.InputStream");b.isZipB=c(b,"isZipB",function(a){return 4<=a.length&&80==a[0]&&75==a[1]&&3==a[2]&&4==a[3]},"~A");b.getMagic=c(b,"getMagic",function(a,g){var b=264<g?P(g,0):null==JU.Rdr.b264?JU.Rdr.b264=P(265,0):JU.Rdr.b264;a.resetStream();try{b[264]=-1,a.mark(g+1),a.read(b,0,g)<g&&(b[0]=b[264]=0)}catch(c){if(!F(c,"java.io.IOException"))throw c;}try{a.reset()}catch(e){if(!F(e,

"java.io.IOException"))throw e;}return b},"java.io.InputStream,~N");b.guessMimeTypeForBytes=c(b,"guessMimeTypeForBytes",function(a){switch(2>a.length?-1:a[1]){case 0:return"image/jpg";case 73:return"image/gif";case 77:return"image/BMP";case 80:return"image/png";default:return"image/unknown"}},"~A");b.getBIS=c(b,"getBIS",function(a){return new java.io.BufferedInputStream(new java.io.ByteArrayInputStream(a))},"~A");b.getBR=c(b,"getBR",function(a){return new java.io.BufferedReader(new java.io.StringReader(a))},

"~S");b.getUnzippedInputStream=c(b,"getUnzippedInputStream",function(a,g){for(;JU.Rdr.isGzipS(g);)g=new java.io.BufferedInputStream(a.newGZIPInputStream(g));return g},"javajs.api.GenericZipTools,java.io.BufferedInputStream");b.getUnzippedInputStreamBZip2=c(b,"getUnzippedInputStreamBZip2",function(a,g){for(;JU.Rdr.isBZip2S(g);)g=new java.io.BufferedInputStream(a.newBZip2InputStream(g));return g},"javajs.api.GenericZipTools,java.io.BufferedInputStream");b.getBytesFromSB=c(b,"getBytesFromSB",function(a){return JU.Rdr.isBase64(a)?

JU.Base64.decodeBase64(a.substring(8)):a.toBytes(0,-1)},"JU.SB");b.getStreamAsBytes=c(b,"getStreamAsBytes",function(a,g){for(var b=P(1024,0),c=null==g?P(4096,0):null,e=0,h=0;0<(e=a.read(b,0,1024));)h+=e,null==g?(h>=c.length&&(c=JU.AU.ensureLengthByte(c,2*h)),System.arraycopy(b,0,c,h-e,e)):g.write(b,0,e);a.close();return null==g?JU.AU.arrayCopyByte(c,h):h+" bytes"},"java.io.BufferedInputStream,JU.OC");b.getBufferedReader=c(b,"getBufferedReader",function(a,g){if(JU.Rdr.getUTFEncodingForStream(a)===

JU.Encoding.NONE)return new JU.Rdr.StreamReader(a,g);var b=JU.Rdr.getLimitedStreamBytes(a,-1);a.close();return JU.Rdr.getBR(null==g?JU.Rdr.fixUTF(b):String.instantialize(b,g))},"java.io.BufferedInputStream,~S");b.getLimitedStreamBytes=c(b,"getLimitedStreamBytes",function(a,g){var b=0<g&&1024>g?g:1024,c=P(b,0),e=P(0>g?4096:g,0),h=0,k=0;for(0>g&&(g=2147483647);k<g&&0<(h=a.read(c,0,b));)k+=h,k>e.length&&(e=JU.AU.ensureLengthByte(e,2*k)),System.arraycopy(c,0,e,k-h,h),2147483647!=g&&k+b>e.length&&(b=e.length-

k);if(k==e.length)return e;c=P(k,0);System.arraycopy(e,0,c,0,k);return c},"java.io.InputStream,~N");b.streamToUTF8String=c(b,"streamToUTF8String",function(a){var g=Array(1);try{JU.Rdr.readAllAsString(JU.Rdr.getBufferedReader(a,"UTF-8"),-1,!0,g,0)}catch(b){if(!F(b,"java.io.IOException"))throw b;}return g[0]},"java.io.BufferedInputStream");b.readAllAsString=c(b,"readAllAsString",function(a,g,b,c,e){try{var h=JU.SB.newN(8192),k;if(0>g){if(k=a.readLine(),b||null!=k&&0>k.indexOf("\x00")&&(4!=k.length||

65533!=k.charAt(0).charCodeAt(0)||1!=k.indexOf("PNG")))for(h.append(k).appendC("\n");null!=(k=a.readLine());)h.append(k).appendC("\n")}else{b=0;for(var m;b<g&&null!=(k=a.readLine());){if(g-b<(m=k.length)+1)k=k.substring(0,g-b-1);h.append(k).appendC("\n");b+=m+1}}a.close();c[e]=h.toString();return!0}catch(A){if(F(A,Exception))return c[e]=A.toString(),!1;throw A;}},"java.io.BufferedReader,~N,~B,~A,~N");b.getPngZipPointAndCount=c(b,"getPngZipPointAndCount",function(a,g){a.mark(75);try{var b=JU.Rdr.getLimitedStreamBytes(a,

74);a.reset();for(var c=0,e=64,h=1;54<--e;h*=10)c+=(b[e]-48)*h;for(var k=0,e=74,h=1;64<--e;h*=10)k+=(b[e]-48)*h;g[0]=c;g[1]=k}catch(m){g[1]=0}},"java.io.BufferedInputStream,~A");b.getPngZipStream=c(b,"getPngZipStream",function(a,g){if(!JU.Rdr.isPngZipStream(a))return a;var b=P(0,0);a.mark(75);try{var c=E(2,0);JU.Rdr.getPngZipPointAndCount(a,c);if(0!=c[1]){for(var e=c[0];0<e;)e-=a.skip(e);if(!g)return a;b=JU.Rdr.getLimitedStreamBytes(a,c[1])}}catch(h){}finally{try{g&&a.close()}catch(k){if(!F(k,Exception))throw k;

}}return JU.Rdr.getBIS(b)},"java.io.BufferedInputStream,~B");b.getZipRoot=c(b,"getZipRoot",function(a){var g=a.indexOf("|");return 0>g?a:a.substring(0,g)},"~S");b.isTar=c(b,"isTar",function(a){a=JU.Rdr.getMagic(a,264);return-1==a[264]&&117==(a[257]&255)&&115==(a[258]&255)&&116==(a[259]&255)&&97==(a[260]&255)&&114==(a[261]&255)},"java.io.BufferedInputStream");b.streamToBytes=c(b,"streamToBytes",function(a){var g=JU.Rdr.getLimitedStreamBytes(a,-1);a.close();return g},"java.io.InputStream");b.streamToString=

c(b,"streamToString",function(a){return String.instantialize(JU.Rdr.streamToBytes(a))},"java.io.InputStream");b.isBinary=c(b,"isBinary",function(a,g){var b=JU.Rdr.getMagic(a,g);if(-1==JU.Rdr.b264[264])for(var c=0;c<g;c++)if(9>b[c])return!0;return!1},"java.io.BufferedInputStream,~N");var a=v(function(){this.stream=null;r(this,arguments)},JU.Rdr,"StreamReader",java.io.BufferedReader);z(a,function(a,g){L(this,JU.Rdr.StreamReader,[new java.io.InputStreamReader(a,null==g?"UTF-8":g)]);this.stream=a},"java.io.BufferedInputStream,~S");

c(a,"getStream",function(){try{this.stream.reset()}catch(a){if(!F(a,"java.io.IOException"))throw a;}return this.stream});b.b264=null});u("JU");n=v(function(){this.z=this.y=this.x=0;r(this,arguments)},JU,"T3d",null,java.io.Serializable);c(n,"set",function(b,a,d){this.x=b;this.y=a;this.z=d},"~N,~N,~N");c(n,"setA",function(b){this.x=b[0];this.y=b[1];this.z=b[2]},"~A");c(n,"setT",function(b){this.x=b.x;this.y=b.y;this.z=b.z},"JU.T3d");c(n,"add2",function(b,a){this.x=b.x+a.x;this.y=b.y+a.y;this.z=b.z+

a.z},"JU.T3d,JU.T3d");c(n,"add",function(b){this.x+=b.x;this.y+=b.y;this.z+=b.z},"JU.T3d");c(n,"sub2",function(b,a){this.x=b.x-a.x;this.y=b.y-a.y;this.z=b.z-a.z},"JU.T3d,JU.T3d");c(n,"sub",function(b){this.x-=b.x;this.y-=b.y;this.z-=b.z},"JU.T3d");c(n,"scale",function(b){this.x*=b;this.y*=b;this.z*=b},"~N");c(n,"scaleAdd",function(b,a,d){this.x=b*a.x+d.x;this.y=b*a.y+d.y;this.z=b*a.z+d.z},"~N,JU.T3d,JU.T3d");c(n,"scaleAdd2",function(b,a,d){this.x=b*a.x+d.x;this.y=b*a.y+d.y;this.z=b*a.z+d.z},"~N,JU.T3d,JU.T3d");

j(n,"hashCode",function(){var b=JU.T3d.doubleToLongBits0(this.x),a=JU.T3d.doubleToLongBits0(this.y),d=JU.T3d.doubleToLongBits0(this.z);return b^b>>32^a^a>>32^d^d>>32});n.doubleToLongBits0=c(n,"doubleToLongBits0",function(b){return 0==b?0:Double.doubleToLongBits(b)},"~N");j(n,"equals",function(b){return!y(b,"JU.T3d")?!1:this.x==b.x&&this.y==b.y&&this.z==b.z},"~O");j(n,"toString",function(){return"{"+this.x+", "+this.y+", "+this.z+"}"});u("JU");C(["JU.T3d"],"JU.V3d",null,function(){var b=H(JU,"V3d",

JU.T3d);c(b,"cross",function(a,d){this.set(a.y*d.z-a.z*d.y,a.z*d.x-a.x*d.z,a.x*d.y-a.y*d.x)},"JU.V3d,JU.V3d");c(b,"normalize",function(){var a=this.length();this.x/=a;this.y/=a;this.z/=a});c(b,"angle",function(a){var d=this.y*a.z-this.z*a.y,g=this.z*a.x-this.x*a.z,b=this.x*a.y-this.y*a.x,d=Math.sqrt(d*d+g*g+b*b);return Math.abs(Math.atan2(d,this.dot(a)))},"JU.V3d");c(b,"dot",function(a){return this.x*a.x+this.y*a.y+this.z*a.z},"JU.V3d");c(b,"lengthSquared",function(){return this.x*this.x+this.y*this.y+

this.z*this.z});c(b,"length",function(){return Math.sqrt(this.lengthSquared())})});u("J.adapter.readers.molxyz");C(["J.adapter.smarter.AtomSetCollectionReader"],"J.adapter.readers.molxyz.MolReader","java.util.Hashtable JU.BS $.Lst $.PT J.adapter.smarter.Atom J.api.JmolAdapter JU.Logger".split(" "),function(){var b=v(function(){this.haveAtomSerials=!1;this.allow2D=!0;this.iatom0=0;this.vr=null;this.atomCount=0;this.bsDeleted=this.atomData=null;this.is3D=this.fixN=this.haveNonzeroZ=!1;this.nC=this.nH=

this.nDouble=0;r(this,arguments)},J.adapter.readers.molxyz,"MolReader",J.adapter.smarter.AtomSetCollectionReader);j(b,"initializeReader",function(){this.fixN=this.checkFilterKey("FIXN")});j(b,"checkLine",function(){var a=this.line.startsWith("$MDL");if(a){if(this.discardLinesUntilStartsWith("$HDR"),this.rd(),null==this.line)return JU.Logger.warn("$HDR not found in MDL RG file"),this.continuing=!1}else if(this.line.equals("M END"))return!0;if(this.doGetModel(++this.modelNumber,null)&&(this.iatom0=

this.asc.ac,this.processMolSdHeader(),this.processCtab(a),this.vr=null,this.isLastModel(this.modelNumber)))return this.continuing=!1;null!=this.line&&0>this.line.indexOf("$$$$")&&this.discardLinesUntilStartsWith("$$$$");return!0});j(b,"finalizeSubclassReader",function(){this.finalizeReaderMR()});c(b,"finalizeReaderMR",function(){this.fixN&&this.addJmolScript("{search('[Nv4+0,nv4+0]')}.formalCharge=1;{search('{[Ov1-0]}[Nv4+1,nv4+1]')}.formalCharge=-1;");this.check2D3D();null!=this.bsDeleted&&this.asc.getBSAtoms(-1).andNot(this.bsDeleted);

this.isTrajectory=!1;this.finalizeReaderASCR()});c(b,"check2D3D",function(){this.haveNonzeroZ?this.is2D&&(this.is2D=this.optimize2D=!1):!this.is2D&&!this.is3D&&(0<this.nC&&0==this.nH&&0!=this.nDouble)&&(this.is2D=!0);if(this.is2D){if(!this.allow2D)throw new Exception("File is 2D, not 3D");this.set2D()}});c(b,"processMolSdHeader",function(){var a="",d=this.line.trim();this.asc.setCollectionName(d);a+=this.line+"\n";this.rd();if(null!=this.line){var a=a+(this.line+"\n"),g=22<=this.line.length?this.line.substring(20,

22):null;this.is3D="3D".equals(g);this.is2D=!this.is3D&&("2D".equals(g)||this.line.startsWith("JME "));this.rd();null!=this.line&&(this.line=this.line.trim(),a+=this.line+"\n",JU.Logger.info(a),this.checkCurrentLineForScript(),this.asc.setInfo("fileHeader",a),this.newAtomSet(d))}});c(b,"processCtab",function(a){a&&this.discardLinesUntilStartsWith("$CTAB");null!=this.rd()&&(0<=this.line.indexOf("V3000")?(this.optimize2D=this.is2D&&!this.noHydrogens,this.vr=this.getInterface("J.adapter.readers.molxyz.V3000Rdr").set(this),

this.discardLinesUntilContains("COUNTS"),this.vr.readAtomsAndBonds(this.getTokens())):this.readAtomsAndBonds(this.parseIntRange(this.line,0,3),this.parseIntRange(this.line,3,6)),this.applySymmetryAndSetTrajectory())},"~B");c(b,"readAtomsAndBonds",function(a,d){this.atomCount=a;for(var g=0;g<a;++g){this.rd();var b=this.line.length,c,e,h,k,m=0,A=0,j=-2147483648;e=this.parseFloatRange(this.line,0,10);h=this.parseFloatRange(this.line,10,20);k=this.parseFloatRange(this.line,20,30);34>b?c=this.line.substring(31).trim():

(c=this.line.substring(31,34).trim(),c.equals("H1")&&(c="H",A=1),39<=b&&(b=this.parseIntRange(this.line,36,39),1<=b&&7>=b&&(m=4-b),b=this.parseIntRange(this.line,34,36),0!=b&&(-3<=b&&4>=b)&&(A=J.api.JmolAdapter.getNaturalIsotope(J.api.JmolAdapter.getElementNumber(c))+b),-2147483648==j&&this.haveAtomSerials&&(j=g+1)));this.addMolAtom(j,A,c,m,e,h,k)}this.asc.setModelInfoForSet("dimension",this.is2D?"2D":"3D",this.asc.iSet);this.rd();this.line.startsWith("V ")&&this.readAtomValues();0==d&&this.asc.setNoAutoBond();

for(g=0;g<d;++g){0<g&&this.rd();h=0;c=this.line.substring(0,3).trim();e=this.line.substring(3,6).trim();k=this.parseIntRange(this.line,6,9);if((this.is2D||!this.is3D)&&1==k&&12<=this.line.length)h=this.parseIntRange(this.line,9,12);0!=h&&!this.is3D&&(this.is2D=!0);k=this.fixOrder(k,h);this.haveAtomSerials?this.asc.addNewBondFromNames(c,e,k):this.asc.addNewBondWithOrder(this.iatom0+this.parseIntStr(c)-1,this.iatom0+this.parseIntStr(e)-1,k)}g=new java.util.Hashtable;c=new JU.Lst;for(this.rd();null!=

this.line&&0!=this.line.indexOf("$$$$");)0==this.line.indexOf(">")?this.readMolData(g,c):this.line.startsWith("M ISO")?this.readIsotopes():this.rd();null!=this.atomData&&(e=g.get("atom_value_name"),g.put(null==e?"atom_values":e.toString(),this.atomData));g.isEmpty()||(this.asc.setCurrentModelInfo("molDataKeys",c),this.asc.setCurrentModelInfo("molData",g))},"~N,~N");c(b,"readAtomValues",function(){this.atomData=Array(this.atomCount);for(var a=this.atomData.length;0<=--a;)this.atomData[a]="";for(;0==

this.line.indexOf("V ");){a=this.parseIntAt(this.line,3);if(1>a||a>this.atomCount){JU.Logger.error("V nnn does not evalute to a valid atom number: "+a);break}var d=this.line.substring(6).trim();this.atomData[a-1]=d;this.rd()}});c(b,"readIsotopes",function(){var a=this.parseIntAt(this.line,6);try{for(var d=this.asc.getLastAtomSetAtomIndex(),g=0,b=9;g<a;g++){var c=this.parseIntAt(this.line,b),e=this.asc.atoms[c+d-1],h=this.parseIntAt(this.line,b+4),b=b+8,k=JU.PT.replaceAllCharacters(e.elementSymbol,

"0123456789","");17==h&&k.equals("C")?e.elementSymbol="N":5==h&&k.equals("H")?this.deleteAtom(e):e.elementSymbol=""+h+k}}catch(m){}this.rd()});c(b,"deleteAtom",function(a){null==this.bsDeleted&&(this.bsDeleted=new JU.BS);this.bsDeleted.set(a.index)},"J.adapter.smarter.Atom");c(b,"readMolData",function(a,d){for(var g=this.asc.atoms,b=JU.PT.trim(this.line,"> <").toLowerCase(),c="",e=null;null!=this.rd()&&!this.line.equals("$$$$")&&0<this.line.length;)c+=81==this.line.length&&"+"==this.line.charAt(80)?

this.line.substring(0,80):this.line+"\n";c=JU.PT.trim(c,"\n");JU.Logger.info(b+":"+JU.PT.esc(c));a.put(b,c);d.addLast(b);var h=0;if(b.toUpperCase().contains("_PARTIAL_CHARGES")){try{for(var e=JU.PT.parseFloatArray(c),k=this.asc.getLastAtomSetAtomIndex(),m=this.asc.ac;k<m;k++)g[k].partialCharge=0;for(var A=0,k=D(e[A++]);0<=--k;){var j=D(e[A++])+this.iatom0-1,q=e[A++];g[j].partialCharge=q;h++}}catch(x){k=this.asc.getLastAtomSetAtomIndex();for(m=this.asc.ac;k<m;k++)g[k].partialCharge=0;JU.Logger.error("error reading "+

b+" field -- partial charges cleared")}JU.Logger.info(h+" partial charges read")}else if(b.toUpperCase().contains("ATOM_NAMES")){h=0;try{for(var s=JU.PT.getTokens(c),A=0,k=this.parseIntStr(s[A++]);0<=--k;){for(var G;-2147483648==(G=this.parseIntStr(s[A++])););var j=G+this.iatom0-1,M=s[A++];M.equals(".")||(g[j].atomName=M);h++}}catch(N){JU.Logger.error("error reading "+b+" field")}JU.Logger.info(h+" atom names read")}},"java.util.Map,JU.Lst");c(b,"addMolAtom",function(a,d,g,b,c,e,h){"H".equals(g)?

this.nH++:"C".equals(g)&&this.nC++;this.haveNonzeroZ=(new Boolean(this.haveNonzeroZ|0!=h)).valueOf();switch(d){case 0:break;case 1:g="1H";break;case 2:g="2H";break;case 3:g="3H";break;default:g=d+g}d=new J.adapter.smarter.Atom;d.elementSymbol=g;d.formalCharge=b;this.setAtomCoordXYZ(d,c,e,h);-2147483648==a?this.asc.addAtom(d):(this.haveAtomSerials=!0,d.atomSerial=a,this.asc.addAtomWithMappedSerialNumber(d));return d},"~N,~N,~S,~N,~N,~N,~N");c(b,"fixOrder",function(a,d){switch(a){default:case 0:case -10:return 1;

case 1:switch(d){case 1:return this.is2D=!0,1025;case 3:case 6:return this.is2D=!0,1041;case 2:case 4:return this.is2D=!0,1057}break;case 2:case 3:this.nDouble++;break;case 4:return 515;case 5:return 66;case 6:return 513;case 7:return 514;case 8:case 9:return 33;case 14:return 4;case 15:return 5;case 16:return 6}return a},"~N,~N");c(b,"addMolBond",function(a,d,g,b){g=this.fixOrder(g,b);return this.haveAtomSerials?this.asc.addNewBondFromNames(a,d,g):this.asc.addNewBondWithOrder(this.iatom0+this.parseIntStr(a)-

1,this.iatom0+this.parseIntStr(d)-1,g)},"~S,~S,~N,~N")});u("J.adapter.readers.molxyz");C(["J.adapter.smarter.AtomSetCollectionReader"],"J.adapter.readers.molxyz.XyzReader",["JU.Logger"],function(){var b=H(J.adapter.readers.molxyz,"XyzReader",J.adapter.smarter.AtomSetCollectionReader);j(b,"checkLine",function(){var a=this.parseIntStr(this.line);if(-2147483648==a)return this.continuing=!1;this.vibrationNumber=++this.modelNumber;if(0>=this.desiredVibrationNumber?this.doGetModel(this.modelNumber,null):

this.doGetVibration(this.vibrationNumber)){this.rd();this.checkCurrentLineForScript();this.asc.newAtomSet();var d=this.line.trim();this.readAtoms(a);this.applySymmetryAndSetTrajectory();this.asc.setAtomSetName(d);if(this.isLastModel(this.modelNumber))return this.continuing=!1}else this.skipAtomSet(a);this.discardLinesUntilNonBlank();return!1});j(b,"finalizeSubclassReader",function(){this.isTrajectory=!1;this.finalizeReaderASCR()});c(b,"skipAtomSet",function(a){for(this.rd();0<=--a;)this.rd()},"~N");

c(b,"readAtoms",function(a){for(var d=0;d<a;++d){this.rd();var g=this.getTokens();if(4>g.length)JU.Logger.warn("line cannot be read for XYZ atom data: "+this.line);else{var b=this.addAtomXYZSymName(g,1,null,null);this.setElementAndIsotope(b,g[0]);var c=4;switch(g.length){case 4:continue;case 5:case 6:case 8:case 9:if(0<=g[4].indexOf("."))b.partialCharge=this.parseFloatStr(g[4]);else{var e=this.parseIntStr(g[4]);-2147483648!=e&&(b.formalCharge=e)}switch(g.length){case 5:continue;case 6:b.radius=this.parseFloatStr(g[5]);

continue;case 9:b.atomSerial=this.parseIntStr(g[8])}c++;default:var e=this.parseFloatStr(g[c++]),h=this.parseFloatStr(g[c++]),g=this.parseFloatStr(g[c++]);if(Float.isNaN(e)||Float.isNaN(h)||Float.isNaN(g))continue;this.asc.addVibrationVector(b.index,e,h,g)}}}},"~N")});u("J.adapter.smarter");C(["JU.P3"],"J.adapter.smarter.Atom",["JU.AU","$.Lst","$.V3"],function(){var b=v(function(){this.index=this.atomSetIndex=0;this.bsSymmetry=null;this.atomSite=0;this.elementSymbol=null;this.elementNumber=-1;this.atomName=

null;this.formalCharge=-2147483648;this.partialCharge=NaN;this.vib=null;this.bfactor=NaN;this.foccupancy=1;this.radius=NaN;this.isHetero=!1;this.atomSerial=-2147483648;this.chainID=0;this.bondingRadius=NaN;this.altLoc="\x00";this.group3=null;this.sequenceNumber=-2147483648;this.insertionCode="\x00";this.typeSymbol=this.tensors=this.anisoBorU=null;this.part=0;r(this,arguments)},J.adapter.smarter,"Atom",JU.P3,Cloneable);z(b,function(){L(this,J.adapter.smarter.Atom,[]);this.set(NaN,NaN,NaN)});c(b,"addTensor",

function(a,d,g){if(null==a)return null;if(g||null==this.tensors)this.tensors=new JU.Lst;this.tensors.addLast(a);null!=d&&a.setType(d);return a},"JU.Tensor,~S,~B");c(b,"getClone",function(){var a;try{a=this.clone()}catch(d){if(F(d,"CloneNotSupportedException"))return null;throw d;}null!=this.vib&&(a.vib=y(this.vib,"JU.Vibration")?this.vib.clone():JU.V3.newV(a.vib));null!=this.anisoBorU&&(a.anisoBorU=JU.AU.arrayCopyF(this.anisoBorU,-1));if(null!=this.tensors){a.tensors=new JU.Lst;for(var g=this.tensors.size();0<=

--g;)a.tensors.addLast(this.tensors.get(g).copyTensor())}return a});c(b,"getElementSymbol",function(){if(null==this.elementSymbol&&null!=this.atomName){for(var a=this.atomName.length,d=0,g=String.fromCharCode(0);d<a&&!J.adapter.smarter.Atom.isValidSymChar1(g=this.atomName.charAt(d));)++d;switch(a-d){case 0:break;default:if(a=this.atomName.charAt(d+1),J.adapter.smarter.Atom.isValidSymNoCase(g,a)){this.elementSymbol=""+g+a;break}case 1:J.adapter.smarter.Atom.isValidSym1(g)&&(this.elementSymbol=""+g)}}return this.elementSymbol});

b.isValidSym1=c(b,"isValidSym1",function(a){return"A"<=a&&"Z">=a&&0>J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-65]},"~S");b.isValidSym2=c(b,"isValidSym2",function(a,d){return"A"<=a&&"Z">=a&&"a"<=d&&"z">=d&&0!=(J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-65]>>d.charCodeAt(0)-97&1)},"~S,~S");b.isValidSymNoCase=c(b,"isValidSymNoCase",function(a,d){return J.adapter.smarter.Atom.isValidSym2(a,"a">d?String.fromCharCode(d.charCodeAt(0)+32):d)},"~S,~S");b.isValidSymChar1=c(b,"isValidSymChar1",

function(a){return"A"<=a&&"Z">=a&&0!=J.adapter.smarter.Atom.elementCharMasks[a.charCodeAt(0)-65]},"~S");c(b,"copyTo",function(a,d){var g=d.newCloneAtom(this);g.setT(a);return g},"JU.P3,J.adapter.smarter.AtomSetCollection");b.elementCharMasks=E(-1,[1972292,-2147351151,-2146019271,-2130706430,1441792,-2147348464,25,-2147205008,-2147344384,0,-2147352576,1179905,548936,-2147434213,-2147221504,-2145759221,0,1056947,-2147339946,-2147477097,-2147483648,-2147483648,-2147483648,8388624,-2147483646,139264])});

u("J.adapter.smarter");C(["J.api.JmolAdapterAtomIterator"],"J.adapter.smarter.AtomIterator",["J.api.JmolAdapter"],function(){var b=v(function(){this.iatom=0;this.atom=null;this.ac=0;this.bsAtoms=this.atoms=null;r(this,arguments)},J.adapter.smarter,"AtomIterator",null,J.api.JmolAdapterAtomIterator);z(b,function(a){this.ac=a.ac;this.atoms=a.atoms;this.bsAtoms=a.bsAtoms;this.iatom=0},"J.adapter.smarter.AtomSetCollection");j(b,"hasNext",function(){if(this.iatom==this.ac)return!1;for(;null==(this.atom=

this.atoms[this.iatom++])||null!=this.bsAtoms&&!this.bsAtoms.get(this.atom.index);)if(this.iatom==this.ac)return!1;this.atoms[this.iatom-1]=null;return!0});j(b,"getAtomSetIndex",function(){return this.atom.atomSetIndex});j(b,"getSymmetry",function(){return this.atom.bsSymmetry});j(b,"getAtomSite",function(){return this.atom.atomSite+1});j(b,"getUniqueID",function(){return Integer.$valueOf(this.atom.index)});j(b,"getElementNumber",function(){return 0<this.atom.elementNumber?this.atom.elementNumber:

J.api.JmolAdapter.getElementNumber(this.atom.getElementSymbol())});j(b,"getAtomName",function(){return this.atom.atomName});j(b,"getFormalCharge",function(){return-2147483648==this.atom.formalCharge?0:this.atom.formalCharge});j(b,"getPartialCharge",function(){return this.atom.partialCharge});j(b,"getTensors",function(){return this.atom.tensors});j(b,"getRadius",function(){return this.atom.radius});j(b,"getBondRadius",function(){return this.atom.bondingRadius});j(b,"getVib",function(){return null==

this.atom.vib||Float.isNaN(this.atom.vib.z)?null:this.atom.vib});j(b,"getSeqID",function(){return null==this.atom.vib||!Float.isNaN(this.atom.vib.y)||1094713365!=this.atom.vib.z?0:D(this.atom.vib.x)});j(b,"getBfactor",function(){return this.atom.bfactor});j(b,"getOccupancy",function(){return 100*this.atom.foccupancy});j(b,"getIsHetero",function(){return this.atom.isHetero});j(b,"getSerial",function(){return this.atom.atomSerial});j(b,"getChainID",function(){return this.atom.chainID});j(b,"getAltLoc",

function(){return J.api.JmolAdapter.canonizeAlternateLocationID(this.atom.altLoc)});j(b,"getGroup3",function(){return this.atom.group3});j(b,"getSequenceNumber",function(){return this.atom.sequenceNumber});j(b,"getInsertionCode",function(){return J.api.JmolAdapter.canonizeInsertionCode(this.atom.insertionCode)});j(b,"getXYZ",function(){return this.atom});j(b,"getElement",function(){return this.getElementNumber()&127});j(b,"getIsotope",function(){return this.getElementNumber()>>7});j(b,"getPart",function(){return this.atom.part})});

u("J.adapter.smarter");C(["java.util.Hashtable"],"J.adapter.smarter.AtomSetCollection","java.util.Collections $.Properties JU.AU $.BS $.Lst $.P3 $.V3 J.adapter.smarter.Atom $.Bond $.SmarterJmolAdapter J.api.Interface JU.BSUtil $.Logger JV.JC".split(" "),function(){var b=v(function(){this.atoms=this.atomSetInfo=this.collectionName=this.fileTypeName=this.bsAtoms=this.reader=null;this.ac=0;this.bonds=null;this.bondCount=0;this.structures=null;this.atomSetCount=this.structureCount=0;this.iSet=-1;this.errorMessage=

this.atomSetAuxiliaryInfo=this.atomSetBondCounts=this.atomSetAtomCounts=this.atomSetAtomIndexes=this.atomSetNumbers=null;this.isTrajectory=this.coordinatesAreFractional=!1;this.trajectoryStepCount=0;this.trajectoryNames=this.vibrationSteps=this.trajectorySteps=null;this.allowMultiple=this.doFixPeriodic=!1;this.readerList=null;this.atomMapAnyCase=!1;this.fixedSite=0;this.bsStructuredModels=null;this.haveAnisou=!1;this.baseSymmetryAtomCount=0;this.crystalReaderLatticeOpsOnly=!1;this.xtalSymmetry=null;

this.bondIndex0=0;this.atomSymbolicMap=null;this.haveUnitCell=!1;this.vibScale=0;this.firstAtomToBond=-1;r(this,arguments)},J.adapter.smarter,"AtomSetCollection",null);Q(b,function(){this.atomSetInfo=new java.util.Hashtable;this.atoms=Array(256);this.bonds=Array(256);this.structures=Array(16);this.atomSetNumbers=E(16,0);this.atomSetAtomIndexes=E(16,0);this.atomSetAtomCounts=E(16,0);this.atomSetBondCounts=E(16,0);this.atomSetAuxiliaryInfo=Array(16);this.atomSymbolicMap=new java.util.Hashtable});z(b,

function(a,d,g,b){this.fileTypeName=a;this.reader=d;this.allowMultiple=null==d||0>d.desiredVibrationNumber;a=new java.util.Properties;a.put("PATH_KEY",".PATH");a.put("PATH_SEPARATOR",J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR);this.setInfo("properties",a);null!=d&&(a=d.htParams.get("appendToModelIndex"),null!=a&&this.setInfo("appendToModelIndex",a),a=d.htParams.get("fixedSite"),null!=a&&(this.fixedSite=a.intValue()));if(null!=g){d=0;this.readerList=new JU.Lst;for(b=0;b<g.length;b++)null!=

g[b]&&(0<g[b].ac||null!=g[b].reader&&g[b].reader.mustFinalizeModelSet)&&this.appendAtomSetCollection(d++,g[b]);1<d&&this.setInfo("isMultiFile",Boolean.TRUE)}else null!=b&&(this.setInfo("isMultiFile",Boolean.TRUE),this.appendAtomSetCollectionList(b))},"~S,J.adapter.smarter.AtomSetCollectionReader,~A,JU.Lst");c(b,"setCollectionName",function(a){if(null!=a&&0<(a=a.trim()).length)this.collectionName=a},"~S");c(b,"clearGlobalBoolean",function(a){this.atomSetInfo.remove(JV.JC.getBoolName(a))},"~N");c(b,

"setGlobalBoolean",function(a){this.setInfo(JV.JC.getBoolName(a),Boolean.TRUE)},"~N");c(b,"getGlobalBoolean",function(a){return this.atomSetInfo.get(JV.JC.getBoolName(a))===Boolean.TRUE},"~N");c(b,"appendAtomSetCollectionList",function(a){var d=a.size();if(0==d)this.errorMessage="No file found!";else for(var g=0;g<d;g++){var b=a.get(g);y(b,"JU.Lst")?this.appendAtomSetCollectionList(b):this.appendAtomSetCollection(g,b)}},"JU.Lst");c(b,"setTrajectory",function(){this.isTrajectory||(this.trajectorySteps=

new JU.Lst);this.isTrajectory=!0;var a=null==this.bsAtoms?this.ac:this.bsAtoms.cardinality();if(!(1>=a)){for(var d=Array(a),g=0<a&&null!=this.atoms[0].vib&&!Float.isNaN(this.atoms[0].vib.z),a=g?Array(a):null,b=0==this.trajectoryStepCount?null:this.trajectorySteps.get(this.trajectoryStepCount-1),c=0,e=0;c<this.ac;c++)if(null==this.bsAtoms||this.bsAtoms.get(c)){var h=JU.P3.newP(this.atoms[c]);this.doFixPeriodic&&null!=b&&(h=J.adapter.smarter.AtomSetCollection.fixPeriodic(h,b[c]));d[e]=h;g&&(a[e]=this.atoms[c].vib);

e++}if(g){if(null==this.vibrationSteps){this.vibrationSteps=new JU.Lst;for(c=0;c<this.trajectoryStepCount;c++)this.vibrationSteps.addLast(null)}this.vibrationSteps.addLast(a)}this.trajectorySteps.addLast(d);this.trajectoryStepCount++}});c(b,"appendAtomSetCollection",function(a,d){null!=d.reader&&d.reader.mustFinalizeModelSet&&this.readerList.addLast(d.reader);var g=this.ac;this.setInfo("loadState",d.atomSetInfo.get("loadState"));if(null!=d.bsAtoms){this.getBSAtoms(0);for(var b=d.bsAtoms.nextSetBit(0);0<=

b;b=d.bsAtoms.nextSetBit(b+1))this.bsAtoms.set(g+b)}for(var b=0,c=this.atomSetCount,e=0;e<d.atomSetCount;e++){this.newAtomSet();var h=(this.atomSetAuxiliaryInfo[this.iSet]=d.atomSetAuxiliaryInfo[e]).get("PDB_CONECT_firstAtom_count_max");null!=h&&(h[0]+=g);this.setCurrentModelInfo("title",d.collectionName);this.setAtomSetName(d.getAtomSetName(e));for(h=0;h<d.atomSetAtomCounts[e];h++)null!=this.bsAtoms&&this.bsAtoms.set(this.ac),this.newCloneAtom(d.atoms[b]),b++;this.atomSetNumbers[this.iSet]=0>a?this.iSet+

1:1E6*(a+1)+d.atomSetNumbers[e]}for(b=0;b<d.bondCount;b++)e=d.bonds[b],this.addNewBondWithOrder(e.atomIndex1+g,e.atomIndex2+g,e.order);for(b=JV.JC.globalBooleans.length;0<=--b;)d.getGlobalBoolean(b)&&this.setGlobalBoolean(b);for(b=0;b<d.structureCount;b++)g=d.structures[b],this.addStructure(g),g.modelStartEnd[0]+=c,g.modelStartEnd[1]+=c},"~N,J.adapter.smarter.AtomSetCollection");c(b,"setNoAutoBond",function(){this.setInfo("noAutoBond",Boolean.TRUE)});c(b,"freeze",function(a){1==this.atomSetCount&&

null==this.collectionName&&(this.collectionName=this.getAtomSetAuxiliaryInfoValue(0,"name"));a&&this.reverseAtomSets();1<this.trajectoryStepCount&&this.finalizeTrajectory();this.getList(!0);this.getList(!1);for(a=0;a<this.atomSetCount;a++)this.setModelInfoForSet("initialAtomCount",Integer.$valueOf(this.atomSetAtomCounts[a]),a),this.setModelInfoForSet("initialBondCount",Integer.$valueOf(this.atomSetBondCounts[a]),a)},"~B");c(b,"reverseAtomSets",function(){this.reverseArray(this.atomSetAtomIndexes);

this.reverseArray(this.atomSetNumbers);this.reverseArray(this.atomSetAtomCounts);this.reverseArray(this.atomSetBondCounts);J.adapter.smarter.AtomSetCollection.reverseList(this.trajectorySteps);J.adapter.smarter.AtomSetCollection.reverseList(this.trajectoryNames);J.adapter.smarter.AtomSetCollection.reverseList(this.vibrationSteps);this.reverseObject(this.atomSetAuxiliaryInfo);for(var a=0;a<this.ac;a++)this.atoms[a].atomSetIndex=this.atomSetCount-1-this.atoms[a].atomSetIndex;for(a=0;a<this.structureCount;a++){var d=

this.structures[a].modelStartEnd[0];0<=d&&(this.structures[a].modelStartEnd[0]=this.atomSetCount-1-this.structures[a].modelStartEnd[1],this.structures[a].modelStartEnd[1]=this.atomSetCount-1-d)}for(a=0;a<this.bondCount;a++)this.bonds[a].atomSetIndex=this.atomSetCount-1-this.atoms[this.bonds[a].atomIndex1].atomSetIndex;this.reverseSets(this.bonds,this.bondCount);for(var g=JU.AU.createArrayOfArrayList(this.atomSetCount),a=0;a<this.atomSetCount;a++)g[a]=new JU.Lst;for(a=0;a<this.ac;a++)g[this.atoms[a].atomSetIndex].addLast(this.atoms[a]);

for(var d=E(this.ac,0),b=this.ac,a=this.atomSetCount;0<=--a;)for(var c=g[a].size();0<=--c;){var e=this.atoms[--b]=g[a].get(c);d[e.index]=b;e.index=b}for(a=0;a<this.bondCount;a++)this.bonds[a].atomIndex1=d[this.bonds[a].atomIndex1],this.bonds[a].atomIndex2=d[this.bonds[a].atomIndex2];for(a=0;a<this.atomSetCount;a++)g=this.getAtomSetAuxiliaryInfoValue(a,"PDB_CONECT_firstAtom_count_max"),null!=g&&(g[0]=d[g[0]],g[1]=this.atomSetAtomCounts[a])});c(b,"reverseSets",function(a,d){for(var g=JU.AU.createArrayOfArrayList(this.atomSetCount),

b=0;b<this.atomSetCount;b++)g[b]=new JU.Lst;for(b=0;b<d;b++){if(0>a[b].atomSetIndex)return;g[a[b].atomSetIndex].addLast(a[b])}for(b=this.atomSetCount;0<=--b;)for(var c=g[b].size();0<=--c;)a[--d]=g[b].get(c)},"~A,~N");c(b,"reverseObject",function(a){for(var d=this.atomSetCount,g=B(d/2);0<=--g;)JU.AU.swap(a,g,d-1-g)},"~A");b.reverseList=c(b,"reverseList",function(a){null!=a&&java.util.Collections.reverse(a)},"JU.Lst");c(b,"reverseArray",function(a){for(var d=this.atomSetCount,g=B(d/2);0<=--g;)JU.AU.swapInt(a,

g,d-1-g)},"~A");c(b,"getList",function(a){var d;for(d=this.ac;0<=--d&&!(null!=this.atoms[d]&&"\x00"!=(a?this.atoms[d].altLoc:this.atoms[d].insertionCode)););if(!(0>d)){var g=Array(this.atomSetCount);for(d=0;d<this.atomSetCount;d++)g[d]="";var b;for(d=0;d<this.ac;d++)if(null!=this.atoms[d]){var c=a?this.atoms[d].altLoc:this.atoms[d].insertionCode;if("\x00"!=c&&0>g[b=this.atoms[d].atomSetIndex].indexOf(c))g[b]+=c}a=a?"altLocs":"insertionCodes";for(d=0;d<this.atomSetCount;d++)0<g[d].length&&this.setModelInfoForSet(a,

g[d],d)}},"~B");c(b,"finish",function(){if(null!=this.reader)this.reader.finalizeModelSet();else if(null!=this.readerList)for(var a=0;a<this.readerList.size();a++)this.readerList.get(a).finalizeModelSet();this.atoms=null;this.atomSetAtomCounts=E(16,0);this.atomSetAuxiliaryInfo=Array(16);this.atomSetInfo=new java.util.Hashtable;this.atomSetCount=0;this.atomSetNumbers=E(16,0);this.atomSymbolicMap=new java.util.Hashtable;this.bonds=null;this.iSet=-1;this.xtalSymmetry=this.readerList=null;this.structures=

Array(16);this.structureCount=0;this.vibrationSteps=this.trajectorySteps=null});c(b,"discardPreviousAtoms",function(){for(var a=this.ac;0<=--a;)this.atoms[a]=null;this.ac=0;this.clearMap();this.atomSetCount=0;this.iSet=-1;for(a=this.atomSetAuxiliaryInfo.length;0<=--a;)this.atomSetAtomCounts[a]=0,this.atomSetBondCounts[a]=0,this.atomSetAuxiliaryInfo[a]=null});c(b,"removeCurrentAtomSet",function(){if(!(0>this.iSet)){var a=this.atomSetAtomIndexes[this.iSet];null!=this.bsAtoms&&this.bsAtoms.clearBits(a,

this.ac);this.ac=a;this.atomSetAtomCounts[this.iSet]=0;this.iSet--;this.atomSetCount--;this.reader.doCheckUnitCell=!1}});c(b,"getHydrogenAtomCount",function(){for(var a=0,d=0;d<this.ac;d++)(1==this.atoms[d].elementNumber||this.atoms[d].elementSymbol.equals("H"))&&a++;return a});c(b,"newCloneAtom",function(a){a=a.getClone();this.addAtom(a);return a},"J.adapter.smarter.Atom");c(b,"cloneFirstAtomSet",function(a){if(!this.allowMultiple)return 0;this.newAtomSet();0==a&&(a=this.atomSetAtomCounts[0]);for(var d=

0;d<a;++d)this.newCloneAtom(this.atoms[d]);return this.ac},"~N");c(b,"cloneAtomSetWithBonds",function(a){var d=this.atomSetBondCounts[a?this.iSet:0];a=a?this.cloneLastAtomSet():this.cloneFirstAtomSet(0);if(0<a)for(var g=0;g<d;g++){var b=this.bonds[this.bondCount-d];this.addNewBondWithOrder(b.atomIndex1+a,b.atomIndex2+a,b.order)}},"~B");c(b,"cloneLastAtomSet",function(){return this.cloneLastAtomSetFromPoints(0,null)});c(b,"cloneLastAtomSetFromPoints",function(a,d){if(!this.allowMultiple)return 0;var g=

0<a?a:this.getLastAtomSetAtomCount(),b=this.getLastAtomSetAtomIndex();this.newAtomSet();for(var c=0;c<g;++c){var e=this.newCloneAtom(this.atoms[b++]);null!=d&&e.setT(d[c])}return g},"~N,~A");c(b,"getLastAtomSetAtomCount",function(){return this.atomSetAtomCounts[this.iSet]});c(b,"getLastAtomSetAtomIndex",function(){return this.ac-this.atomSetAtomCounts[this.iSet]});c(b,"addNewAtom",function(){return this.addAtom(new J.adapter.smarter.Atom)});c(b,"addAtom",function(a){this.ac==this.atoms.length&&(this.atoms=

2E5<this.ac?JU.AU.ensureLength(this.atoms,this.ac+5E4):JU.AU.doubleLength(this.atoms));0==this.atomSetCount&&this.newAtomSet();a.index=this.ac;this.atoms[this.ac++]=a;a.atomSetIndex=this.iSet;a.atomSite=0<this.fixedSite?this.fixedSite-1:this.atomSetAtomCounts[this.iSet]++;return a},"J.adapter.smarter.Atom");c(b,"addAtomWithMappedName",function(a){var d=this.addAtom(a).atomName;null!=d&&this.atomSymbolicMap.put(d,a)},"J.adapter.smarter.Atom");c(b,"addAtomWithMappedSerialNumber",function(a){var d=this.addAtom(a).atomSerial;

-2147483648!=d&&this.atomSymbolicMap.put(""+d,a)},"J.adapter.smarter.Atom");c(b,"getAtomFromName",function(a){return this.atomSymbolicMap.get(a)},"~S");c(b,"setAtomMapAnyCase",function(){this.atomMapAnyCase=!0;var a=new java.util.Hashtable;a.putAll(this.atomSymbolicMap);for(var d,g=this.atomSymbolicMap.entrySet().iterator();g.hasNext()&&((d=g.next())||1);){var b=d.getKey(),c=b.toUpperCase();c.equals(b)||a.put(c,d.getValue())}this.atomSymbolicMap=a});c(b,"getAtomIndex",function(a){var d=this.atomSymbolicMap.get(a);

null==d&&this.atomMapAnyCase&&(d=this.atomSymbolicMap.get(a.toUpperCase()));return null==d?-1:d.index},"~S");c(b,"addNewBondWithOrder",function(a,d,g){var b=null;0<=a&&(a<this.ac&&0<=d&&d<this.ac&&a!=d)&&(b=new J.adapter.smarter.Bond(a,d,g),this.addBond(b));return b},"~N,~N,~N");c(b,"addNewBondFromNames",function(a,d,g){return this.addNewBondWithOrderA(this.getAtomFromName(a),this.getAtomFromName(d),g)},"~S,~S,~N");c(b,"addNewBondWithOrderA",function(a,d,g){return null!=a&&null!=d?this.addNewBondWithOrder(a.index,

d.index,g):null},"J.adapter.smarter.Atom,J.adapter.smarter.Atom,~N");c(b,"addBond",function(a){0<this.trajectoryStepCount||(0>a.atomIndex1||0>a.atomIndex2||0>a.order||a.atomIndex1==a.atomIndex2||this.atoms[a.atomIndex1].atomSetIndex!=this.atoms[a.atomIndex2].atomSetIndex?JU.Logger.debugging&&JU.Logger.debug(">>>>>>BAD BOND:"+a.atomIndex1+"-"+a.atomIndex2+" order="+a.order):this.addBondNoCheck(a))},"J.adapter.smarter.Bond");c(b,"addBondNoCheck",function(a){this.bondCount==this.bonds.length&&(this.bonds=

JU.AU.arrayCopyObject(this.bonds,this.bondCount+1024));this.bonds[this.bondCount++]=a;this.atomSetBondCounts[this.iSet]++},"J.adapter.smarter.Bond");c(b,"finalizeStructures",function(){if(0!=this.structureCount){this.bsStructuredModels=new JU.BS;for(var a=new java.util.Hashtable,d=0;d<this.structureCount;d++){var g=this.structures[d];-1==g.modelStartEnd[0]&&(g.modelStartEnd[0]=0,g.modelStartEnd[1]=this.atomSetCount-1);this.bsStructuredModels.setBits(g.modelStartEnd[0],g.modelStartEnd[1]+1);if(0!=

g.strandCount){var g=g.structureID+" "+g.modelStartEnd[0],b=a.get(g),b=(null==b?0:b.intValue())+1;a.put(g,Integer.$valueOf(b))}}for(d=0;d<this.structureCount;d++)g=this.structures[d],1==g.strandCount&&(g.strandCount=a.get(g.structureID+" "+g.modelStartEnd[0]).intValue())}});c(b,"addStructure",function(a){this.structureCount==this.structures.length&&(this.structures=JU.AU.arrayCopyObject(this.structures,this.structureCount+32));this.structures[this.structureCount++]=a},"J.adapter.smarter.Structure");

c(b,"addVibrationVectorWithSymmetry",function(a,d,g,b,c){if(c){c=this.atoms[a].atomSite;for(var e=this.atoms[a].atomSetIndex;a<this.ac&&this.atoms[a].atomSetIndex==e;a++)this.atoms[a].atomSite==c&&this.addVibrationVector(a,d,g,b)}else this.addVibrationVector(a,d,g,b)},"~N,~N,~N,~N,~B");c(b,"addVibrationVector",function(a,d,g,b){this.allowMultiple||(a%=this.ac);return this.atoms[a].vib=JU.V3.new3(d,g,b)},"~N,~N,~N,~N");c(b,"setCoordinatesAreFractional",function(a){this.coordinatesAreFractional=a;this.setCurrentModelInfo("coordinatesAreFractional",

Boolean.$valueOf(a));a&&this.setGlobalBoolean(0)},"~B");c(b,"setAnisoBorU",function(a,d,g){this.haveAnisou=!0;a.anisoBorU=d;d[6]=g},"J.adapter.smarter.Atom,~A,~N");c(b,"setU",function(a,d,g){var b=a.anisoBorU;null==b&&this.setAnisoBorU(a,b=K(8,0),8);b[d]=g},"J.adapter.smarter.Atom,~N,~N");c(b,"getXSymmetry",function(){null==this.xtalSymmetry&&(this.xtalSymmetry=J.api.Interface.getOption("adapter.smarter.XtalSymmetry",this.reader.vwr,"file").set(this.reader));return this.xtalSymmetry});c(b,"getSymmetry",

function(){return this.getXSymmetry().getSymmetry()});c(b,"setSymmetry",function(a){return null==a?null:this.getXSymmetry().setSymmetry(a)},"J.adapter.smarter.XtalSymmetry.FileSymmetry");c(b,"newFileSymmetry",function(){return this.getXSymmetry().newFileSymmetry()});c(b,"setTensors",function(){this.haveAnisou&&this.getXSymmetry().setTensors()});c(b,"setInfo",function(a,d){null==d?this.atomSetInfo.remove(a):this.atomSetInfo.put(a,d)},"~S,~O");c(b,"setAtomSetCollectionPartialCharges",function(a){if(!this.atomSetInfo.containsKey(a))return!1;

for(var d=this.atomSetInfo.get(a),g=d.size(),b=this.ac;0<=--b;)this.atoms[b].partialCharge=d.get(b%g).floatValue();JU.Logger.info("Setting partial charges type "+a);return!0},"~S");c(b,"mapPartialCharge",function(a,d){this.getAtomFromName(a).partialCharge=d},"~S,~N");b.fixPeriodic=c(b,"fixPeriodic",function(a,d){a.x=J.adapter.smarter.AtomSetCollection.fixPoint(a.x,d.x);a.y=J.adapter.smarter.AtomSetCollection.fixPoint(a.y,d.y);a.z=J.adapter.smarter.AtomSetCollection.fixPoint(a.z,d.z);return a},"JU.P3,JU.P3");

b.fixPoint=c(b,"fixPoint",function(a,d){for(;0.9<a-d;)a-=1;for(;-0.9>a-d;)a+=1;return a},"~N,~N");c(b,"finalizeTrajectoryAs",function(a,d){this.trajectorySteps=a;this.vibrationSteps=d;this.trajectoryStepCount=a.size();this.finalizeTrajectory()},"JU.Lst,JU.Lst");c(b,"finalizeTrajectory",function(){if(0!=this.trajectoryStepCount){var a=this.trajectorySteps.get(0),d=null==this.vibrationSteps?null:this.vibrationSteps.get(0),g=null==this.bsAtoms?this.ac:this.bsAtoms.cardinality();if(null!=this.vibrationSteps&&

null!=d&&d.length<g||a.length<g)this.errorMessage="File cannot be loaded as a trajectory";else{for(var g=new JU.V3,b=0,c=0;b<this.ac;b++)if(null==this.bsAtoms||this.bsAtoms.get(b))null!=this.vibrationSteps&&(this.atoms[b].vib=null==d?g:d[c]),null!=a[c]&&this.atoms[b].setT(a[c]),c++;this.setInfo("trajectorySteps",this.trajectorySteps);null!=this.vibrationSteps&&this.setInfo("vibrationSteps",this.vibrationSteps);0==this.ac&&(this.ac=a.length)}}});c(b,"newAtomSet",function(){this.newAtomSetClear(!0)});

c(b,"newAtomSetClear",function(a){!this.allowMultiple&&0<=this.iSet&&this.reader.discardPreviousAtoms();this.bondIndex0=this.bondCount;this.isTrajectory&&this.reader.discardPreviousAtoms();this.iSet=this.atomSetCount++;this.atomSetCount>this.atomSetNumbers.length&&(this.atomSetAtomIndexes=JU.AU.doubleLengthI(this.atomSetAtomIndexes),this.atomSetAtomCounts=JU.AU.doubleLengthI(this.atomSetAtomCounts),this.atomSetBondCounts=JU.AU.doubleLengthI(this.atomSetBondCounts),this.atomSetAuxiliaryInfo=JU.AU.doubleLength(this.atomSetAuxiliaryInfo));

this.atomSetAtomIndexes[this.iSet]=this.ac;this.atomSetCount+this.trajectoryStepCount>this.atomSetNumbers.length&&(this.atomSetNumbers=JU.AU.doubleLengthI(this.atomSetNumbers));this.isTrajectory?this.atomSetNumbers[this.iSet+this.trajectoryStepCount]=this.atomSetCount+this.trajectoryStepCount:this.atomSetNumbers[this.iSet]=this.atomSetCount;a&&this.clearMap();this.setCurrentModelInfo("title",this.collectionName)},"~B");c(b,"clearMap",function(){this.atomSymbolicMap.clear();this.atomMapAnyCase=!1});

c(b,"getAtomSetAtomIndex",function(a){return this.atomSetAtomIndexes[a]},"~N");c(b,"getAtomSetAtomCount",function(a){return this.atomSetAtomCounts[a]},"~N");c(b,"getAtomSetBondCount",function(a){return this.atomSetBondCounts[a]},"~N");c(b,"setAtomSetName",function(a){if(null!=a)if(this.isTrajectory)this.setTrajectoryName(a);else{var d=0>this.iSet?null:this.getAtomSetName(this.iSet);this.setModelInfoForSet("name",a,this.iSet);null!=this.reader&&(0<a.length&&!a.equals(d))&&this.reader.appendLoadNote(a);

this.allowMultiple||this.setCollectionName(a)}},"~S");c(b,"setTrajectoryName",function(a){if(0!=this.trajectoryStepCount){null==this.trajectoryNames&&(this.trajectoryNames=new JU.Lst);for(var d=this.trajectoryNames.size();d<this.trajectoryStepCount;d++)this.trajectoryNames.addLast(null);this.trajectoryNames.set(this.trajectoryStepCount-1,a)}},"~S");c(b,"setCurrentAtomSetNumber",function(a){this.setAtomSetNumber(this.iSet+(this.isTrajectory?this.trajectoryStepCount:0),a)},"~N");c(b,"setAtomSetNumber",

function(a,d){this.atomSetNumbers[a]=d},"~N,~N");c(b,"setAtomSetModelProperty",function(a,d){this.setAtomSetModelPropertyForSet(a,d,this.iSet)},"~S,~S");c(b,"setAtomSetModelPropertyForSet",function(a,d,g){var b=this.getAtomSetAuxiliaryInfoValue(g,"modelProperties");null==b&&this.setModelInfoForSet("modelProperties",b=new java.util.Properties,g);b.put(a,d);a.startsWith(".")&&b.put(a.substring(1),d)},"~S,~S,~N");c(b,"setAtomProperties",function(a,d,g){"string"==typeof d&&!d.endsWith("\n")&&(d+="\n");

0>g&&(g=this.iSet);var b=this.getAtomSetAuxiliaryInfoValue(g,"atomProperties");null==b&&this.setModelInfoForSet("atomProperties",b=new java.util.Hashtable,g);b.put(a,d)},"~S,~O,~N,~B");c(b,"setAtomSetPartialCharges",function(a){if(!this.atomSetAuxiliaryInfo[this.iSet].containsKey(a))return!1;a=this.getAtomSetAuxiliaryInfoValue(this.iSet,a);for(var d=a.size();0<=--d;)this.atoms[d].partialCharge=a.get(d).floatValue();return!0},"~S");c(b,"getAtomSetAuxiliaryInfoValue",function(a,d){return this.atomSetAuxiliaryInfo[0<=

a?a:this.iSet].get(d)},"~N,~S");c(b,"setCurrentModelInfo",function(a,d){this.setModelInfoForSet(a,d,this.iSet)},"~S,~O");c(b,"setModelInfoForSet",function(a,d,g){0>g||(null==this.atomSetAuxiliaryInfo[g]&&(this.atomSetAuxiliaryInfo[g]=new java.util.Hashtable),null==d?this.atomSetAuxiliaryInfo[g].remove(a):this.atomSetAuxiliaryInfo[g].put(a,d))},"~S,~O,~N");c(b,"getAtomSetNumber",function(a){return this.atomSetNumbers[a>=this.atomSetCount?0:a]},"~N");c(b,"getAtomSetName",function(a){if(null!=this.trajectoryNames&&

a<this.trajectoryNames.size())return this.trajectoryNames.get(a);a>=this.atomSetCount&&(a=this.atomSetCount-1);return this.getAtomSetAuxiliaryInfoValue(a,"name")},"~N");c(b,"getAtomSetAuxiliaryInfo",function(a){a=a>=this.atomSetCount?this.atomSetCount-1:a;return 0>a?null:this.atomSetAuxiliaryInfo[a]},"~N");c(b,"setAtomSetEnergy",function(a,d){0>this.iSet||(JU.Logger.info("Energy for model "+(this.iSet+1)+" = "+a),this.setCurrentModelInfo("EnergyString",a),this.setCurrentModelInfo("Energy",Float.$valueOf(d)),

this.setAtomSetModelProperty("Energy",""+d))},"~S,~N");c(b,"setAtomSetFrequency",function(a,d,g,b,c){this.setAtomSetModelProperty("FreqValue",b);b+=" "+(null==c?"cm^-1":c);c=(null==g?"":g+" ")+b;this.setAtomSetName(c);this.setAtomSetModelProperty("Frequency",b);this.setAtomSetModelProperty("Mode",""+a);this.setModelInfoForSet("vibrationalMode",Integer.$valueOf(a),this.iSet);null!=g&&this.setAtomSetModelProperty("FrequencyLabel",g);this.setAtomSetModelProperty(".PATH",(null==d?"":d+J.adapter.smarter.SmarterJmolAdapter.PATH_SEPARATOR+

"Frequencies")+"Frequencies");return c},"~N,~S,~S,~S,~S");c(b,"getBondList",function(){for(var a=Array(this.bondCount),d=0;d<this.bondCount;d++)a[d]=w(-1,[this.atoms[this.bonds[d].atomIndex1].atomName,this.atoms[this.bonds[d].atomIndex2].atomName,""+this.bonds[d].order]);return a});c(b,"centralize",function(){for(var a=new JU.P3,d=0;d<this.atomSetCount;d++){var g=this.atomSetAtomCounts[d],b=this.atomSetAtomIndexes[d];a.set(0,0,0);for(var c=b+g;--c>=b;)a.add(this.atoms[c]);a.scale(1/g);for(c=b+g;--c>=

b;)this.atoms[c].sub(a)}});c(b,"mergeTrajectories",function(a){if(this.isTrajectory&&a.isTrajectory&&null==this.vibrationSteps){for(var d=0;d<a.trajectoryStepCount;d++)this.trajectorySteps.add(this.trajectoryStepCount++,a.trajectorySteps.get(d));this.setInfo("trajectorySteps",this.trajectorySteps);this.setInfo("ignoreUnitCell",a.atomSetInfo.get("ignoreUnitCell"))}},"J.adapter.smarter.AtomSetCollection");c(b,"removeAtomSet",function(a){null==this.bsAtoms&&(this.bsAtoms=JU.BSUtil.newBitSet2(0,this.ac));

var d=this.atomSetAtomIndexes[a],g=d+this.atomSetAtomCounts[a];this.bsAtoms.clearBits(d,g);for(d=g;d<this.ac;d++)this.atoms[d].atomSetIndex--;for(d=a+1;d<this.atomSetCount;d++)this.atomSetAuxiliaryInfo[d-1]=this.atomSetAuxiliaryInfo[d],this.atomSetAtomIndexes[d-1]=this.atomSetAtomIndexes[d],this.atomSetBondCounts[d-1]=this.atomSetBondCounts[d],this.atomSetAtomCounts[d-1]=this.atomSetAtomCounts[d],this.atomSetNumbers[d-1]=this.atomSetNumbers[d];for(d=0;d<this.bondCount;d++)this.bonds[d].atomSetIndex=

this.atoms[this.bonds[d].atomIndex1].atomSetIndex;this.atomSetAuxiliaryInfo[--this.atomSetCount]=null;for(d=g=0;d<this.structureCount;d++){var b=this.structures[d];b.modelStartEnd[0]==a&&b.modelStartEnd[1]==a&&(this.structures[d]=null,g++)}if(0<g){a=Array(this.structureCount-g);for(g=d=0;d<this.structureCount;d++)null!=this.structures[d]&&(a[g++]=this.structures[d]);this.structures=a}},"~N");c(b,"removeLastUnselectedAtoms",function(){for(var a=this.ac,d=0,g=this.getLastAtomSetAtomIndex(),b=0,c=g;c<

a;c++)this.bsAtoms.get(c)?(0<d&&(this.atoms[this.atoms[c].index=c-d]=this.atoms[c],this.atoms[c]=null),b++):(d++,this.ac--,this.atoms[c]=null);this.atomSetAtomCounts[this.iSet]=b;0==b?(this.iSet--,this.atomSetCount--):this.bsAtoms.setBits(g,g+b)});c(b,"checkNoEmptyModel",function(){for(;0<this.atomSetCount&&0==this.atomSetAtomCounts[this.atomSetCount-1];)this.atomSetCount--});c(b,"getBSAtoms",function(a){null==this.bsAtoms&&(this.bsAtoms=new JU.BS,0!=a&&this.bsAtoms.setBits(0,0>a?this.ac:a));return this.bsAtoms},

"~N");c(b,"setBSAtomsForSet",function(a){if(null!=this.bsAtoms){0>a&&(a=this.iSet);var d=this.atomSetAtomIndexes[a];0>this.bsAtoms.nextSetBit(d)&&this.bsAtoms.setBits(d,d+this.atomSetAtomCounts[a])}},"~N");c(b,"fix2Stereo",function(){this.getBSAtoms(-1);for(var a=this.bondCount;0<=--a;){var d=this.bonds[a];this.atoms[d.atomIndex2].elementSymbol.equals("H")&&1025!=d.order&&1041!=d.order&&this.atoms[d.atomIndex1].elementSymbol.equals("C")?this.bsAtoms.clear(d.atomIndex2):this.atoms[d.atomIndex1].elementSymbol.equals("H")&&

this.atoms[d.atomIndex2].elementSymbol.equals("C")&&this.bsAtoms.clear(d.atomIndex1)}})});u("J.adapter.smarter");C(["javajs.api.GenericLineReader","JU.SB","JV.Viewer"],"J.adapter.smarter.AtomSetCollectionReader","JU.BS $.Lst $.M3 $.P3 $.PT $.Quat $.V3 J.adapter.smarter.Atom $.AtomSetCollection J.api.Interface $.JmolAdapter JU.BSUtil $.Logger $.SimpleUnitCell JV.FileManager $.JC".split(" "),function(){var b=v(function(){this.requiresBSFilter=this.debugging=this.isBinary=!1;this.dssr=this.validation=

this.domains=this.trajectorySteps=this.htParams=this.readerName=this.binaryDoc=this.reader=this.asc=this.primitiveToCrystal=null;this.isConcatenated=!1;this.lstNCS=this.thisBiomolecule=this.addedDataKey=this.addedData=null;this.floatifyJavaDouble=!0;this.next=this.prevline=this.line=null;this.ptLine=0;this.checkNearAtoms=!0;this.fillRange=this.latticeCells=this.latticeType=null;this.iHaveSymmetryOperators=this.iHaveUnitCell=this.doProcessLines=!1;this.continuing=!0;this.vwr=null;this.isMolecular=

this.is2D=this.noMinimize=this.noHydrogens=this.optimize2D=this.isSequential=this.getHeader=this.doCheckUnitCell=this.applySymmetryToBonds=this.isTrajectory=this.ignoreFileSymmetryOperators=this.doApplySymmetry=!1;this.vibrationNumber=this.modelNumber=this.templateAtomCount=0;this.desiredVibrationNumber=-2147483648;this.bsModels=null;this.havePartialChargeFilter=this.useFileModelNumbers=!1;this.calculationType="?";this.sgName=null;this.ignoreFileSpaceGroupName=this.ignoreFileUnitCell=!1;this.unitCellParams=

null;this.desiredModelNumber=-2147483648;this.out=this.symmetry=null;this.doPackUnitCell=this.iHaveFractionalCoordinates=!1;this.ptSupercell=null;this.forcePacked=this.mustFinalizeModelSet=!1;this.packingRange=null;this.cellSlop=1E-4;this.isPrimitive=this.rotateHexCell=!1;this.modDim=0;this.highprecision0=this.lowPrecision=!1;this.loadNote=null;this.merging=this.fileCoordinatesAreFractional=this.doConvertToFractional=!1;this.symmetryRange=0;this.firstLastStep=null;this.lastModelNumber=2147483647;

this.desiredSpaceGroupIndex=-1;this.latticeScaling=NaN;this.unitCellOffset=null;this.unitCellOffsetFractional=!1;this.paramsLattice=this.moreUnitCellInfo=null;this.paramsPacked=this.paramsCentroid=!1;this.fileName=this.filePath=this.fileOffsetFractional=this.fileOffset=this.fileScaling=null;this.baseBondIndex=this.baseAtomIndex=0;this.stateScriptVersionInt=2147483647;this.isSUPERCELL=this.noPack=this.isFinalized=!1;this.precision=0;this.haveModel=!1;this.previousUnitCell=this.previousSpaceGroup=null;

this.nMatrixElements=0;this.filterCased=this.filter=this.bsFilter=this.matUnitCellOrientation=this.ucItems=null;this.filterAtomType=this.filterAtomName=this.filterChain=this.filterGroup3=this.filterAltLoc=this.haveAtomFilter=!1;this.filterAtomTypeStr=null;this.filterAtomNameTerminator=";";this.filterEveryNth=this.filterAllHetero=this.filterHetero=this.filterElement=!1;this.filterSymop=null;this.nFiltered=this.filterN=0;this.reverseModels=this.doReadMolecularOrbitals=this.allowPDBFilter=this.isDSSP1=

this.ignoreStructure=this.useAltNames=this.addVibrations=this.doCentralize=this.doSetOrientation=!1;this.nameRequired=null;this.centroidPacked=this.doCentroidUnitCell=!1;this.strSupercell=null;this.filteredPrecision=this.fixUnitCell=this.polymerX=this.slabXY=this.allow_a_len_1=!1;this.ms=this.matRot=this.filter2Cased=this.filter1Cased=this.filter2=this.filter1=null;this.vibsFractional=!1;this.siteScript=this.previousScript=null;r(this,arguments)},J.adapter.smarter,"AtomSetCollectionReader",null,javajs.api.GenericLineReader);

Q(b,function(){this.next=E(1,0);this.highprecision0=JV.Viewer.isHighPrecision;this.loadNote=new JU.SB});c(b,"getPackingRangeValue",function(a){return null!=this.packingRange?this.packingRange.floatValue():0!=a?a:0.02},"~N");c(b,"setup",function(a,d,g){this.setupASCR(a,d,g)},"~S,java.util.Map,~O");c(b,"setupASCR",function(a,d,g){null!=a&&(this.debugging=JU.Logger.debugging,this.htParams=d,this.filePath=JV.FileManager.stripTypePrefix(""+d.get("fullPathName")),a=this.filePath.lastIndexOf("/"),this.fileName=

this.filePath.substring(a+1),y(g,"java.io.BufferedReader")?this.reader=g:y(g,"javajs.api.GenericBinaryDocument")&&(this.binaryDoc=g))},"~S,java.util.Map,~O");c(b,"readData",function(){this.initialize();this.asc=new J.adapter.smarter.AtomSetCollection(this.readerName,this,null,null);try{this.initializeReader();if(null==this.binaryDoc)for(null==this.line&&this.continuing&&this.rd();null!=this.line&&this.continuing;)this.checkLine()&&this.rd();else this.binaryDoc.setOutputChannel(this.out),this.processBinaryDocument();

this.finalizeSubclassReader();this.isFinalized||this.finalizeReaderASCR()}catch(a){JU.Logger.info("Reader error: "+a),a.printStackTrace(),this.setError(a)}null!=this.reader&&this.reader.close();null!=this.binaryDoc&&this.binaryDoc.close();return this.finish()});c(b,"fixBaseIndices",function(){try{var a=this.htParams.get("baseModelIndex");if(null!=a){var d=a.intValue();this.baseAtomIndex+=this.asc.ac;this.baseBondIndex+=this.asc.bondCount;d+=this.asc.atomSetCount;this.htParams.put("baseAtomIndex",

Integer.$valueOf(this.baseAtomIndex));this.htParams.put("baseBondIndex",Integer.$valueOf(this.baseBondIndex));this.htParams.put("baseModelIndex",Integer.$valueOf(d))}}catch(g){if(!F(g,Exception))throw g;}});c(b,"readDataObject",function(a){this.initialize();this.asc=new J.adapter.smarter.AtomSetCollection(this.readerName,this,null,null);this.initializeReader();this.processDOM(a);return this.finish()},"~O");c(b,"processDOM",function(){},"~O");c(b,"processBinaryDocument",function(){});c(b,"initializeReader",

function(){});c(b,"checkLine",function(){return!0});c(b,"checkLastModel",function(){if(this.isLastModel(this.modelNumber)&&this.doProcessLines)return this.continuing=this.doProcessLines=!1;this.doProcessLines=!1;return!0});c(b,"isLastModel",function(a){return 0<this.desiredModelNumber||a>=this.lastModelNumber},"~N");c(b,"appendLoadNote",function(a){null==a?this.loadNote=new JU.SB:(this.loadNote.append(a).append("\n"),JU.Logger.info(a))},"~S");c(b,"initializeTrajectoryFile",function(){this.asc.addAtom(new J.adapter.smarter.Atom);

this.trajectorySteps=this.htParams.get("trajectorySteps");null==this.trajectorySteps&&this.htParams.put("trajectorySteps",this.trajectorySteps=new JU.Lst)});c(b,"finalizeSubclassReader",function(){});c(b,"finalizeReaderASCR",function(){this.isFinalized=!0;if(0<this.asc.atomSetCount){1==this.asc.atomSetCount&&(this.asc.setCurrentModelInfo("dbName",this.htParams.get("dbName")),this.asc.setCurrentModelInfo("auxFiles",this.htParams.get("auxFiles")));this.applySymmetryAndSetTrajectory();this.asc.finalizeStructures();

this.doCentralize&&this.asc.centralize();null!=this.fillRange&&this.asc.setInfo("boundbox",this.fillRange);var a=this.asc.getAtomSetAuxiliaryInfo(0);if(null!=a){if(null!=this.domains){this.asc.setGlobalBoolean(5);var d=this.domains.getMapKeys(2,!0),g=d.indexOf("{ ",2);0<=g&&(d=d.substring(g+2));g=d.indexOf("_metadata");0>g&&(g=d.indexOf("metadata"));0<=g&&(d=d.substring(0,g));d=JU.PT.rep(JU.PT.replaceAllCharacters(d,"{}","").trim(),"\n","\n ")+"\n\nUse SHOW DOMAINS for details.";this.appendLoadNote("\nDomains loaded:\n "+

d);for(d=this.asc.atomSetCount;0<=--d;)a=this.asc.getAtomSetAuxiliaryInfo(d),a.put("domains",this.domains)}if(null!=this.validation)for(d=this.asc.atomSetCount;0<=--d;)a=this.asc.getAtomSetAuxiliaryInfo(d),a.put("validation",this.validation);if(null!=this.dssr){a.put("dssrJSON",Boolean.TRUE);for(d=this.asc.atomSetCount;0<=--d;)a=this.asc.getAtomSetAuxiliaryInfo(d),a.put("dssr",this.dssr)}}}this.floatifyJavaDouble||this.asc.setInfo("highPrecision",Boolean.TRUE);this.setLoadNote()});c(b,"setLoadNote",

function(){var a=this.loadNote.toString();0<this.loadNote.length()&&this.asc.setInfo("modelLoadNote",a);return a});c(b,"setIsPDB",function(){this.asc.setGlobalBoolean(4);null!=this.htParams.get("pdbNoHydrogens")&&this.asc.setInfo("pdbNoHydrogens",this.htParams.get("pdbNoHydrogens"));this.checkFilterKey("ADDHYDROGENS")&&this.asc.setInfo("pdbAddHydrogens",Boolean.TRUE)});c(b,"setModelPDB",function(a){a?this.asc.setGlobalBoolean(4):this.asc.clearGlobalBoolean(4);this.asc.setCurrentModelInfo(JV.JC.getBoolName(4),

a?Boolean.TRUE:null)},"~B");c(b,"finish",function(){!1!=this.highprecision0&&this.vwr.setBooleanPropertyTok("doubleprecision",603979831,this.highprecision0);var a=this.htParams.get("loadState");this.asc.setInfo("loadState",null==a?"":a);a=this.htParams.get("smilesString");null!=a&&this.asc.setInfo("smilesString",a);this.htParams.containsKey("templateAtomCount")||this.htParams.put("templateAtomCount",Integer.$valueOf(this.asc.ac));null!=this.bsFilter&&(this.htParams.put("filteredAtomCount",Integer.$valueOf(JU.BSUtil.cardinalityOf(this.bsFilter))),

this.htParams.put("bsFilter",this.bsFilter));this.calculationType.equals("?")||this.asc.setInfo("calculationType",this.calculationType);var d=a=this.asc.fileTypeName;0<=d.indexOf("(")&&(d=d.substring(0,d.indexOf("(")));for(var g=this.asc.atomSetCount;0<=--g;)this.asc.setModelInfoForSet("fileName",this.filePath,g),this.asc.setModelInfoForSet("fileType",d,g);this.asc.freeze(this.reverseModels);if(null!=this.asc.errorMessage)return this.asc.errorMessage+"\nfor file "+this.filePath+"\ntype "+a;if(!this.merging&&

(null==this.asc.bsAtoms?0==this.asc.ac:0>this.asc.bsAtoms.nextSetBit(0))&&0>d.indexOf("DataOnly")&&null==this.asc.atomSetInfo.get("dataOnly"))return"No atoms found\nfor file "+this.filePath+"\ntype "+a;this.fixBaseIndices();return this.asc});c(b,"setError",function(a){var d=a.getMessage();this.asc.errorMessage=null==this.line?"Error reading file at end of file \n"+d:"Error reading file at line "+this.ptLine+":\n"+this.line+"\n"+d;a.printStackTrace()},"Throwable");c(b,"initialize",function(){this.htParams.containsKey("baseAtomIndex")&&

(this.baseAtomIndex=this.htParams.get("baseAtomIndex").intValue());this.htParams.containsKey("baseBondIndex")&&(this.baseBondIndex=this.htParams.get("baseBondIndex").intValue());this.initializeSymmetry();this.vwr=this.htParams.remove("vwr");this.htParams.containsKey("stateScriptVersionInt")&&(this.stateScriptVersionInt=this.htParams.get("stateScriptVersionInt").intValue());this.packingRange=this.htParams.get("packingRange");var a=null!=this.htParams.get("highPrecision");null==this.packingRange&&a&&

(this.floatifyJavaDouble=!1,this.packingRange=Float.$valueOf(1E-4));this.merging=this.htParams.containsKey("merging");this.getHeader=this.htParams.containsKey("getHeader");this.isSequential=this.htParams.containsKey("isSequential");this.readerName=this.htParams.get("readerName");this.htParams.containsKey("outputChannel")&&(this.out=this.htParams.get("outputChannel"));this.htParams.containsKey("vibrationNumber")?this.desiredVibrationNumber=this.htParams.get("vibrationNumber").intValue():this.htParams.containsKey("modelNumber")&&

(this.desiredModelNumber=this.htParams.get("modelNumber").intValue());this.applySymmetryToBonds=this.htParams.containsKey("applySymmetryToBonds");this.bsFilter=this.requiresBSFilter?this.htParams.get("bsFilter"):null;this.setFilter(null);this.fillRange=this.htParams.get("fillRange");this.paramsLattice=this.htParams.get("lattice");a=this.htParams.get("supercell");this.noPack=this.checkFilterKey("NOPACK");null!=this.strSupercell&&!this.noPack&&(this.forcePacked=!0);y(a,"JU.P3")?(a=this.ptSupercell=

a,1!=a.length()&&(this.strSupercell=D(a.x)+"a,"+D(a.y)+"b,"+D(a.z)+"c",this.isSUPERCELL=!0)):"string"==typeof a&&(this.strSupercell=a,this.isSUPERCELL=!0);a=this.htParams.containsKey("ptFile")?this.htParams.get("ptFile").intValue():-1;this.isTrajectory=this.htParams.containsKey("isTrajectory");0<a&&this.htParams.containsKey("firstLastSteps")?(a=this.htParams.get("firstLastSteps").get(a-1),y(a,"JU.BS")?this.bsModels=a:this.firstLastStep=a):this.htParams.containsKey("firstLastStep")?this.firstLastStep=

this.htParams.get("firstLastStep"):this.htParams.containsKey("bsModels")&&(this.bsModels=this.htParams.get("bsModels"));this.useFileModelNumbers=this.htParams.containsKey("useFileModelNumbers")||this.checkFilterKey("USEFILEMODELNUMBERS");this.htParams.containsKey("templateAtomCount")&&(this.templateAtomCount=this.htParams.get("templateAtomCount").intValue());if(null!=this.bsModels||null!=this.firstLastStep)this.desiredModelNumber=-2147483648;if(null==this.bsModels&&null!=this.firstLastStep){0>this.firstLastStep[0]&&

(this.firstLastStep[0]=0);if(0==this.firstLastStep[2]||this.firstLastStep[1]<this.firstLastStep[0])this.firstLastStep[1]=-1;1>this.firstLastStep[2]&&(this.firstLastStep[2]=1);this.bsModels=JU.BSUtil.newAndSetBit(this.firstLastStep[0]);if(this.firstLastStep[1]>this.firstLastStep[0])for(a=this.firstLastStep[0];a<=this.firstLastStep[1];a+=this.firstLastStep[2])this.bsModels.set(a)}if(null!=this.bsModels&&(null==this.firstLastStep||-1!=this.firstLastStep[1]))this.lastModelNumber=this.bsModels.length();

this.symmetryRange=this.htParams.containsKey("symmetryRange")?this.htParams.get("symmetryRange").floatValue():0;this.paramsCentroid=this.htParams.containsKey("centroid");this.paramsPacked=this.htParams.containsKey("packed");this.initializeSymmetryOptions();this.htParams.containsKey("spaceGroupIndex")&&(this.desiredSpaceGroupIndex=this.htParams.get("spaceGroupIndex").intValue(),-2==this.desiredSpaceGroupIndex&&(this.sgName=this.htParams.get("spaceGroupName")),this.ignoreFileSpaceGroupName=-2==this.desiredSpaceGroupIndex||

0<=this.desiredSpaceGroupIndex,this.ignoreFileSymmetryOperators=-1!=this.desiredSpaceGroupIndex);this.htParams.containsKey("unitCellOffset")&&(this.fileScaling=JU.P3.new3(1,1,1),this.fileOffset=this.htParams.get("unitCellOffset"),this.fileOffsetFractional=JU.P3.newP(this.fileOffset),this.unitCellOffsetFractional=this.htParams.containsKey("unitCellOffsetFractional"));this.htParams.containsKey("unitcell")&&(a=this.htParams.get("unitcell"),this.merging&&this.setFractionalCoordinates(!0),9==a.length?

(this.addExplicitLatticeVector(0,a,0),this.addExplicitLatticeVector(1,a,3),this.addExplicitLatticeVector(2,a,6)):this.setUnitCell(a[0],a[1],a[2],a[3],a[4],a[5]),this.ignoreFileUnitCell=this.iHaveUnitCell,this.merging&&!this.iHaveUnitCell&&this.setFractionalCoordinates(!1));this.domains=this.htParams.get("domains");this.validation=this.htParams.get("validation");this.dssr=this.htParams.get("dssr");this.isConcatenated=this.htParams.containsKey("concatenate")});c(b,"parsePrecision",function(a){if(!this.filteredPrecision){var d=

a.indexOf(".")+1;if(0<=d){var g=a.indexOf("(");0>g?this.precision=Math.max(this.precision,a.length-d):(0==this.precision&&(this.precision=g),this.precision=Math.min(this.precision,g-1-d))}}return this.parseFloatStr(a)},"~S");c(b,"setLowPrecision",function(){this.lowPrecision=!0;this.cellSlop=1E-4;null==this.packingRange&&(this.packingRange=Double.$valueOf(1E-4))});c(b,"setPrecision",function(){var a;if(this.lowPrecision)a=!1,this.precision=4;else if(this.precision=1E3<this.precision?this.precision-

1E3:Math.min(12,Math.max(4,this.precision)),a=7<=this.precision)this.vwr.setBooleanProperty("doubleprecision",!0),JV.Viewer.isHighPrecision?(this.cellSlop=1E-12,this.paramsPacked||(this.packingRange=Double.$valueOf(this.cellSlop)),this.asc.setInfo("highPrecision",Boolean.TRUE)):(a=!1,this.precision=6,this.appendLoadNote("Structure read has high precision but this version of Jmol uses float precision.\nUse JmolD.jar or JavaScript for full precision."));!a&&10>this.precision&&(this.cellSlop=Math.pow(10,

-this.precision));this.symmetry.setPrecision(this.cellSlop);this.unitCellParams[26]=this.cellSlop;if(this.fileCoordinatesAreFractional){a=this.asc.ac;for(var d=this.asc.getLastAtomSetAtomIndex();--a>=d;)this.symmetry.twelfthify(this.asc.atoms[a])}this.appendLoadNote("Precision set to "+this.precision+"; packing set to "+(null==this.packingRange?0.02:this.packingRange.floatValue()))});c(b,"initializeSymmetryOptions",function(){this.latticeCells=E(4,0);this.doApplySymmetry=!1;var a=this.paramsLattice;

if(null==a||0==a.length()){if(!this.forcePacked&&null==this.strSupercell)return;a=JU.P3.new3(1,1,1)}this.latticeCells[0]=D(a.x);this.latticeCells[1]=D(a.y);this.latticeCells[2]=D(a.z);y(a,"JU.T4")&&(this.latticeCells[3]=D(a.w));if((this.doCentroidUnitCell=this.paramsCentroid)&&(-1==this.latticeCells[2]||0==this.latticeCells[2]))this.latticeCells[2]=1;a=this.forcePacked||this.paramsPacked;this.centroidPacked=this.doCentroidUnitCell&&a;this.doPackUnitCell=!this.doCentroidUnitCell&&(a||0>this.latticeCells[2]);

this.doApplySymmetry=0<this.latticeCells[0]&&0<this.latticeCells[1];this.doApplySymmetry||(this.latticeCells=E(3,0))});c(b,"doGetModel",function(a,d){if(null!=d&&null!=this.nameRequired&&0<this.nameRequired.length&&0>d.toUpperCase().indexOf(this.nameRequired))return!1;var g=null==this.bsModels?1>this.desiredModelNumber||a==this.desiredModelNumber:a>this.lastModelNumber?!1:0<a&&this.bsModels.get(a-1)||this.haveModel&&null!=this.firstLastStep&&0>this.firstLastStep[1]&&(2>this.firstLastStep[2]||0==(a-

1-this.firstLastStep[0])%this.firstLastStep[2]);g&&0==this.desiredModelNumber&&this.discardPreviousAtoms();this.haveModel=(new Boolean(this.haveModel|g)).valueOf();g&&(this.doProcessLines=!0);return g},"~N,~S");c(b,"discardPreviousAtoms",function(){this.asc.discardPreviousAtoms()});c(b,"initializeSymmetry",function(){this.previousSpaceGroup=this.sgName;this.previousUnitCell=this.unitCellParams;this.iHaveUnitCell=this.ignoreFileUnitCell;if(!this.ignoreFileUnitCell){this.unitCellParams=K(27,0);for(var a=

27;0<=--a;)this.unitCellParams[a]=NaN;this.unitCellParams[25]=this.latticeScaling;this.unitCellParams[26]=this.cellSlop;this.symmetry=null}this.ignoreFileSpaceGroupName||(this.sgName="unspecified!");this.doCheckUnitCell=!1});c(b,"newAtomSet",function(a){0<=this.asc.iSet?(this.asc.newAtomSet(),this.asc.setCollectionName("<collection of "+(this.asc.iSet+1)+" models>")):this.asc.setCollectionName(a);this.asc.setModelInfoForSet("name",a,Math.max(0,this.asc.iSet));this.asc.setAtomSetName(a)},"~S");c(b,

"cloneLastAtomSet",function(a,d){var g=this.asc.getLastAtomSetAtomCount();this.asc.cloneLastAtomSetFromPoints(a,d);this.asc.haveUnitCell&&(this.doCheckUnitCell=this.iHaveUnitCell=!0,this.sgName=this.previousSpaceGroup,this.unitCellParams=this.previousUnitCell);return g},"~N,~A");c(b,"setSpaceGroupName",function(a){this.ignoreFileSpaceGroupName||null==a||(a=a.trim(),0==a.length||(a.equals("HM:")||a.equals(this.sgName))||(a.equals("P1")||JU.Logger.info("Setting space group name to "+a),this.sgName=

a))},"~S");c(b,"setSymmetryOperator",function(a){if(this.ignoreFileSymmetryOperators)return-1;var d=this.asc.getXSymmetry().addSpaceGroupOperation(a,!0);0>d&&JU.Logger.warn("Skipping symmetry operation "+a);this.iHaveSymmetryOperators=!0;return d},"~S");c(b,"initializeCartesianToFractional",function(){for(var a=0;16>a;a++)if(!Float.isNaN(this.unitCellParams[6+a]))return;for(a=0;16>a;a++)this.unitCellParams[6+a]=0==a%5?1:0;this.nMatrixElements=0});c(b,"clearUnitCell",function(){if(!this.ignoreFileUnitCell){for(var a=

6;22>a;a++)this.unitCellParams[a]=NaN;this.checkUnitCell(6)}});c(b,"setUnitCellItem",function(a,d){this.ignoreFileUnitCell||(0==a&&1==d&&!this.allow_a_len_1||3==a&&0==d?(null==this.ucItems&&(this.ucItems=K(6,0)),this.ucItems[a]=d):(null!=this.ucItems&&6>a&&(this.ucItems[a]=d),!Float.isNaN(d)&&(6<=a&&Float.isNaN(this.unitCellParams[6]))&&this.initializeCartesianToFractional(),this.unitCellParams[a]=d,this.debugging&&JU.Logger.debug("setunitcellitem "+a+" "+d),6>a||Float.isNaN(d)?this.iHaveUnitCell=

this.checkUnitCell(6):12==++this.nMatrixElements&&(this.iHaveUnitCell=this.checkUnitCell(22))))},"~N,~N");c(b,"setUnitCell",function(a,d,g,b,c,e){this.ignoreFileUnitCell||(this.clearUnitCell(),this.unitCellParams[0]=a,this.unitCellParams[1]=d,this.unitCellParams[2]=g,0!=b&&(this.unitCellParams[3]=b),0!=c&&(this.unitCellParams[4]=c),0!=e&&(this.unitCellParams[5]=e),this.iHaveUnitCell=this.checkUnitCell(6))},"~N,~N,~N,~N,~N,~N");c(b,"addExplicitLatticeVector",function(a,d,g){if(!this.ignoreFileUnitCell){if(0==

a)for(var b=0;6>b;b++)this.unitCellParams[b]=0;a=6+3*a;this.unitCellParams[a++]=d[g++];this.unitCellParams[a++]=d[g++];this.unitCellParams[a]=d[g];if(Float.isNaN(this.unitCellParams[0]))for(a=0;6>a;a++)this.unitCellParams[a]=-1;if(this.iHaveUnitCell=this.checkUnitCell(15)){if(this.slabXY||this.polymerX)this.unitCellParams[2]=-1;this.polymerX&&(this.unitCellParams[1]=-1)}}},"~N,~A,~N");c(b,"checkUnitCell",function(a){for(var d=0;d<a;d++)if(Float.isNaN(this.unitCellParams[d]))return!1;this.fixFloatA(this.unitCellParams);

if(22==a&&1==this.unitCellParams[0]&&1==this.unitCellParams[1]&&1==this.unitCellParams[2]&&1==this.unitCellParams[6]&&1==this.unitCellParams[11]&&1==this.unitCellParams[16])return!1;6==a&&Float.isNaN(this.unitCellParams[6])&&(this.slabXY&&0<this.unitCellParams[2]?(JU.SimpleUnitCell.addVectors(this.unitCellParams),this.unitCellParams[2]=-1):this.polymerX&&0<this.unitCellParams[1]&&(JU.SimpleUnitCell.addVectors(this.unitCellParams),this.unitCellParams[1]=this.unitCellParams[2]=-1));this.doApplySymmetry&&

(this.getSymmetry(),this.doConvertToFractional=!this.fileCoordinatesAreFractional);return!0},"~N");c(b,"getSymmetry",function(){if(!this.iHaveUnitCell)return null;null==this.symmetry&&((this.symmetry=this.asc.newFileSymmetry()).setUnitCellFromParams(this.unitCellParams,!1,this.cellSlop),this.checkUnitCellOffset());null==this.symmetry?this.iHaveUnitCell=!1:this.symmetry.setSpaceGroupName(this.sgName);return this.symmetry});c(b,"checkUnitCellOffset",function(){null==this.fileOffsetFractional||null==

this.symmetry||(this.fileOffset.setT(this.fileOffsetFractional),this.unitCellOffsetFractional!=this.fileCoordinatesAreFractional&&(this.unitCellOffsetFractional?this.symmetry.toCartesian(this.fileOffset,!1):this.symmetry.toFractional(this.fileOffset,!1)))});c(b,"fractionalizeCoordinates",function(a){if(null!=this.getSymmetry()){var d=this.asc.atoms;if(a)for(var g=this.asc.ac;0<=--g;)this.symmetry.toFractional(d[g],!1);else for(g=this.asc.ac;0<=--g;)this.symmetry.toCartesian(d[g],!1);this.setFractionalCoordinates(a)}},

"~B");c(b,"setFractionalCoordinates",function(a){this.iHaveFractionalCoordinates=this.fileCoordinatesAreFractional=a;this.checkUnitCellOffset()},"~B");c(b,"setFilterAtomTypeStr",function(a){this.filterAtomTypeStr=a;this.filterAtomNameTerminator="\x00"},"~S");c(b,"setFilter",function(a){null==a?a=this.htParams.get("filter"):this.filterCased=this.bsFilter=null;null==this.filterCased&&(this.filterCased=null==a?null:a+";");null!=a&&(a=a.toUpperCase());this.filter=a;this.doSetOrientation=!this.checkFilterKey("NOORIENT");

this.doCentralize=!this.checkFilterKey("NOCENTER")&&this.checkFilterKey("CENTER");this.addVibrations=!this.checkFilterKey("NOVIB");this.ignoreStructure=this.checkFilterKey("DSSP");this.isDSSP1=this.checkFilterKey("DSSP1");this.doReadMolecularOrbitals=!this.checkFilterKey("NOMO");this.useAltNames=this.checkFilterKey("ALTNAME");this.reverseModels=this.checkFilterKey("REVERSEMODELS");this.allow_a_len_1=this.checkFilterKey("TOPOS");this.slabXY=this.checkFilterKey("SLABXY");this.polymerX=!this.slabXY&&

this.checkFilterKey("POLYMERX");this.noHydrogens=this.checkFilterKey("NOH");this.noMinimize=this.checkFilterKey("NOMIN");this.optimize2D=this.checkFilterKey("2D")&&!this.noHydrogens&&!this.noMinimize;if(null!=this.filter){this.fixUnitCell=this.checkFilterKey("FIXUNITCELL");this.checkFilterKey("LOWPRECISION")&&this.setLowPrecision();this.checkFilterKey("HETATM")&&(this.filterHetero=!0,this.filter=JU.PT.rep(this.filter,"HETATM","HETATM-Y"),this.filterCased=JU.PT.rep(this.filterCased,"HETATM","HETATM-Y"));

this.checkFilterKey("ATOM")&&(this.filterHetero=!0,this.filter=JU.PT.rep(this.filter,"ATOM","HETATM-N"),this.filterCased=JU.PT.rep(this.filterCased,"ATOM","HETATM-N"));this.checkFilterKey("CELL=")&&(this.strSupercell=this.filter.substring(this.filter.indexOf("CELL=")+5).toLowerCase());this.nameRequired=JU.PT.getQuotedAttribute(this.filter,"NAME");null!=this.nameRequired&&(this.nameRequired.startsWith("'")?this.nameRequired=JU.PT.split(this.nameRequired,"'")[1]:this.nameRequired.startsWith('"')&&(this.nameRequired=

JU.PT.split(this.nameRequired,'"')[1]),this.filter=JU.PT.rep(this.filter,this.nameRequired,""),this.filter=JU.PT.rep(this.filter,"NAME=",""));this.filterAtomName=this.checkFilterKey("*.")||this.checkFilterKey("!.");if(this.filter.startsWith("_")||this.filter.startsWith("!_")||0<=this.filter.indexOf(";_"))this.filterElement=this.checkFilterKey("_");this.filterGroup3=this.checkFilterKey("[");this.filterChain=this.checkFilterKey(":");this.filterAltLoc=this.checkFilterKey("%");this.filterEveryNth=this.checkFilterKey("/=");

this.filterAllHetero=this.checkFilterKey("ALLHET");if(this.filterEveryNth)this.filterN=this.parseIntAt(this.filter,this.filter.indexOf("/=")+2);else if(this.filter.startsWith("=")||0<=this.filter.indexOf(";="))this.filterAtomType=this.checkFilterKey("=");-2147483648==this.filterN&&(this.filterEveryNth=!1);this.haveAtomFilter=this.filterAtomName||this.filterAtomType||this.filterElement||this.filterGroup3||this.filterChain||this.filterAltLoc||this.filterHetero||this.filterEveryNth||this.checkFilterKey("/=");

if(null==this.bsFilter&&(this.bsFilter=new JU.BS,this.htParams.put("bsFilter",this.bsFilter),this.filter=(";"+this.filter+";").$replace(",",";"),a=this.getFilter("PRECISION="),null!=a&&(a=JU.PT.parseInt(a),0<a&&16>=a&&(this.precision=1E3+a,this.filteredPrecision=!0)),a=this.getFilter("LATTICESCALING="),null!=a&&25<this.unitCellParams.length&&(this.unitCellParams[25]=this.latticeScaling=this.parseFloatStr(a)),a=this.getFilter("SYMOP="),null!=a&&(this.filterSymop=" "+a+" "),JU.Logger.info("filtering with "+

this.filter),this.haveAtomFilter)){this.filter1Cased=this.filterCased;this.filter2Cased="";if(0<=(a=this.filter.indexOf("|")))this.filter1Cased=this.filter.substring(0,a).trim()+";",this.filter2Cased=";"+this.filter.substring(a).trim();this.filter1=this.filter1Cased.toUpperCase();this.filter2=0==this.filter2Cased.length?null:this.filter2Cased.toUpperCase()}}},"~S");c(b,"getFilterWithCase",function(a){var d=null==this.filterCased?-1:this.filterCased.toUpperCase().indexOf(a.toUpperCase());return 0>

d?null:this.filterCased.substring(d+a.length,this.filterCased.indexOf(";",d))},"~S");c(b,"getFilter",function(a){var d=null==this.filter?-1:this.filter.indexOf(a);return 0>d?null:this.filter.substring(d+a.length,this.filter.indexOf(";",d))},"~S");c(b,"checkFilterKey",function(a){return null!=this.filter&&0<=this.filter.indexOf(a)},"~S");c(b,"checkAndRemoveFilterKey",function(a){if(!this.checkFilterKey(a))return!1;this.filter=JU.PT.rep(this.filter,a,"");3>this.filter.length&&(this.filter=null);return!0},

"~S");c(b,"filterAtom",function(a,d){if(!this.haveAtomFilter)return!0;var g=this.checkFilter(a,this.filter1,this.filter1Cased);null!=this.filter2&&(g=(new Boolean(g|this.checkFilter(a,this.filter2,this.filter2Cased))).valueOf());if(g&&this.filterEveryNth&&(!a.isHetero||!this.filterAllHetero))g=0==this.nFiltered++%this.filterN;this.bsFilter.setBitTo(0<=d?d:this.asc.ac,g);return g},"J.adapter.smarter.Atom,~N");c(b,"checkFilter",function(a,d,g){return a.isHetero&&this.filterAllHetero?!0:(!this.filterGroup3||

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d);a.put("readerName",d);return J.adapter.smarter.Resolver.getReader("XmlReader",a)},"java.util.Map");b.determineAtomSetCollectionReader=c(b,"determineAtomSetCollectionReader",function(a,d){var g;if(y(a,"javajs.api.GenericBinaryDocument"))return g=J.adapter.smarter.Resolver.getBinaryType(a.getInputStream()),null==g?"binary file type not recognized":g;if(y(a,"java.io.InputStream")){g=J.adapter.smarter.Resolver.getBinaryType(a);if(null!=g)return g;a=JU.Rdr.getBufferedReader(new java.io.BufferedInputStream(a),

null)}var b=a,c=new JU.LimitedLineReader(b,16384),e=c.getHeader(64).trim();if(0==e.length)throw new java.io.EOFException("File contains no data.");if(1==e.indexOf("PNG")&&0<=e.indexOf("PNGJ"))return"pngj";if(1==e.indexOf("PNG")||1==e.indexOf("JPG")||6==e.indexOf("JFIF"))return"spt";if(0<=e.indexOf('"num_pairs"'))return"dssr";if(0<=e.indexOf("output.31\n"))return"GenNBO|output.31";if(null!=(g=J.adapter.smarter.Resolver.checkFileStart(e)))return g.equals("Xml")?J.adapter.smarter.Resolver.getXmlType(c.getHeader(0)):

g;for(var h="{"==e.charAt(0),k=Array(16),m=g=0;m<k.length;++m)k[m]=c.readLineWithNewline(),0<k[m].length&&g++;if(null!=(g=J.adapter.smarter.Resolver.checkSpecial1(g,k,e))||null!=(g=J.adapter.smarter.Resolver.checkLineStarts(k))||null!=(g=J.adapter.smarter.Resolver.checkHeaderContains(c.getHeader(0)))||null!=(g=J.adapter.smarter.Resolver.checkSpecial2(k)))return g;if(h){b=b.readLine();if(null!=(g=J.adapter.smarter.Resolver.checkJSONContains(b)))return null!=d&&d.put("fileData",b),g;b=null==d?null:

b.substring(0,Math.min(100,b.length))}else b=null==d?null:"\n"+k[0]+"\n"+k[1]+"\n"+k[2]+"\n";return b},"~O,java.util.Map");b.getBinaryType=c(b,"getBinaryType",function(a){a=JU.Rdr.getMagic(a,100);var d=a[0]&255;return JU.Rdr.isPickleB(a)?"PyMOL":222==d?J.adapter.smarter.Resolver.bytesMatch(a,4,J.adapter.smarter.Resolver.mmtfMagic)?"MMTF":null:131==d?J.adapter.smarter.Resolver.checkBCIF(a,!0)?"BCIF":null:J.adapter.smarter.Resolver.bytesMatch(a,0,J.adapter.smarter.Resolver.cdxMagic)?"CDX":J.adapter.smarter.Resolver.bytesMatch(a,

0,J.adapter.smarter.Resolver.cmdfMagic)?"Cmdf":null},"java.io.InputStream");b.checkBCIF=c(b,"checkBCIF",function(a,d){return J.adapter.smarter.Resolver.bytesMatch(a,10,J.adapter.smarter.Resolver.bcifMolstarMagic)||J.adapter.smarter.Resolver.bytesMatch(a,10,J.adapter.smarter.Resolver.bcifModelMagic)||J.adapter.smarter.Resolver.bytesMatch(a,10,J.adapter.smarter.Resolver.bcifModelMagic)||J.adapter.smarter.Resolver.bytesMatch(a,10,J.adapter.smarter.Resolver.bcifCoordMagic)?d:J.adapter.smarter.Resolver.bytesMatch(a,

10,J.adapter.smarter.Resolver.bcifDensityMagic)||J.adapter.smarter.Resolver.bytesMatch(a,10,J.adapter.smarter.Resolver.bcifVolumeMagic)?!d:0>J.adapter.smarter.Resolver.findBytes(a,J.adapter.smarter.Resolver.bcifServerMagic)==d},"~A,~B");b.findBytes=c(b,"findBytes",function(a,d){var g=a.length-d.length;a:for(;0<=--g;){for(var b=d.length;0<=--b;)if(a[g+b]!=d[b])continue a;return g}return-1},"~A,~A");b.bytesMatch=c(b,"bytesMatch",function(a,d,g){if(g.length>a.length-d)return!1;for(var b=g.length;0<=

--b;)if(a[d+b]!=g[b])return!1;return!0},"~A,~N,~A");b.checkFileStart=c(b,"checkFileStart",function(a){for(var d=0;d<J.adapter.smarter.Resolver.fileStartsWithRecords.length;++d)for(var g=J.adapter.smarter.Resolver.fileStartsWithRecords[d],b=1;b<g.length;++b)if(a.startsWith(g[b]))return g[0];return null},"~S");b.checkSpecial1=c(b,"checkSpecial1",function(a,d,g){if(1==a&&0<d[0].length&&JU.PT.isDigit(d[0].charAt(0)))return"Jme";if(J.adapter.smarter.Resolver.checkMopacGraphf(d))return"MopacGraphf";if(J.adapter.smarter.Resolver.checkOdyssey(d))return"Odyssey";

switch(J.adapter.smarter.Resolver.checkMol(d)){case 1:case 3:case 2E3:case 3E3:return"Mol"}switch(J.adapter.smarter.Resolver.checkXyz(d)){case 1:return"Xyz";case 2:return"Bilbao";case 3:return"PWmat"}return J.adapter.smarter.Resolver.checkAlchemy(d[0])?"Alchemy":J.adapter.smarter.Resolver.checkFoldingXyz(d)?"FoldingXyz":J.adapter.smarter.Resolver.checkXSF(d)?"Xcrysden":J.adapter.smarter.Resolver.checkCube(d)?"Cube":J.adapter.smarter.Resolver.checkWien2k(d)?"Wien2k":J.adapter.smarter.Resolver.checkAims(d)?

"Aims":J.adapter.smarter.Resolver.checkGenNBO(d,g)?"GenNBO":null},"~N,~A,~S");b.checkXSF=c(b,"checkXSF",function(a){for(var d=0;0==a[d].length;)d++;return a[d].startsWith("ANIMSTEPS ")||a[d].equals("ATOMS\n")&&0<JU.PT.parseInt(a[d+1])},"~A");b.checkAims=c(b,"checkAims",function(a){for(var d=0;d<a.length&&!a[d].startsWith("mol 1");d++){var g=JU.PT.getTokens(a[d]);if(0!=g.length&&(g[0].startsWith("atom")&&4<g.length&&Float.isNaN(JU.PT.parseFloat(g[4]))||g[0].startsWith("multipole")&&6<=g.length||g[0].startsWith("lattice_vector")&&

4<=g.length))return!0}return!1},"~A");b.checkAlchemy=c(b,"checkAlchemy",function(a){var d;return 0<(d=a.indexOf("ATOMS"))&&a.indexOf("BONDS")>d?0<JU.PT.parseInt(a.substring(0,d).trim()):!1},"~S");b.isInt=c(b,"isInt",function(a){J.adapter.smarter.Resolver.n[0]=0;a=a.trim();return 0<a.length&&-2147483648!=JU.PT.parseIntNext(a,J.adapter.smarter.Resolver.n)&&J.adapter.smarter.Resolver.n[0]==a.length},"~S");b.isFloat=c(b,"isFloat",function(a){return!Float.isNaN(JU.PT.parseFloat(a))},"~S");b.checkCube=

c(b,"checkCube",function(a){for(var d=2;5>=d;d++){var g=new java.util.StringTokenizer(a[d]),b=g.countTokens();if(!(4==b||2==d&&5==b)||!J.adapter.smarter.Resolver.isInt(g.nextToken()))return!1;for(var c=3;0<=--c;)if(!J.adapter.smarter.Resolver.isFloat(g.nextToken()))return!1;if(5==b&&!J.adapter.smarter.Resolver.isInt(g.nextToken()))return!1}return!0},"~A");b.checkFoldingXyz=c(b,"checkFoldingXyz",function(a){var d=new java.util.StringTokenizer(a[0].trim()," \t");if(2>d.countTokens()||!J.adapter.smarter.Resolver.isInt(d.nextToken().trim()))return!1;

d=a[1].trim();0==d.length&&(d=a[2].trim());d=new java.util.StringTokenizer(d," \t");return 0<d.countTokens()&&J.adapter.smarter.Resolver.isInt(d.nextToken().trim())},"~A");b.checkGenNBO=c(b,"checkGenNBO",function(a,d){return 0<=d.indexOf("$GENNBO")||a[1].startsWith(" Basis set information needed for plotting orbitals")||0<=a[1].indexOf("s in the AO basis:")||0<=a[1].indexOf("***** NBO ")||0<=a[2].indexOf(" N A T U R A L A T O M I C O R B I T A L")},"~A,~S");b.checkMol=c(b,"checkMol",function(a){var d=

("X"+a[3]).trim().toUpperCase();if(7>d.length||0<=d.indexOf(".")||a[0].startsWith("data_"))return 0;if(d.endsWith("V2000"))return 2E3;if(d.endsWith("V3000"))return 3E3;var d=JU.PT.parseInt(a[3].substring(0,3).trim()),g=JU.PT.parseInt(a[3].substring(3,6).trim());return 0<d&&0<=g&&0!=a[0].indexOf("@<TRIPOS>")&&0!=a[1].indexOf("@<TRIPOS>")&&0!=a[2].indexOf("@<TRIPOS>")?3:0},"~A");b.checkMopacGraphf=c(b,"checkMopacGraphf",function(a){return 2<a[0].indexOf("MOPAC-Graphical data")},"~A");b.checkOdyssey=

c(b,"checkOdyssey",function(a){var d;for(d=0;d<a.length&&(a[d].startsWith("C ")||0==a[d].length);d++);if(d>=a.length||" "!=a[d].charAt(0)||(d+=2)+1>=a.length)return!1;var g=a[d];if(3>g.length)return!1;var b=JU.PT.parseInt(g.substring(2).trim()),c=JU.PT.parseInt(g.substring(0,2).trim());if(2>(g=a[d+1]).length)return!1;a=JU.PT.parseInt(g.substring(0,2).trim());if(0>b||5<b||0>=a||-2147483648==c||5<c)return!1;g=J.adapter.smarter.AtomSetCollectionReader.getTokensFloat(g,null,5);return!Float.isNaN(g[1])&&

!Float.isNaN(g[2])&&!Float.isNaN(g[3])&&Float.isNaN(g[4])},"~A");b.checkWien2k=c(b,"checkWien2k",function(a){return a[2].startsWith("MODE OF CALC=")||a[2].startsWith(" RELA")||a[2].startsWith(" NREL")},"~A");b.checkXyz=c(b,"checkXyz",function(a){var d=!1,g=JU.PT.parseInt(a[0]);if(0<=g&&a[0].trim().equals(""+g)){if(J.adapter.smarter.Resolver.isInt(a[2]))return 2;d=!0}if(0<=a[0].indexOf("Bilbao Crys"))return 2;var b;return(d||5<a.length&&0<g)&&((b=a[1].trim().toUpperCase()).startsWith("LATTICE VECTOR")||

b.equals("LATTICE"))?3:d?1:0},"~A");b.checkLineStarts=c(b,"checkLineStarts",function(a){for(var d=0;d<J.adapter.smarter.Resolver.lineStartsWithRecords.length;++d)for(var g=J.adapter.smarter.Resolver.lineStartsWithRecords[d],b=1;b<g.length;++b)for(var c=g[b],e=0;e<a.length;e++)if(a[e].startsWith(c))return g[0];return null},"~A");b.checkHeaderContains=c(b,"checkHeaderContains",function(a){for(var d=0;d<J.adapter.smarter.Resolver.headerContainsRecords.length;++d){var g=J.adapter.smarter.Resolver.checkHeaderRecords(a,

J.adapter.smarter.Resolver.headerContainsRecords[d]);if(null!=g)return g}return null},"~S");b.checkJSONContains=c(b,"checkJSONContains",function(a){for(var d=0;d<J.adapter.smarter.Resolver.jsonContainsRecords.length;++d){var g=J.adapter.smarter.Resolver.checkHeaderRecords(a,J.adapter.smarter.Resolver.jsonContainsRecords[d]);if(null!=g)return g}return null},"~S");b.checkHeaderRecords=c(b,"checkHeaderRecords",function(a,d){for(var g=1;g<d.length;++g)if(!(0>a.indexOf(d[g])))return g=d[0],!g.equals("Xml")?

g:0<=a.indexOf("/AFLOWDATA/")||0<=a.indexOf("-- Structure PRE --")?"AFLOW":0>a.indexOf("<!DOCTYPE HTML PUBLIC")&&0>a.indexOf("XHTML")&&(0>a.indexOf("xhtml")||0<=a.indexOf("<cml"))?J.adapter.smarter.Resolver.getXmlType(a):null;return null},"~S,~A");b.getXmlType=c(b,"getXmlType",function(a){return 0<=a.indexOf("http://www.molpro.net/")?"XmlMolpro":0<=a.indexOf("odyssey")?"XmlOdyssey":0<=a.indexOf("C3XML")?"XmlChem3d":0<=a.indexOf("CDXML")?"XmlCdx":0<=a.indexOf("arguslab")?"XmlArgus":0<=a.indexOf("jvxl")||

0<=a.indexOf("http://www.xml-cml.org/schema")||0<=a.indexOf("cml:")||0<=a.indexOf("<cml>")?"XmlCml":0<=a.indexOf("XSD")?"XmlXsd":0<=a.indexOf(">vasp")?"XmlVasp":0<=a.indexOf("<GEOMETRY_INFO>")?"XmlQE":"XmlCml(unidentified)"},"~S");b.checkSpecial2=c(b,"checkSpecial2",function(a){if(J.adapter.smarter.Resolver.checkGromacs(a))return"Gromacs";if(J.adapter.smarter.Resolver.checkCrystal(a))return"Crystal";if(J.adapter.smarter.Resolver.checkFAH(a))return"FAH";a=J.adapter.smarter.Resolver.checkCastepVaspSiesta(a);

return null!=a?a:null},"~A");b.checkFAH=c(b,"checkFAH",function(a){return(a[0].trim()+a[2].trim()).equals('{"atoms": [')},"~A");b.checkCrystal=c(b,"checkCrystal",function(a){var d=a[1].trim();if(d.equals("SLAB")||d.equals("MOLECULE")||d.equals("CRYSTAL")||d.equals("POLYMER")||(d=a[3]).equals("SLAB")||d.equals("MOLECULE")||d.equals("POLYMER"))return!0;for(d=0;d<a.length;d++)if(a[d].trim().equals("OPTGEOM")||a[d].trim().equals("FREQCALC")||a[d].contains("DOVESI")||a[d].contains("TORINO")||a[d].contains("http://www.crystal.unito.it")||

a[d].contains("Pcrystal")||a[d].contains("MPPcrystal")||a[d].contains("crystal executable"))return!0;return!1},"~A");b.checkGromacs=c(b,"checkGromacs",function(a){if(-2147483648==JU.PT.parseInt(a[1]))return!1;for(var d=-1,g=2;16>g&&0!=d;g++)if(69!=(d=a[g].length)&&45!=d&&0!=d)return!1;return!0},"~A");b.checkCastepVaspSiesta=c(b,"checkCastepVaspSiesta",function(a){for(var d=0;d<a.length;d++){var g=a[d].toUpperCase();if(1==g.indexOf("FREQUENCIES IN CM-1")||g.contains("CASTEP")||g.startsWith("%BLOCK LATTICE_ABC")||

g.startsWith("%BLOCK LATTICE_CART")||g.startsWith("%BLOCK POSITIONS_FRAC")||g.startsWith("%BLOCK POSITIONS_ABS")||g.contains("<-- E"))return"Castep";if(g.contains("%BLOCK"))return"Siesta";if(6<=d&&10>d&&(g.startsWith("DIRECT")||g.startsWith("CARTESIAN")))return"VaspPoscar"}return null},"~A");b.getFileTypefromFilter=c(b,"getFileTypefromFilter",function(a){var d=null==a?-1:a.toLowerCase().indexOf("filetype");return 0>d?null:a.substring(d+8,(a+";").indexOf(";",d)).$replace("="," ").trim()},"~S");b.fixDOSName=

c(b,"fixDOSName",function(a){return 0<=a.indexOf(":\\")?a.$replace("\\","/"):a},"~S");b.readerSets=w(-1,"cif. ;Cif;Cif2;MMCif;MMTF;MagCif;BCIF; molxyz. ;Mol3D;Mol;Xyz; more. ;AFLOW;BinaryDcd;CDX;Gromacs;Jcampdx;MdCrd;MdTop;Mol2;TlsDataOnly; quantum. ;Adf;Csf;Dgrid;GamessUK;GamessUS;Gaussian;GaussianFchk;GaussianWfn;Jaguar;Molden;MopacGraphf;GenNBO;NWChem;Psi;Qchem;QCJSON;WebMO;Orca;MO;Ams; pdb. ;Pdb;Pqr;P2n;JmolData; pymol. ;PyMOL; simple. ;Alchemy;Ampac;Cube;FoldingXyz;GhemicalMM;HyperChem;Jme;JSON;Mopac;MopacArchive;Tinker;Input;FAH; spartan. ;Spartan;SpartanSmol;Odyssey; xtal. ;Abinit;Aims;Bilbao;Castep;Cgd;Crystal;Dmol;Espresso;Gulp;Jana;Magres;Shelx;Siesta;VaspOutcar;VaspPoscar;Wien2k;Xcrysden;PWmat;Optimade;Cmdf; xml. ;XmlCdx;XmlArgus;XmlCml;XmlChem3d;XmlMolpro;XmlOdyssey;XmlXsd;XmlVasp;XmlQE;".split(" "));

b.cdxMagic=P(-1,[86,106,67,68]);b.cmdfMagic=P(-1,[67,77,68,70]);b.mmtfMagic=P(-1,[109,109,116,102]);b.bcifMolstarMagic=P(-1,[109,111,108,42]);b.bcifDensityMagic=P(-1,[68,101,110,115]);b.bcifVolumeMagic=P(-1,[86,111,108,117]);b.bcifModelMagic=P(-1,[77,111,100,101]);b.bcifCoordMagic=P(-1,[67,111,111,114,100]);b.bcifServerMagic=P(-1,[83,69,82,86,69,82]);b.sptRecords=w(-1,["spt","# Jmol state","# Jmol script","JmolManifest"]);b.m3dStartRecords=w(-1,["Alchemy","STRUCTURE 1.00 1"]);b.cubeFileStartRecords=

w(-1,["Cube","JVXL","#JVXL"]);b.mol2Records=w(-1,["Mol2","mol2","@<TRIPOS>"]);b.webmoFileStartRecords=w(-1,["WebMO","[HEADER]"]);b.moldenFileStartRecords=w(-1,["Molden","[Molden","MOLDEN","[MOLDEN"]);b.dcdFileStartRecords=w(-1,["BinaryDcd","T\x00\x00\x00CORD","\x00\x00\x00TCORD"]);b.tlsDataOnlyFileStartRecords=w(-1,["TlsDataOnly","REFMAC\n\nTL","REFMAC\r\n\r\n","REFMAC\r\rTL"]);b.inputFileStartRecords=w(-1,["Input","#ZMATRIX","%mem=","AM1","$rungauss"]);b.magresFileStartRecords=w(-1,["Magres","#$magres",

"# magres"]);b.pymolStartRecords=w(-1,["PyMOL","}q"]);b.janaStartRecords=w(-1,["Jana","Version Jana"]);b.jsonStartRecords=w(-1,["JSON",'{"mol":']);b.jcampdxStartRecords=w(-1,["Jcampdx","##TITLE"]);b.jmoldataStartRecords=w(-1,["JmolData","REMARK 6 Jmol"]);b.pqrStartRecords=w(-1,["Pqr","REMARK 1 PQR","REMARK The B-factors"]);b.p2nStartRecords=w(-1,["P2n","REMARK 1 P2N"]);b.cif2StartRecords=w(-1,["Cif2","#\\#CIF_2","\u00ef\u00bb\u00bf#\\#CIF_2"]);b.xmlStartRecords=w(-1,["Xml","<?xml"]);b.cfiStartRecords=

w(-1,["Input","$CFI"]);b.fileStartsWithRecords=w(-1,[J.adapter.smarter.Resolver.xmlStartRecords,J.adapter.smarter.Resolver.sptRecords,J.adapter.smarter.Resolver.m3dStartRecords,J.adapter.smarter.Resolver.cubeFileStartRecords,J.adapter.smarter.Resolver.mol2Records,J.adapter.smarter.Resolver.webmoFileStartRecords,J.adapter.smarter.Resolver.moldenFileStartRecords,J.adapter.smarter.Resolver.dcdFileStartRecords,J.adapter.smarter.Resolver.tlsDataOnlyFileStartRecords,J.adapter.smarter.Resolver.inputFileStartRecords,

J.adapter.smarter.Resolver.magresFileStartRecords,J.adapter.smarter.Resolver.pymolStartRecords,J.adapter.smarter.Resolver.janaStartRecords,J.adapter.smarter.Resolver.jsonStartRecords,J.adapter.smarter.Resolver.jcampdxStartRecords,J.adapter.smarter.Resolver.jmoldataStartRecords,J.adapter.smarter.Resolver.pqrStartRecords,J.adapter.smarter.Resolver.p2nStartRecords,J.adapter.smarter.Resolver.cif2StartRecords,J.adapter.smarter.Resolver.cfiStartRecords]);b.n=E(1,0);b.mmcifLineStartRecords=w(-1,"MMCif _entry.id _database_PDB_ _pdbx_ _chem_comp.pdbx_type _audit_author.name _atom_site.".split(" "));

b.cifLineStartRecords=w(-1,["Cif","data_","_publ"]);b.pdbLineStartRecords=w(-1,"Pdb;HEADER;OBSLTE;TITLE ;CAVEAT;COMPND;SOURCE;KEYWDS;EXPDTA;AUTHOR;REVDAT;SPRSDE;JRNL ;REMARK ;DBREF ;SEQADV;SEQRES;MODRES;HELIX ;SHEET ;TURN ;CRYST1;ORIGX1;ORIGX2;ORIGX3;SCALE1;SCALE2;SCALE3;ATOM ;HETATM;MODEL ;LINK ;USER MOD ".split(";"));b.cgdLineStartRecords=w(-1,["Cgd","EDGE ","edge "]);b.shelxLineStartRecords=w(-1,"Shelx;TITL ;ZERR ;LATT ;SYMM ;CELL ;TITL\t".split(";"));b.ghemicalMMLineStartRecords=w(-1,["GhemicalMM",

"!Header mm1gp","!Header gpr"]);b.jaguarLineStartRecords=w(-1,["Jaguar"," | Jaguar version"]);b.mdlLineStartRecords=w(-1,["Mol","$MDL "]);b.spartanSmolLineStartRecords=w(-1,["SpartanSmol","INPUT="]);b.csfLineStartRecords=w(-1,["Csf","local_transform"]);b.mdTopLineStartRecords=w(-1,["MdTop","%FLAG TITLE"]);b.hyperChemLineStartRecords=w(-1,["HyperChem","mol 1"]);b.vaspOutcarLineStartRecords=w(-1,["VaspOutcar"," vasp."," INCAR:"]);b.orcaInputLineStartRecords=w(-1,["Orca","* xyz","*xyz"]);b.lineStartsWithRecords=

w(-1,[J.adapter.smarter.Resolver.mmcifLineStartRecords,J.adapter.smarter.Resolver.cifLineStartRecords,J.adapter.smarter.Resolver.pdbLineStartRecords,J.adapter.smarter.Resolver.cgdLineStartRecords,J.adapter.smarter.Resolver.shelxLineStartRecords,J.adapter.smarter.Resolver.ghemicalMMLineStartRecords,J.adapter.smarter.Resolver.jaguarLineStartRecords,J.adapter.smarter.Resolver.mdlLineStartRecords,J.adapter.smarter.Resolver.spartanSmolLineStartRecords,J.adapter.smarter.Resolver.csfLineStartRecords,J.adapter.smarter.Resolver.mol2Records,

J.adapter.smarter.Resolver.mdTopLineStartRecords,J.adapter.smarter.Resolver.hyperChemLineStartRecords,J.adapter.smarter.Resolver.vaspOutcarLineStartRecords,J.adapter.smarter.Resolver.orcaInputLineStartRecords]);b.bilbaoContainsRecords=w(-1,["Bilbao",">Bilbao Crystallographic Server<"]);b.xmlContainsRecords=w(-1,'Xml <?xml <atom <molecule <reaction <cml <bond .dtd" <list> <entry <identifier http://www.xml-cml.org/schema/cml2/core'.split(" "));b.gaussianContainsRecords=w(-1,["Gaussian","Entering Gaussian System",

"Entering Link 1","1998 Gaussian, Inc."]);b.ampacContainsRecords=w(-1,["Ampac","AMPAC Version"]);b.mopacContainsRecords=w(-1,"Mopac;MOPAC 93 (c) Fujitsu;MOPAC FOR LINUX (PUBLIC DOMAIN VERSION);MOPAC: VERSION 6;MOPAC 7;MOPAC2;MOPAC (PUBLIC".split(";"));b.qchemContainsRecords=w(-1,["Qchem","Welcome to Q-Chem","A Quantum Leap Into The Future Of Chemistry"]);b.gamessUKContainsRecords=w(-1,["GamessUK","GAMESS-UK","G A M E S S - U K"]);b.gamessUSContainsRecords=w(-1,["GamessUS","GAMESS","$CONTRL"]);

b.spartanBinaryContainsRecords=w(-1,["SpartanSmol","|PropertyArchive","_spartan","spardir","BEGIN Directory Entry Molecule"]);b.spartanContainsRecords=w(-1,["Spartan","Spartan","converted archive file"]);b.adfContainsRecords=w(-1,["Adf","Amsterdam Density Functional"]);b.amsContainsRecords=w(-1,["Ams","Amsterdam Modeling Suite"]);b.psiContainsRecords=w(-1,["Psi"," PSI 3","PSI3:"]);b.nwchemContainsRecords=w(-1,["NWChem"," argument 1 = "]);b.uicrcifContainsRecords=w(-1,["Cif","Crystallographic Information File"]);

b.dgridContainsRecords=w(-1,["Dgrid","BASISFILE created by DGrid"]);b.crystalContainsRecords=w(-1,["Crystal","* CRYSTAL","TORINO","DOVESI"]);b.dmolContainsRecords=w(-1,["Dmol","DMol^3"]);b.gulpContainsRecords=w(-1,["Gulp","GENERAL UTILITY LATTICE PROGRAM"]);b.espressoContainsRecords=w(-1,["Espresso","Program PWSCF","Program PHONON"]);b.siestaContainsRecords=w(-1,["Siesta","MD.TypeOfRun","SolutionMethod","MeshCutoff","WELCOME TO SIESTA"]);b.xcrysDenContainsRecords=

w(-1,["Xcrysden","PRIMVEC","CONVVEC","PRIMCOORD","ANIMSTEP"]);b.mopacArchiveContainsRecords=w(-1,["MopacArchive","SUMMARY OF PM"]);b.abinitContainsRecords=w(-1,["Abinit","http://www.abinit.org","Catholique","Louvain"]);b.qcJsonContainsRecords=w(-1,["QCJSON",'"QCJSON']);b.optimadeContainsRecords=w(-1,["Optimade",'"cartesian_site_positions":','"api_version":',"optimade"]);b.jsonArrayContainsRecords=w(-1,["JSON",'"atomArray":[','"atomArray" : [']);b.orcaContainsRecords=w(-1,["Orca","* O R C A *"]);

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1,d)):(g<this.minRight?this.minRight=g:g>this.maxRight&&(this.maxRight=g),this.eleRight=this.eleRight.addTuple(a+1,d));return this},"~N,JU.T3");b.getDimensionValue=c(b,"getDimensionValue",function(a,d){null==a&&System.out.println("bspt.Node ???");switch(d){case 0:return a.x;case 1:return a.y;default:return a.z}},"JU.T3,~N")});u("J.c");C(["java.lang.Enum"],"J.c.CBK",["JU.SB"],function(){var b=H(J.c,"CBK",Enum);b.getCallback=c(b,"getCallback",function(a){a=a.toUpperCase();var d=a.indexOf("CALLBACK");

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b;this.shadesA=x.getShades(this.colixA=a);this.shadesB=x.getShades(this.colixB=d);this.calcArgbEndcap(!0,!1);this.calcCosSin(this.dxB,this.dyB,this.dzB);this.calcPoints(3,!1);this.interpolate(0,1,this.xyzfRaster,this.xyztRaster);this.interpolate(1,2,this.xyzfRaster,this.xyztRaster);k=this.xyzfRaster;2==b&&this.renderFlatEndcap(!0,!1,k);x.setZMargin(5);a=x.width;d=x.zbuf;c=k[0];e=k[1];h=k[2];k=k[3];j=x.pixel;for(p=this.rasterCount;0<=--p;)s=k[p]>>8,G=s>>1,M=c[p],q=e[p],N=h[p],this.endCapHidden&&0!=

this.argbEndcap&&(this.clipped?(x.plotPixelClippedArgb(this.argbEndcap,this.xEndcap+M,this.yEndcap+q,this.zEndcap-N-1,a,d,j),x.plotPixelClippedArgb(this.argbEndcap,this.xEndcap-M,this.yEndcap-q,this.zEndcap+N-1,a,d,j)):(x.plotPixelUnclipped(this.argbEndcap,this.xEndcap+M,this.yEndcap+q,this.zEndcap-N-1,a,d,j),x.plotPixelUnclipped(this.argbEndcap,this.xEndcap-M,this.yEndcap-q,this.zEndcap+N-1,a,d,j))),this.line3d.plotLineDeltaAOld(this.shadesA,this.shadesB,g,s,this.xA+M,this.yA+q,this.zA-N,this.dxB,

this.dyB,this.dzB,this.clipped),m&&this.line3d.plotLineDeltaOld(this.shadesA[G],this.shadesB[G],this.xA-M,this.yA-q,this.zA+N,this.dxB,this.dyB,this.dzB,this.clipped);x.setZMargin(0);3==b&&this.renderSphericalEndcaps()}},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");c(b,"renderBitsFloat",function(a,d,g,b,c,e,h){var k=this.g3d;null==this.ptA0&&(this.ptA0=new JU.P3,this.ptB0=new JU.P3);this.ptA0.setT(e);var m=B(c/2)+1,j=Math.round(e.x),p=Math.round(e.y),q=Math.round(e.z),x=Math.round(h.x),s=Math.round(h.y),G=

Math.round(h.z),M=k.clipCode3(j-m,p-m,q-m),j=k.clipCode3(j+m,p+m,q+m),p=k.clipCode3(x-m,s-m,G-m),m=k.clipCode3(x+m,s+m,G+m),x=M|j|p|m;this.clipped=0!=x;if(!(-1==x||0!=(M&m&j&p))){this.dxBf=h.x-e.x;this.dyBf=h.y-e.y;this.dzBf=h.z-e.z;0<c&&(this.diameter=c,this.xAf=e.x,this.yAf=e.y,this.zAf=e.z);e=0==g&&(this.clipped||2==b||0==b);this.xA=D(this.xAf);this.yA=D(this.yAf);this.zA=D(this.zAf);this.dxB=D(this.dxBf);this.dyB=D(this.dyBf);this.dzB=D(this.dzBf);this.shadesA=k.getShades(this.colixA=a);this.shadesB=

k.getShades(this.colixB=d);this.endcaps=b;this.calcArgbEndcap(!0,!0);x=this.xyzfRaster;0<c&&this.generateBaseEllipsePrecisely(!1);2==b&&this.renderFlatEndcap(!0,!0,x);this.line3d.setLineBits(this.dxBf,this.dyBf);k.setZMargin(5);c=k.pixel;a=k.width;d=k.zbuf;h=x[0];M=x[1];m=x[2];x=x[3];for(s=this.rasterCount;0<=--s;){var G=x[s]>>8,j=G>>1,p=h[s],q=M[s],N=m[s];this.endCapHidden&&0!=this.argbEndcap&&(this.clipped?(k.plotPixelClippedArgb(this.argbEndcap,this.xEndcap+p,this.yEndcap+q,this.zEndcap-N-1,a,

d,c),k.plotPixelClippedArgb(this.argbEndcap,this.xEndcap-p,this.yEndcap-q,this.zEndcap+N-1,a,d,c)):(k.plotPixelUnclipped(this.argbEndcap,this.xEndcap+p,this.yEndcap+q,this.zEndcap-N-1,a,d,c),k.plotPixelUnclipped(this.argbEndcap,this.xEndcap-p,this.yEndcap-q,this.zEndcap+N-1,a,d,c)));this.ptA0.set(this.xA+p,this.yA+q,this.zA-N);this.ptB0.setT(this.ptA0);this.ptB0.x+=this.dxB;this.ptB0.y+=this.dyB;this.ptB0.z+=this.dzB;this.line3d.plotLineDeltaABitsFloat(this.shadesA,this.shadesB,G,this.ptA0,this.ptB0,

g,this.clipped);e&&(this.ptA0.set(this.xA-p,this.yA-q,this.zA+N),this.ptB0.setT(this.ptA0),this.ptB0.x+=this.dxB,this.ptB0.y+=this.dyB,this.ptB0.z+=this.dzB,this.line3d.plotLineDeltaABitsFloat(this.shadesA,this.shadesB,j,this.ptA0,this.ptB0,g,this.clipped))}k.setZMargin(0);3==b&&this.renderSphericalEndcaps();this.xAf+=this.dxBf;this.yAf+=this.dyBf;this.zAf+=this.dzBf}},"~N,~N,~N,~N,~N,JU.P3,JU.P3");c(b,"renderBits",function(a,d,g,b,c,e,h){var k=this.g3d;if(0==c||1==c)this.line3d.plotLineBits(k.getColorArgbOrGray(a),

k.getColorArgbOrGray(d),e,h,0,0,!1);else{this.ptA0i.setT(e);var m=B(c/2)+1,j=e.x,p=e.y,q=e.z,x=h.x,s=h.y,G=h.z,M=k.clipCode3(j-m,p-m,q-m),j=k.clipCode3(j+m,p+m,q+m),p=k.clipCode3(x-m,s-m,G-m),m=k.clipCode3(x+m,s+m,G+m),x=M|j|p|m;this.clipped=0!=x;if(!(-1==x||0!=(M&m&j&p))){this.dxBf=h.x-e.x;this.dyBf=h.y-e.y;this.dzBf=h.z-e.z;0<c&&(this.diameter=c,this.xAf=e.x,this.yAf=e.y,this.zAf=e.z);e=0==g&&(this.clipped||2==b||0==b);this.xA=D(this.xAf);this.yA=D(this.yAf);this.zA=D(this.zAf);this.dxB=D(this.dxBf);

this.dyB=D(this.dyBf);this.dzB=D(this.dzBf);this.shadesA=k.getShades(this.colixA=a);this.shadesB=k.getShades(this.colixB=d);this.endcaps=b;this.calcArgbEndcap(!0,!0);x=this.xyzfRaster;0<c&&this.generateBaseEllipsePrecisely(!1);2==b&&this.renderFlatEndcap(!0,!0,x);this.line3d.setLineBits(this.dxBf,this.dyBf);k.setZMargin(5);c=k.pixel;a=k.width;d=k.zbuf;h=x[0];M=x[1];m=x[2];x=x[3];for(s=this.rasterCount;0<=--s;){var G=x[s]>>8,j=G>>1,p=h[s],q=M[s],N=m[s];this.endCapHidden&&0!=this.argbEndcap&&(this.clipped?

(k.plotPixelClippedArgb(this.argbEndcap,this.xEndcap+p,this.yEndcap+q,this.zEndcap-N-1,a,d,c),k.plotPixelClippedArgb(this.argbEndcap,this.xEndcap-p,this.yEndcap-q,this.zEndcap+N-1,a,d,c)):(k.plotPixelUnclipped(this.argbEndcap,this.xEndcap+p,this.yEndcap+q,this.zEndcap-N-1,a,d,c),k.plotPixelUnclipped(this.argbEndcap,this.xEndcap-p,this.yEndcap-q,this.zEndcap+N-1,a,d,c)));this.ptA0i.set(this.xA+p,this.yA+q,this.zA-N);this.ptB0i.setT(this.ptA0i);this.ptB0i.x+=this.dxB;this.ptB0i.y+=this.dyB;this.ptB0i.z+=

this.dzB;this.line3d.plotLineDeltaABitsInt(this.shadesA,this.shadesB,G,this.ptA0i,this.ptB0i,g,this.clipped);e&&(this.ptA0i.set(this.xA-p,this.yA-q,this.zA+N),this.ptB0i.setT(this.ptA0i),this.ptB0i.x+=this.dxB,this.ptB0i.y+=this.dyB,this.ptB0i.z+=this.dzB,this.line3d.plotLineDeltaABitsInt(this.shadesA,this.shadesB,j,this.ptA0i,this.ptB0i,g,this.clipped))}k.setZMargin(0);3==b&&this.renderSphericalEndcaps();this.xAf+=this.dxBf;this.yAf+=this.dyBf;this.zAf+=this.dzBf}}},"~N,~N,~N,~N,~N,JU.P3i,JU.P3i");

c(b,"renderConeOld",function(a,d,g,b,c,e,h,k,m,j,p){this.dxBf=h-(this.xAf=b);this.dyBf=k-(this.yAf=c);this.dzBf=m-(this.zAf=e);this.xA=B(Math.floor(this.xAf));this.yA=B(Math.floor(this.yAf));this.zA=B(Math.floor(this.zAf));this.dxB=B(Math.floor(this.dxBf));this.dyB=B(Math.floor(this.dyBf));this.dzB=B(Math.floor(this.dzBf));this.xTip=h;this.yTip=k;this.zTip=m;this.shadesA=this.g3d.getShades(this.colixA=a);var q=this.shader.getShadeIndex(this.dxB,this.dyB,-this.dzB);a=this.g3d;b=a.pixel;c=a.width;e=

a.zbuf;a.plotPixelClippedArgb(this.shadesA[q],D(h),D(k),D(m),c,e,b);this.diameter=g;if(1>=g)1==g&&this.line3d.plotLineDeltaOld(this.colixA,this.colixA,this.xA,this.yA,this.zA,this.dxB,this.dyB,this.dzB,this.clipped);else{this.endcaps=d;this.calcArgbEndcap(!1,!0);this.generateBaseEllipsePrecisely(p);!p&&2==this.endcaps&&this.renderFlatEndcap(!1,!0,this.xyzfRaster);a.setZMargin(5);d=this.xyztRaster[0];g=this.xyztRaster[1];h=this.xyztRaster[2];k=this.xyzfRaster[3];m=this.shadesA;for(var q=this.endCapHidden&&

0!=this.argbEndcap,x=this.rasterCount;0<=--x;){var s=d[x],G=g[x],M=h[x],N=k[x]>>8,n=this.xAf+s,u=this.yAf+G,r=this.zAf-M,s=this.xAf-s,G=this.yAf-G,M=this.zAf+M,v=m[0];q&&(a.plotPixelClippedArgb(this.argbEndcap,D(n),D(u),D(r),c,e,b),a.plotPixelClippedArgb(this.argbEndcap,D(s),D(G),D(M),c,e,b));0!=v&&(this.line3d.plotLineDeltaAOld(m,m,0,N,D(n),D(u),D(r),B(Math.ceil(this.xTip-n)),B(Math.ceil(this.yTip-u)),B(Math.ceil(this.zTip-r)),!0),j&&(this.line3d.plotLineDeltaAOld(m,m,0,N,D(n),D(u)+1,D(r),B(Math.ceil(this.xTip-

n)),B(Math.ceil(this.yTip-u))+1,B(Math.ceil(this.zTip-r)),!0),this.line3d.plotLineDeltaAOld(m,m,0,N,D(n)+1,D(u),D(r),B(Math.ceil(this.xTip-n))+1,B(Math.ceil(this.yTip-u)),B(Math.ceil(this.zTip-r)),!0)),!p&&!(2!=this.endcaps&&0<this.dzB)&&this.line3d.plotLineDeltaOld(v,v,D(s),D(G),D(M),B(Math.ceil(this.xTip-s)),B(Math.ceil(this.yTip-G)),B(Math.ceil(this.zTip-M)),!0))}a.setZMargin(0)}},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~B,~B");c(b,"generateBaseEllipsePrecisely",function(a){this.calcCosSin(this.dxBf,this.dyBf,

this.dzBf);this.calcPoints(a?2:3,!0);this.interpolatePrecisely(0,1,this.xyzfRaster,this.xyztRaster);a||this.interpolatePrecisely(1,2,this.xyzfRaster,this.xyztRaster);for(a=3;0<=--a;)for(var d=this.rasterCount;0<=--d;)this.xyzfRaster[a][d]=B(Math.floor(this.xyztRaster[a][d]))},"~B");c(b,"calcPoints",function(a,d){this.calcRotatedPoint(0,0,d,this.xyzfRaster,this.xyztRaster);this.calcRotatedPoint(0.5,1,d,this.xyzfRaster,this.xyztRaster);3==(this.rasterCount=a)&&this.calcRotatedPoint(1,2,d,this.xyzfRaster,

this.xyztRaster)},"~N,~B");c(b,"calcCosSin",function(a,d,g){var b=a*a+d*d;if(0==b)this.cosPhi=this.cosTheta=1,this.sinPhi=0;else{var c=Math.sqrt(b),b=Math.sqrt(b+g*g);this.cosTheta=g/b;this.cosPhi=a/c;this.sinPhi=d/c}},"~N,~N,~N");c(b,"calcRotatedPoint",function(a,d,g,b,c){c[3][d]=a;a*=3.141592653589793;var e=Math.sin(a)*this.cosTheta,h=Math.cos(a);a=this.radius*(e*this.cosPhi-h*this.sinPhi);e=this.radius*(e*this.sinPhi+h*this.cosPhi);h=this.radius2-(a*a+e*e);h=0<h?Math.sqrt(h):0;g?(c[0][d]=a,c[1][d]=

e,c[2][d]=h):(this.tEvenDiameter?(b[0][d]=B(a-0.5),b[1][d]=B(e-0.5)):(b[0][d]=B(a),b[1][d]=B(e)),b[2][d]=B(h+0.5));b[3][d]=this.shader.getShadeFp8(a,e,h)},"~N,~N,~B,~A,~A");c(b,"allocRaster",function(a,d,g){if(this.rasterCount>=d[0].length)for(;this.rasterCount>=d[0].length;){for(var b=4;0<=--b;)d[b]=JU.AU.doubleLengthI(d[b]);g[3]=JU.AU.doubleLengthF(g[3])}if(a)for(;this.rasterCount>=g[0].length;)for(b=3;0<=--b;)g[b]=JU.AU.doubleLengthF(g[b]);return this.rasterCount++},"~B,~A,~A");c(b,"interpolate",

function(a,d,g,b){var c=g[0],e=g[1],c=c[d]-c[a];0>c&&(c=-c);e=e[d]-e[a];0>e&&(e=-e);if(!(1>=c+e)){for(var h=this.allocRaster(!1,g,b),c=g[0],e=g[1],k=g[3],m=b[3][a],j=b[3][d],p=4;0<=--p;){var q=(m+j)/2;this.calcRotatedPoint(q,h,!1,g,b);if(c[h]==c[a]&&e[h]==e[a])k[a]=k[a]+k[h]>>>1,m=q;else if(c[h]==c[d]&&e[h]==e[d])k[d]=k[d]+k[h]>>>1,j=q;else{this.interpolate(a,h,g,b);this.interpolate(h,d,g,b);return}}c[h]=c[a];e[h]=e[d]}},"~N,~N,~A,~A");c(b,"interpolatePrecisely",function(a,d,g,b){var c=b[0],e=b[1],

h=B(Math.floor(c[d]))-B(Math.floor(c[a]));0>h&&(h=-h);e=B(Math.floor(e[d]))-B(Math.floor(e[a]));0>e&&(e=-e);if(!(1>=h+e)){for(var e=b[3],h=e[a],k=e[d],m=this.allocRaster(!0,g,b),c=b[0],e=b[1],j=g[3],p=4;0<=--p;){var q=(h+k)/2;this.calcRotatedPoint(q,m,!0,g,b);if(B(Math.floor(c[m]))==B(Math.floor(c[a]))&&B(Math.floor(e[m]))==B(Math.floor(e[a])))j[a]=j[a]+j[m]>>>1,h=q;else if(B(Math.floor(c[m]))==B(Math.floor(c[d]))&&B(Math.floor(e[m]))==B(Math.floor(e[d])))j[d]=j[d]+j[m]>>>1,k=q;else{this.interpolatePrecisely(a,

m,g,b);this.interpolatePrecisely(m,d,g,b);return}}c[m]=c[a];e[m]=e[d]}},"~N,~N,~A,~A");c(b,"renderFlatEndcap",function(a,d,g){var b,c;if(d){if(0==this.dzBf||0==this.colixEndcap||!this.g3d.setC(this.colixEndcap))return;d=this.xAf;b=this.yAf;c=this.zAf;a&&0>this.dzBf&&(d+=this.dxBf,b+=this.dyBf,c+=this.dzBf);d=D(d);b=D(b);c=D(c)}else{if(0==this.dzB||0==this.colixEndcap||!this.g3d.setC(this.colixEndcap))return;d=this.xAend;b=this.yAend;c=this.zAend;a&&0>this.dzB&&(d+=this.dxB,b+=this.dyB,c+=this.dzB)}var e=

g[1][0];a=g[1][0];var h=0,k=0,m=g[0],j=g[1];g=g[2];for(var p=this.rasterCount;0<--p;){var q=j[p];q<e?e=q:q>a?a=q:(q=-q,q<e?e=q:q>a&&(a=q))}for(q=e;q<=a;++q){for(var e=2147483647,x=-2147483648,p=this.rasterCount;0<=--p;){if(j[p]==q){var s=m[p];s<e&&(e=s,h=g[p]);s>x&&(x=s,k=g[p])}j[p]==-q&&(s=-m[p],s<e&&(e=s,h=-g[p]),s>x&&(x=s,k=-g[p]))}p=x-e+1;this.g3d.setColorNoisy(this.endcapShadeIndex);this.g3d.plotPixelsClippedRaster(p,d+e,b+q,c-h-1,c-k-1,null,null)}},"~B,~B,~A");c(b,"renderSphericalEndcaps",function(){0!=

this.colixA&&this.g3d.setC(this.colixA)&&this.g3d.fillSphereXYZ(this.diameter,this.xA,this.yA,this.zA+1);0!=this.colixB&&this.g3d.setC(this.colixB)&&this.g3d.fillSphereXYZ(this.diameter,this.xA+this.dxB,this.yA+this.dyB,this.zA+this.dzB+1)});c(b,"calcArgbEndcap",function(a,d){this.tEvenDiameter=0==(this.diameter&1);this.radius=this.diameter/2;this.radius2=this.radius*this.radius;this.endCapHidden=!1;var g=d?this.dzBf:this.dzB;if(!(3==this.endcaps||0==g)){this.xEndcap=this.xAend=this.xA;this.yEndcap=

this.yAend=this.yA;this.zEndcap=this.zAend=this.zA;var b=d?this.dxBf:this.dxB,c=d?this.dyBf:this.dyB;0<=g||!a?(this.endcapShadeIndex=this.shader.getShadeIndex(-b,-c,g),0==this.colixA?(this.xAend+=B(this.dxB/2),this.yAend+=B(this.dyB/2),this.zAend+=B(this.dzB/2),this.colixEndcap=this.colixB):this.colixEndcap=this.colixA):(this.endcapShadeIndex=this.shader.getShadeIndex(b,c,-g),0==this.colixB?(this.colixEndcap=this.colixA,this.xAend-=B(this.dxB/2),this.yAend-=B(this.dyB/2),this.zAend-=B(this.dzB/2)):

(this.colixEndcap=this.colixB,this.xEndcap+=this.dxB,this.yEndcap+=this.dyB,this.zEndcap+=this.dzB));g=this.colixEndcap==this.colixA?this.shadesA:this.shadesB;56<this.endcapShadeIndex&&(this.endcapShadeIndex=56);this.argbEndcap=g[this.endcapShadeIndex];this.endCapHidden=1==this.endcaps}},"~B,~B")});u("J.g3d");O(J.g3d,"G3DRenderer");u("J.g3d");C(["J.api.JmolRendererInterface","JU.GData","JU.P3i","$.V3"],"J.g3d.Graphics3D","java.util.Arrays JU.AU J.api.Interface J.c.STER J.g3d.CylinderRenderer $.LineRenderer $.Pixelator $.PixelatorScreened $.PixelatorShaded $.PixelatorT $.Platform3D $.SphereRenderer $.TextRenderer $.TextString JU.C $.Normix".split(" "),

function(){var b=v(function(){this.hermite3d=this.circle3d=this.triangle3d=this.cylinder3d=this.sphere3d=this.line3d=this.platform=null;this.antialias2=this.isFullSceneAntialiasingEnabled=!1;this.strings=null;this.stringCount=0;this.anaglyphChannelBytes=null;this.$haveTranslucentObjects=this.twoPass=!1;this.zbufT=this.zbuf=this.pbufT=this.pbuf=null;this.translucencyMask=0;this.renderLow=!1;this.shadesCurrent=null;this.anaglyphLength=0;this.pixelShaded=this.pixelScreened=this.pixelT0=this.pixel0=this.pixel=

null;this.zMargin=0;this.aobuf=null;this.translucencyLog=this.lastRawColor=this.currentShadeIndex=0;this.wasScreened=!1;this.saveDiffuse=this.saveAmbient=0;this.shadeIndexes2Sided=this.shadeIndexes=this.vectorNormal=this.vectorAC=this.vectorAB=this.sC=this.sB=this.sA=null;this.pass2Flag01=0;r(this,arguments)},J.g3d,"Graphics3D",JU.GData,J.api.JmolRendererInterface);Q(b,function(){this.sA=new JU.P3i;this.sB=new JU.P3i;this.sC=new JU.P3i;this.vectorAB=new JU.V3;this.vectorAC=new JU.V3;this.vectorNormal=

new JU.V3;this.shadeIndexes=P(JU.GData.normixCount,0);this.shadeIndexes2Sided=P(JU.GData.normixCount,0)});z(b,function(){L(this,J.g3d.Graphics3D,[]);for(var a=JU.GData.normixCount;0<=--a;)this.transformedVectors[a]=new JU.V3});j(b,"isWebGL",function(){return!1});j(b,"clear",function(){this.stringCount=0;this.strings=null;J.g3d.TextRenderer.clearFontCache()});j(b,"destroy",function(){this.releaseBuffers();this.graphicsForMetrics=this.pixelScreened=this.pixelT0=this.pixel=this.pixel0=this.pixelShaded=

this.platform=null});c(b,"setZMargin",function(a){this.zMargin=a},"~N");j(b,"initialize",function(a,d){this.vwr=a;this.apiPlatform=d;this.platform=new J.g3d.Platform3D(d);this.pixel=this.pixel0=new J.g3d.Pixelator(this);this.graphicsForMetrics=this.platform.getGraphicsForMetrics();this.line3d=new J.g3d.LineRenderer(this);this.sphere3d=new J.g3d.SphereRenderer(this);this.cylinder3d=new J.g3d.CylinderRenderer(this)},"JV.Viewer,J.api.GenericPlatform");j(b,"addRenderer",function(a){switch(a){case 1073741880:null==

this.circle3d&&(this.circle3d=this.getRenderer("Circle"));break;case 553648143:null==this.hermite3d&&(this.hermite3d=this.getRenderer("Hermite"));case 1073742182:null==this.triangle3d&&(this.triangle3d=this.getRenderer("Triangle"),this.triangle3d.isOrthographic=!this.vwr.tm.perspectiveDepth)}},"~N");c(b,"getRenderer",function(a){a=J.api.Interface.getOption("g3d."+a+"Renderer",this.vwr,"render");if(null==a)throw new NullPointerException("Interface");a.set(this,this);return a},"~S");j(b,"setWindowParameters",

function(a,d,g){this.setWinParams(a,d,g);this.currentlyRendering&&this.endRendering()},"~N,~N,~B");j(b,"checkTranslucent",function(a){a&&(this.$haveTranslucentObjects=!0);return!this.twoPass||this.twoPass&&this.isPass2==a},"~B");j(b,"beginRendering",function(a,d,g,b){this.currentlyRendering&&this.endRendering();this.renderLow=b;if(this.windowWidth!=this.newWindowWidth||this.windowHeight!=this.newWindowHeight||this.newAntialiasing!=this.isFullSceneAntialiasingEnabled)this.windowWidth=this.newWindowWidth,

this.windowHeight=this.newWindowHeight,this.isFullSceneAntialiasingEnabled=this.newAntialiasing,this.releaseBuffers();this.setRotationMatrix(a);this.line3d.isOrthographic=!this.vwr.tm.perspectiveDepth;null!=this.triangle3d&&(this.triangle3d.isOrthographic=!this.vwr.tm.perspectiveDepth);this.antialiasEnabled=this.antialiasThisFrame=this.newAntialiasing;this.currentlyRendering=!0;if(null!=this.strings)for(a=Math.min(this.strings.length,this.stringCount);0<=--a;)this.strings[a]=null;this.stringCount=

0;this.twoPass=!0;this.isPass2=!1;this.colixCurrent=this.pass2Flag01=0;this.$haveTranslucentObjects=this.wasScreened=!1;this.pixel=this.pixel0;this.pixel.bgcolor=this.bgcolor;this.contrastColix=JU.C.getBgContrast(this.bgcolor);this.translucentCoverOnly=!d;null==this.pbuf&&(this.platform.allocateBuffers(this.windowWidth,this.windowHeight,this.antialiasThisFrame,g),this.pbuf=this.platform.pBuffer,this.zbuf=this.platform.zBuffer,this.aobuf=null,this.pixel0.setBuf(),null!=this.pixelT0&&this.pixelT0.setBuf(),

null!=this.pixelShaded&&this.pixelShaded.setBuf());this.setWidthHeight(this.antialiasThisFrame);null!=this.pixelScreened&&(this.pixelScreened.width=this.width);this.platform.clearBuffer();null!=this.backgroundImage&&this.plotImage(-2147483648,0,-2147483648,this.backgroundImage,null,0,0,0);this.textY=0},"JU.M3,~B,~B,~B");j(b,"setBackgroundTransparent",function(a){null!=this.platform&&this.platform.setBackgroundTransparent(a)},"~B");c(b,"releaseBuffers",function(){this.aobuf=this.zbufT=this.pbufT=this.zbuf=

this.pbuf=null;this.platform.releaseBuffers();this.line3d.clearLineCache()});j(b,"setPass2",function(a){if(!this.$haveTranslucentObjects||!this.currentlyRendering)return!1;this.isPass2=!0;this.pass2Flag01=1;this.colixCurrent=0;if(null==this.pbufT||this.antialias2!=a)this.platform.allocateTBuffers(a),this.pbufT=this.platform.pBufferT,this.zbufT=this.platform.zBufferT;this.antialias2=a;this.antialiasThisFrame&&!this.antialias2&&this.downsampleFullSceneAntialiasing(!0);this.platform.clearTBuffer();null==

this.pixelT0&&(this.pixelT0=new J.g3d.PixelatorT(this));null==this.pixel.p0?this.pixel=this.pixelT0:this.pixel.p0=this.pixelT0;return!0},"~B");j(b,"endRendering",function(){if(this.currentlyRendering){if(null!=this.pbuf){if(this.isPass2&&null!=this.pbufT)for(var a=this.pbufT.length;0<=--a;)this.pbuf[a]=J.g3d.Graphics3D.mergeBufferPixel(this.pbuf[a],this.pbufT[a],this.bgcolor);this.pixel===this.pixelShaded&&0==this.pixelShaded.zShadePower&&this.pixelShaded.showZBuffer();this.antialiasThisFrame&&this.downsampleFullSceneAntialiasing(!1)}this.platform.setBackgroundColor(this.bgcolor);

this.platform.notifyEndOfRendering();this.currentlyRendering=this.isPass2=!1}});b.mergeBufferPixel=c(b,"mergeBufferPixel",function(a,d,g){if(0==d||a==d)return a;0==a&&(a=g);g=a&16711935;a&=65280;var b=d&16711935,c=d&65280;switch(d>>24&15){case 0:g=b;a=c;break;case 1:g=(b<<2)+(b<<1)+b+g>>3&16711935;a=(c<<2)+ +(c<<1)+c+a>>3&65280;break;case 2:g=(b<<1)+b+g>>2&16711935;a=(c<<1)+c+a>>2&65280;break;case 3:g=(b<<2)+b+(g<<1)+g>>3&16711935;a=(c<<2)+c+(a<<1)+a>>3&65280;break;case 4:g=g+b>>1&16711935;a=a+c>>

1&65280;break;case 5:g=(b<<1)+b+(g<<2)+g>>3&16711935;a=(c<<1)+c+(a<<2)+a>>3&65280;break;case 6:g=(g<<1)+g+b>>2&16711935;a=(a<<1)+a+c>>2&65280;break;case 7:g=(g<<2)+(g<<1)+g+b>>3&16711935,a=(a<<2)+(a<<1)+a+c>>3&65280}return 4278190080|g|a},"~N,~N,~N");j(b,"getScreenImage",function(a){var d=this.platform.bufferedImage;a&&this.releaseBuffers();return d},"~B");j(b,"applyAnaglygh",function(a,d){switch(a){case J.c.STER.REDCYAN:for(var g=this.anaglyphLength;0<=--g;){var b=this.anaglyphChannelBytes[g]&255;

this.pbuf[g]=this.pbuf[g]&4294901760|b<<8|b}break;case J.c.STER.CUSTOM:for(var b=d[0],c=d[1]&16777215,g=this.anaglyphLength;0<=--g;){var e=this.anaglyphChannelBytes[g]&255,e=(e|(e|e<<8)<<8)&c;this.pbuf[g]=this.pbuf[g]&b|e}break;case J.c.STER.REDBLUE:for(g=this.anaglyphLength;0<=--g;)b=this.anaglyphChannelBytes[g]&255,this.pbuf[g]=this.pbuf[g]&4294901760|b;break;case J.c.STER.REDGREEN:for(g=this.anaglyphLength;0<=--g;)this.pbuf[g]=this.pbuf[g]&4294901760|(this.anaglyphChannelBytes[g]&255)<<8}},"J.c.STER,~A");

j(b,"snapshotAnaglyphChannelBytes",function(){if(this.currentlyRendering)throw new NullPointerException;this.anaglyphLength=this.windowWidth*this.windowHeight;if(null==this.anaglyphChannelBytes||this.anaglyphChannelBytes.length!=this.anaglyphLength)this.anaglyphChannelBytes=P(this.anaglyphLength,0);for(var a=this.anaglyphLength;0<=--a;)this.anaglyphChannelBytes[a]=this.pbuf[a]});j(b,"releaseScreenImage",function(){this.platform.clearScreenBufferThreaded()});j(b,"haveTranslucentObjects",function(){return this.$haveTranslucentObjects});

j(b,"setSlabAndZShade",function(a,d,g,b,c){this.setSlab(a);this.setDepth(d);g<b?(null==this.pixelShaded&&(this.pixelShaded=new J.g3d.PixelatorShaded(this)),this.pixel=this.pixelShaded.set(g,b,c)):this.pixel=this.pixel0},"~N,~N,~N,~N,~N");c(b,"downsampleFullSceneAntialiasing",function(a){var d=this.bgcolor;a&&(d+=255==(d&255)?-1:1);J.g3d.Graphics3D.downsample2d(this.pbuf,this.windowWidth,this.windowHeight,d);a&&(J.g3d.Graphics3D.downsample2dZ(this.pbuf,this.zbuf,this.windowWidth,this.windowHeight,

d),this.antialiasThisFrame=!1,this.setWidthHeight(!1))},"~B");b.downsample2d=c(b,"downsample2d",function(a,d,g,b){var c=d<<1;if(0!=b){b&=16777215;for(var e=a.length;0<=--e;)0==a[e]&&(a[e]=b)}for(var h=(b>>2&1061109567)<<2,h=h+((h&3233857728)>>6),k=0,m=0,e=g;0<=--e;m+=c)for(g=d;0<=--g;++k){var j=(a[m]>>2&1061109567)+(a[m++ +c]>>2&1061109567)+(a[m]>>2&1061109567)+(a[m++ +c]>>2&1061109567),j=j+((j&3233857728)>>6);j==h&&(j=b);a[k]=j&16777215|4278190080}},"~A,~N,~N,~N");b.downsample2dZ=c(b,"downsample2dZ",

function(a,d,g,b,c){for(var e=g<<1,h=0,k=0;0<=--b;k+=e)for(var m=g;0<=--m;++h,++k){var j=Math.min(d[k],d[k+e]),j=Math.min(j,d[++k]),j=Math.min(j,d[k+e]);2147483647!=j&&(j>>=1);d[h]=a[h]==c?2147483647:j}},"~A,~A,~N,~N,~N");c(b,"hasContent",function(){return this.platform.hasContent()});j(b,"setC",function(a){var d=JU.C.isColixLastAvailable(a);if(!d&&a==this.colixCurrent&&-1==this.currentShadeIndex)return!0;var g=a&30720;if(16384==g)return!1;this.renderLow&&(g=0);var b=0!=g,c=b&&30720==g;this.setScreened(c);

if(!this.checkTranslucent(b&&!c))return!1;this.isPass2?(this.translucencyMask=g<<13|16777215,this.translucencyLog=g>>11):this.translucencyLog=0;this.colixCurrent=a;d&&this.argbCurrent!=this.lastRawColor&&(0==this.argbCurrent&&(this.argbCurrent=4294967295),this.lastRawColor=this.argbCurrent,this.shader.setLastColix(this.argbCurrent,this.inGreyscaleMode));this.shadesCurrent=this.getShades(a);this.currentShadeIndex=-1;this.setColor(this.getColorArgbOrGray(a));return!0},"~N");c(b,"setScreened",function(a){this.wasScreened!=

a&&((this.wasScreened=a)?(null==this.pixelScreened&&(this.pixelScreened=new J.g3d.PixelatorScreened(this,this.pixel0)),null==this.pixel.p0?this.pixel=this.pixelScreened:this.pixel.p0=this.pixelScreened):null==this.pixel.p0||this.pixel===this.pixelScreened?this.pixel=this.isPass2?this.pixelT0:this.pixel0:this.pixel.p0=this.isPass2?this.pixelT0:this.pixel0);return this.pixel},"~B");j(b,"drawFilledCircle",function(a,d,g,b,c,e){if(!this.isClippedZ(e)){var h=B((g+1)/2),h=b<h||b+h>=this.width||c<h||c+h>=

this.height;if(!h||!this.isClippedXY(g,b,c))0!=a&&this.setC(a)&&(h?this.isClippedXY(g,b,c)||this.circle3d.plotCircleCenteredClipped(b,c,e,g):this.circle3d.plotCircleCenteredUnclipped(b,c,e,g)),0!=d&&this.setC(d)&&(h?this.circle3d.plotFilledCircleCenteredClipped(b,c,e,g):this.circle3d.plotFilledCircleCenteredUnclipped(b,c,e,g))}},"~N,~N,~N,~N,~N,~N");j(b,"volumeRender4",function(a,d,g,b){if(1==a)this.plotPixelClippedArgb(this.argbCurrent,d,g,b,this.width,this.zbuf,this.pixel);else if(!this.isClippedZ(b)){var c=

B((a+1)/2),c=d<c||d+c>=this.width||g<c||g+c>=this.height;if(!c||!this.isClippedXY(a,d,g))c?this.circle3d.plotFilledCircleCenteredClipped(d,g,b,a):this.circle3d.plotFilledCircleCenteredUnclipped(d,g,b,a)}},"~N,~N,~N,~N");j(b,"fillSphereXYZ",function(a,d,g,b){switch(a){case 1:this.plotPixelClippedArgb(this.argbCurrent,d,g,b,this.width,this.zbuf,this.pixel);return;case 0:return}a<=(this.antialiasThisFrame?2E3:1E3)&&this.sphere3d.render(this.shadesCurrent,a,d,g,b,null,null,null,-1,null)},"~N,~N,~N,~N");

j(b,"volumeRender",function(a){a?(this.saveAmbient=this.getAmbientPercent(),this.saveDiffuse=this.getDiffusePercent(),this.setAmbientPercent(100),this.setDiffusePercent(0),this.addRenderer(1073741880)):(this.setAmbientPercent(this.saveAmbient),this.setDiffusePercent(this.saveDiffuse))},"~B");j(b,"fillSphereI",function(a,d){this.fillSphereXYZ(a,d.x,d.y,d.z)},"~N,JU.P3i");j(b,"fillSphereBits",function(a,d){this.fillSphereXYZ(a,Math.round(d.x),Math.round(d.y),Math.round(d.z))},"~N,JU.P3");j(b,"fillEllipsoid",

function(a,d,g,b,c,e,h,k,m,j,p){switch(e){case 1:this.plotPixelClippedArgb(this.argbCurrent,g,b,c,this.width,this.zbuf,this.pixel);return;case 0:return}e<=(this.antialiasThisFrame?2E3:1E3)&&this.sphere3d.render(this.shadesCurrent,e,g,b,c,h,k,m,j,p)},"JU.P3,~A,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A");j(b,"drawRect",function(a,d,g,b,c,e){if(!(0!=b&&this.isClippedZ(b))){b=c-1;e-=1;c=a+b;var h=d+e;0<=d&&d<this.height&&this.drawHLine(a,d,g,b);0<=h&&h<this.height&&this.drawHLine(a,h,g,b);0<=a&&a<this.width&&

this.drawVLine(a,d,g,e);0<=c&&c<this.width&&this.drawVLine(c,d,g,e)}},"~N,~N,~N,~N,~N,~N");c(b,"drawHLine",function(a,d,g,b){0>b&&(a+=b,b=-b);0>a&&(b+=a,a=0);a+b>=this.width&&(b=this.width-1-a);var c=this.pixel,e=this.argbCurrent;a+=this.width*d;for(d=0;d<=b;d++)g<this.zbuf[a]&&c.addPixel(a,g,e),a++},"~N,~N,~N,~N");c(b,"drawVLine",function(a,d,g,b){0>b&&(d+=b,b=-b);0>d&&(b+=d,d=0);d+b>=this.height&&(b=this.height-1-d);a+=this.width*d;d=this.pixel;for(var c=this.argbCurrent,e=0;e<=b;e++)g<this.zbuf[a]&&

d.addPixel(a,g,c),a+=this.width},"~N,~N,~N,~N");j(b,"fillTextRect",function(a,d,g,b,c,e){if(!this.isClippedZ(b)){b=this.width;if(0>a){c+=a;if(0>=c)return;a=0}if(a+c>b&&(c=b-a,0>=c))return;if(0>d){e+=d;if(0>=e)return;d=0}d+e>this.height&&(e=this.height-d);var h=this.argbCurrent;this.isAntialiased()&&(h=J.g3d.Graphics3D.fixTextImageRGB(h));for(var k=this.zbuf,m=this.pixel;0<=--e;)this.plotPixelsUnclippedCount(h,c,a,d++,g,b,k,m)}},"~N,~N,~N,~N,~N,~N");j(b,"drawString",function(a,d,g,b,c,e,h){this.currentShadeIndex=

0;null!=a&&(this.isClippedZ(e)||this.drawStringNoSlab(a,d,g,b,c,h))},"~S,JU.Font,~N,~N,~N,~N,~N");j(b,"drawStringNoSlab",function(a,d,g,b,c,e){if(null!=a){null==this.strings&&(this.strings=Array(10));this.stringCount==this.strings.length&&(this.strings=JU.AU.doubleLength(this.strings));var h=new J.g3d.TextString;h.setText(a,null==d?this.currentFont:this.currentFont=d,this.argbCurrent,JU.C.isColixTranslucent(e)?this.getColorArgbOrGray(e)&16777215|(e&30720)<<13:0,g,b,c);this.strings[this.stringCount++]=

h}},"~S,JU.Font,~N,~N,~N,~N");j(b,"renderAllStrings",function(a){if(null!=this.strings){2<=this.stringCount&&(null==J.g3d.Graphics3D.sort&&(J.g3d.Graphics3D.sort=new J.g3d.TextString),java.util.Arrays.sort(this.strings,J.g3d.Graphics3D.sort));for(var d=0;d<this.stringCount;d++){var g=this.strings[d];this.plotText(g.x,g.y,g.z,g.argb,g.bgargb,g.text,g.font,a)}this.strings=null;this.stringCount=0}},"~O");j(b,"plotText",function(a,d,g,b,c,e,h,k){J.g3d.TextRenderer.plot(a,d,g,b,c,e,h,this,k,this.antialiasThisFrame)},

"~N,~N,~N,~N,~N,~S,JU.Font,J.api.JmolRendererInterface");j(b,"drawImage",function(a,d,g,b,c,e,h,k){null!=a&&(0<h&&0<k&&!this.isClippedZ(c))&&this.plotImage(d,g,b,a,null,e,h,k)},"~O,~N,~N,~N,~N,~N,~N,~N");j(b,"plotImage",function(a,d,g,b,c,e,h,k){this.setC(e);this.isPass2||(this.translucencyMask=-1);0==e&&(this.argbCurrent=0);var m=-2147483648==a;e=m?this.bgcolor:this.argbCurrent;m&&(a=0,g=2147483646,h=this.width,k=this.height);if(!(0>=a+h||a>=this.width||0>=d+k||d>=this.height))if(b=this.apiPlatform.drawImageToBuffer(null,

this.platform.offscreenImage,b,h,k,m?e:0),null!=b){var m=this.zbuf,j=this.width,p=this.pixel,q=this.height,x=this.translucencyLog;if(null==c&&0<=a&&a+h<=j&&0<=d&&d+k<=q){var s=0,G=0;for(a=d*j+a;s<k;s++,a+=j-h)for(var M=0;M<h;M++,G++,a++)if(g<m[a]){var N=b[G];-16777216==(N&4278190080)&&p.addPixel(a,g,N)}}else{null==c&&(c=this);for(G=s=0;s<k;s++)for(M=0;M<h;M++)N=b[G++],-16777216==(N&4278190080)&&c.plotImagePixel(N,a+M,d+s,g,8,e,j,q,m,p,x)}}},"~N,~N,~N,~O,J.api.JmolRendererInterface,~N,~N,~N");j(b,

"setFont",function(a){this.currentFont=a},"JU.Font");j(b,"drawPixel",function(a,d,g){this.plotPixelClippedArgb(this.argbCurrent,a,d,g,this.width,this.zbuf,this.pixel)},"~N,~N,~N");j(b,"drawPoints",function(a,d,g){if(1<g)for(var b=0.8*g*g,c=-g;c<g;c++)for(var e=-g;e<g;e++)c*c+e*e>b||(this.plotPoints(a,d,c,e),this.plotPoints(a,d,c,e));else this.plotPoints(a,d,0,0)},"~N,~A,~N");j(b,"drawDashedLineBits",function(a,d,g,b){this.isAntialiased()&&(a+=a,d+=d);this.setScreeni(g,this.sA);this.setScreeni(b,this.sB);

this.drawLineABBits(a,d,!0)},"~N,~N,JU.P3,JU.P3");c(b,"drawLineABBits",function(a,d,g){this.line3d.plotLineBits(this.argbCurrent,this.argbCurrent,this.sA,this.sB,a,d,g);Math.abs(this.sA.x-this.sB.x)<Math.abs(this.sA.y-this.sB.y)?(this.sA.x+=1,this.sB.x+=1):(this.sA.y+=1,this.sB.y+=1);this.line3d.plotLineBits(this.argbCurrent,this.argbCurrent,this.sA,this.sB,a,d,g)},"~N,~N,~B");c(b,"setScreeni",function(a,d){d.x=Math.round(a.x);d.y=Math.round(a.y);d.z=Math.round(a.z)},"JU.P3,JU.P3i");j(b,"drawLineXYZ",

function(a,d,g,b,c,e){this.line3d.plotLineOld(this.argbCurrent,this.argbCurrent,a,d,g,b,c,e)},"~N,~N,~N,~N,~N,~N");j(b,"drawLine",function(a,d,g,b,c,e,h,k){this.setC(a)||(a=0);var m=this.argbCurrent;this.setC(d)||(d=0);(0!=a||0!=d)&&this.line3d.plotLineOld(m,this.argbCurrent,g,b,c,e,h,k)},"~N,~N,~N,~N,~N,~N,~N,~N");j(b,"drawLineBits",function(a,d,g,b){this.setC(a)||(a=0);var c=this.argbCurrent;this.setC(d)||(d=0);if(0!=a||0!=d)this.setScreeni(g,this.sA),this.setScreeni(b,this.sB),this.line3d.plotLineBits(c,

this.argbCurrent,this.sA,this.sB,0,0,!1)},"~N,~N,JU.P3,JU.P3");j(b,"drawLinePixels",function(a,d,g,b){this.sA.setT(a);this.sB.setT(d);this.sA.z=this.sB.z=g;a=this.slab;-2147483648==b&&(this.slab=0);this.drawLineABBits(0,0,!1);this.slab=a},"JU.P3i,JU.P3i,~N,~N");j(b,"drawLineAB",function(a,d){this.setScreeni(a,this.sA);this.setScreeni(d,this.sB);this.line3d.plotLineBits(this.argbCurrent,this.argbCurrent,this.sA,this.sB,0,0,!1)},"JU.P3,JU.P3");j(b,"fillCylinderXYZ",function(a,d,g,b,c,e,h,k,m,j){if(!(b>

this.ht3)){var p=0;this.currentShadeIndex=0;this.setC(d)||(d=0);this.wasScreened&&(p=2);this.setC(a)||(a=0);this.wasScreened&&(p+=1);0==a&&0==d||this.cylinder3d.renderOld(a,d,p,g,b,c,e,h,k,m,j)}},"~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");j(b,"fillCylinderScreen3I",function(a,d,g,b){d<=this.ht3&&this.cylinder3d.renderOld(this.colixCurrent,this.colixCurrent,0,a,d,D(g.x),D(g.y),D(g.z),D(b.x),D(b.y),D(b.z))},"~N,~N,JU.P3,JU.P3,JU.P3,JU.P3,~N");j(b,"fillCylinder",function(a,d,g,b){d<=this.ht3&&this.cylinder3d.renderOld(this.colixCurrent,

this.colixCurrent,0,a,d,g.x,g.y,g.z,b.x,b.y,b.z)},"~N,~N,JU.P3i,JU.P3i");j(b,"fillCylinderBits",function(a,d,g,b){d<=this.ht3&&(1!=g.z&&1!=b.z)&&(0==d||1==d?(this.setScreeni(g,this.sA),this.setScreeni(b,this.sB),this.line3d.plotLineBits(this.getColorArgbOrGray(this.colixCurrent),this.getColorArgbOrGray(this.colixCurrent),this.sA,this.sB,0,0,!1)):this.cylinder3d.renderBitsFloat(this.colixCurrent,this.colixCurrent,0,a,d,g,b))},"~N,~N,JU.P3,JU.P3");j(b,"fillCylinderBits2",function(a,d,g,b,c,e){if(!(b>

this.ht3)){var h=0;this.currentShadeIndex=0;this.setC(d)||(d=0);this.wasScreened&&(h=2);this.setC(a)||(a=0);this.wasScreened&&(h+=1);0==a&&0==d||(this.setScreeni(c,this.sA),this.setScreeni(e,this.sB),this.cylinder3d.renderBits(a,d,h,g,b,this.sA,this.sB))}},"~N,~N,~N,~N,JU.P3,JU.P3");j(b,"fillConeScreen3f",function(a,d,g,b,c){d<=this.ht3&&this.cylinder3d.renderConeOld(this.colixCurrent,a,d,g.x,g.y,g.z,b.x,b.y,b.z,!0,c)},"~N,~N,JU.P3,JU.P3,~B");j(b,"drawHermite4",function(a,d,g,b,c){this.hermite3d.renderHermiteRope(!1,

a,0,0,0,d,g,b,c)},"~N,JU.P3,JU.P3,JU.P3,JU.P3");j(b,"drawHermite7",function(a,d,g,b,c,e,h,k,m,j,p,q,x){if(0==x)this.hermite3d.renderHermiteRibbon(a,d,g,b,c,e,h,k,m,j,p,q,0);else{this.hermite3d.renderHermiteRibbon(a,d,g,b,c,e,h,k,m,j,p,q,1);var s=this.colixCurrent;this.setC(x);this.hermite3d.renderHermiteRibbon(a,d,g,b,c,e,h,k,m,j,p,q,-1);this.setC(s)}},"~B,~B,~N,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,~N,~N");j(b,"fillHermite",function(a,d,g,b,c,e,h,k){this.hermite3d.renderHermiteRope(!0,

a,d,g,b,c,e,h,k)},"~N,~N,~N,~N,JU.P3,JU.P3,JU.P3,JU.P3");j(b,"drawTriangle3C",function(a,d,g,b,c,e,h){1==(h&1)&&this.drawLine(d,b,a.x,a.y,a.z,g.x,g.y,g.z);2==(h&2)&&this.drawLine(b,e,g.x,g.y,g.z,c.x,c.y,c.z);4==(h&4)&&this.drawLine(d,e,a.x,a.y,a.z,c.x,c.y,c.z)},"JU.P3i,~N,JU.P3i,~N,JU.P3i,~N,~N");j(b,"fillTriangleTwoSided",function(a,d,g,b){this.setColorNoisy(this.getShadeIndex(a));this.fillTriangleP3f(d,g,b,!1)},"~N,JU.P3,JU.P3,JU.P3");c(b,"fillTriangleP3f",function(a,d,g,b){this.setScreeni(a,this.sA);

this.setScreeni(d,this.sB);this.setScreeni(g,this.sC);this.triangle3d.fillTriangle(this.sA,this.sB,this.sC,b)},"JU.P3,JU.P3,JU.P3,~B");j(b,"fillTriangle3f",function(a,d,g,b){var c=this.getShadeIndexP3(a,d,g,b);0>c||(b?this.setColorNoisy(c):this.setColor(this.shadesCurrent[c]),this.fillTriangleP3f(a,d,g,!1))},"JU.P3,JU.P3,JU.P3,~B");j(b,"fillTriangle3i",function(a,d,g,b,c,e,h){h&&(b=this.vectorAB,b.set(d.x-a.x,d.y-a.y,d.z-a.z),null==g?b=this.shader.getShadeIndex(-b.x,-b.y,b.z):(this.vectorAC.set(g.x-

a.x,g.y-a.y,g.z-a.z),b.cross(b,this.vectorAC),b=0<=b.z?this.shader.getShadeIndex(-b.x,-b.y,b.z):this.shader.getShadeIndex(b.x,b.y,-b.z)),56<b&&(b=56),this.setColorNoisy(b));this.fillTriangleP3f(a,d,g,!1)},"JU.P3,JU.P3,JU.P3,JU.T3,JU.T3,JU.T3,~B");j(b,"fillTriangle3CN",function(a,d,g,b,c,e,h,k,m){this.triangle3d.fillTriangle(a,b,h,this.checkGouraud(d,c,k,g,e,m))},"JU.P3i,~N,~N,JU.P3i,~N,~N,JU.P3i,~N,~N");j(b,"fillTriangle3CNBits",function(a,d,g,b,c,e,h,k,m){this.fillTriangleP3f(a,b,h,this.checkGouraud(d,

c,k,g,e,m))},"JU.P3,~N,~N,JU.P3,~N,~N,JU.P3,~N,~N,~B");c(b,"checkGouraud",function(a,d,g,b,c,e){if(!this.isPass2&&b==c&&b==e&&a==d&&a==g){d=this.getShadeIndex(b);if(a!=this.colixCurrent||this.currentShadeIndex!=d)this.currentShadeIndex=-1,this.setC(a),this.setColorNoisy(d);return!1}this.setTriangleTranslucency(a,d,g);this.triangle3d.setGouraud(this.getShades(a)[this.getShadeIndex(b)],this.getShades(d)[this.getShadeIndex(c)],this.getShades(g)[this.getShadeIndex(e)]);return!0},"~N,~N,~N,~N,~N,~N");

c(b,"getShadeIndex",function(a){return-1E4==a||9999==a?J.g3d.Graphics3D.nullShadeIndex:0>a?this.shadeIndexes2Sided[~a]:this.shadeIndexes[a]},"~N");c(b,"setTriangleTranslucency",function(a,d,g){this.isPass2&&(a&=14336,d&=14336,g&=14336,this.translucencyMask=(JU.GData.roundInt(B((a+d+g)/3))&30720)<<13|16777215)},"~N,~N,~N");j(b,"fillQuadrilateral",function(a,d,g,b,c){c=this.getShadeIndexP3(a,d,g,c);0>c||(this.setColorNoisy(c),this.fillTriangleP3f(a,d,g,!1),this.fillTriangleP3f(a,g,b,!1))},"JU.P3,JU.P3,JU.P3,JU.P3,~B");

j(b,"drawSurface",function(){},"JU.MeshSurface,~N");j(b,"plotPixelClippedP3i",function(a){this.plotPixelClippedArgb(this.argbCurrent,a.x,a.y,a.z,this.width,this.zbuf,this.pixel)},"JU.P3i");c(b,"plotPixelClippedArgb",function(a,d,g,b,c,e,h){this.isClipped3(d,g,b)||(d=g*c+d,b<e[d]&&h.addPixel(d,b,a))},"~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(b,"plotPixelUnclipped",function(a,d,g,b,c,e,h){d=g*c+d;b<e[d]&&h.addPixel(d,b,a)},"~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(b,"plotImagePixel",function(a,d,g,b,c,e,

h,k,m,j,p){0>d||(d>=h||0>g||g>=k)||j.addImagePixel(c,p,g*h+d,b,a,e)},"~N,~N,~N,~N,~N,~N,~N,~N,~A,~O,~N");c(b,"plotPixelsClippedRaster",function(a,d,g,b,c,e,h){var k,m;if(!(0>=a||0>g||g>=this.height||d>=this.width||b<(m=this.slab)&&c<m||b>(k=this.depth)&&c>k)){var j=this.zbuf,p=(d<<16)+(g<<1)^858993459,q=(b<<10)+512;b=c-b;c=B(a/2);b=JU.GData.roundInt(B(((b<<10)+(0<=b?c:-c))/a));if(0>d){d=-d;q+=b*d;a-=d;if(0>=a)return;d=0}a+d>this.width&&(a=this.width-d);d=g*this.width+d;g=this.pixel;if(null==e){e=

this.argbNoisyDn;c=this.argbNoisyUp;for(var x=this.argbCurrent;0<=--a;){h=q>>10;if(h>=m&&h<=k&&h<j[d]){var p=(p<<16)+(p<<1)+p&2147483647,s=p>>16&7;g.addPixel(d,h,0==s?e:1==s?c:x)}++d;q+=b}}else{p=e.r<<8;c=B((h.r-e.r<<8)/a);x=e.g;s=B((h.g-x)/a);e=e.b;for(var G=B((h.b-e)/a);0<=--a;)h=q>>10,h>=m&&(h<=k&&h<j[d])&&g.addPixel(d,h,4278190080|p&16711680|x&65280|e>>8&255),++d,q+=b,p+=c,x+=s,e+=G}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16");c(b,"plotPixelsUnclippedRaster",function(a,d,b,c,f,e,h){if(!(0>=a)){var k=

((d<<16)+(b<<1)^858993459)&2147483647,m=(c<<10)+512;c=f-c;f=B(a/2);c=JU.GData.roundInt(B(((c<<10)+(0<=c?f:-f))/a));d=b*this.width+d;b=this.zbuf;f=this.pixel;if(null==e){e=this.argbNoisyDn;for(var j=this.argbNoisyUp,p=this.argbCurrent;0<=--a;){h=m>>10;if(h<b[d]){var k=(k<<16)+(k<<1)+k&2147483647,q=k>>16&7;f.addPixel(d,h,0==q?e:1==q?j:p)}++d;m+=c}}else{k=e.r<<8;j=JU.GData.roundInt(B((h.r-e.r<<8)/a));p=e.g;q=JU.GData.roundInt(B((h.g-p)/a));e=e.b;for(var x=JU.GData.roundInt(B((h.b-e)/a));0<=--a;)h=m>>

10,h<b[d]&&f.addPixel(d,h,4278190080|k&16711680|p&65280|e>>8&255),++d,m+=c,k+=j,p+=q,e+=x}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16");c(b,"plotPixelsClippedRasterBits",function(a,d,b,c,f,e,h,k,m){var j,p;if(!(0>=a||0>b||b>=this.height||d>=this.width||c<(p=this.slab)&&f<p||c>(j=this.depth)&&f>j)){c=this.zbuf;var q=(d<<16)+(b<<1)^858993459;if(0>d){a-=-d;if(0>=a)return;d=0}a+d>this.width&&(a=this.width-d);b=b*this.width+d;f=this.pixel;if(null==e){e=this.argbNoisyDn;for(var x=this.argbNoisyUp,s=this.argbCurrent;0<=

--a;){h=this.line3d.getZCurrent(k,m,d++);if(h>=p&&h<=j&&h<c[b]){var q=(q<<16)+(q<<1)+q&2147483647,G=q>>16&7;f.addPixel(b,h,2>G?e:6>G?x:s)}++b}}else{q=e.r<<8;x=B((h.r-e.r<<8)/a);s=e.g;G=B((h.g-s)/a);e=e.b;for(var M=B((h.b-e)/a);0<=--a;)h=this.line3d.getZCurrent(k,m,d++),h>=p&&(h<=j&&h<c[b])&&f.addPixel(b,h,4278190080|q&16711680|s&65280|e>>8&255),++b,q+=x,s+=G,e+=M}}},"~N,~N,~N,~N,~N,JU.Rgb16,JU.Rgb16,~N,~N");c(b,"plotPixelsUnclippedRasterBits",function(a,d,b,c,f,e,h){if(!(0>=a)){var k=((d<<16)+(b<<

1)^858993459)&2147483647;b=b*this.width+d;var m=this.zbuf,j=this.pixel;if(null==c)for(var p=this.argbNoisyDn,q=this.argbNoisyUp,x=this.argbCurrent;0<=--a;)f=this.line3d.getZCurrent(e,h,d++),f<m[b]&&(k=(k<<16)+(k<<1)+k&2147483647,c=k>>16&7,j.addPixel(b,f,0==c?p:1==c?q:x)),++b;else{k=c.r<<8;p=JU.GData.roundInt(B((f.r-c.r<<8)/a));q=c.g;x=JU.GData.roundInt(B((f.g-q)/a));c=c.b;for(var s=JU.GData.roundInt(B((f.b-c)/a));0<=--a;)f=this.line3d.getZCurrent(e,h,d++),f<m[b]&&j.addPixel(b,f,4278190080|k&16711680|

q&65280|c>>8&255),++b,k+=p,q+=x,c+=s}}},"~N,~N,~N,JU.Rgb16,JU.Rgb16,~N,~N");c(b,"plotPixelsUnclippedCount",function(a,d,b,c,f,e,h,k){for(b=c*e+b;0<=--d;)f<h[b]&&k.addPixel(b,f,a),++b},"~N,~N,~N,~N,~N,~N,~A,J.g3d.Pixelator");c(b,"plotPoints",function(a,d,b,c){var f=this.pixel,e=this.argbCurrent,h=this.zbuf,k=this.width,m=this.antialiasThisFrame;for(a*=3;0<a;){var j=d[--a],p=d[--a]+c,q=d[--a]+b;if(!this.isClipped3(q,p,j)){var x=p*k+q++;j<h[x]&&f.addPixel(x,j,e);m&&(x=p*k+q,!this.isClipped3(q,p,j)&&

j<h[x]&&f.addPixel(x,j,e),x=++p*k+q,!this.isClipped3(q,p,j)&&j<h[x]&&f.addPixel(x,j,e),x=p*k+--q,!this.isClipped3(q,p,j)&&j<h[x]&&f.addPixel(x,j,e))}}},"~N,~A,~N,~N");c(b,"setColorNoisy",function(a){this.currentShadeIndex=a;this.argbCurrent=this.shadesCurrent[a];this.argbNoisyUp=this.shadesCurrent[63>a?a+1:63];this.argbNoisyDn=this.shadesCurrent[0<a?a-1:0]},"~N");c(b,"getShadeIndexP3",function(a,d,b,c){this.vectorAB.sub2(d,a);this.vectorAC.sub2(b,a);a=this.vectorNormal;a.cross(this.vectorAB,this.vectorAC);

return 0>a.z?this.shader.getShadeIndex(a.x,a.y,-a.z):c?-1:this.shader.getShadeIndex(-a.x,-a.y,a.z)},"JU.P3,JU.P3,JU.P3,~B");j(b,"renderBackground",function(a){null!=this.backgroundImage&&this.plotImage(-2147483648,0,-2147483648,this.backgroundImage,a,0,0,0)},"J.api.JmolRendererInterface");j(b,"drawAtom",function(a){this.fillSphereXYZ(a.sD,a.sX,a.sY,a.sZ)},"JM.Atom,~N");j(b,"getExportType",function(){return 0});j(b,"getExportName",function(){return null});c(b,"canDoTriangles",function(){return!0});

c(b,"isCartesianExport",function(){return!1});j(b,"initializeExporter",function(){return null},"JV.Viewer,~N,JU.GData,java.util.Map");j(b,"finalizeOutput",function(){return null});j(b,"drawBond",function(){},"JU.P3,JU.P3,~N,~N,~N,~N,~N");j(b,"drawEllipse",function(){return!1},"JU.P3,JU.P3,JU.P3,~B,~B");c(b,"getPrivateKey",function(){return 0});j(b,"clearFontCache",function(){J.g3d.TextRenderer.clearFontCache()});c(b,"setRotationMatrix",function(a){for(var d=JU.Normix.getVertexVectors(),b=JU.GData.normixCount;0<=

--b;){var c=this.transformedVectors[b];a.rotate2(d[b],c);this.shadeIndexes[b]=this.shader.getShadeB(c.x,-c.y,c.z);this.shadeIndexes2Sided[b]=0<=c.z?this.shadeIndexes[b]:this.shader.getShadeB(-c.x,c.y,-c.z)}},"JU.M3");j(b,"renderCrossHairs",function(a,d,b,c,f){d=this.isAntialiased();this.setC(0>f?10:100<f?11:23);f=Math.max(Math.min(this.width,Math.round(c.x)),0);b=Math.max(Math.min(this.height,Math.round(c.y)),0);var e=Math.round(c.z)+1,h=d?8:4,k=d?20:10;d=d?2:1;this.drawRect(f-h,b,e,0,k,d);this.drawRect(f,

b-h,e,0,d,k);this.drawRect(f-h,b-h,e,0,k,k);h=k;k>>=1;this.setC(a[1]<c.x?21:11);this.drawRect(f-h,b,e,0,k,d);this.setC(a[0]>c.x?21:11);this.drawRect(f+k,b,e,0,k,d);this.setC(a[3]<c.y?21:11);this.drawRect(f,b-h,e,0,d,k);this.setC(a[2]>c.y?21:11);this.drawRect(f,b+k,e,0,d,k)},"~A,~N,~N,JU.P3,~N");j(b,"initializeOutput",function(){return!1},"JV.Viewer,~N,java.util.Map");b.fixTextImageRGB=c(b,"fixTextImageRGB",function(a){return 0==(a&12632256)?a|263172:a},"~N");b.sort=null;b.nullShadeIndex=50});u("J.g3d");

C(["J.g3d.PrecisionRenderer","java.util.Hashtable"],"J.g3d.LineRenderer",["JU.BS"],function(){var b=v(function(){this.lineBits=this.shader=this.g3d=null;this.slope=0;this.lineTypeX=!1;this.nBits=0;this.slopeKey=this.lineCache=null;this.z2t=this.y2t=this.x2t=this.z1t=this.y1t=this.x1t=0;r(this,arguments)},J.g3d,"LineRenderer",J.g3d.PrecisionRenderer);Q(b,function(){this.lineCache=new java.util.Hashtable});z(b,function(a){L(this,J.g3d.LineRenderer,[]);this.g3d=a;this.shader=a.shader},"J.g3d.Graphics3D");

c(b,"setLineBits",function(a,d){this.slope=0!=a?d/a:0<=d?3.4028235E38:-3.4028235E38;this.nBits=(this.lineTypeX=1>=this.slope&&-1<=this.slope)?this.g3d.width:this.g3d.height;this.slopeKey=Float.$valueOf(this.slope);if(this.lineCache.containsKey(this.slopeKey))this.lineBits=this.lineCache.get(this.slopeKey);else{this.lineBits=JU.BS.newN(this.nBits);d=Math.abs(d);a=Math.abs(a);if(d>a){var b=a;a=d;d=b}for(var b=0,c=a+a,f=d+d,e=0;e<this.nBits;e++)b+=f,b>a&&(this.lineBits.set(e),b-=c);this.lineCache.put(this.slopeKey,

this.lineBits)}},"~N,~N");c(b,"clearLineCache",function(){this.lineCache.clear()});c(b,"plotLineOld",function(a,d,b,c,f,e,h,k){this.x1t=b;this.x2t=e;this.y1t=c;this.y2t=h;this.z1t=f;this.z2t=k;var m=!0;switch(this.getTrimmedLineImpl()){case 0:m=!1;break;case 2:return}this.plotLineClippedOld(a,d,b,c,f,e-b,h-c,k-f,m,0,0)},"~N,~N,~N,~N,~N,~N,~N,~N");c(b,"plotLineDeltaOld",function(a,d,b,c,f,e,h,k,m){this.x1t=b;this.x2t=b+e;this.y1t=c;this.y2t=c+h;this.z1t=f;this.z2t=f+k;if(m)switch(this.getTrimmedLineImpl()){case 2:return;

case 0:m=!1}this.plotLineClippedOld(a,d,b,c,f,e,h,k,m,0,0)},"~N,~N,~N,~N,~N,~N,~N,~N,~B");c(b,"plotLineDeltaAOld",function(a,d,b,c,f,e,h,k,m,j,p){this.x1t=f;this.x2t=f+k;this.y1t=e;this.y2t=e+m;this.z1t=h;this.z2t=h+j;if(p)switch(this.getTrimmedLineImpl()){case 2:return;case 0:p=!1}var q=this.g3d.zbuf,x=this.g3d.width,s=0,G=e*x+f,M=this.g3d.bufferSize,N=63>c?c+1:c,n=0<c?c-1:c,u=a[N],r=a[n],v=d[c],N=d[N];d=d[n];a=a[c];c=this.g3d.pixel;0!=b&&(c=this.g3d.setScreened(1==(b&1)),this.g3d.currentShadeIndex=

0);0!=a&&(!p&&0<=G&&G<M&&h<q[G])&&c.addPixel(G,h,a);if(!(0==k&&0==m)){p=1;n=x;f+=k;var y=e+m;0>k&&(k=-k,p=-1);0>m&&(m=-m,n=-x);x=k+k;e=m+m;h<<=10;if(m<=k){var w=k-1;0>j&&(w=-w);j=B(((j<<10)+w)/k);m=0;w=Math.abs(f-this.x2t)-1;f=Math.abs(f-this.x1t)-1;for(var y=k-1,z=B(y/2);--y>=w;){if(y==z){a=v;if(0==a)break;u=N;r=d;0!=b%3&&(c=this.g3d.setScreened(2==(b&2)),this.g3d.currentShadeIndex=0)}G+=p;h+=j;m+=e;m>k&&(G+=n,m-=x);if(0!=a&&y<f&&0<=G&&G<M&&2147483647>s){var C=h>>10;if(C<q[G]){var D=this.shader.nextRandom8Bit();

c.addPixel(G,C,85>D?r:170<D?u:a)}}s=(s+1)%1}}else{w=m-1;0>j&&(w=-w);j=B(((j<<10)+w)/m);k=0;w=Math.abs(y-this.y2t)-1;f=Math.abs(y-this.y1t)-1;y=m-1;for(z=B(y/2);--y>=w;){if(y==z){a=v;if(0==a)break;u=N;r=d;0!=b%3&&(c=this.g3d.setScreened(2==(b&2)),this.g3d.currentShadeIndex=0)}G+=n;h+=j;k+=x;k>m&&(G+=p,k-=e);0!=a&&(y<f&&0<=G&&G<M&&2147483647>s)&&(C=h>>10,C<q[G]&&(D=this.g3d.shader.nextRandom8Bit(),c.addPixel(G,C,85>D?r:170<D?u:a)));s=(s+1)%1}}}},"~A,~A,~N,~N,~N,~N,~N,~N,~N,~N,~B");c(b,"plotLineDeltaABitsFloat",

function(a,d,b,c,f,e,h){var k=Math.round(c.x),m=Math.round(c.y),j=Math.round(c.z),p=Math.round(f.x),q=Math.round(f.y),x=Math.round(f.z),s=p-k,G=q-m;this.x1t=k;this.x2t=p;this.y1t=m;this.y2t=q;this.z1t=j;this.z2t=x;if(!(h&&2==this.getTrimmedLineImpl())){h=this.g3d.zbuf;var M=this.g3d.width,p=0,x=63>b?b+1:b,q=0<b?b-1:b,N=a[b],n=a[x],u=a[q];b=d[b];a=d[x];d=d[q];var q=m*M+k,x=this.g3d.bufferSize,r,v,y,w;this.lineTypeX?(r=k,v=this.x1t,y=this.x2t,k+=B(s/2),w=m=0<=s?1:-1,s=0<=G?M:-M,this.setRastABFloat(c.x,

c.z,f.x,f.z)):(r=m,v=this.y1t,y=this.y2t,k=m+B(G/2),m=0<=G?1:-1,w=0<=G?M:-M,s=0<=s?1:-1,this.setRastABFloat(c.y,c.z,f.y,f.z));c=j;f=N;j=n;G=u;n=!1;u=this.g3d.pixel;0!=e&&(u=this.g3d.setScreened(1==(e&1)),this.g3d.currentShadeIndex=0);for(N=r;;N+=m,r+=m){N==v&&(n=!0);if(N==k){f=b;if(0==f)break;j=a;G=d;0!=e%3&&(u=this.g3d.setScreened(2==(e&2)),this.g3d.currentShadeIndex=0)}0!=f&&(n&&0<=q&&q<x&&2147483647>p)&&(c=this.getZCurrent(this.a,this.b,N),c<h[q]&&(M=this.shader.nextRandom8Bit(),u.addPixel(q,D(c),

85>M?G:170<M?j:f)));if(N==y)break;p=(p+1)%1;for(q+=w;0>r;)r+=this.nBits;this.lineBits.get(r%this.nBits)&&(q+=s)}}},"~A,~A,~N,JU.P3,JU.P3,~N,~B");c(b,"plotLineDeltaABitsInt",function(a,d,b,c,f,e,h){var k=c.x,m=c.y,j=c.z,p=f.x,q=f.y,x=f.z,s=p-k,G=q-m;this.x1t=k;this.x2t=p;this.y1t=m;this.y2t=q;this.z1t=j;this.z2t=x;if(!(h&&2==this.getTrimmedLineImpl())){h=this.g3d.zbuf;var M=this.g3d.width,p=0,x=63>b?b+1:b,q=0<b?b-1:b,N=a[b],n=a[x],r=a[q];b=d[b];a=d[x];d=d[q];var q=m*M+k,x=this.g3d.bufferSize,u,v,y,

w;this.lineTypeX?(u=k,v=this.x1t,y=this.x2t,k+=B(s/2),w=m=0<=s?1:-1,s=0<=G?M:-M,this.setRastAB(c.x,c.z,f.x,f.z)):(u=m,v=this.y1t,y=this.y2t,k=m+B(G/2),m=0<=G?1:-1,w=0<=G?M:-M,s=0<=s?1:-1,this.setRastAB(c.y,c.z,f.y,f.z));c=j;f=N;j=n;G=r;n=!1;r=this.g3d.pixel;0!=e&&(r=this.g3d.setScreened(1==(e&1)),this.g3d.currentShadeIndex=0);for(N=u;;N+=m,u+=m){N==v&&(n=!0);if(N==k){f=b;if(0==f)break;j=a;G=d;0!=e%3&&(r=this.g3d.setScreened(2==(e&2)),this.g3d.currentShadeIndex=0)}0!=f&&(n&&0<=q&&q<x&&2147483647>p)&&

(c=this.getZCurrent(this.a,this.b,N),c<h[q]&&(M=this.shader.nextRandom8Bit(),r.addPixel(q,D(c),85>M?G:170<M?j:f)));if(N==y)break;p=(p+1)%1;for(q+=w;0>u;)u+=this.nBits;this.lineBits.get(u%this.nBits)&&(q+=s)}}},"~A,~A,~N,JU.P3i,JU.P3i,~N,~B");c(b,"plotLineBits",function(a,d,b,c,f,e,h){if(!(1>=b.z||1>=c.z)){var k=!0;this.x1t=b.x;this.y1t=b.y;this.z1t=b.z;this.x2t=c.x;this.y2t=c.y;this.z2t=c.z;switch(this.getTrimmedLineImpl()){case 2:return;case 0:k=!1;break;default:h&&(b.set(this.x1t,this.y1t,this.z1t),

c.set(this.x2t,this.y2t,this.z2t))}h=this.g3d.zbuf;var m=this.g3d.width,j=0;0==f&&(e=2147483647,f=1);var p=b.x,q=b.y,x=b.z,s=c.x-p,G=p+s,M=c.y-q,N=q+M,n=q*m+p,u=this.g3d.bufferSize,r=this.g3d.pixel;0!=a&&(!k&&0<=n&&n<u&&x<h[n])&&r.addPixel(n,x,a);if(!(0==s&&0==M)){var v=k=1,x=m;0>s&&(s=-s,k=-1);0>M&&(M=-M,x=-m,v=-1);var m=s+s,y=M+M;if(M<=s){this.setRastAB(b.x,b.z,c.x,c.z);q=0;b=Math.abs(G-this.x2t)-1;G=Math.abs(G-this.x1t)-1;N=s-1;for(c=B(N/2);--N>=b&&!(N==c&&(a=d,0==a));){n+=k;p+=k;q+=y;q>s&&(n+=

x,q-=m);if(0!=a&&N<G&&0<=n&&n<u&&j<e){var w=this.getZCurrent(this.a,this.b,p);w<h[n]&&r.addPixel(n,w,a)}j=(j+1)%f}}else{this.setRastAB(b.y,b.z,c.y,c.z);p=0;b=Math.abs(N-this.y2t)-1;G=Math.abs(N-this.y1t)-1;N=M-1;for(c=B(N/2);--N>=b&&!(N==c&&(a=d,0==a));)n+=x,q+=v,p+=m,p>M&&(n+=k,p-=y),0!=a&&(N<G&&0<=n&&n<u&&j<e)&&(w=this.getZCurrent(this.a,this.b,q),w<h[n]&&r.addPixel(n,w,a)),j=(j+1)%f}}}},"~N,~N,JU.P3i,JU.P3i,~N,~N,~B");c(b,"getTrimmedLineImpl",function(){var a=this.g3d.clipCode3(this.x1t,this.y1t,

this.z1t),d=this.g3d.clipCode3(this.x2t,this.y2t,this.z2t);if(0==(a|d))return 0;if(-1==(a|d))return 2;var b=this.g3d.xLast,c=this.g3d.yLast,f=this.g3d.slab,e=this.g3d.depth;do{if(0!=(a&d))return 2;var h=this.x2t-this.x1t,k=this.y2t-this.y1t,m=this.z2t-this.z1t;0!=a?(0!=(a&8)?(this.y1t+=D(-this.x1t*k/h),this.z1t+=D(-this.x1t*m/h),this.x1t=0):0!=(a&4)?(this.y1t+=D((b-this.x1t)*k/h),this.z1t+=D((b-this.x1t)*m/h),this.x1t=b):0!=(a&2)?(this.x1t+=D(-this.y1t*h/k),this.z1t+=D(-this.y1t*m/k),this.y1t=0):

0!=(a&1)?(this.x1t+=D((c-this.y1t)*h/k),this.z1t+=D((c-this.y1t)*m/k),this.y1t=c):0!=(a&32)?(this.x1t+=D((f-this.z1t)*h/m),this.y1t+=D((f-this.z1t)*k/m),this.z1t=f):(this.x1t+=D((e-this.z1t)*h/m),this.y1t+=D((e-this.z1t)*k/m),this.z1t=e),a=this.g3d.clipCode3(this.x1t,this.y1t,this.z1t)):(0!=(d&8)?(this.y2t+=D(-this.x2t*k/h),this.z2t+=D(-this.x2t*m/h),this.x2t=0):0!=(d&4)?(this.y2t+=D((b-this.x2t)*k/h),this.z2t+=D((b-this.x2t)*m/h),this.x2t=b):0!=(d&2)?(this.x2t+=D(-this.y2t*h/k),this.z2t+=D(-this.y2t*

m/k),this.y2t=0):0!=(d&1)?(this.x2t+=D((c-this.y2t)*h/k),this.z2t+=D((c-this.y2t)*m/k),this.y2t=c):0!=(d&32)?(this.x2t+=D((f-this.z2t)*h/m),this.y2t+=D((f-this.z2t)*k/m),this.z2t=f):(this.x2t+=D((e-this.z2t)*h/m),this.y2t+=D((e-this.z2t)*k/m),this.z2t=e),d=this.g3d.clipCode3(this.x2t,this.y2t,this.z2t))}while(0!=(a|d));return 1});c(b,"plotLineClippedOld",function(a,d,b,c,f,e,h,k,m,j,p){var q=this.g3d.zbuf,x=this.g3d.width,s=0;0==j&&(p=2147483647,j=1);var G=c*x+b,M=this.g3d.bufferSize,n=this.g3d.pixel;

0!=a&&(!m&&0<=G&&G<M&&f<q[G])&&n.addPixel(G,f,a);if(!(0==e&&0==h)){m=1;var u=x;b+=e;var r=c+h;0>e&&(e=-e,m=-1);0>h&&(h=-h,u=-x);x=e+e;c=h+h;f<<=10;if(h<=e){var v=e-1;0>k&&(v=-v);k=B(((k<<10)+v)/e);h=0;v=Math.abs(b-this.x2t)-1;b=Math.abs(b-this.x1t)-1;for(var r=e-1,w=B(r/2);--r>=v&&!(r==w&&(a=d,0==a));){G+=m;f+=k;h+=c;h>e&&(G+=u,h-=x);if(0!=a&&r<b&&0<=G&&G<M&&s<p){var y=f>>10;y<q[G]&&n.addPixel(G,y,a)}s=(s+1)%j}}else{v=h-1;0>k&&(v=-v);k=B(((k<<10)+v)/h);e=0;v=Math.abs(r-this.y2t)-1;b=Math.abs(r-this.y1t)-

1;r=h-1;for(w=B(r/2);--r>=v&&!(r==w&&(a=d,0==a));)G+=u,f+=k,e+=x,e>h&&(G+=m,e-=c),0!=a&&(r<b&&0<=G&&G<M&&s<p)&&(y=f>>10,y<q[G]&&n.addPixel(G,y,a)),s=(s+1)%j}}},"~N,~N,~N,~N,~N,~N,~N,~N,~B,~N,~N")});u("J.g3d");C(null,"J.g3d.Pixelator",["J.g3d.Graphics3D"],function(){var b=v(function(){this.pb=this.zb=this.p0=this.g=null;this.bgcolor=this.width=0;r(this,arguments)},J.g3d,"Pixelator",null);z(b,function(a){this.g=a;this.bgcolor=this.g.bgcolor;this.setBuf()},"J.g3d.Graphics3D");c(b,"setBuf",function(){this.zb=

this.g.zbuf;this.pb=this.g.pbuf});c(b,"clearPixel",function(a,d){this.zb[a]>d&&(this.zb[a]=2147483647)},"~N,~N");c(b,"addPixel",function(a,d,b){this.zb[a]=d;this.pb[a]=b},"~N,~N,~N");c(b,"addImagePixel",function(a,d,b,c,f,e){if(c<this.zb[b])switch(a){case 0:break;case 8:this.addPixel(b,c,f);break;default:a+=d,7>=a&&(d=this.pb[b],0!=e&&(d=J.g3d.Graphics3D.mergeBufferPixel(d,e,e)),d=J.g3d.Graphics3D.mergeBufferPixel(d,f&16777215|a<<24,this.bgcolor),this.addPixel(b,c,d))}},"~N,~N,~N,~N,~N,~N")});u("J.g3d");

C(["J.g3d.Pixelator"],"J.g3d.PixelatorT",["J.g3d.Graphics3D"],function(){var b=H(J.g3d,"PixelatorT",J.g3d.Pixelator);j(b,"clearPixel",function(){},"~N,~N");j(b,"addPixel",function(a,d,b){var c=this.g.zbufT[a];if(d<c){var f=this.g.pbufT[a];!this.g.translucentCoverOnly&&(0!=f&&c-d>this.g.zMargin)&&(this.pb[a]=J.g3d.Graphics3D.mergeBufferPixel(this.pb[a],f,this.g.bgcolor));this.g.zbufT[a]=d;this.g.pbufT[a]=b&this.g.translucencyMask}else d!=c&&!this.g.translucentCoverOnly&&d-c>this.g.zMargin&&(this.pb[a]=

J.g3d.Graphics3D.mergeBufferPixel(this.pb[a],b&this.g.translucencyMask,this.g.bgcolor))},"~N,~N,~N")});u("J.g3d");C(["J.g3d.Pixelator"],"J.g3d.PixelatorShaded",null,function(){var b=v(function(){this.tmp=this.bgRGB=null;this.zShadePower=this.zDepth=this.zSlab=0;r(this,arguments)},J.g3d,"PixelatorShaded",J.g3d.Pixelator);z(b,function(a){L(this,J.g3d.PixelatorShaded,[a]);this.tmp=E(3,0)},"J.g3d.Graphics3D");c(b,"set",function(a,d,b){this.bgcolor=this.g.bgcolor;this.bgRGB=E(-1,[this.bgcolor&255,this.bgcolor>>

8&255,this.g.bgcolor>>16&255]);this.zSlab=0>a?0:a;this.zDepth=0>d?0:d;this.zShadePower=b;this.p0=this.g.pixel0;return this},"~N,~N,~N");j(b,"addPixel",function(a,d,b){if(!(d>this.zDepth)){if(d>=this.zSlab&&0<this.zShadePower){var c=this.tmp,f=this.bgRGB;c[0]=b;c[1]=b>>8;c[2]=b>>16;var e=(this.zDepth-d)/(this.zDepth-this.zSlab);if(1<this.zShadePower)for(var h=0;h<this.zShadePower;h++)e*=e;for(h=0;3>h;h++)c[h]=f[h]+D(e*((c[h]&255)-f[h]));b=c[2]<<16|c[1]<<8|c[0]|b&4278190080}this.p0.addPixel(a,d,b)}},

"~N,~N,~N");c(b,"showZBuffer",function(){for(var a=this.p0.zb.length;0<=--a;)if(0!=this.p0.pb[a]){var d=D(Math.min(255,Math.max(0,255*(this.zDepth-this.p0.zb[a])/(this.zDepth-this.zSlab))));this.p0.pb[a]=4278190080|d|d<<8|d<<16}})});u("J.g3d");C(["J.g3d.Pixelator"],"J.g3d.PixelatorScreened",null,function(){var b=H(J.g3d,"PixelatorScreened",J.g3d.Pixelator);z(b,function(a,d){L(this,J.g3d.PixelatorScreened,[a]);this.width=a.width;this.p0=d},"J.g3d.Graphics3D,J.g3d.Pixelator");j(b,"addPixel",function(a,

d,b){a%this.width%2==B(a/this.width)%2&&this.p0.addPixel(a,d,b)},"~N,~N,~N")});u("J.g3d");n=v(function(){this.bufferSizeT=this.bufferSize=this.bufferHeight=this.bufferWidth=this.windowSize=this.windowHeight=this.windowWidth=0;this.zBufferT=this.zBuffer=this.pBufferT=this.pBuffer=this.bufferedImage=null;this.heightOffscreen=this.widthOffscreen=0;this.apiPlatform=this.graphicsForTextOrImage=this.offscreenImage=null;r(this,arguments)},J.g3d,"Platform3D",null);z(n,function(b){this.apiPlatform=b},"J.api.GenericPlatform");

c(n,"getGraphicsForMetrics",function(){return this.apiPlatform.getGraphics(this.allocateOffscreenImage(1,1))});c(n,"allocateTBuffers",function(b){this.bufferSizeT=b?this.bufferSize:this.windowSize;this.zBufferT=E(this.bufferSizeT,0);this.pBufferT=E(this.bufferSizeT,0)},"~B");c(n,"allocateBuffers",function(b,a,d,g){this.windowWidth=b;this.windowHeight=a;this.windowSize=b*a;d&&(b*=2,a*=2);this.bufferWidth=b;this.bufferHeight=a;this.bufferSize=this.bufferWidth*this.bufferHeight;this.zBuffer=E(this.bufferSize,

0);this.pBuffer=E(this.bufferSize,0);this.bufferedImage=this.apiPlatform.allocateRgbImage(this.windowWidth,this.windowHeight,this.pBuffer,this.windowSize,J.g3d.Platform3D.backgroundTransparent,g)},"~N,~N,~B,~B");c(n,"releaseBuffers",function(){this.windowWidth=this.windowHeight=this.bufferWidth=this.bufferHeight=this.bufferSize=-1;null!=this.bufferedImage&&(this.apiPlatform.flushImage(this.bufferedImage),this.bufferedImage=null);this.zBufferT=this.pBufferT=this.zBuffer=this.pBuffer=null});c(n,"hasContent",

function(){for(var b=this.bufferSize;0<=--b;)if(2147483647!=this.zBuffer[b])return!0;return!1});c(n,"clearScreenBuffer",function(){for(var b=this.bufferSize;0<=--b;)this.zBuffer[b]=2147483647,this.pBuffer[b]=0});c(n,"setBackgroundColor",function(b){if(null!=this.pBuffer)for(var a=this.bufferSize;0<=--a;)0==this.pBuffer[a]&&(this.pBuffer[a]=b)},"~N");c(n,"clearTBuffer",function(){for(var b=this.bufferSizeT;0<=--b;)this.zBufferT[b]=2147483647,this.pBufferT[b]=0});c(n,"clearBuffer",function(){this.clearScreenBuffer()});

c(n,"clearScreenBufferThreaded",function(){});c(n,"notifyEndOfRendering",function(){this.apiPlatform.notifyEndOfRendering()});c(n,"getGraphicsForTextOrImage",function(b,a){if(b>this.widthOffscreen||a>this.heightOffscreen)null!=this.offscreenImage&&(this.apiPlatform.disposeGraphics(this.graphicsForTextOrImage),this.apiPlatform.flushImage(this.offscreenImage)),b>this.widthOffscreen&&(this.widthOffscreen=b),a>this.heightOffscreen&&(this.heightOffscreen=a),this.offscreenImage=this.allocateOffscreenImage(this.widthOffscreen,

this.heightOffscreen),this.graphicsForTextOrImage=this.apiPlatform.getStaticGraphics(this.offscreenImage,J.g3d.Platform3D.backgroundTransparent);return this.graphicsForTextOrImage},"~N,~N");c(n,"allocateOffscreenImage",function(b,a){return this.apiPlatform.newOffScreenImage(b,a)},"~N,~N");c(n,"setBackgroundTransparent",function(b){J.g3d.Platform3D.backgroundTransparent=b},"~B");n.backgroundTransparent=!1;u("J.g3d");n=v(function(){this.b=this.a=0;this.isOrthographic=!1;r(this,arguments)},J.g3d,"PrecisionRenderer",

null);c(n,"getZCurrent",function(b,a,d){return Math.round(1.4E-45==b?a:this.isOrthographic?b*d+a:b/(a-d))},"~N,~N,~N");c(n,"setRastABFloat",function(b,a,d,g){var c=g-a,f=d-b;0==c||0==f?(this.a=1.4E-45,this.b=a):this.isOrthographic?(this.a=c/f,this.b=a-this.a*b):(this.a=f*a*(g/c),this.b=(d*g-b*a)/c)},"~N,~N,~N,~N");c(n,"setRastAB",function(b,a,d,g){var c=g-a,f=d-b;1.4E-45==b||0==c||0==f?(this.a=1.4E-45,this.b=g):this.isOrthographic?(this.a=c/f,this.b=a-this.a*b):(this.a=f*a*(g/c),this.b=(d*g-b*a)/

c)},"~N,~N,~N,~N");u("J.g3d");C(["JU.P3"],"J.g3d.SphereRenderer",null,function(){var b=v(function(){this.mDeriv=this.coef=this.mat=this.zroot=this.shader=this.g3d=null;this.planeShade=this.selectedOctant=0;this.zbuf=null;this.offsetPbufBeginLine=this.slab=this.depth=this.height=this.width=0;this.dxyz=this.planeShades=this.ptTemp=null;r(this,arguments)},J.g3d,"SphereRenderer",null);Q(b,function(){this.zroot=R(2,0);this.ptTemp=new JU.P3;this.planeShades=E(3,0);this.dxyz=K(3,3,0)});z(b,function(a){this.g3d=

a;this.shader=a.shader},"J.g3d.Graphics3D");c(b,"render",function(a,d,b,c,f,e,h,k,m,j){if(1!=f&&(49<d&&(d&=-2),!this.g3d.isClippedXY(d,b,c))){this.slab=this.g3d.slab;this.depth=this.g3d.depth;var p=d+1>>1,q=f-p;if(!(f+p<this.slab||q>this.depth)){var x=b-p,s=b+p,G=c-p,M=c+p;this.shader.nOut=this.shader.nIn=0;this.zbuf=this.g3d.zbuf;this.height=this.g3d.height;this.width=this.g3d.width;this.offsetPbufBeginLine=this.width*c+b;var n=this.shader;this.mat=e;if(null!=e&&(this.coef=h,this.mDeriv=k,this.selectedOctant=

m,null==n.ellipsoidShades&&n.createEllipsoidShades(),null!=j)){this.planeShade=-1;for(h=0;3>h;h++)if(p=this.dxyz[h][0]=j[h].x-b,k=this.dxyz[h][1]=j[h].y-c,m=this.dxyz[h][2]=j[h].z-f,this.planeShades[h]=n.getShadeIndex(p,k,-m),0==p&&0==k){this.planeShade=this.planeShades[h];break}}if(null!=e||128<d)this.renderQuadrant(-1,-1,b,c,f,d,a),this.renderQuadrant(-1,1,b,c,f,d,a),this.renderQuadrant(1,-1,b,c,f,d,a),this.renderQuadrant(1,1,b,c,f,d,a),null!=e&&(this.mDeriv=this.coef=this.mat=null);else{var r=

n.sphereShapeCache[d-1];if(null==r){r=0;e=0!=(d&1);j=d/2;k=j*j;p=B((d+1)/2);m=e?0:0.5;for(h=0;h<p;++h,++m)for(var u=m*m,v=e?0:0.5,y=0;y<p;++y,++v){var w=v*v,w=k-u-w;0<=w&&++r}var r=E(r,0),z=0;m=e?0:0.5;for(h=0;h<p;++h,++m){u=m*m;v=e?0:0.5;for(y=0;y<p;++y,++v)if(w=v*v,w=k-u-w,0<=w){var C=Math.sqrt(w),w=D(C),F=n.getShadeN(v,m,C,j),H=n.getShadeN(-v,m,C,j),I=n.getShadeN(v,-m,C,j),C=n.getShadeN(-v,-m,C,j),w=w|F<<7|H<<13|I<<19|C<<25;r[z++]=w}r[z-1]|=2147483648}n.sphereShapeCache[d-1]=r}0>x||s>=this.width||

0>G||M>=this.height||q<this.slab||f>this.depth?this.renderSphereClipped(r,b,c,f,d,a):this.renderSphereUnclipped(r,f,d,a)}this.zbuf=null}}},"~A,~N,~N,~N,~N,JU.M3,~A,JU.M4,~N,~A");c(b,"renderSphereUnclipped",function(a,d,b,c){var f=0,e=1-(b&1),h=this.offsetPbufBeginLine,k=h-e*this.width;b=B((b+1)/2);var m=this.zbuf,j=this.width,p=this.g3d.pixel;do{var q=h,x=h-e,s=k,G=k-e,M;do{M=a[f++];var n=d-(M&127);n<m[q]&&p.addPixel(q,n,c[M>>7&63]);n<m[x]&&p.addPixel(x,n,c[M>>13&63]);n<m[s]&&p.addPixel(s,n,c[M>>

19&63]);n<m[G]&&p.addPixel(G,n,c[M>>25&63]);++q;--x;++s;--G}while(0<=M);h+=j;k-=j}while(0<--b)},"~A,~N,~N,~A");c(b,"renderSphereClipped",function(a,d,b,c,f,e){var h=this.width,k=this.height,m=0,j=1-(f&1),p=this.offsetPbufBeginLine,q=p-j*h;f=B((f+1)/2);var x=b,s=b-j;b=(d<<16)+(b<<1)^858993459;var G=this.zbuf,M=this.g3d.pixel,n=this.slab,r=this.depth;do{var u=0<=x&&x<k,v=0<=s&&s<k,w=p,y=p-j,z=q,C=q-j,D,E=d,F=d-j;do{var H=0<=F&&F<h,I=0<=E&&E<h;D=a[m++];var L;L=D&127;var K;c<n?(K=c+L,L=K>=n):(K=c-L,L=

K<n);L&&(K=n);if(K>=n&&K<=r){if(u){if(I&&K<G[w]){var O=L?44+(b>>7&7):D>>7&63;M.addPixel(w,K,e[O])}H&&K<G[y]&&(O=L?44+(b>>13&7):D>>13&63,M.addPixel(y,K,e[O]))}v&&(I&&K<G[z]&&(O=L?44+(b>>19&7):D>>19&63,M.addPixel(z,K,e[O])),H&&K<G[C]&&(O=L?44+(b>>25&7):D>>25&63,M.addPixel(C,K,e[O])))}++w;--y;++z;--C;++E;--F;L&&(b=(b<<16)+(b<<1)+b&2147483647)}while(0<=D);p+=h;q-=h;++x;--s}while(0<--f)},"~A,~N,~N,~N,~N,~A");c(b,"renderQuadrant",function(a,d,b,c,f,e,h){e=B(e/2);var k=b+e*a,m=(0>b?-1:b<this.width?0:1)+

(0>k?-2:k<this.width?0:2);-3==m||3==m||(k=c+e*d,k=(0>c?-1:c<this.height?0:1)+(0>k?-2:k<this.height?0:2),-3==k||3==k||(null==this.mat&&0==m&&0==k&&f-e>=this.slab&&f<=this.depth?this.renderQuadrantUnclipped(e,a,d,f,h):this.renderQuadrantClipped(e,a,d,b,c,f,h)))},"~N,~N,~N,~N,~N,~N,~A");c(b,"renderQuadrantUnclipped",function(a,d,b,c,f){for(var e=a*a,h=2*a+1,k=0>b?-this.width:this.width,m=this.offsetPbufBeginLine,j=this.zbuf,p=this.g3d.pixel,q=this.shader.sphereShadeIndexes,x=0,s=0;s<=e;s+=x+ ++x,m+=

k)for(var G=m,n=e-s,r=c-a,u=B((x*b+a<<8)/h),v=0,w=0;w<=n;w+=v+ ++v,G+=d)if(!(j[G]<=r)&&(r=B(Math.sqrt(n-w)),r=c-r,!(j[G]<=r))){var y=B((v*d+a<<8)/h);p.addPixel(G,r,f[q[(u<<8)+y]])}},"~N,~N,~N,~N,~A");c(b,"renderQuadrantClipped",function(a,d,b,c,f,e,h){for(var k=null!=this.mat,m=0<=this.selectedOctant,j=a*a,p=2*a+1,q=0>b?-this.width:this.width,x=this.offsetPbufBeginLine,s=(c<<16)+(f<<1)^858993459,G=0,n=0,r=this.g3d.pixel,u=0,v=this.height,w=this.width,y=this.zbuf,z=this.dxyz,C=this.slab,D=this.depth,

E=this.ptTemp,F=this.coef,H=this.zroot,I=this.selectedOctant,K=this.shader,L=this.planeShades,O=K.sphereShadeIndexes,P=this.planeShade,Q=this.mat,U=0,V=0,R=f;V<=j;V+=U+ ++U,x+=q,R+=b)if(0>R){if(0>b)break}else if(R>=v){if(0<b)break}else{var W=j-(k?0:V);k||(G=B((U*b+a<<8)/p));for(var s=(s<<16)+(s<<1)+s&2147483647,T=c,Y=0,$=0,aa=-1,ba=1,Z=x;$<=W;$+=Y+ ++Y,Z+=d,T+=d)if(0>T){if(0>d)break}else if(T>=w){if(0<d)break}else{var S;if(k){S=(F[4]*T+F[5]*R+F[8])/F[2]/2;var X=S*S-(F[0]*T*T+F[1]*R*R+F[3]*T*R+F[6]*

T+F[7]*R-1)/F[2];if(0>X){if(0<=aa)break;continue}X=Math.sqrt(X);H[0]=-S-X;H[1]=-S+X;aa=e<C?1:0;if(0==(S=B(H[aa])))S=e;ba=2;u=S;if(m){E.set(T-c,R-f,S-e);Q.rotate(E);X=0;0>E.x&&(X|=1);0>E.y&&(X|=2);0>E.z&&(X|=4);if(X==I){if(0<=P)n=P;else{ba=3;n=3.4028235E38;for(S=0;3>S;S++)if(0!=(X=z[S][2]))X=e+(-z[S][0]*(T-c)-z[S][1]*(R-f))/X,X<n&&(n=X,ba=S);3==ba&&(ba=0,n=e);H[0]=n;n=L[ba]}S=B(H[0]);ba=3}if(X=e<C?S>=C:S<C)u=S=C,ba=0}if(S<C||S>D||y[Z]<=u)continue}else{S=B(Math.sqrt(W-$));S=e+(e<C?S:-S);if(X=e<C?S>=

C:S<C)S=C,ba=0;if(S<C||S>D||y[Z]<=S)continue}switch(ba){case 0:n=44+(s>>8&7);s=(s<<16)+(s<<1)+s&2147483647;ba=1;break;case 2:n=K.getEllipsoidShade(T,R,H[aa],a,this.mDeriv);break;case 3:r.clearPixel(Z,u);break;default:n=B((Y*d+a<<8)/p),n=O[(G<<8)+n]}r.addPixel(Z,S,h[n])}s=(s+T+R|1)&2147483647}},"~N,~N,~N,~N,~N,~N,~A")});u("J.g3d");C(["java.util.Hashtable"],"J.g3d.TextRenderer",["JU.CU","J.g3d.Graphics3D"],function(){var b=v(function(){this.size=this.mapWidth=this.width=this.ascent=this.height=0;this.tmap=

null;this.isInvalid=!1;r(this,arguments)},J.g3d,"TextRenderer",null);z(b,function(a,d){this.ascent=d.getAscent();this.height=d.getHeight();this.width=d.stringWidth(a);0!=this.width&&(this.mapWidth=this.width,this.size=this.mapWidth*this.height)},"~S,JU.Font");b.clearFontCache=c(b,"clearFontCache",function(){J.g3d.TextRenderer.working||(J.g3d.TextRenderer.htFont3d.clear(),J.g3d.TextRenderer.htFont3dAntialias.clear())});b.plot=c(b,"plot",function(a,d,b,c,f,e,h,k,m,j){if(0==e.length)return 0;if(0<=e.indexOf("<su")||

0<=e.indexOf("<color"))return J.g3d.TextRenderer.plotByCharacter(a,d,b,c,f,e,h,k,m,j);var p=h.getAscent();d-=p;e=J.g3d.TextRenderer.getPlotText3D(a,d,k,e,h,j);if(e.isInvalid)return e.width;j&&(c=J.g3d.Graphics3D.fixTextImageRGB(c));j=e.height;h=e.width;var p=e.tmap,q=k.width,x=k.height,s=k.zbuf,G=k.pixel,n=k.translucencyLog;if(null!=m||(0>a||a+e.width>q||0>d||d+e.height>x)&&null!=(m=k))for(var r=k=0;r<j;r++)for(var u=0;u<h;u++){var v=p[k++];0!=v&&m.plotImagePixel(c,a+u,d+r,b,v,f,q,x,s,G,n)}else{k=

r=0;for(a=d*q+a;r<j;r++,a+=q-h)for(u=0;u<h;u++)G.addImagePixel(p[k++],n,a++,b,c,f)}return e.width},"~N,~N,~N,~N,~N,~S,JU.Font,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B");b.plotByCharacter=c(b,"plotByCharacter",function(a,d,b,c,f,e,h,k,m,j){for(var p=0,q=e.length,x=Math.round(0.25*h.getHeight()),s=-Math.round(0.3*h.getHeight()),G=0,n=0;n<q;n++){if("<"==e.charAt(n)){if(n+5<q&&e.substring(n,n+6).equals("<color")){var G=c,r=e.indexOf(">",n);if(0>r)continue;c=JU.CU.getArgbFromString(e.substring(n+

7,r).trim());n=r;continue}if(n+7<q&&e.substring(n,n+8).equals("</color>")){n+=7;c=G;continue}if(n+4<q&&e.substring(n,n+5).equals("<sub>")){n+=4;d+=x;continue}if(n+4<q&&e.substring(n,n+5).equals("<sup>")){n+=4;d+=s;continue}if(n+5<q&&e.substring(n,n+6).equals("</sub>")){n+=5;d-=x;continue}if(n+5<q&&e.substring(n,n+6).equals("</sup>")){n+=5;d-=s;continue}}r=J.g3d.TextRenderer.plot(a+p,d,b,c,f,e.substring(n,n+1),h,k,m,j);p+=r}return p},"~N,~N,~N,~N,~N,~S,JU.Font,J.g3d.Graphics3D,J.api.JmolRendererInterface,~B");

b.getPlotText3D=c(b,"getPlotText3D",function(a,d,b,c,f,e){J.g3d.TextRenderer.working=!0;e=e?J.g3d.TextRenderer.htFont3dAntialias:J.g3d.TextRenderer.htFont3d;var h=e.get(f),k=null,m=!1,j=!1;null!=h?k=h.get(c):(h=new java.util.Hashtable,m=!0);null==k&&(k=new J.g3d.TextRenderer(c,f),j=!0);k.isInvalid=0==k.width||0>=a+k.width||a>=b.width||0>=d+k.height||d>=b.height;if(k.isInvalid)return k;m&&e.put(f,h);j&&(k.setTranslucency(c,f,b),h.put(c,k));J.g3d.TextRenderer.working=!1;return k},"~N,~N,J.g3d.Graphics3D,~S,JU.Font,~B");

c(b,"setTranslucency",function(a,d,b){a=b.apiPlatform.getTextPixels(a,d,b.platform.getGraphicsForTextOrImage(this.mapWidth,this.height),b.platform.offscreenImage,this.mapWidth,this.height,this.ascent);if(null!=a){this.tmap=P(this.size,0);for(d=a.length;0<=--d;)b=a[d]&255,0!=b&&(this.tmap[d]=J.g3d.TextRenderer.translucency[b>>5])}},"~S,JU.Font,J.g3d.Graphics3D");b.translucency=P(-1,[7,6,5,4,3,2,1,8]);b.working=!1;b.htFont3d=new java.util.Hashtable;b.htFont3dAntialias=new java.util.Hashtable});u("J.g3d");

C(["JU.P3i"],"J.g3d.TextString",null,function(){var b=v(function(){this.font=this.text=null;this.bgargb=this.argb=0;r(this,arguments)},J.g3d,"TextString",JU.P3i,java.util.Comparator);c(b,"setText",function(a,d,b,c,f,e,h){this.text=a;this.font=d;this.argb=b;this.bgargb=c;this.x=f;this.y=e;this.z=h},"~S,JU.Font,~N,~N,~N,~N,~N");j(b,"compare",function(a,d){return null==a||null==d?0:a.z>d.z?-1:a.z<d.z?1:0},"J.g3d.TextString,J.g3d.TextString");j(b,"toString",function(){return this.asString()+" "+this.text})});

u("J.g3d");C(["J.g3d.G3DRenderer","$.PrecisionRenderer","JU.Rgb16"],"J.g3d.TriangleRenderer",["JU.GData"],function(){var b=v(function(){this.rgb16t2=this.rgb16t1=this.rgb16sGouraud=this.rgb16sE=this.rgb16sW=this.azE=this.axE=this.azW=this.axW=this.bb=this.aa=this.az=this.ay=this.ax=this.g3d=null;r(this,arguments)},J.g3d,"TriangleRenderer",J.g3d.PrecisionRenderer,J.g3d.G3DRenderer);Q(b,function(){this.ax=E(3,0);this.ay=E(3,0);this.az=E(3,0);this.aa=K(64,0);this.bb=K(64,0);this.axW=E(64,0);this.azW=

E(64,0);this.axE=E(64,0);this.azE=E(64,0);this.rgb16t1=new JU.Rgb16;this.rgb16t2=new JU.Rgb16});z(b,function(){L(this,J.g3d.TriangleRenderer,[])});j(b,"set",function(a){try{this.rgb16sW=Array(64);this.rgb16sE=Array(64);for(var d=64;0<=--d;)this.rgb16sW[d]=new JU.Rgb16,this.rgb16sE[d]=new JU.Rgb16;this.g3d=a;this.rgb16sGouraud=Array(3);for(d=3;0<=--d;)this.rgb16sGouraud[d]=new JU.Rgb16}catch(b){if(!F(b,Exception))throw b;}return this},"J.api.JmolRendererInterface,JU.GData");c(b,"reallocRgb16s",function(a,

d){var b=Array(d);System.arraycopy(a,0,b,0,a.length);for(var c=a.length;c<d;++c)b[c]=new JU.Rgb16;return b},"~A,~N");c(b,"setGouraud",function(a,d,b){this.rgb16sGouraud[0].setInt(a);this.rgb16sGouraud[1].setInt(d);this.rgb16sGouraud[2].setInt(b)},"~N,~N,~N");c(b,"fillTriangle",function(a,d,b,c){this.ax[0]=a.x;this.ax[1]=d.x;this.ax[2]=b.x;this.ay[0]=a.y;this.ay[1]=d.y;this.ay[2]=b.y;this.az[0]=a.z;this.az[1]=d.z;this.az[2]=b.z;if(!(1>=this.az[0]||1>=this.az[1]||1>=this.az[2])){d=this.g3d.clipCode3(this.ax[0],

this.ay[0],this.az[0]);b=this.g3d.clipCode3(this.ax[1],this.ay[1],this.az[1]);var f=this.g3d.clipCode3(this.ax[2],this.ay[2],this.az[2]),e=d|b|f;a=0!=e;if(!a||!(-1==e||0!=(d&b&f))){f=0;this.ay[1]<this.ay[f]&&(f=1);this.ay[2]<this.ay[f]&&(f=2);var e=(f+1)%3,h=(f+2)%3;if(this.ay[e]>this.ay[h])var k=e,e=h,h=k;d=this.ay[f];var m=this.ay[e],j=this.ay[h];b=j-d+1;if(!(b>3*this.g3d.height)){if(b>this.axW.length){var p=b+31&-32;this.axW=E(p,0);this.azW=E(p,0);this.axE=E(p,0);this.azE=E(p,0);this.aa=K(p,0);

this.bb=K(p,0);this.rgb16sW=this.reallocRgb16s(this.rgb16sW,p);this.rgb16sE=this.reallocRgb16s(this.rgb16sE,p)}var q;c?(p=this.rgb16sW,q=this.rgb16sE):p=q=null;k=m-d;0==k?(this.ax[e]<this.ax[f]&&(k=e,e=f,f=k),this.generateRaster(b,f,h,this.axW,this.azW,0,p),this.generateRaster(b,e,h,this.axE,this.azE,0,q)):m==j?(this.ax[h]<this.ax[e]&&(k=e,e=h,h=k),this.generateRaster(b,f,e,this.axW,this.azW,0,p),this.generateRaster(b,f,h,this.axE,this.azE,0,q)):(m=this.ax[h]-this.ax[f],j=JU.GData.roundInt(B(b/2)),

0>m&&(j=-j),this.ax[f]+B((m*k+j)/b)<this.ax[e]?(this.generateRaster(b,f,h,this.axW,this.azW,0,p),this.generateRaster(k+1,f,e,this.axE,this.azE,0,q),this.generateRaster(b-k,e,h,this.axE,this.azE,k,q)):(this.generateRaster(k+1,f,e,this.axW,this.azW,0,p),this.generateRaster(b-k,e,h,this.axW,this.azW,k,p),this.generateRaster(b,f,h,this.axE,this.azE,0,q)));this.g3d.setZMargin(5);f=this.g3d.pass2Flag01;e=1-f;h=0;0>d&&(b+=d,h-=d,d=0);d+b>this.g3d.height&&(b=this.g3d.height-d);if(c)if(a)for(;--b>=f;++d,++h)a=

this.axE[h]-(c=this.axW[h])+e,0<a&&this.g3d.plotPixelsClippedRaster(a,c,d,this.azW[h],this.azE[h],this.rgb16sW[h],this.rgb16sE[h]);else for(;--b>=f;++d,++h)a=this.axE[h]-(c=this.axW[h])+e,1==f&&0>a&&(a=1,c--),0<a&&this.g3d.plotPixelsUnclippedRaster(a,c,d,this.azW[h],this.azE[h],this.rgb16sW[h],this.rgb16sE[h]);else if(a)for(;--b>=f;++d,++h)a=this.axE[h]-(c=this.axW[h])+e,0<a&&this.g3d.plotPixelsClippedRasterBits(a,c,d,this.azW[h],this.azE[h],null,null,this.aa[h],this.bb[h]);else for(;--b>=f;++d,++h)a=

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this.vectorT=this.pointT3=this.pointT2=this.pointT=this.s2=this.s1=this.pt2i=this.pt0i=this.font3d=this.tickBs=this.tickAs=this.tickB=this.tickA=null;this.draw000=!0;this.width=0;this.endcap=3;this.pt1=this.pt0=null;r(this,arguments)},J.render,"FontLineShapeRenderer",J.render.ShapeRenderer);Q(b,function(){this.pt0i=new JU.P3i;this.pt2i=new JU.P3i;this.s1=new JU.P3i;this.s2=new JU.P3i;this.pointT=new JU.P3;this.pointT2=new JU.P3;this.pointT3=new JU.P3;this.vectorT=new JU.V3;this.vectorT2=new JU.V3;

this.vectorT3=new JU.V3;this.pt0=new JU.P3;this.pt1=new JU.P3});c(b,"getDiameter",function(a,d){var b;b=20<d;switch(this.exportType){case 1:b=b?d:B(Math.floor(1E3*this.vwr.tm.unscaleToScreen(a,2*d/10)));break;default:b?b=D(this.vwr.tm.scaleToScreen(a,B(d/10))):(this.g3d.isAntialiased()&&(d+=d),b=d)}return b},"~N,~N");c(b,"renderLine",function(a,d,b,c){0>b?this.g3d.drawDashedLineBits(8,4,a,d):this.g3d.fillCylinderBits(this.endcap,1==this.exportType?-b:b,a,d);c&&null!=this.tickInfo&&(this.checkTickTemps(),

this.tickAs.setT(a),this.tickBs.setT(d),this.drawTicks(b,!0))},"JU.P3,JU.P3,~N,~B");c(b,"checkTickTemps",function(){null==this.tickA&&(this.tickA=new JU.P3,this.tickB=new JU.P3,this.tickAs=new JU.P3,this.tickBs=new JU.P3)});c(b,"drawTicks",function(a,d){Float.isNaN(this.tickInfo.first)&&(this.tickInfo.first=0);this.drawTicks2(this.tickInfo.ticks.x,8,a,!d?null:null==this.tickInfo.tickLabelFormats?w(-1,["%0.2f"]):this.tickInfo.tickLabelFormats);this.drawTicks2(this.tickInfo.ticks.y,4,a,null);this.drawTicks2(this.tickInfo.ticks.z,

2,a,null)},"~N,~B");c(b,"drawTicks2",function(a,d,b,c){if(0!=a&&(this.g3d.isAntialiased()&&(d*=2),this.vectorT2.set(this.tickBs.x,this.tickBs.y,0),this.vectorT.set(this.tickAs.x,this.tickAs.y,0),this.vectorT2.sub(this.vectorT),!(50>this.vectorT2.length()))){var f=this.tickInfo.signFactor;this.vectorT.sub2(this.tickB,this.tickA);var e=this.vectorT.length();if(null!=this.tickInfo.scale)if(Float.isNaN(this.tickInfo.scale.x)){var h=this.vwr.getUnitCellInfo(0);Float.isNaN(h)||this.vectorT.set(this.vectorT.x/

h,this.vectorT.y/this.vwr.getUnitCellInfo(1),this.vectorT.z/this.vwr.getUnitCellInfo(2))}else this.vectorT.set(this.vectorT.x*this.tickInfo.scale.x,this.vectorT.y*this.tickInfo.scale.y,this.vectorT.z*this.tickInfo.scale.z);h=this.vectorT.length()+1E-4*a;if(!(h<a)){this.vectorT.scale(a/h*e/h);var e=(this.tickBs.z-this.tickAs.z)/(h/a),h=h+this.tickInfo.first,k=B(Math.floor(this.tickInfo.first/a))*a-this.tickInfo.first;this.pointT.scaleAdd2(k/a,this.vectorT,this.tickA);var k=k+this.tickInfo.first,m=

this.tickAs.z;0>b&&(b=1);this.vectorT2.set(-this.vectorT2.y,this.vectorT2.x,0);this.vectorT2.scale(d/this.vectorT2.length());d=this.tickInfo.reference;null==d?(this.pointT3.setT(this.vwr.getBoundBoxCenter()),603979809==this.vwr.g.axesMode&&this.pointT3.add3(1,1,1)):this.pointT3.setT(d);this.tm.transformPtScr(this.pointT3,this.pt2i);d=0.2>Math.abs(this.vectorT2.x/this.vectorT2.y);for(var j=!d,p=!d&&0>this.vectorT2.x,q=null!=c&&0<c.length,x,s,n=Array(1),r=this.draw000?0:-1;k<h;){if(k>=this.tickInfo.first&&

(this.pointT2.setT(this.pointT),this.tm.transformPt3f(this.pointT2,this.pointT2),this.drawLine(B(Math.floor(this.pointT2.x)),B(Math.floor(this.pointT2.y)),D(m),x=B(Math.floor(this.pointT2.x+this.vectorT2.x)),s=B(Math.floor(this.pointT2.y+this.vectorT2.y)),D(m),b),q&&(this.draw000||0!=k))){n[0]=Float.$valueOf(0==k?0:k*f);var u=JU.PT.sprintf(c[r%c.length],"f",n);this.drawString(x,s,D(m),4,p,d,j,B(Math.floor(this.pointT2.y)),u)}this.pointT.add(this.vectorT);k+=a;m+=e;r++}}}},"~N,~N,~N,~A");c(b,"drawLine",

function(a,d,b,c,f,e,h){return this.drawLine2(this.g3d,a,d,b,c,f,e,h)},"~N,~N,~N,~N,~N,~N,~N");c(b,"drawLine2",function(a,d,b,c,f,e,h,k){this.pt0.set(d,b,c);this.pt1.set(f,e,h);if(this.dotsOrDashes)null!=this.dashDots&&J.render.FontLineShapeRenderer.drawDashedCylinder(a,d,b,c,f,e,h,this.dashDots,this.width,this.colixA,this.colixB,!this.isExport||1==this.mad?this.width:this.mad,this.asLineOnly,this.s1);else{if(0>k)return a.drawDashedLineBits(8,4,this.pt0,this.pt1),1;a.fillCylinderBits(2,k,this.pt0,

this.pt1)}return B((k+1)/2)},"J.api.JmolRendererInterface,~N,~N,~N,~N,~N,~N,~N");c(b,"drawString",function(a,d,b,c,f,e,h,k,m){if(null!=m){var j=this.font3d.stringWidth(m),p=this.font3d.getAscent();a=f?a-(B(c/2)+2+j):e?a-(B(c/2)+2+B(j/2)):a+(B(c/2)+2);f=d;f=h?f+B(p/2):0==k||k<d?f+p:f-B(c/2);d=b-c-2;1>d&&(d=1);this.g3d.drawString(m,this.font3d,a,f,d,d,0)}},"~N,~N,~N,~N,~B,~B,~B,~N,~S");b.drawDashedCylinder=c(b,"drawDashedCylinder",function(a,d,b,c,f,e,h,k,m,j,p,q,x,s){if(!(null==k||0>m)){var n=k[0];

f-=d;e-=b;h-=c;var r=0,u=k===J.render.FontLineShapeRenderer.ndots,v=u||k===J.render.FontLineShapeRenderer.sixdots;if(v){null==s&&(s=new JU.P3i);var w=(f*f+e*e)/(m*m);u?(n=Math.sqrt(w)/1.5,r=D(n)+2):8>w?k=J.render.FontLineShapeRenderer.twodots:32>w&&(k=J.render.FontLineShapeRenderer.fourdots)}var w=k[1],y=k[2],z=j,C=0==y?p:j;0==r&&(r=k.length);for(var E=0,F=3;F<r;F++){var E=u?E+1:k[F],H=B(Math.floor(d+f*E/n)),I=B(Math.floor(b+e*E/n)),K=B(Math.floor(c+h*E/n));if(v)s.set(H,I,K),F==w?a.setC(j):F==y&&

a.setC(p),a.fillSphereI(m,s);else{F==w&&(z=p);E=k[++F];F==y&&(C=p);var L=B(Math.floor(d+f*E/n)),O=B(Math.floor(b+e*E/n)),P=B(Math.floor(c+h*E/n));J.render.FontLineShapeRenderer.fillCylinder(a,z,C,2,H,I,K,L,O,P,q,x)}}}},"J.api.JmolRendererInterface,~N,~N,~N,~N,~N,~N,~A,~N,~N,~N,~N,~B,JU.P3i");b.fillCylinder=c(b,"fillCylinder",function(a,d,b,c,f,e,h,k,m,j,p,q){q?a.drawLine(d,b,f,e,h,k,m,j):a.fillCylinderXYZ(d,b,c,p,f,e,h,k,m,j)},"J.api.JmolRendererInterface,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~B");b.dashes=

E(-1,[12,0,0,2,5,7,10]);b.hDashes=E(-1,[10,7,6,1,3,4,6,7,9]);b.pymoldashes=E(-1,[30,0,0,2,4,7,9,12,14,17,19,22,24,27,30]);b.ndots=E(-1,[0,3,1E3]);b.sixdots=E(-1,[12,3,6,1,3,5,7,9,11]);b.fourdots=E(-1,[13,3,5,2,5,8,11]);b.twodots=E(-1,[12,3,4,3,9])});u("J.render");C(["J.render.ShapeRenderer"],"J.render.FrankRenderer",["J.shape.Frank","JV.Viewer"],function(){var b=H(J.render,"FrankRenderer",J.render.ShapeRenderer);j(b,"render",function(){var a=this.shape,d=this.vwr.getBooleanProperty("allowKeyStrokes"),

b=this.vwr.getBoolean(603983903);this.colix=b?20:this.vwr.isSignedApplet?d||(JV.Viewer.isJS||JV.Viewer.isSwingJS)&&!this.vwr.isWebGL?5:10:d?7:12;if(this.isExport||!this.vwr.getShowFrank()||!this.g3d.setC(this.colix))return!1;if(this.vwr.frankOn&&!this.vwr.noFrankEcho)return this.vwr.noFrankEcho;this.vwr.noFrankEcho=!0;d=this.vwr.imageFontScaling;a.getFont(d);d=D(a.frankWidth+4*d);this.g3d.drawStringNoSlab(J.shape.Frank.frankString,a.font3d,this.vwr.gdata.width-d,this.vwr.gdata.height-a.frankDescent,

0,0);a=b?this.vwr.getModelkit(!1):null;b&&!a.isHidden()&&(this.g3d.setC(12),this.g3d.fillTextRect(0,0,1,0,10,104),b=a.getActiveMenu(),null!=b&&("atomMenu".equals(b)?(this.g3d.setC(21),this.g3d.fillTextRect(0,0,0,0,10,26)):"bondMenu".equals(b)?(this.g3d.setC(7),this.g3d.fillTextRect(0,26,0,0,10,26)):"xtalMenu".equals(b)&&(this.g3d.setC(8),this.g3d.fillTextRect(0,52,0,0,10,26))));return!1})});u("J.render");C(["J.api.JmolRepaintManager","JU.BS"],"J.render.RepaintManager",["J.api.Interface","JU.Logger",

"JV.JC","$.Viewer"],function(){var b=v(function(){this.bsTranslucent=this.renderers=this.shapeManager=this.vwr=null;this.holdRepaint=0;this.repaintPending=!1;r(this,arguments)},J.render,"RepaintManager",null,J.api.JmolRepaintManager);Q(b,function(){this.bsTranslucent=JU.BS.newN(37)});z(b,function(){});j(b,"set",function(a,d){this.vwr=a;this.shapeManager=d},"JV.Viewer,JV.ShapeManager");j(b,"isRepaintPending",function(){return this.repaintPending});j(b,"pushHoldRepaint",function(){++this.holdRepaint},

"~S");j(b,"popHoldRepaint",function(a,d){null!=d&&d.startsWith("CLEAR HOLD")&&(this.holdRepaint=0,a=!0);--this.holdRepaint;0>=this.holdRepaint&&(this.holdRepaint=0,a&&(this.repaintPending=!0,this.repaintNow(d)))},"~B,~S");j(b,"requestRepaintAndWait",function(a){var d=null;JV.Viewer.isJS&&!JV.Viewer.isSwingJS&&(d=self.Jmol&&Jmol.repaint?Jmol:null);if(null==d)try{this.repaintNow(a),JV.Viewer.isJS||this.wait(this.vwr.g.repaintWaitMs),this.repaintPending&&(JU.Logger.error("repaintManager requestRepaintAndWait timeout"),

this.repaintDone())}catch(b){if(F(b,"InterruptedException"))System.out.println("repaintManager requestRepaintAndWait interrupted thread="+Thread.currentThread().getName());else throw b;}else d.repaint(this.vwr.html5Applet,!1),this.repaintDone()},"~S");j(b,"repaintIfReady",function(a){if(this.repaintPending)return!1;this.repaintPending=!0;0==this.holdRepaint&&this.repaintNow(a);return!0},"~S");c(b,"repaintNow",function(){this.vwr.haveDisplay&&this.vwr.apiPlatform.repaint(this.vwr.display)},"~S");j(b,

"repaintDone",function(){this.repaintPending=!1});j(b,"clear",function(a){if(null!=this.renderers)if(0<=a)this.renderers[a]=null;else for(a=0;37>a;++a)this.renderers[a]=null},"~N");c(b,"getRenderer",function(a){if(null!=this.renderers[a])return this.renderers[a];var d=JV.JC.getShapeClassName(a,!0)+"Renderer";if(null==(d=J.api.Interface.getInterface(d,this.vwr,"render")))return null;d.setViewerG3dShapeID(this.vwr,a);return this.renderers[a]=d},"~N");j(b,"render",function(a,d,b,c){null==this.renderers&&

(this.renderers=Array(37));this.getAllRenderers();try{var f=this.vwr.getBoolean(603979934);a.renderBackground(null);if(b){this.bsTranslucent.clearAll();null!=c&&a.renderCrossHairs(c,this.vwr.getScreenWidth(),this.vwr.getScreenHeight(),this.vwr.tm.getNavigationOffset(),this.vwr.tm.navigationDepthPercent);var e=this.vwr.getRubberBandSelection();null!=e&&a.setC(this.vwr.cm.colixRubberband)&&a.drawRect(e.x,e.y,0,0,e.width,e.height);this.vwr.noFrankEcho=!0}c=null;for(e=0;37>e&&a.currentlyRendering;++e){var h=

this.shapeManager.getShape(e);null!=h&&(f&&(c="rendering "+JV.JC.getShapeClassName(e,!1),JU.Logger.startTimer(c)),(b||this.bsTranslucent.get(e))&&this.getRenderer(e).renderShape(a,d,h)&&this.bsTranslucent.set(e),f&&JU.Logger.checkTimer(c,!1))}a.renderAllStrings(null)}catch(k){if(F(k,Exception)){k.printStackTrace();if(this.vwr.async&&"Interface".equals(k.getMessage()))throw new NullPointerException;JU.Logger.error("rendering error? "+k)}else throw k;}},"JU.GData,JM.ModelSet,~B,~A");c(b,"getAllRenderers",

function(){for(var a=!0,d=0;37>d;++d)null==this.shapeManager.getShape(d)||null!=this.getRenderer(d)||(a=this.repaintPending=!this.vwr.async);if(!a)throw new NullPointerException;});j(b,"renderExport",function(a,d,b){this.shapeManager.finalizeAtoms(null,!0);a=this.vwr.initializeExporter(b);if(null==a)return JU.Logger.error("Cannot export "+b.get("type")),null;null==this.renderers&&(this.renderers=Array(37));this.getAllRenderers();b=null;try{var c=this.vwr.getBoolean(603979934);a.renderBackground(a);

for(var f=0;37>f;++f){var e=this.shapeManager.getShape(f);null!=e&&(c&&(b="rendering "+JV.JC.getShapeClassName(f,!1),JU.Logger.startTimer(b)),this.getRenderer(f).renderShape(a,d,e),c&&JU.Logger.checkTimer(b,!1))}a.renderAllStrings(a);b=a.finalizeOutput()}catch(h){if(F(h,Exception))h.printStackTrace(),JU.Logger.error("rendering error? "+h);else throw h;}return b},"JU.GData,JM.ModelSet,java.util.Map")});u("J.render");C(null,"J.render.ShapeRenderer",["JV.JC"],function(){var b=v(function(){this.shape=

this.ms=this.g3d=this.tm=this.vwr=null;this.exportType=this.mad=this.colix=this.shapeID=this.myVisibilityFlag=0;this.isExport=!1;r(this,arguments)},J.render,"ShapeRenderer",null);c(b,"initRenderer",function(){});c(b,"setViewerG3dShapeID",function(a,d){this.vwr=a;this.tm=a.tm;this.shapeID=d;this.myVisibilityFlag=JV.JC.getShapeVisibilityFlag(d);this.initRenderer()},"JV.Viewer,~N");c(b,"renderShape",function(a,d,b){this.setup(a,d,b);a=this.render();this.exportType=0;this.isExport=!1;return a},"J.api.JmolRendererInterface,JM.ModelSet,J.shape.Shape");

c(b,"setup",function(a,d,b){this.g3d=a;this.ms=d;this.shape=b;this.exportType=a.getExportType();this.isExport=0!=this.exportType},"J.api.JmolRendererInterface,JM.ModelSet,J.shape.Shape");c(b,"isVisibleForMe",function(a){return a.isVisible(this.myVisibilityFlag|9)},"JM.Atom")});u("J.render");C(["J.render.FontLineShapeRenderer","JU.BS","$.P3","$.V3"],"J.render.SticksRenderer",["JU.A4","$.M3","J.c.PAL","JU.C","$.Edge"],function(){var b=v(function(){this.showMultipleBonds=!1;this.multipleBondRadiusFactor=

this.multipleBondSpacing=0;this.useBananas=this.bondsPerp=!1;this.modeMultipleBond=0;this.isCartesian=!1;this.endcaps=0;this.hbondsSolid=this.bondsBackbone=this.hbondsBackbone=this.ssbondsBackbone=!1;this.bond=this.b=this.a=null;this.bondOrder=this.mag2d=this.dy=this.dx=this.zB=this.yB=this.xB=this.zA=this.yA=this.xA=0;this.slabByAtom=this.slabbing=this.isAntialiased=this.wireframeOnly=!1;this.bsForPass2=this.p2=this.p1=this.z=this.y=this.x=null;this.isPass2=!1;this.dyStep=this.dxStep=this.yAxis2=

this.xAxis2=this.yAxis1=this.xAxis1=0;this.a4=this.rot=null;r(this,arguments)},J.render,"SticksRenderer",J.render.FontLineShapeRenderer);Q(b,function(){this.x=new JU.V3;this.y=new JU.V3;this.z=new JU.V3;this.p1=new JU.P3;this.p2=new JU.P3;this.bsForPass2=JU.BS.newN(64)});j(b,"render",function(){var a=this.ms.bo;if(null==a)return!1;(this.isPass2=this.vwr.gdata.isPass2)||this.bsForPass2.clearAll();this.slabbing=this.tm.slabEnabled;this.slabByAtom=this.vwr.getBoolean(603979939);this.endcaps=3;this.dashDots=

this.vwr.getBoolean(603979893)?J.render.FontLineShapeRenderer.sixdots:J.render.FontLineShapeRenderer.dashes;this.isCartesian=1==this.exportType;this.getMultipleBondSettings(!1);this.wireframeOnly=!this.vwr.checkMotionRendering(1677721602);this.ssbondsBackbone=this.vwr.getBoolean(603979952);this.hbondsBackbone=this.vwr.getBoolean(603979852);this.bondsBackbone=(new Boolean(this.hbondsBackbone|this.ssbondsBackbone)).valueOf();this.hbondsSolid=this.vwr.getBoolean(603979854);this.isAntialiased=this.g3d.isAntialiased();

var d=!1;if(this.isPass2){if(!this.isExport)for(var b=this.bsForPass2.nextSetBit(0);0<=b;b=this.bsForPass2.nextSetBit(b+1))this.bond=a[b],null!=this.bond&&this.renderBond()}else for(b=this.ms.bondCount;0<=--b;)this.bond=a[b],null!=this.bond&&(0!=(this.bond.shapeVisibilityFlags&this.myVisibilityFlag)&&this.renderBond())&&(d=!0,this.bsForPass2.set(b));return d});c(b,"getMultipleBondSettings",function(a){this.useBananas=this.vwr.getBoolean(603979886)&&!a;this.multipleBondSpacing=a?0.26:this.vwr.getFloat(570425370);

this.multipleBondRadiusFactor=a?0.4:this.vwr.getFloat(570425369);this.bondsPerp=this.useBananas||0<this.multipleBondSpacing&&0>this.multipleBondRadiusFactor;this.useBananas&&(this.multipleBondSpacing=0>this.multipleBondSpacing?0.4*-this.multipleBondSpacing:this.multipleBondSpacing);this.multipleBondRadiusFactor=Math.abs(this.multipleBondRadiusFactor);0==this.multipleBondSpacing&&this.isCartesian&&(this.multipleBondSpacing=0.2);this.modeMultipleBond=this.vwr.g.modeMultipleBond;this.showMultipleBonds=

0!=this.multipleBondSpacing&&0!=this.modeMultipleBond&&this.vwr.getBoolean(603979928)},"~B");c(b,"renderBond",function(){var a,d;this.a=a=this.bond.atom1;this.b=d=this.bond.atom2;var b=this.bond.order&131071;this.bondsBackbone&&(this.ssbondsBackbone&&0!=(b&256)?(this.a=this.a.group.getLeadAtomOr(this.a),this.b=this.b.group.getLeadAtomOr(this.b)):this.hbondsBackbone&&JU.Edge.isOrderH(b)&&(this.a=this.a.group.getLeadAtomOr(this.a),this.b=this.b.group.getLeadAtomOr(this.b)));if(!this.isPass2&&(!this.a.isVisible(9)||

!this.b.isVisible(9)||!this.g3d.isInDisplayRange(this.a.sX,this.a.sY)||!this.g3d.isInDisplayRange(this.b.sX,this.b.sY)))return!1;if(this.slabbing){var c=this.vwr.gdata.isClippedZ(this.a.sZ);if(c&&this.vwr.gdata.isClippedZ(this.b.sZ)||this.slabByAtom&&(c||this.vwr.gdata.isClippedZ(this.b.sZ)))return!1}this.zA=this.a.sZ;this.zB=this.b.sZ;if(1==this.zA||1==this.zB)return!1;this.colixA=a.colixAtom;this.colixB=d.colixAtom;2==((this.colix=this.bond.colix)&-30721)?(this.colix&=30720,this.colixA=JU.C.getColixInherited(this.colix|

this.vwr.cm.getColixAtomPalette(a,J.c.PAL.CPK.id),this.colixA),this.colixB=JU.C.getColixInherited(this.colix|this.vwr.cm.getColixAtomPalette(d,J.c.PAL.CPK.id),this.colixB)):(this.colixA=JU.C.getColixInherited(this.colix,this.colixA),this.colixB=JU.C.getColixInherited(this.colix,this.colixB));a=!1;if(!this.isExport&&!this.isPass2&&(d=!JU.C.renderPass2(this.colixA),c=!JU.C.renderPass2(this.colixB),!d||!c)){if(!d&&!c&&!a)return this.g3d.setC(!d?this.colixA:this.colixB),!0;a=!0}this.bondOrder=b&131071;

if(0==(this.bondOrder&224)&&(0!=(this.bondOrder&256)&&(this.bondOrder&=-257),0!=(this.bondOrder&1023)&&(!this.showMultipleBonds||2==this.modeMultipleBond&&500<this.mad||65536==(this.bondOrder&98304))))this.bondOrder=1;d=0;switch(this.bondOrder){case 1025:case 1041:case 1057:this.bondOrder=1;case 1:case 2:case 3:case 4:case 5:case 6:break;case 17:case 513:this.bondOrder=1;d=513==b?0:1;break;case 515:case 514:this.bondOrder=2;d=515==b?this.getAromaticDottedBondMask():0;break;default:0!=(this.bondOrder&

224)?(this.bondOrder=JU.Edge.getPartialBondOrder(b),d=JU.Edge.getPartialBondDotted(b)):JU.Edge.isOrderH(this.bondOrder)?(this.bondOrder=1,this.hbondsSolid||(d=-1)):32768==this.bondOrder?this.bondOrder=1:98304==(this.bondOrder&98304)&&(this.getMultipleBondSettings(!0),this.bondOrder&=3,d=-2)}this.xA=this.a.sX;this.yA=this.a.sY;this.xB=this.b.sX;this.yB=this.b.sY;this.mad=this.bond.mad;0<this.multipleBondRadiusFactor&&1<this.bondOrder&&(this.mad*=this.multipleBondRadiusFactor);this.dx=this.xB-this.xA;

this.dy=this.yB-this.yA;this.width=D(this.vwr.tm.scaleToScreen(B((this.zA+this.zB)/2),this.mad));this.wireframeOnly&&0<this.width&&(this.width=1);if(!this.isCartesian&&(this.asLineOnly=1>=this.width)&&this.isAntialiased)this.width=3,this.asLineOnly=!1;b=!this.isExport||1==this.mad?this.width:this.mad;switch(d){case -2:this.drawBond(0);this.getMultipleBondSettings(!1);break;case -1:J.render.FontLineShapeRenderer.drawDashedCylinder(this.g3d,this.xA,this.yA,this.zA,this.xB,this.yB,this.zB,J.render.FontLineShapeRenderer.hDashes,

this.width,this.colixA,this.colixB,b,this.asLineOnly,this.s1);break;default:switch(this.bondOrder){case 4:this.bondOrder=2;b=this.multipleBondRadiusFactor;0==b&&1<this.width&&(this.width=B(0.5*this.width));b=this.multipleBondSpacing;0>b&&(this.multipleBondSpacing=0.3);this.drawBond(d);this.bondsPerp=!this.bondsPerp;this.bondOrder=2;this.drawBond(d>>2);this.bondsPerp=!this.bondsPerp;this.multipleBondSpacing=b;break;case 5:this.bondOrder=3;b=this.multipleBondRadiusFactor;0==b&&1<this.width&&(this.width=

B(0.5*this.width));b=this.multipleBondSpacing;0>b&&(this.multipleBondSpacing=0.2);this.drawBond(d);this.bondsPerp=!this.bondsPerp;this.bondOrder=2;this.multipleBondSpacing*=1.5;this.drawBond(d>>3);this.bondsPerp=!this.bondsPerp;this.multipleBondSpacing=b;break;case 6:this.bondOrder=4;b=this.multipleBondRadiusFactor;0==b&&1<this.width&&(this.width=B(0.5*this.width));b=this.multipleBondSpacing;0>b&&(this.multipleBondSpacing=0.15);this.drawBond(d);this.bondsPerp=!this.bondsPerp;this.bondOrder=2;this.multipleBondSpacing*=

1.5;this.drawBond(d>>4);this.bondsPerp=!this.bondsPerp;this.multipleBondSpacing=b;break;default:this.drawBond(d)}}return a});c(b,"drawBond",function(a){var d=0!=(a&1),b=16384==(this.colixA&30720)||16384==(this.colixB&30720)?2:this.endcaps;if(this.isCartesian&&1==this.bondOrder&&!d)this.g3d.drawBond(this.a,this.b,this.colixA,this.colixB,b,this.mad,-1);else{var c=0==this.dx&&0==this.dy;if(!c||!this.asLineOnly||this.isCartesian){var f=!this.isExport||1==this.mad?this.width:this.mad,e=1<this.bondOrder&&

0<this.multipleBondSpacing,h=e&&(null!=this.vwr.getHybridizationAndAxes(this.a.i,this.z,this.x,"pz")||null!=this.vwr.getHybridizationAndAxes(this.b.i,this.z,this.x,"pz"))&&!Float.isNaN(this.x.x);if(c&&!e){a=B(this.width/8)+3;a=this.width+a;d=this.yA-B((this.bondOrder-1)*a/2);do J.render.FontLineShapeRenderer.fillCylinder(this.g3d,this.colixA,this.colixB,b,this.xA,d,this.zA,this.xB,d,this.zB,f,this.asLineOnly),d+=a;while(0<--this.bondOrder)}else if(1==this.bondOrder)d?J.render.FontLineShapeRenderer.drawDashedCylinder(this.g3d,

this.xA,this.yA,this.zA,this.xB,this.yB,this.zB,this.dashDots,this.width,this.colixA,this.colixB,f,this.asLineOnly,this.s1):J.render.FontLineShapeRenderer.fillCylinder(this.g3d,this.colixA,this.colixB,b,this.xA,this.yA,this.zA,this.xB,this.yB,this.zB,f,this.asLineOnly);else if(e)if(h||this.z.setT(JU.P3.getUnlikely()),this.x.sub2(this.b,this.a),this.y.cross(this.x,this.z),this.y.normalize(),Float.isNaN(this.y.x)&&(this.z.setT(JU.P3.getUnlikely()),this.y.cross(this.x,this.z),this.y.cross(this.y,this.x),

this.y.normalize()),this.bondsPerp&&this.y.cross(this.y,this.x),this.y.scale(this.multipleBondSpacing),this.x.setT(this.y),this.x.scale((this.bondOrder-1)/2),this.useBananas)switch(this.drawBanana(this.a,this.b,this.x,0),this.bondOrder){case 4:this.drawBanana(this.a,this.b,this.x,90),this.drawBanana(this.a,this.b,this.x,-90);default:this.drawBanana(this.a,this.b,this.x,180);break;case 3:this.drawBanana(this.a,this.b,this.x,120),this.drawBanana(this.a,this.b,this.x,-120)}else{this.p1.sub2(this.a,this.x);

for(this.p2.sub2(this.b,this.x);;){this.isCartesian?this.g3d.drawBond(this.p1,this.p2,this.colixA,this.colixB,b,this.mad,-2):(this.tm.transformPtScr(this.p1,this.s1),this.tm.transformPtScr(this.p2,this.s2),d?J.render.FontLineShapeRenderer.drawDashedCylinder(this.g3d,this.s1.x,this.s1.y,this.s1.z,this.s2.x,this.s2.y,this.s2.z,this.dashDots,this.width,this.colixA,this.colixB,f,this.asLineOnly,this.s1):J.render.FontLineShapeRenderer.fillCylinder(this.g3d,this.colixA,this.colixB,b,this.s1.x,this.s1.y,

this.s1.z,this.s2.x,this.s2.y,this.s2.z,f,this.asLineOnly));a>>=1;d=0!=(a&1);if(0>=--this.bondOrder)break;this.p1.add(this.y);this.p2.add(this.y);this.stepAxisCoordinates()}}else if(this.mag2d=Math.round(Math.sqrt(this.dx*this.dx+this.dy*this.dy)),this.resetAxisCoordinates(),this.isCartesian&&3==this.bondOrder)J.render.FontLineShapeRenderer.fillCylinder(this.g3d,this.colixA,this.colixB,b,this.xAxis1,this.yAxis1,this.zA,this.xAxis2,this.yAxis2,this.zB,f,this.asLineOnly),this.stepAxisCoordinates(),

this.x.sub2(this.b,this.a),this.x.scale(0.05),this.p1.sub2(this.a,this.x),this.p2.add2(this.b,this.x),this.g3d.drawBond(this.p1,this.p2,this.colixA,this.colixB,b,this.mad,-2),this.stepAxisCoordinates(),J.render.FontLineShapeRenderer.fillCylinder(this.g3d,this.colixA,this.colixB,b,this.xAxis1,this.yAxis1,this.zA,this.xAxis2,this.yAxis2,this.zB,f,this.asLineOnly);else for(;;){0!=(a&1)?J.render.FontLineShapeRenderer.drawDashedCylinder(this.g3d,this.xAxis1,this.yAxis1,this.zA,this.xAxis2,this.yAxis2,

this.zB,this.dashDots,this.width,this.colixA,this.colixB,f,this.asLineOnly,this.s1):J.render.FontLineShapeRenderer.fillCylinder(this.g3d,this.colixA,this.colixB,b,this.xAxis1,this.yAxis1,this.zA,this.xAxis2,this.yAxis2,this.zB,f,this.asLineOnly);a>>=1;if(0>=--this.bondOrder)break;this.stepAxisCoordinates()}}}},"~N");c(b,"resetAxisCoordinates",function(){var a=this.mag2d>>3;-1!=this.multipleBondSpacing&&0>this.multipleBondSpacing&&(a*=-this.multipleBondSpacing);a=this.width+a;this.dxStep=B(a*this.dy/

this.mag2d);this.dyStep=B(a*-this.dx/this.mag2d);this.xAxis1=this.xA;this.yAxis1=this.yA;this.xAxis2=this.xB;this.yAxis2=this.yB;a=this.bondOrder-1;this.xAxis1-=B(this.dxStep*a/2);this.yAxis1-=B(this.dyStep*a/2);this.xAxis2-=B(this.dxStep*a/2);this.yAxis2-=B(this.dyStep*a/2)});c(b,"stepAxisCoordinates",function(){this.xAxis1+=this.dxStep;this.yAxis1+=this.dyStep;this.xAxis2+=this.dxStep;this.yAxis2+=this.dyStep});c(b,"getAromaticDottedBondMask",function(){var a=this.b.findAromaticNeighbor(this.a.i);

return null==a?1:0>this.dx*(a.sY-this.yA)-this.dy*(a.sX-this.xA)?2:1});c(b,"drawBanana",function(a,d,b,c){this.g3d.addRenderer(553648143);this.vectorT.sub2(d,a);null==this.rot&&(this.rot=new JU.M3,this.a4=new JU.A4);this.a4.setVA(this.vectorT,3.141592653589793*c/180);this.rot.setAA(this.a4);this.pointT.setT(a);this.pointT3.setT(d);this.pointT2.ave(a,d);this.rot.rotate2(b,this.vectorT);this.pointT2.add(this.vectorT);this.tm.transformPtScrT3(a,this.pointT);this.tm.transformPtScrT3(this.pointT2,this.pointT2);

this.tm.transformPtScrT3(d,this.pointT3);a=Math.max(this.width,1);this.g3d.setC(this.colixA);this.g3d.fillHermite(5,a,a,a,this.pointT,this.pointT,this.pointT2,this.pointT3);this.g3d.setC(this.colixB);this.g3d.fillHermite(5,a,a,a,this.pointT,this.pointT2,this.pointT3,this.pointT3)},"JM.Atom,JM.Atom,JU.V3,~N")});u("JS");C(["JS.T"],"JS.ContextToken",["java.util.Hashtable","JS.SV"],function(){var b=v(function(){this.name0=this.forVars=this.contextVariables=null;r(this,arguments)},JS,"ContextToken",JS.T);

b.newContext=c(b,"newContext",function(a){a=a?JS.ContextToken.newCmd(1275335685,"{"):JS.ContextToken.newCmd(1275334681,"}");a.intValue=0;return a},"~B");b.newCmd=c(b,"newCmd",function(a,d){var b=new JS.ContextToken;b.tok=a;b.value=d;return b},"~N,~O");c(b,"addName",function(a){null==this.contextVariables&&(this.contextVariables=new java.util.Hashtable);this.contextVariables.put(a,JS.SV.newS("").setName(a))},"~S")});u("JS");C(null,"JS.ScriptContext",["java.util.Hashtable","JS.SV"],function(){var b=

v(function(){this.aatoken=null;this.chk=this.allowJSThreads=!1;this.contextPath=" >> ";this.vars=null;this.displayLoadErrorsSave=!1;this.errorType=this.errorMessageUntranslated=this.errorMessage=null;this.isEditorScript=this.isEditor=this.executionStepping=this.executionPaused=!1;this.functionName=null;this.iCommandError=-1;this.id=0;this.isComplete=!0;this.isTryCatch=this.isStateScript=this.isJSThread=this.isFunction=!1;this.forVars=null;this.iToken=0;this.lineEnd=2147483647;this.lineNumbers=this.lineIndices=

null;this.mustResumeEval=!1;this.parentContext=this.parallelProcessor=this.outputBuffer=null;this.pc0=this.pc=0;this.pcEnd=2147483647;this.scriptFileName=this.scriptExtensions=this.script=null;this.scriptLevel=0;this.htFileCache=this.statement=null;this.statementLength=0;this.token=null;this.tryPt=0;this.theToken=null;this.theTok=0;this.privateFuncs=this.why=this.pointers=null;r(this,arguments)},JS,"ScriptContext",null);z(b,function(){this.id=++JS.ScriptContext.contextCount});c(b,"setMustResume",

function(){for(var a=this;null!=a;)a.mustResumeEval=!0,a.pc=a.pc0,a=a.parentContext});c(b,"getVariable",function(a){for(var d=this,b;null!=d&&!d.isFunction;){if(null!=d.vars&&null!=(b=d.vars.get(a)))return b;d=d.parentContext}return null},"~S");c(b,"getFullMap",function(){var a=new java.util.Hashtable,d=this;for(null!=this.contextPath&&a.put("_path",JS.SV.newS(this.contextPath));null!=d&&!d.isFunction;){if(null!=d.vars)for(var b,c=d.vars.keySet().iterator();c.hasNext()&&((b=c.next())||1);)if(!a.containsKey(b)){var f=

d.vars.get(b);(2!=f.tok||2147483647!=f.intValue)&&a.put(b,f)}d=d.parentContext}return a});c(b,"saveTokens",function(a){this.aatoken=a;if(null==a)this.pointers=null;else{this.pointers=E(a.length,0);for(var d=this.pointers.length;0<=--d;)this.pointers[d]=null==a[d]?-1:a[d][0].intValue}},"~A");c(b,"restoreTokens",function(){if(null!=this.pointers)for(var a=this.pointers.length;0<=--a;)null!=this.aatoken[a]&&(this.aatoken[a][0].intValue=this.pointers[a]);return this.aatoken});c(b,"getTokenCount",function(){return null==

this.aatoken?-1:this.aatoken.length});c(b,"getToken",function(a){return this.aatoken[a]},"~N");b.contextCount=0});u("JS");C(["java.lang.Exception"],"JS.ScriptException",null,function(){var b=v(function(){this.untranslated=this.message=this.eval=null;this.isError=!1;r(this,arguments)},JS,"ScriptException",Exception);z(b,function(a,d,b,c){this.eval=a;this.message=d;(this.isError=c)&&this.eval.setException(this,d,b)},"JS.ScriptError,~S,~S,~B");c(b,"getErrorMessageUntranslated",function(){return this.untranslated});

j(b,"getMessage",function(){return this.message});j(b,"toString",function(){return this.message})});u("JS");C(["javajs.api.JSONEncodable","JS.T","JU.P3"],"JS.SV","java.util.Arrays $.Collections $.Hashtable JU.AU $.BArray $.BS $.Base64 $.Lst $.Measure $.PT $.SB JM.BondSet JU.BSUtil $.Escape JV.Viewer".split(" "),function(){var b=v(function(){this.index=2147483647;this.myName=null;V("JS.SV.Sort")||JS.SV.$SV$Sort$();r(this,arguments)},JS,"SV",JS.T,javajs.api.JSONEncodable);b.newV=c(b,"newV",function(a,

d){var b=new JS.SV;b.tok=a;b.value=d;return b},"~N,~O");b.newI=c(b,"newI",function(a){var d=new JS.SV;d.tok=2;d.intValue=a;return d},"~N");b.newF=c(b,"newF",function(a){if(a!=a)return JS.SV.vNaN;var d=new JS.SV;d.tok=3;d.value=Float.$valueOf(a);return d},"~N");b.newS=c(b,"newS",function(a){return JS.SV.newV(4,a)},"~S");b.newT=c(b,"newT",function(a){return JS.SV.newSV(a.tok,a.intValue,a.value)},"JS.T");b.newSV=c(b,"newSV",function(a,d,b){a=JS.SV.newV(a,b);a.intValue=d;return a},"~N,~N,~O");c(b,"setv",

function(a){this.index=a.index;this.intValue=a.intValue;this.tok=a.tok;this.value=a.value;return this},"JS.SV");b.copySafely=c(b,"copySafely",function(a){return null==a.myName?a:(new JS.SV).setv(a)},"JS.SV");b.sizeOf=c(b,"sizeOf",function(a){switch(null==a?0:a.tok){case 10:return JS.SV.bsSelectToken(a).cardinality();case 15:return a.value.data.length;case 4:return a.value.length;case 7:return 2147483647==a.intValue?a.getList().size():JS.SV.sizeOf(JS.SV.selectItemTok(a,-2147483648));case 6:return a.value.size();

case 14:return a.value.getFullMap().size();case 1073742335:case 1073742334:return-1;case 2:return-2;case 3:return-4;case 8:return-8;case 9:return-16;case 11:return-32;case 12:return-64;default:return 0}},"JS.T");b.isVariableType=c(b,"isVariableType",function(a){return y(a,"JS.SV")||y(a,Boolean)||y(a,Integer)||y(a,Float)||"string"==typeof a||y(a,"JU.T3")||y(a,"JU.BS")||y(a,"JU.P4")||y(a,"JU.Quat")||y(a,"JU.M34")||y(a,"java.util.Map")||y(a,"JU.Lst")||y(a,"JU.BArray")||y(a,"JS.ScriptContext")||JS.SV.isArray(a)},

"~O");b.isArray=c(b,"isArray",function(a){return y(a,Array)},"~O");b.getVariable=c(b,"getVariable",function(a){return null==a?JS.SV.newS(""):y(a,"JS.SV")?a:y(a,Boolean)?JS.SV.getBoolean(a.booleanValue()):y(a,Integer)?JS.SV.newI(a.intValue()):y(a,Float)?JS.SV.newV(3,a):"string"==typeof a?(a=JS.SV.unescapePointOrBitsetAsVariable(a),y(a,"JS.SV")?a:JS.SV.newV(4,a)):y(a,"JU.P3")?JS.SV.newV(8,a):y(a,"JU.V3")?JS.SV.newV(8,JU.P3.newP(a)):y(a,"JU.BS")?JS.SV.newV(10,a):y(a,"JU.P4")?JS.SV.newV(9,a):y(a,"JU.Quat")?

JS.SV.newV(9,a.toPoint4f()):y(a,"JU.M34")?JS.SV.newV(y(a,"JU.M4")?12:11,a):y(a,"java.util.Map")?JS.SV.getVariableMap(a):y(a,"JU.Lst")?JS.SV.getVariableList(a):y(a,"JU.BArray")?JS.SV.newV(15,a):y(a,"JS.ScriptContext")?JS.SV.newV(14,a):JS.SV.isASV(a)?JS.SV.getVariableAV(a):JU.AU.isAI(a)?JS.SV.getVariableAI(a):JU.AU.isAB(a)?JS.SV.getVariableAB(a):JU.AU.isAF(a)?JS.SV.getVariableAF(a):JU.AU.isAD(a)?JS.SV.getVariableAD(a):JU.AU.isAS(a)?JS.SV.getVariableAS(a):JU.AU.isAP(a)?JS.SV.getVariableAP(a):JU.AU.isAII(a)?

JS.SV.getVariableAII(a):JU.AU.isAFF(a)?JS.SV.getVariableAFF(a):JU.AU.isASS(a)?JS.SV.getVariableASS(a):JU.AU.isADD(a)?JS.SV.getVariableADD(a):JU.AU.isAFloat(a)?JS.SV.newV(13,a):JS.SV.newJSVar(a)},"~O");b.isASV=c(b,"isASV",function(a){return!JV.Viewer.isSwingJS?a&&a[0]&&"JS.SV"==a[0].__CLASS_NAME__:y(a,Array)},"~O");b.newJSVar=c(b,"newJSVar",function(a){var d,b,c,f,e;switch(a.BYTES_PER_ELEMENT?Array:a.constructor){case Boolean:d=0;b=a;break;case Number:d=1;c=a;break;case Array:d=2;f=a;break;case Object:d=

3,f=a,e=Object.keys(a)}switch(d){case 0:return b?JS.SV.vT:JS.SV.vF;case 1:return 2147483647<c||c!=Math.floor(c)?JS.SV.newF(c):JS.SV.newI(D(c));case 2:e=new JU.Lst;a=0;for(d=f.length;a<d;a++)e.addLast(JS.SV.newJSVar(f[a]));return JS.SV.getVariableList(e);case 3:d=new java.util.Hashtable;for(a=e.length;0<=--a;)b=null,b=f[e[a]],d.put(e[a],JS.SV.newJSVar(b));return JS.SV.getVariableMap(d)}return JS.SV.newS(a.toString())},"~O");b.getVariableMap=c(b,"getVariableMap",function(a){for(var d=a,b=null,c,f=d.values().iterator();f.hasNext()&&

((c=f.next())||1);){b=c;break}if(!y(b,"JS.SV")){a=new java.util.Hashtable;for(var e,d=d.entrySet().iterator();d.hasNext()&&((e=d.next())||1);)a.put(e.getKey(),JS.SV.getVariable(e.getValue()))}return JS.SV.newV(6,a)},"java.util.Map");b.getVariableList=c(b,"getVariableList",function(a){var d=a.size();if(0<d&&y(a.get(0),"JS.SV"))return JS.SV.newV(7,a);for(var b=new JU.Lst,c=0;c<d;c++)b.addLast(JS.SV.getVariable(a.get(c)));return JS.SV.newV(7,b)},"JU.Lst");b.getVariableAV=c(b,"getVariableAV",function(a){for(var d=

new JU.Lst,b=0;b<a.length;b++)d.addLast(a[b]);return JS.SV.newV(7,d)},"~A");b.getVariableAD=c(b,"getVariableAD",function(a){for(var d=new JU.Lst,b=0;b<a.length;b++)d.addLast(JS.SV.newV(3,Float.$valueOf(a[b])));return JS.SV.newV(7,d)},"~A");b.getVariableAO=c(b,"getVariableAO",function(a){for(var d=new JU.Lst,b=0;b<a.length;b++)d.addLast(JS.SV.getVariable(a[b]));return JS.SV.newV(7,d)},"~A");b.getVariableAS=c(b,"getVariableAS",function(a){for(var d=new JU.Lst,b=0;b<a.length;b++)d.addLast(JS.SV.newV(4,

a[b]));return JS.SV.newV(7,d)},"~A");b.getVariableAP=c(b,"getVariableAP",function(a){for(var d=new JU.Lst,b=0;b<a.length;b++)d.addLast(JS.SV.newV(8,a[b]));return JS.SV.newV(7,d)},"~A");b.getVariableAFF=c(b,"getVariableAFF",function(a){for(var d=new JU.Lst,b=0;b<a.length;b++)d.addLast(JS.SV.getVariableAF(a[b]));return JS.SV.newV(7,d)},"~A");b.getVariableADD=c(b,"getVariableADD",function(a){for(var d=new JU.Lst,b=0;b<a.length;b++)d.addLast(JS.SV.getVariableAD(a[b]));return JS.SV.newV(7,d)},"~A");b.getVariableASS=

c(b,"getVariableASS",function(a){for(var d=new JU.Lst,b=0;b<a.length;b++)d.addLast(JS.SV.getVariableAS(a[b]));return JS.SV.newV(7,d)},"~A");b.getVariableAII=c(b,"getVariableAII",function(a){for(var d=new JU.Lst,b=0;b<a.length;b++)d.addLast(JS.SV.getVariableAI(a[b]));return JS.SV.newV(7,d)},"~A");b.getVariableAF=c(b,"getVariableAF",function(a){for(var d=new JU.Lst,b=0;b<a.length;b++)d.addLast(JS.SV.newV(3,Float.$valueOf(a[b])));return JS.SV.newV(7,d)},"~A");b.getVariableAI=c(b,"getVariableAI",function(a){for(var d=

new JU.Lst,b=0;b<a.length;b++)d.addLast(JS.SV.newI(a[b]));return JS.SV.newV(7,d)},"~A");b.getVariableAB=c(b,"getVariableAB",function(a){for(var d=new JU.Lst,b=0;b<a.length;b++)d.addLast(JS.SV.newI(a[b]));return JS.SV.newV(7,d)},"~A");c(b,"setName",function(a){this.myName=a;return this},"~S");c(b,"increment",function(a){switch(this.tok){case 2:return this.intValue+=a,!0;case 3:return this.value=Float.$valueOf(this.value.floatValue()+a),!0;default:return!1}},"~N");c(b,"asBoolean",function(){return JS.SV.bValue(this)});

c(b,"asInt",function(){return JS.SV.iValue(this)});c(b,"asFloat",function(){return JS.SV.fValue(this)});c(b,"asString",function(){return JS.SV.sValue(this)});b.oValue=c(b,"oValue",function(a){if(!y(a,"JS.SV"))return a;switch(a.tok){case 1073742335:return Boolean.TRUE;case 0:case 1073742334:return Boolean.FALSE;case 2:return Integer.$valueOf(a.intValue);case 10:case 1275068418:return JS.SV.selectItemVar(a).value;default:return a.value}},"~O");b.nValue=c(b,"nValue",function(a){switch(null==a?0:a.tok){case 3:return a.value;

case 2:a=a.intValue;break;case 4:if(0<=a.value.indexOf("."))return Float.$valueOf(JS.SV.toFloat(a.value));a=D(JS.SV.toFloat(a.value));break;case 8:return Float.$valueOf(a.value.length());default:a=0}return Integer.$valueOf(a)},"JS.T");b.bValue=c(b,"bValue",function(a){switch(null==a?0:a.tok){case 1073742335:case 14:return!0;case 1073742334:return!1;case 2:return 0!=a.intValue;case 3:case 4:case 7:return 0!=JS.SV.fValue(a);case 10:case 15:return 0!=JS.SV.iValue(a);case 8:case 9:case 11:case 12:return 1E-4<

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case 1073742334:return 0;case 2:return a.intValue;case 3:return a.value.floatValue();case 7:if(2147483647==a.intValue)return a.getList().size();case 4:return JS.SV.toFloat(JS.SV.sValue(a));case 10:case 15:return JS.SV.iValue(a);case 8:return a.value.length();case 9:return JU.Measure.distanceToPlane(a.value,JS.SV.pt0);case 11:var d=new JU.P3;a.value.rotate(d);return d.length();case 12:return d=new JU.P3,a.value.rotTrans(d),d.length();default:return 0}},"JS.T");b.sValue=c(b,"sValue",function(a){if(null==

a)return"";var d;switch(a.tok){case 1073742335:return"true";case 1073742334:return"false";case 2:return""+a.intValue;case 10:return d=JS.SV.bsSelectToken(a),y(a.value,"JM.BondSet")?JU.Escape.eBond(d):JU.Escape.eBS(d);case 7:var b=a.getList();d=a.intValue;0>=d&&(d=b.size()-d);if(2147483647!=d)return 1>d||d>b.size()?"":JS.SV.sValue(b.get(d-1));case 6:case 14:if("string"==typeof a.value)return a.value;d=new JU.SB;JS.SV.sValueArray(d,a,"","",!1,!0,!0,2147483647,!1);return JU.PT.rep(d.toString(),"\n\x00",

" ");case 4:return b=a.value,d=a.intValue,0>=d&&(d=b.length-d),2147483647==d?b:1>d||d>b.length?"":""+b.charAt(d-1);case 8:return JU.Escape.eP(a.value);case 9:return JU.Escape.eP4(a.value);case 11:case 12:return JU.Escape.e(a.value);default:return a.value.toString()}},"JS.T");b.sValueArray=c(b,"sValueArray",function(a,d,b,c,f,e,h,k,m){switch(d.tok){case 6:case 14:case 7:var j=";"+d.hashCode()+";";if(0<=b.indexOf(j)){a.append(f?7==d.tok?"[ ]":"{ }":(7==d.tok?"":"\x00")+'"<'+(null==d.myName?"circular reference":

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c(b,"sValueAddKeys",function(a,d,b,c,f,e,h,k){if(!(0>h)){var m=b.keySet(),m=b.keySet().toArray(Array(m.size()));java.util.Arrays.sort(m);if(f){a.append("{ ");for(var j="",p=0;p<m.length;p++){f=m[p];var q=b.get(f);if(!k||!(7==q.tok&&0==q.getList().size()||6==q.tok&&q.getMap().isEmpty()))e?a.append(j).append(JU.PT.esc(f)).append(":"):a.appendC(" ").append(f),JS.SV.sValueArray(a,q,d,c+" ",!0,!1,e,h,k),j=","}a.append(" }");e||a.append("\n")}else{a.append(c).append("{\n");c+=" ";for(p=0;p<m.length;p++)a.append(c),

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function(a,d,b){var c=a.getList(),f=d.getList();if(!b){if(null==f)c.addLast(JS.SV.newT(d));else for(b=0;b<f.size();b++)c.addLast(f.get(b));return a}var e=new JU.Lst;if(null==c)e.addLast(a);else for(b=0;b<c.size();b++)e.addLast(c.get(b));if(null==f)e.addLast(d);else for(b=0;b<f.size();b++)e.addLast(f.get(b));return JS.SV.getVariableList(e)},"JS.SV,JS.SV,~B");b.bsSelectToken=c(b,"bsSelectToken",function(a){return JS.SV.selectItemTok(a,-2147483648).value},"JS.T");b.bsSelectRange=c(b,"bsSelectRange",

function(a,d){a=JS.SV.selectItemTok(a,-2147483648);a=JS.SV.selectItemTok(a,0>=d?d:1);a=JS.SV.selectItemTok(a,0>=d?2147483646:d);return a.value},"JS.T,~N");b.selectItemVar=c(b,"selectItemVar",function(a){return 2147483647!=a.index||(7==a.tok||15==a.tok)&&2147483647==a.intValue?a:JS.SV.selectItemTok(a,-2147483648)},"JS.SV");b.selectItemTok=c(b,"selectItemTok",function(a,d){switch(a.tok){case 11:case 12:case 10:case 7:case 15:case 4:break;default:return y(a,"JS.SV")&&null!=a.myName?JS.SV.copySafely(a):

a}var b=null,c=null,f=a.intValue,e=-2147483648==d;if(2147483647==f)return e&&4==a.tok?a:JS.SV.newSV(a.tok,e?f:d,a.value);var h=0,k=y(a,"JS.SV")&&2147483647!=a.index,m=JS.SV.newSV(a.tok,2147483647,null);switch(a.tok){case 10:y(a.value,"JM.BondSet")?(b=JM.BondSet.newBS(a.value),h=b.cardinality()):(b=JU.BSUtil.copy(a.value),h=k?1:b.cardinality());break;case 15:h=a.value.data.length;break;case 7:h=a.getList().size();break;case 4:c=a.value;h=c.length;break;case 11:h=-3;break;case 12:h=-4}if(0>h){h=-h;

if(0<f&&Math.abs(f)>h)return m=f%10,f=B((f-m)/10),0<m&&m<=h&&f<=h?JS.SV.newV(3,Float.$valueOf(a.value.getElement(f-1,m-1))):JS.SV.newV(4,"");if(Math.abs(f)>h)return JS.SV.newV(4,"");b=K(h,0);0>f?a.value.getColumn(-1-f,b):a.value.getRow(f-1,b);return e?JS.SV.getVariableAF(b):1>d||d>h?JS.SV.newV(4,""):JS.SV.newV(3,Float.$valueOf(b[d-1]))}0>=f&&(f=h+f);e||(1>f&&(f=1),0==d?d=h:0>d&&(d=h+d),d<f&&(d=f));switch(a.tok){case 10:m.value=b;if(k){1<f&&b.clearAll();break}if(e){f==h?d=b.length()-1:1==f&&(d=b.nextSetBit(0));

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a;d++)f.addLast(JS.SV.newV(4,""));f.set(a,b)}}},"~N,~N,JS.SV");c(b,"escape",function(){switch(this.tok){case 4:return JU.PT.esc(this.value);case 11:case 12:return JU.PT.toJSON(null,this.value);case 7:case 6:case 14:var a=new JU.SB;JS.SV.sValueArray(a,this,"","",!0,!1,!0,2147483647,!1);return a.toString();default:return JS.SV.sValue(this)}});b.unescapePointOrBitsetAsVariable=c(b,"unescapePointOrBitsetAsVariable",function(a){if(null==a)return a;var d=null,b=null;if(y(a,"JS.SV"))switch(a.tok){case 8:case 9:case 11:case 12:case 10:d=

a.value;break;case 4:b=a.value;break;default:b=JS.SV.sValue(a)}else"string"==typeof a&&(b=a);if(null!=b&&0==b.length)return b;null==d&&(d=JU.Escape.uABsM(b));return y(d,"JU.P3")?JS.SV.newV(8,d):y(d,"JU.P4")?JS.SV.newV(9,d):y(d,"JU.BS")?(null!=b&&0==b.indexOf("[{")&&(d=JM.BondSet.newBS(d)),JS.SV.newV(10,d)):y(d,"JU.M34")?JS.SV.newV(y(d,"JU.M3")?11:12,d):a},"~O");b.getBoolean=c(b,"getBoolean",function(a){return JS.SV.newT(a?JS.SV.vT:JS.SV.vF)},"~B");b.sprintf=c(b,"sprintf",function(a,d){if(null==d)return a;

var b=7==d.tok,c=0<=a.indexOf("d")||0<=a.indexOf("i")?E(1,0):null,f=0<=a.indexOf("f")?K(1,0):null,e=0<=a.indexOf("e")?R(1,0):null,h=0<=a.indexOf("s"),k=0<=a.indexOf("p")&&(b||8==d.tok),m=0<=a.indexOf("q")&&(b||9==d.tok),j=w(-1,[c,f,e,null,null,null]);if(!b)return JS.SV.sprintf(a,d,j,c,f,e,h,k,m);for(var b=d.getList(),p=Array(b.size()),q=0;q<p.length;q++)p[q]=JS.SV.sprintf(a,b.get(q),j,c,f,e,h,k,m);return p},"~S,JS.SV");b.sprintf=c(b,"sprintf",function(a,d,b,c,f,e,h,k,m){if(6==d.tok){var j=a.indexOf("[");

if(0<=j){var p;d=d.getMap().get(a.substring(j+1,p=a.indexOf("]")));a=a.substring(0,j)+a.substring(p+1)}}null!=c&&(c[0]=JS.SV.iValue(d));null!=f&&(f[0]=JS.SV.fValue(d));null!=e&&(e[0]=JS.SV.fValue(d));h&&(b[3]=JS.SV.sValue(d));k&&(b[4]=d.value);m&&(b[5]=d.value);return JU.PT.sprintf(a,"IFDspq",b)},"~S,JS.SV,~A,~A,~A,~A,~B,~B,~B");b.getFormatType=c(b,"getFormatType",function(a){return 0<=a.indexOf(";")?-1:";json;base64;bytearray;array;xyz;abc;".indexOf(";"+a.toLowerCase()+";")},"~S");b.format=c(b,"format",

function(a,d){switch(a.length){case 0:return"";case 1:return JS.SV.sValue(a[0]);case 2:if(2147483647==d&&(d=JS.SV.getFormatType(a[0].asString())),0<=d)return JS.SV.getFormat(a[1],d)}var b=JU.PT.split(JU.PT.rep(JS.SV.sValue(a[0]),"%%","\u0001"),"%");if(0==b.length)return"";var c=new JU.SB;c.append(b[0]);for(var f=1;f<b.length;f++){var e=JS.SV.sprintf(JU.PT.formatCheck("%"+b[f]),6==a[1].tok?a[1]:7==a[1].tok?a[1].getList().get(f-1):f<a.length?a[f]:null);if(JU.AU.isAS(e))for(var h=0;h<e.length;h++)c.append(e[h]).append("\n");

else c.append(e)}return c.toString()},"~A,~N");b.getFormat=c(b,"getFormat",function(a,d){switch(d){case 0:var b=a.myName;a.myName=null;var c=a.toJSON();a.myName=b;return c;case 5:case 12:case 22:var f;switch(a.tok){case 15:f=JU.AU.arrayCopyByte(a.value.data,-1);break;case 7:b=a.getList();if(22==d){f=new JU.Lst;for(c=b.size();0<=--c;)f.addLast(b.get(c));return f}f=P(b.size(),0);for(c=f.length;0<=--c;)f[c]=b.get(c).asInt();break;default:if(b=a.asString(),b.startsWith(";base64,")){if(5==d)return b;f=

JU.Base64.decodeBase64(b)}else f=b.getBytes()}switch(d){case 12:return new JU.BArray(f);case 5:return";base64,"+JU.Base64.getBase64(f).toString();case 22:return JS.SV.getVariable(f)}}return null},"JS.SV,~N");b.getBitSet=c(b,"getBitSet",function(a,d){switch(a.tok){case 10:return(2147483647==a.index?JS.SV.selectItemTok(a,-2147483648):a).value;case 7:return JS.SV.unEscapeBitSetArray(a.getList(),d);default:return d?null:new JU.BS}},"JS.SV,~B");b.unEscapeBitSetArray=c(b,"unEscapeBitSetArray",function(a,

d){for(var b=new JU.BS,c=0;c<a.size();c++){var f=a.get(c);if(2==f.tok&&0<=f.intValue)b.set(f.intValue);else if(7==f.tok){f=JS.SV.unEscapeBitSetArray(f.getList(),!0);if(null==f)return d?null:new JU.BS;b.or(f)}else if(!JS.SV.unEscapeBitSet(f,b))return d?null:new JU.BS}return b},"JU.Lst,~B");b.areEqual=c(b,"areEqual",function(a,d){if(null==a||null==d)return!1;if(null!=a.value&&a.value===d.value)return!0;if(a.tok==d.tok)switch(a.tok){case 2:if(2==d.tok)return a.intValue==d.intValue;break;case 4:return a.value.equalsIgnoreCase(d.value);

case 10:case 15:case 6:case 7:case 14:return a.equals(d);case 8:return 1E-6>a.value.distance(d.value);case 9:return 1E-6>a.value.distance4(d.value);case 11:return a.value.equals(d.value);case 12:return a.value.equals(d.value)}return a.isNaN()?d.isNaN():1E-6>Math.abs(JS.SV.fValue(a)-JS.SV.fValue(d))},"JS.SV,JS.SV");b.isLike=c(b,"isLike",function(a,d){return null!=a&&null!=d&&4==a.tok&&4==d.tok&&JU.PT.isLike(a.value,d.value)},"JS.SV,JS.SV");c(b,"sortOrReverse",function(a){var d=this.getList();if(null!=

d&&1<d.size())if(-2147483648==a){a=d.size();for(var b=0;b<a;b++){var c=d.get(b);d.set(b,d.get(--a));d.set(a,c)}}else java.util.Collections.sort(this.getList(),U(JS.SV.Sort,this,null,--a,null));return this},"~N");c(b,"pushPop",function(a,d){if(null==a){if(4==this.tok){if(null==d){var b=this.value,c=b.length-1;if(0>c)return JS.SV.newS("");var f=b.substring(c);this.value=b.substring(0,c);return JS.SV.newS(f)}this.value+=JS.SV.sValue(d);return this}c=this.getMap();if(null==c){b=this.getList();if(null==

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"J.atomdata.RadiusData,JU.BS");j(b,"setProperty",function(a,d,b){if("color"===a){var c=JU.C.getColixO(d);0==c&&(c=2);null==this.bsColixSet&&(this.bsColixSet=new JU.BS);var f=J.c.PAL.pidOf(d);for(a=b.nextSetBit(0);0<=a;a=b.nextSetBit(a+1)){var e=this.ms.at[a];e.colixAtom=this.getColixA(c,f,e);this.bsColixSet.setBitTo(a,2!=c||f!=J.c.PAL.NONE.id);e.paletteID=f}this.vwr.setModelkitPropertySafely("updateatomkeys",b)}else if("colorValues"===a){if(0!=d.length){null==this.bsColixSet&&(this.bsColixSet=new JU.BS);

var h=0,f=null;for(a=b.nextSetBit(0);0<=a&&!(h>=d.length);a=b.nextSetBit(a+1))f=Integer.$valueOf(d[h++]),c=JU.C.getColixO(f),0==c&&(c=2),f=J.c.PAL.pidOf(f),e=this.ms.at[a],e.colixAtom=this.getColixA(c,f,e),this.bsColixSet.setBitTo(a,2!=c||f!=J.c.PAL.NONE.id),e.paletteID=f}}else if("colors"===a){h=d[0];null==this.bsColixSet&&(this.bsColixSet=new JU.BS);d=this.ms.at;for(a=b.nextSetBit(0);0<=a;a=b.nextSetBit(a+1))if(!(a>=h.length||0==(c=h[a])))d[a].colixAtom=c,d[a].paletteID=J.c.PAL.UNKNOWN.id,this.bsColixSet.set(a)}else if("translucency"===

a){c=d.equals("translucent");null==this.bsColixSet&&(this.bsColixSet=new JU.BS);d=this.ms.at;for(a=b.nextSetBit(0);0<=a;a=b.nextSetBit(a+1))d[a].setTranslucent(c,this.translucentLevel),c&&this.bsColixSet.set(a)}else a.startsWith("ball")&&(a=a.substring(4).intern()),this.setPropAS(a,d,b)},"~S,~O,JU.BS");j(b,"setAtomClickability",function(){for(var a=this.vwr.slm.bsDeleted,d=this.ms.ac;0<=--d;){var b=this.ms.at[d];null!=b&&(b.setClickable(0),null!=a&&a.get(d)||(0==(b.shapeVisibilityFlags&this.vf)||

this.ms.isAtomHidden(d))||b.setClickable(this.vf))}})});u("J.shape");C(["J.shape.Shape"],"J.shape.FontLineShape",null,function(){var b=v(function(){this.font3d=this.tickInfos=null;r(this,arguments)},J.shape,"FontLineShape",J.shape.Shape);j(b,"initShape",function(){this.translucentAllowed=!1});c(b,"setPropFLS",function(a,d){if("tickInfo"===a){var b=d.type;if(null==d.ticks)if(" "==d.type)this.tickInfos=null;else{if(null!=this.tickInfos){for(var b=!1,c=0;4>c;c++)null!=this.tickInfos[c]&&this.tickInfos[c].type==

d.type?this.tickInfos[c]=null:b=!0;b||(this.tickInfos=null)}}else null==this.tickInfos&&(this.tickInfos=Array(4)),this.tickInfos["xyz".indexOf(b)+1]=d}else"font"===a&&(this.font3d=d)},"~S,~O");j(b,"getShapeState",function(){return null})});u("J.shape");C(["J.shape.Shape"],"J.shape.Frank",["J.i18n.GT","JV.Viewer"],function(){var b=v(function(){this.baseFont3d=this.currentMetricsFont3d=null;this.scaling=this.dy=this.dx=this.y=this.x=this.frankDescent=this.frankAscent=this.frankWidth=0;this.font3d=null;

r(this,arguments)},J.shape,"Frank",J.shape.Shape);j(b,"initShape",function(){this.myType="frank";this.baseFont3d=this.font3d=this.vwr.gdata.getFont3DFSS("SansSerif","Plain",16);if(JV.Viewer.isJS||JV.Viewer.isSwingJS)J.shape.Frank.frankString="JSmol";this.calcMetrics()});j(b,"setProperty",function(a,d){"font"===a&&10<=d.fontSize&&(this.baseFont3d=d,this.scaling=0)},"~S,~O,JU.BS");j(b,"wasClicked",function(a,d){var b=this.vwr.getScreenWidth(),c=this.vwr.getScreenHeight();return 0<b&&0<c&&a>b-this.frankWidth-

4&&d>c-this.frankAscent-4},"~N,~N");j(b,"checkObjectHovered",function(a,d){if(!this.vwr.getShowFrank()||!this.wasClicked(a,d)||!this.vwr.menuEnabled())return!1;this.vwr.hoverOnPt(a,d,J.i18n.GT.$("Click for menu..."),null,null);return!0},"~N,~N,JU.BS");c(b,"calcMetrics",function(){this.font3d!==this.currentMetricsFont3d&&(this.currentMetricsFont3d=this.font3d,this.frankWidth=this.font3d.stringWidth(J.shape.Frank.frankString),this.frankDescent=this.font3d.getDescent(),this.frankAscent=this.font3d.getAscent())});

c(b,"getFont",function(a){a!=this.scaling&&(this.scaling=a,this.font3d=this.vwr.gdata.getFont3DScaled(this.baseFont3d,a),this.calcMetrics())},"~N");j(b,"getShapeState",function(){return null});b.frankString="Jmol"});u("J.shape");C(null,"J.shape.Shape",["J.c.PAL","JU.C","$.Logger","JV.JC"],function(){var b=v(function(){this.ms=this.vwr=this.myType=null;this.translucentLevel=this.vf=this.shapeID=0;this.translucentAllowed=!0;this.isBioShape=!1;this.bsColixSet=this.bsSizeSet=null;r(this,arguments)},J.shape,

"Shape",null);c(b,"initializeShape",function(a,d,b){this.vwr=a;this.shapeID=b;this.vf=JV.JC.getShapeVisibilityFlag(b);this.setModelSet(d);this.initShape()},"JV.Viewer,JM.ModelSet,~N");c(b,"setModelVisibilityFlags",function(){},"JU.BS");c(b,"getSize",function(){return 0},"~N");c(b,"getSizeG",function(){return 0},"JM.Group");c(b,"replaceGroup",function(){},"JM.Group,JM.Group");c(b,"setModelSet",function(a){this.ms=a;this.initModelSet()},"JM.ModelSet");c(b,"initModelSet",function(){});c(b,"setShapeSizeRD",

function(a,d,b){null==d?this.setSize(a,b):this.setSizeRD(d,b)},"~N,J.atomdata.RadiusData,JU.BS");c(b,"setSize",function(){},"~N,JU.BS");c(b,"setSizeRD",function(){},"J.atomdata.RadiusData,JU.BS");c(b,"setPropS",function(a,d){"setProperties"===a?this.setProperties(d):"translucentLevel"===a?this.translucentLevel=d.floatValue():"refreshTrajectories"!==a&&JU.Logger.warn("unassigned "+JV.JC.shapeClassBases[this.shapeID]+" + shape setProperty:"+a+":"+d)},"~S,~O,JU.BS");c(b,"getPropertyData",function(a,

d){return this.getPropShape(a,d)},"~S,~A");c(b,"getPropShape",function(a,d){if(y(d[1],Integer)){var b=d[1].intValue();d[1]=this.getProperty(a,b);return null!=d[1]}return!1},"~S,~A");c(b,"getProperty",function(){return null},"~S,~N");c(b,"getIndexFromName",function(){return-1},"~S");c(b,"wasClicked",function(){return!1},"~N,~N");c(b,"findNearestAtomIndex",function(){},"~N,~N,~A,JU.BS");c(b,"checkBoundsMinMax",function(){},"JU.P3,JU.P3");c(b,"setAtomClickability",function(){});c(b,"checkObjectClicked",

function(){return null},"~N,~N,~N,JU.BS,~B");c(b,"checkObjectHovered",function(){return!1},"~N,~N,JU.BS");c(b,"checkObjectDragged",function(){return!1},"~N,~N,~N,~N,~N,JU.BS");c(b,"coordinateInRange",function(a,d,b,c,f){this.vwr.tm.transformPtScr(b,f);a=(a-f.x)*(a-f.x)+(d-f.y)*(d-f.y);return a<=c?a:-1},"~N,~N,JU.T3,~N,JU.P3i");c(b,"getColixI",function(a,d,b){return this.getColixA(a,d,this.ms.at[b])},"~N,~N,~N");c(b,"getColixA",function(a,d,b){return 2==a?this.vwr.cm.getColixAtomPalette(b,d):a},"~N,~N,JM.Atom");

c(b,"getColixB",function(a,d,b){return 2==a?this.vwr.cm.getColixBondPalette(b,d):a},"~N,~N,JM.Bond");c(b,"getShapeDetail",function(){return null});b.getColix=c(b,"getColix",function(a,d,b){return JU.C.getColixInherited(null==a||d>=a.length?0:a[d],b.colixAtom)},"~A,~N,JM.Atom");b.getFontCommand=c(b,"getFontCommand",function(a,d){return null==d?"":"font "+a+" "+d.getInfo()},"~S,JU.Font");b.getColorCommandUnk=c(b,"getColorCommandUnk",function(a,d,b){return J.shape.Shape.getColorCommand(a,J.c.PAL.UNKNOWN.id,

d,b)},"~S,~N,~B");b.getColorCommand=c(b,"getColorCommand",function(a,d,b,c){if(d==J.c.PAL.UNKNOWN.id&&0==b)return"";d=d==J.c.PAL.UNKNOWN.id&&0==b?"":(c?J.shape.Shape.getTranslucentLabel(b)+" ":"")+(d!=J.c.PAL.UNKNOWN.id&&!J.c.PAL.isPaletteVariable(d)?J.c.PAL.getPaletteName(d):J.shape.Shape.encodeColor(b));return"color "+a+" "+d},"~S,~N,~N,~B");b.encodeColor=c(b,"encodeColor",function(a){return JU.C.isColixColorInherited(a)?"none":JU.C.getHexCode(a)},"~N");b.getTranslucentLabel=c(b,"getTranslucentLabel",

function(a){return JU.C.isColixTranslucent(a)?JU.C.getColixTranslucencyLabel(a):"opaque"},"~N");b.appendCmd=c(b,"appendCmd",function(a,d){0!=d.length&&a.append(" ").append(d).append(";\n")},"JU.SB,~S");c(b,"setProperties",function(a){var d=this.vwr.bsA();if(y(a,"JU.Lst"))for(;0<a.size();){var b=a.removeItemAt(0);this.setProperty(b[0].intern(),b[1],d)}else{b=a;a=0;for(var c=b.length;a<c;a++)this.setProperty(b[a][0].intern(),b[a][1],d)}},"~O")});u("J.shape");C(["J.shape.Shape","JU.P3i"],"J.shape.Sticks",

"java.util.Hashtable JU.BS $.P3 J.c.PAL JU.BSUtil $.C $.Edge $.Escape".split(" "),function(){var b=v(function(){this.myMask=0;this.reportAll=!1;this.ptXY=this.closestAtom=this.selectedBonds=this.bsOrderSet=null;r(this,arguments)},J.shape,"Sticks",J.shape.Shape);Q(b,function(){this.closestAtom=E(1,0);this.ptXY=new JU.P3i});j(b,"initShape",function(){this.myMask=1023;this.reportAll=!1});j(b,"setSize",function(a,d){if(2147483647==a)this.selectedBonds=JU.BSUtil.copy(d);else if(-2147483648==a)null==this.bsOrderSet&&

(this.bsOrderSet=new JU.BS),this.bsOrderSet.or(d);else{null==this.bsSizeSet&&(this.bsSizeSet=new JU.BS);for(var b=null!=this.selectedBonds?this.ms.getBondIterator(this.selectedBonds):this.ms.getBondIteratorForType(this.myMask,d);b.hasNext();)this.bsSizeSet.set(b.nextIndex()),b.next().setMad(a)}},"~N,JU.BS");j(b,"setProperty",function(a,d,b){if("type"===a)this.myMask=d.intValue();else if("reportAll"===a)this.reportAll=!0;else if("reset"===a)this.selectedBonds=this.bsColixSet=this.bsSizeSet=this.bsOrderSet=

null;else if("bondOrder"===a){null==this.bsOrderSet&&(this.bsOrderSet=new JU.BS);a=d.intValue();for(b=null!=this.selectedBonds?this.ms.getBondIterator(this.selectedBonds):this.ms.getBondIteratorForType(65535,b);b.hasNext();)this.bsOrderSet.set(b.nextIndex()),b.next().setOrder(a)}else if("color"===a)if(null==this.bsColixSet&&(this.bsColixSet=new JU.BS),a=JU.C.getColixO(d),d=y(d,"J.c.PAL")?d:null,d===J.c.PAL.TYPE||d===J.c.PAL.ENERGY){var c=d===J.c.PAL.ENERGY;for(b=null!=this.selectedBonds?this.ms.getBondIterator(this.selectedBonds):

this.ms.getBondIteratorForType(this.myMask,b);b.hasNext();){this.bsColixSet.set(b.nextIndex());var f=b.next();f.colix=c?this.getColixB(a,d.id,f):JU.C.getColix(JU.Edge.getArgbHbondType(f.order))}}else{if(!(2==a&&d!==J.c.PAL.CPK))for(b=null!=this.selectedBonds?this.ms.getBondIterator(this.selectedBonds):this.ms.getBondIteratorForType(this.myMask,b);b.hasNext();)d=b.nextIndex(),b.next().colix=a,this.bsColixSet.setBitTo(d,0!=a&&2!=a)}else if("translucency"===a){null==this.bsColixSet&&(this.bsColixSet=

new JU.BS);a=d.equals("translucent");for(b=null!=this.selectedBonds?this.ms.getBondIterator(this.selectedBonds):this.ms.getBondIteratorForType(this.myMask,b);b.hasNext();)this.bsColixSet.set(b.nextIndex()),b.next().setTranslucent(a,this.translucentLevel)}else"deleteModelAtoms"!==a&&this.setPropS(a,d,b)},"~S,~O,JU.BS");j(b,"getProperty",function(a){return a.equals("selectionState")?null!=this.selectedBonds?"select BONDS "+JU.Escape.eBS(this.selectedBonds)+"\n":"":a.equals("sets")?w(-1,[this.bsOrderSet,

this.bsSizeSet,this.bsColixSet]):null},"~S,~N");j(b,"setAtomClickability",function(){for(var a=this.ms.bo,d=this.ms.bondCount;0<=--d;){var b=a[d];null==b||(0==(b.shapeVisibilityFlags&this.vf)||this.ms.isAtomHidden(b.atom1.i)||this.ms.isAtomHidden(b.atom2.i))||(b.atom1.setClickable(this.vf),b.atom2.setClickable(this.vf))}});j(b,"getShapeState",function(){return null});j(b,"checkObjectHovered",function(a,d,b){var c=new JU.P3;b=this.findPickedBond(a,d,b,c,this.closestAtom);if(null==b)return!1;this.vwr.highlightBond(b.index,

this.closestAtom[0],a,d);return!0},"~N,~N,JU.BS");j(b,"checkObjectClicked",function(a,d,b,c){b=new JU.P3;a=this.findPickedBond(a,d,c,b,this.closestAtom);if(null==a)return null;d=a.atom1.mi;c=a.getIdentity();var f=new java.util.Hashtable;f.put("pt",b);f.put("index",Integer.$valueOf(a.index));f.put("modelIndex",Integer.$valueOf(d));f.put("model",this.vwr.getModelNumberDotted(d));f.put("type","bond");f.put("info",c);this.vwr.setStatusAtomPicked(-3,'["bond","'+a.getIdentity()+'",'+b.x+","+b.y+","+b.z+

"]",f,!1);return f},"~N,~N,~N,JU.BS,~B");c(b,"findPickedBond",function(a,d,b,c,f){b=100;this.vwr.gdata.isAntialiased()&&(a<<=1,d<<=1,b<<=1);for(var e=null,h=new JU.P3,k=this.ms.bo,m=this.ms.bondCount;0<=--m;){var j=k[m];if(!(null==j||0==j.shapeVisibilityFlags)){var p=j.atom1,q=j.atom2;if(p.checkVisible()&&q.checkVisible()){h.ave(p,q);var x=this.coordinateInRange(a,d,h,b,this.ptXY);if(0<=x&&40<Math.abs(p.sY-q.sY)+Math.abs(p.sX-q.sX)){var s=1*(this.ptXY.x-p.sX)/(q.sX-p.sX);0.4>s||0.6<s||(b=x,e=j,null!=

f&&(f[0]=0.5>s?p.i:q.i),c.setT(h))}}}}return e},"~N,~N,JU.BS,JU.P3,~A")});u("J.thread");C(["J.thread.JmolThread"],"J.thread.HoverWatcherThread",null,function(){var b=v(function(){this.moved=this.current=this.actionManager=null;this.hoverDelay=0;r(this,arguments)},J.thread,"HoverWatcherThread",J.thread.JmolThread);z(b,function(a,d,b,c){this.setViewer(c,"HoverWatcher");this.actionManager=a;this.current=d;this.moved=b;this.start()},"JV.ActionManager,JV.MouseState,JV.MouseState,JV.Viewer");j(b,"run1",

function(a){for(;;)switch(a){case -1:this.isJS||Thread.currentThread().setPriority(1);a=0;break;case 0:this.hoverDelay=this.vwr.getHoverDelay();if(this.stopped||0>=this.hoverDelay||!this.runSleep(this.hoverDelay,1))return;a=1;break;case 1:this.moved.is(this.current)&&(this.currentTime=System.currentTimeMillis(),this.currentTime-this.moved.time>(this.vwr.acm.zoomTrigger?100:this.hoverDelay)&&!this.stopped&&this.actionManager.checkHover()),a=0}},"~N")});u("J.thread");C(["java.lang.Thread"],"J.thread.JmolThread",

["JU.Logger","JV.Viewer"],function(){var b=v(function(){this.$name="JmolThread";this.sc=this.eval=this.vwr=null;this.hoverEnabled=this.haveReference=!1;this.sleepTime=this.currentTime=this.lastRepaintTime=this.targetTime=this.startTime=0;this.isReset=this.stopped=this.isJS=!1;this.useTimeout=!0;this.junk=0;r(this,arguments)},J.thread,"JmolThread",Thread);c(b,"setManager",function(){return 0},"~O,JV.Viewer,~O");c(b,"setViewer",function(a,d){this.setName(d);this.$name=d+"_"+ ++J.thread.JmolThread.threadIndex;

this.vwr=a;this.isJS=a.isSingleThreaded},"JV.Viewer,~S");c(b,"setEval",function(a){this.eval=a;this.sc=this.vwr.getEvalContextAndHoldQueue(a);null!=this.sc&&(this.useTimeout=a.getAllowJSThreads())},"J.api.JmolScriptEvaluator");c(b,"resumeEval",function(){if(!(null==this.eval||!this.isJS&&!this.vwr.testAsync||!this.useTimeout)){this.sc.mustResumeEval=!this.stopped;var a=this.eval,d=this.sc;this.sc=this.eval=null;setTimeout(function(){a.resumeEval(d)},1)}});j(b,"start",function(){this.run()});j(b,"run",

function(){this.startTime=System.currentTimeMillis();try{this.run1(-1)}catch(a){if(F(a,"InterruptedException")){var d=a;JU.Logger.debugging&&!y(this,"J.thread.HoverWatcherThread")&&this.oops(d)}else if(F(a,Exception))this.oops(a);else throw a;}});c(b,"oops",function(a){JU.Logger.debug(this.$name+" exception "+a);(!JV.Viewer.isJS||JV.Viewer.isSwingJS)&&a.printStackTrace();this.vwr.queueOnHold=!1},"Exception");c(b,"runSleep",function(a,d){if(this.isJS&&!this.useTimeout)return!0;var b=this;setTimeout(function(){b.run1(d)},

Math.max(a,0));return!1},"~N,~N");c(b,"interrupt",function(){this.stopped=!0;this.vwr.startHoverWatcher(!0);this.isJS||$(this,J.thread.JmolThread,"interrupt",[])});c(b,"checkInterrupted",function(a){return this.haveReference&&(null==a||!a.$name.equals(this.$name))?!0:this.stopped},"J.thread.JmolThread");c(b,"reset",function(){this.isReset=!0;this.interrupt()});c(b,"toString",function(){return $(this,J.thread.JmolThread,"toString",[])+"["+this.$name+"]"});b.threadIndex=0});u("J.thread");C(["J.thread.JmolThread"],

"J.thread.TimeoutThread",["JU.SB"],function(){var b=v(function(){this.script=null;this.status=0;this.triggered=!0;r(this,arguments)},J.thread,"TimeoutThread",J.thread.JmolThread);z(b,function(a,d,b,c){this.setViewer(a,d);this.$name=d;this.set(b,c)},"JV.Viewer,~S,~N,~S");c(b,"set",function(a,d){this.sleepTime=a;null!=d&&(this.script=d)},"~N,~S");j(b,"toString",function(){return"timeout name="+this.$name+" executions="+this.status+" mSec="+this.sleepTime+" secRemaining="+(this.targetTime-System.currentTimeMillis())/

1E3+" script="+this.script});j(b,"run1",function(a){for(;;)switch(a){case -1:this.isJS||Thread.currentThread().setPriority(1);this.targetTime=System.currentTimeMillis()+Math.abs(this.sleepTime);a=0;break;case 0:if(this.checkInterrupted(null)||(null==this.script||0==this.script.length)||!this.runSleep(26,1))return;a=1;break;case 1:a=System.currentTimeMillis()<this.targetTime?0:2;break;case 2:this.currentTime=System.currentTimeMillis();if(null==this.vwr.timeouts.get(this.$name))return;this.status++;

(a=0>this.sleepTime)?this.targetTime=System.currentTimeMillis()+Math.abs(this.sleepTime):this.vwr.timeouts.remove(this.$name);this.triggered&&(this.triggered=!1,this.$name.equals("_SET_IN_MOTION_")?this.vwr.checkInMotion(2):this.vwr.evalStringQuiet(a?this.script+';\ntimeout ID "'+this.$name+'";':this.script));a=a?0:-2;break;case -2:this.vwr.timeouts.remove(this.$name);return}},"~N");b.clear=c(b,"clear",function(a){for(var d,b=a.values().iterator();b.hasNext()&&((d=b.next())||1);){var c=d;c.script.equals("exitJmol")||

c.interrupt()}a.clear()},"java.util.Map");b.setTimeout=c(b,"setTimeout",function(a,d,b,c,f){var e=d.get(b);0==c?null!=e&&(e.interrupt(),d.remove(b)):null!=e?e.set(c,f):(e=new J.thread.TimeoutThread(a,b,c,f),d.put(b,e),e.start())},"JV.Viewer,java.util.Map,~S,~N,~S");b.trigger=c(b,"trigger",function(a,d){var b=a.get(d);null!=b&&(b.triggered=0>b.sleepTime)},"java.util.Map,~S");b.showTimeout=c(b,"showTimeout",function(a,d){var b=new JU.SB;if(null!=a)for(var c,f=a.values().iterator();f.hasNext()&&((c=

f.next())||1);){var e=c;(null==d||e.$name.equalsIgnoreCase(d))&&b.append(e.toString()).append("\n")}return 0<b.length()?b.toString():"<no timeouts set>"},"java.util.Map,~S")});u("JM");C(["JU.Node","$.Point3fi","J.c.PAL"],"JM.Atom","JU.BS $.CU $.P3 $.PT $.SB J.atomdata.RadiusData J.c.VDW JM.Group JU.C $.Elements JV.JC".split(" "),function(){var b=v(function(){this.altloc="\x00";this.atomSite=this.atomID=0;this.group=null;this.atomNumberFlags=this.valence=this.userDefinedVanDerWaalRadius=0;this.atomSymmetry=

null;this.paletteID=this.colixAtom=this.madAtom=this.formalChargeAndFlags=0;this.bonds=null;this.shapeVisibilityFlags=this.clickabilityFlags=this.nBackbonesDisplayed=this.nBondsDisplayed=0;r(this,arguments)},JM,"Atom",JU.Point3fi,JU.Node);Q(b,function(){this.paletteID=J.c.PAL.CPK.id});j(b,"setAtom",function(a,d,b,c,f,e,h,k,m){this.mi=a;this.atomSymmetry=f;this.atomSite=e;this.i=d;this.atomNumberFlags=h;m&&(this.formalChargeAndFlags=2);0!=k&&-2147483648!=k&&this.setFormalCharge(k);this.userDefinedVanDerWaalRadius=

c;null!=b&&this.setT(b);return this},"~N,~N,JU.P3,~N,JU.BS,~N,~N,~N,~B,~B");c(b,"setShapeVisibility",function(a,d){this.shapeVisibilityFlags=d?this.shapeVisibilityFlags|a:this.shapeVisibilityFlags&~a},"~N,~B");c(b,"isCovalentlyBonded",function(a){if(null!=this.bonds)for(var d=this.bonds.length;0<=--d;)if(this.bonds[d].isCovalent()&&this.bonds[d].getOtherAtom(this)===a)return!0;return!1},"JM.Atom");c(b,"isBonded",function(a){if(null!=this.bonds)for(var d=this.bonds.length;0<=--d;)if(this.bonds[d].getOtherAtom(this)===

a)return!0;return!1},"JM.Atom");c(b,"getBond",function(a){if(null!=this.bonds)for(var d=this.bonds.length;0<=--d;)if(null!=this.bonds[d].getOtherAtom(a))return this.bonds[d];return null},"JM.Atom");c(b,"addDisplayedBond",function(a,d){this.nBondsDisplayed+=d?1:-1;this.setShapeVisibility(a,0<this.nBondsDisplayed)},"~N,~B");c(b,"deleteBond",function(a){if(null!=this.bonds)for(var d=this.bonds.length;0<=--d;)if(this.bonds[d]===a){this.deleteBondAt(d);break}},"JM.Bond");c(b,"deleteBondAt",function(a){this.setCIPChirality(0);

case J.atomdata.RadiusData.EnumType.FACTOR:case J.atomdata.RadiusData.EnumType.OFFSET:var c=0;switch(d.vdwType){case J.c.VDW.TEMP:c=a.ms.getBfactor100Hi();c=0<c?this.getBfactor100()/c:0;break;case J.c.VDW.HYDRO:c=Math.abs(this.getHydrophobicity());break;case J.c.VDW.BONDING:c=this.getBondingRadius();break;case J.c.VDW.ADPMIN:case J.c.VDW.ADPMAX:c=this.getADPMinMax(d.vdwType===J.c.VDW.ADPMAX);break;default:c=this.getVanderwaalsRadiusFloat(a,d.vdwType)}b=d.factorType===J.atomdata.RadiusData.EnumType.FACTOR?

b*c:b+c;break;case J.atomdata.RadiusData.EnumType.ABSOLUTE:if(16.1==b)return JM.Atom.MAD_GLOBAL}c=ca(0>b?b:2E3*b);0>c&&0<b&&(c=0);return c},"JV.Viewer,J.atomdata.RadiusData");c(b,"getADPMinMax",function(a){var d=this.getTensors();if(null==d)return 0;var b=d[0];if(null==b||1!=b.iType)return 0;this.group.chain.model.ms.isModulated(this.i)&&b.isUnmodulated&&(b=d[1]);return b.getFactoredValue(a?2:1)},"~B");c(b,"getTensors",function(){return this.group.chain.model.ms.getAtomTensorList(this.i)});c(b,"getRasMolRadius",

function(){return Math.abs(B(this.madAtom/8))});j(b,"getEdges",function(){return null==this.bonds?[]:this.bonds});j(b,"getBondCount",function(){return null==this.bonds?0:this.bonds.length});c(b,"setTranslucent",function(a,d){this.colixAtom=JU.C.getColixTranslucent3(this.colixAtom,a,d)},"~B,~N");j(b,"getElementNumber",function(){return JU.Elements.getElementNumber(this.atomNumberFlags)});j(b,"getIsotopeNumber",function(){return JU.Elements.getIsotopeNumber(this.atomNumberFlags)});j(b,"getAtomicAndIsotopeNumber",

function(){return this.atomNumberFlags});c(b,"setAtomicAndIsotopeNumber",function(a){if(0>a||(a&127)>=JU.Elements.elementNumberMax||32767<a)a=0;this.atomNumberFlags=a},"~N");c(b,"getElementSymbolIso",function(a){return JU.Elements.elementSymbolFromNumber(a?this.atomNumberFlags:this.atomNumberFlags&127)},"~B");c(b,"getElementSymbol",function(){return this.getElementSymbolIso(!0)});c(b,"isHetero",function(){return 0!=(this.formalChargeAndFlags&2)});c(b,"hasVibration",function(){return 0!=(this.formalChargeAndFlags&

1)});c(b,"setFormalCharge",function(a){this.formalChargeAndFlags=this.formalChargeAndFlags&15|(-2147483648==a?0:7<a?7:-3>a?-3:a)<<24},"~N");c(b,"setVibrationVector",function(){this.formalChargeAndFlags|=1});c(b,"setNegativeDisorder",function(){this.formalChargeAndFlags|=4});c(b,"isNegativeDisorder",function(){return 0!=(this.formalChargeAndFlags&4)});j(b,"getFormalCharge",function(){return this.formalChargeAndFlags>>24});c(b,"getOccupancy100",function(){var a=this.group.chain.model.ms.occupancies;

return null==a?100:Math.round(a[this.i])});c(b,"isOccupied",function(){var a=this.group.chain.model.ms.occupancies;return null==a||50<=a[this.i]});c(b,"getBfactor100",function(){var a=this.group.chain.model.ms.bfactor100s;return null==a?0:a[this.i]});c(b,"getHydrophobicity",function(){var a=this.group.chain.model.ms.hydrophobicities;return null==a?JU.Elements.getHydrophobicity(this.group.groupID):a[this.i]});c(b,"setRadius",function(a){return!Float.isNaN(this.userDefinedVanDerWaalRadius=0<a?a:NaN)},

"~N");c(b,"$delete",function(a){this.valence=-1;if(null!=this.bonds)for(var d=this.bonds.length;0<=--d;){var b=this.bonds[d];b.getOtherAtom(this).deleteBond(b);a.set(b.index)}this.bonds=null},"JU.BS");j(b,"isDeleted",function(){return 0>this.valence});c(b,"setValence",function(a){this.isDeleted()||(this.valence=0>a?0:127>=a?a:127)},"~N");j(b,"getValence",function(){return this.isDeleted()?-1:0<this.valence?this.valence:this.getValenceAromatic(!0)});c(b,"getValenceAromatic",function(a){if(this.isDeleted())return-1;

this.bonds[d];b.isCovalent()&&!b.getOtherAtom(this).isDeleted()&&++a}return a});j(b,"getCovalentHydrogenCount",function(){if(null==this.bonds)return 0;for(var a=0,d=this.bonds.length;0<=--d;)if(this.bonds[d].isCovalentNotPartial0()){var b=this.bonds[d].getOtherAtom(this);0<=b.valence&&1==b.getElementNumber()&&++a}return a});j(b,"getImplicitHydrogenCount",function(){return this.group.chain.model.ms.getMissingHydrogenCount(this,!1)});j(b,"getTotalHydrogenCount",function(){return this.getCovalentHydrogenCount()+

this.getImplicitHydrogenCount()});j(b,"getTotalValence",function(){var a=this.getValence();if(0>a)return a;var d=this.getImplicitHydrogenCount();return a+d+this.group.chain.model.ms.aaRet[4]});j(b,"getCovalentBondCountPlusMissingH",function(){return this.getCovalentBondCount()+this.getImplicitHydrogenCount()});c(b,"getTargetValence",function(){switch(this.getElementNumber()){case 6:case 14:case 32:return 4;case 5:case 7:case 15:return 3;case 8:case 16:return 2;case 1:case 9:case 17:case 35:case 53:return 1}return-1});

c(b,"getDimensionValue",function(a){return 0==a?this.x:1==a?this.y:this.z},"~N");c(b,"getVanderwaalsRadiusFloat",function(a,d){return Float.isNaN(this.userDefinedVanDerWaalRadius)?a.getVanderwaalsMarType(this.atomNumberFlags,this.getVdwType(d))/1E3:this.userDefinedVanDerWaalRadius},"JV.Viewer,J.c.VDW");c(b,"getVdwType",function(a){switch(a){case J.c.VDW.AUTO:a=this.group.chain.model.ms.getDefaultVdwType(this.mi);break;case J.c.VDW.NOJMOL:a=this.group.chain.model.ms.getDefaultVdwType(this.mi),a===

J.c.VDW.AUTO_JMOL&&(a=J.c.VDW.AUTO_BABEL)}return a},"J.c.VDW");c(b,"getBondingRadius",function(){var a=this.group.chain.model.ms.bondingRadii,a=null==a||this.i>=a.length?0:a[this.i];return 0==a?JU.Elements.getBondingRadius(this.atomNumberFlags,this.getFormalCharge()):a});c(b,"getVolume",function(a,d){var b=null==d?this.userDefinedVanDerWaalRadius:NaN;Float.isNaN(b)&&(b=a.getVanderwaalsMarType(this.getElementNumber(),this.getVdwType(d))/1E3);var c=0;if(null!=this.bonds)for(var f=0;f<this.bonds.length;f++)if(this.bonds[f].isCovalent()){var e=

this.bonds[f].getOtherAtom(this),h=null==d?e.userDefinedVanDerWaalRadius:NaN;Float.isNaN(h)&&(h=a.getVanderwaalsMarType(e.getElementNumber(),e.getVdwType(d))/1E3);e=this.distance(e);if(!(e>b+h)){if(e+b<=h)return 0;h=b-(b*b+e*e-h*h)/(2*e);c-=1.0471975511965976*h*h*(3*b-h)}}return c+4.1887902047863905*b*b*b},"JV.Viewer,J.c.VDW");c(b,"getCurrentBondCount",function(){return null==this.bonds?0:this.bonds.length});c(b,"getRadius",function(){return Math.abs(this.madAtom/2E3)});j(b,"getIndex",function(){return this.i});

j(b,"getAtomSite",function(){return this.atomSite});j(b,"getGroupBits",function(a){this.group.setAtomBits(a)},"JU.BS");j(b,"getAtomName",function(){return 0<this.atomID?JM.Group.specialAtomNames[this.atomID]:null==this.group.chain.model.ms.atomNames?"":this.group.chain.model.ms.atomNames[this.i]});j(b,"getAtomType",function(){var a=this.group.chain.model.ms.atomTypes,a=null==a?null:a[this.i];return null==a?this.getAtomName():a});j(b,"getAtomNumber",function(){var a=this.group.chain.model.ms.atomSerials;

return null==a?this.i:a[this.i]});c(b,"getSeqID",function(){var a=this.group.chain.model.ms.atomSeqIDs;return null==a?0:a[this.i]});c(b,"isVisible",function(a){return(this.shapeVisibilityFlags&a)==a},"~N");c(b,"getPartialCharge",function(){var a=this.group.chain.model.ms.partialCharges;return null==a?0:a[this.i]});c(b,"getSymmetryTranslation",function(a,d,b){for(var c=0;c<d.length;c++)if(this.atomSymmetry.get(a+=b))return d[c];return 0},"~N,~A,~N");c(b,"getCellTranslation",function(a,d,b){for(var c=

b,f=0;f<d.length;f++)for(var e=0;e<b;e++,c++)if(this.atomSymmetry.get(c)&&d[f]==a)return d[f];return 0},"~N,~A,~N");c(b,"getSymmetryOperatorList",function(a){var d="",b=this.group.chain.model.ms,c=b.getModelSymmetryCount(this.mi);if(0==c||null==this.atomSymmetry)return"";for(var b=b.getModelCellRange(this.mi),f=c,e=null==b?1:b.length,h=a?null:new JU.BS,k=0;k<e;k++)for(var m=0;m<c;m++)this.atomSymmetry.get(f++)&&(a?d+=","+(m+1)+(null==b?555:b[k]):h.set(m+1));if(!a)for(k=h.nextSetBit(0);0<=k;k=h.nextSetBit(k+

1))d+=","+k;return 0==d.length?"":d.substring(1)},"~B");j(b,"getModelIndex",function(){return this.mi});j(b,"getMoleculeNumber",function(a){return this.group.chain.model.ms.getMoleculeIndex(this.i,a)+1},"~B");c(b,"getFractionalCoord",function(a,d,b,c){c=this.getFractionalCoordPt(a,b,c);return"X"==d?c.x:"Y"==d?c.y:c.z},"~B,~S,~B,JU.P3");j(b,"getXYZ",function(){return this});c(b,"getFractionalCoordPt",function(a,d,b){var c=this.getUnitCell();null==b?b=JU.P3.newP(this):b.setT(this);null!=c&&(c=c.getUnitCellMultiplied(),

c.toFractional(b,d),a&&JU.PT.fixPtFloats(b,1E5));return b},"~B,~B,JU.P3");c(b,"getUnitCell",function(){return this.group.chain.model.ms.getUnitCellForAtom(this.i)});c(b,"getFractionalUnitCoord",function(a,d,b){b=this.getFractionalUnitCoordPt(a,!1,b);return"X"==d?b.x:"Y"==d?b.y:b.z},"~B,~S,JU.P3");c(b,"getFractionalUnitCoordPt",function(a,d,b){var c=this.getUnitCell();null==b?b=JU.P3.newP(this):b.setT(this);if(null==c)return b;c=c.getUnitCellMultiplied();this.group.chain.model.isJmolDataFrame?(c.toFractional(b,

!1),d&&c.toCartesian(b,!1)):(c.toUnitCell(b,null),d||c.toFractional(b,!1));a&&JU.PT.fixPtFloats(b,d?1E4:1E5);return b},"~B,~B,JU.P3");c(b,"getFractionalUnitDistance",function(a,d,b){var c=this.getUnitCell();if(null==c)return this.distance(a);d.setT(this);b.setT(a);this.group.chain.model.isJmolDataFrame?(c.toFractional(d,!0),c.toFractional(b,!0)):(c.toUnitCell(d,null),c.toUnitCell(b,null));return d.distance(b)},"JU.T3,JU.T3,JU.T3");c(b,"setFractionalCoord",function(a,d,b){var c=this.getUnitCell();

null!=c&&c.toFractional(this,b);switch(a){case 1111492615:case 1111492612:this.x=d;break;case 1111492616:case 1111492613:this.y=d;break;case 1111492617:case 1111492614:this.z=d}null!=c&&c.toCartesian(this,b)},"~N,~N,~B");c(b,"setFractionalCoordTo",function(a,d){this.setFractionalCoordPt(this,a,d)},"JU.P3,~B");c(b,"setFractionalCoordPt",function(a,d,b){a.setT(d);d=this.getUnitCell();null!=d&&d.toCartesian(a,b&&!this.group.chain.model.isJmolDataFrame)},"JU.P3,JU.P3,~B");c(b,"isCursorOnTopOf",function(a,

d,b,c){var f=B(this.sD/2);f<b&&(f=b);b=f*f;f=this.sX-a;f*=f;if(f>b)return!1;var e=this.sY-d;b-=f+e*e;if(0>b)return!1;if(null==c)return!0;var f=this.sZ,e=c.sZ,h=B(c.sD/2);if(f<e-h)return!0;a=c.sX-a;d=c.sY-d;d=h*h-(a*a+d*d);return f-Math.sqrt(b)<e-Math.sqrt(d)},"~N,~N,~N,JM.Atom");c(b,"getInfo",function(){return this.getIdentity(2)});c(b,"getIdentityXYZ",function(a,d){a=3==d||this.group.chain.model.isJmolDataFrame?this.getFractionalCoordPt(!this.group.chain.model.ms.vwr.g.legacyJavaFloat,!1,a):this;

return(3==d?"":this.getIdentity(d)+" ")+JU.PT.formatF(a.x,0,3,!0,!0)+" "+JU.PT.formatF(a.y,0,3,!0,!0)+" "+JU.PT.formatF(a.z,0,3,!0,!0)},"JU.P3,~N");c(b,"getIdentity",function(a){var d=new JU.SB,b=this.getGroup3(!0);if(null!=b&&0<b.length&&(!b.equals("UNK")||this.group.chain.model.isBioModel)){d.append("[");d.append(b);d.append("]");b=this.group.getSeqcodeString();null!=b&&d.append(b);b=this.group.chain.chainID;if(0!=b&&32!=b){d.append(":");var c=this.getChainIDStr();256<=b&&(c=JU.PT.esc(c));d.append(c)}if(2!=

a&&5!=a)return d.toString();d.append(".")}d.append(this.getAtomName());0==d.length()&&(d.append(this.getElementSymbolIso(!1)),d.append(" "),d.appendI(this.getAtomNumber()));2==a&&("\x00"!=this.altloc&&(d.append("%"),d.appendC(this.altloc)),1<this.group.chain.model.ms.mc&&!this.group.chain.model.isJmolDataFrame&&(d.append("/"),d.append(this.getModelNumberForLabel())),d.append(" #"),d.appendI(this.getAtomNumber()));return d.toString()},"~N");j(b,"getGroup3",function(a){var d=this.group.getGroup3();

return a||null!=d&&0<d.length?d:"UNK"},"~B");j(b,"getGroup1",function(a){var d=this.group.getGroup1();return"\x00"!=d?""+d:"\x00"!=a?""+a:""},"~S");j(b,"getBioSmilesType",function(){return this.group.isProtein()?"p":this.group.isDna()?"d":this.group.isRna()?"r":this.group.isCarbohydrate()?"c":" "});j(b,"isPurine",function(){return this.group.isPurine()});j(b,"isPyrimidine",function(){return this.group.isPyrimidine()});j(b,"getResno",function(){return this.group.getResno()});c(b,"isClickable",function(){return this.checkVisible()&&

0!=this.clickabilityFlags&&0!=((this.shapeVisibilityFlags|this.group.shapeVisibilityFlags)&this.clickabilityFlags)});c(b,"setClickable",function(a){0==a?this.clickabilityFlags=0:(this.clickabilityFlags|=a,1040384!=a&&(this.shapeVisibilityFlags|=a))},"~N");c(b,"checkVisible",function(){if(this.isVisible(2))return this.isVisible(4);var a=this.isVisible(9);if(a){a=this.shapeVisibilityFlags;if(0!=this.group.shapeVisibilityFlags&&(8192!=this.group.shapeVisibilityFlags||this.isLeadAtom()))a|=this.group.shapeVisibilityFlags;

a&=-10;32==a&&0==this.clickabilityFlags&&(a=0);if(a=0!=a)this.shapeVisibilityFlags|=4}this.shapeVisibilityFlags|=2;return a});j(b,"isLeadAtom",function(){return this.group.isLeadAtom(this.i)});j(b,"getChainID",function(){return this.group.chain.chainID});j(b,"getChainIDStr",function(){return this.group.chain.getIDStr()});c(b,"getSurfaceDistance100",function(){return this.group.chain.model.ms.getSurfaceDistance100(this.i)});c(b,"getVibrationVector",function(){return this.group.chain.model.ms.getVibration(this.i,

!1)});c(b,"getModulation",function(){return this.group.chain.model.ms.getModulation(this.i)});c(b,"getModelNumberForLabel",function(){return this.group.chain.model.ms.getModelNumberForAtomLabel(this.mi)});c(b,"getModelNumber",function(){return this.group.chain.model.ms.getModelNumber(this.mi)%1E6});j(b,"getBioStructureTypeName",function(){return this.group.getProteinStructureType().getBioStructureTypeName(!0)});j(b,"equals",function(a){return this===a},"~O");j(b,"hashCode",function(){return this.i});

c(b,"findAromaticNeighbor",function(a){if(null==this.bonds)return null;for(var d=this.bonds.length;0<=--d;){var b=this.bonds[d],c=b.getOtherAtom(this);if(b.isAromatic()&&c.i!=a)return c}return null},"~N");c(b,"atomPropertyInt",function(a){switch(a){case 1094715393:return this.getAtomNumber();case 1094713365:return this.getSeqID();case 1094713346:return this.atomID;case 1094713368:return Math.max(0,this.altloc.charCodeAt(0)-32);case 1094713347:return this.i;case 1228931586:return this.getCovalentBondCount();

case 1094713351:return this.group.chain.chainNo;case 1765808134:return this.group.chain.model.ms.vwr.gdata.getColorArgbOrGray(this.colixAtom);case 1086326789:case 1094715402:return this.getElementNumber();case 1094713353:return this.atomNumberFlags;case 1228935687:return this.group.chain.model.fileIndex+1;case 1631586315:return this.getFormalCharge();case 1094713356:return this.group.groupID;case 1094713357:return this.group.groupIndex;case 1094717454:return this.getModelNumber();case -1094717454:return this.group.chain.model.ms.modelFileNumbers[this.mi];

case 1094713359:return this.mi;case 1094713360:return this.getMoleculeNumber(!0);case 1094713361:return this.group.getMonomerIndex()+1;case 1128269825:return this.getOccupancy100();case 1094713362:return this.group.getBioPolymerIndexInModel()+1;case 1094713363:return this.group.getBioPolymerLength();case 1665140738:return this.getRasMolRadius();case 1094715412:return this.getResno();case 1094713366:return this.getAtomSite();case 1639976963:return this.group.getProteinStructureType().getId();case 1237320707:return this.group.getProteinStructureSubType().getId();

case 1094713367:return this.group.getStrucNo();case 1296041985:return this.getSymOp();case 1094715418:return this.getValence()}return 0},"~N");c(b,"getSymOp",function(){return null==this.atomSymmetry?0:this.atomSymmetry.nextSetBit(0)+1});c(b,"atomPropertyFloat",function(a,d,b){switch(d){case 1111490561:return this.getADPMinMax(!0);case 1111490562:return this.getADPMinMax(!1);case 1111492609:case 1111492629:return this.x;case 1111492610:case 1111492630:return this.y;case 1111492611:case 1111492631:return this.z;

case 1111490587:return this.group.chain.model.ms.getAtomicDSSRData(this.i);case 1114249217:case 1112152066:case 1112150019:case 1112150020:case 1112150021:case 1112152070:case 1112152071:case 1112152073:case 1112152074:case 1112152076:case 1649022989:case 1112152078:return a.shm.getAtomShapeValue(d,this.group,this.i);case 1111492618:return this.getBondingRadius();case 1111490563:return a.getNMRCalculation().getChemicalShift(this);case 1111490564:return JU.Elements.getCovalentRadius(this.atomNumberFlags);

case 1111490565:case 1111490576:case 1111490574:return this.group.getGroupParameter(d);case 1111492615:case 1111492612:return this.getFractionalCoord(!a.g.legacyJavaFloat,"X",!1,b);case 1111492616:case 1111492613:return this.getFractionalCoord(!a.g.legacyJavaFloat,"Y",!1,b);case 1111492617:case 1111492614:return this.getFractionalCoord(!a.g.legacyJavaFloat,"Z",!1,b);case 1113589786:return this.getHydrophobicity();case 1111490566:return a.getNMRCalculation().getMagneticShielding(this);case 1111490567:return this.getMass();

case 1128269825:return this.getOccupancy100()/100;case 1111492619:return this.getPartialCharge();case 1111490569:case 1111490570:case 1111490568:if(this.group.chain.model.isJmolDataFrame&&this.group.chain.model.jmolFrameType.startsWith("plot ramachandran"))switch(d){case 1111490569:return this.getFractionalCoord(!a.g.legacyJavaFloat,"X",!1,b);case 1111490570:return this.getFractionalCoord(!a.g.legacyJavaFloat,"Y",!1,b);case 1111490568:return a=this.getFractionalCoord(!a.g.legacyJavaFloat,"Z",!1,b)-

180,-180>a?360+a:a}return this.group.getGroupParameter(d);case 1665140738:case 1112152075:return this.getRadius();case 1111490571:return a.antialiased?B(this.sX/2):this.sX;case 1111490572:return a.getScreenHeight()-(a.antialiased?B(this.sY/2):this.sY);case 1111490573:return a.antialiased?B(this.sZ/2):this.sZ;case 1113589787:return a.slm.isAtomSelected(this.i)?1:0;case 1111490575:return a.ms.getSurfaceDistanceMax(),this.getSurfaceDistance100()/100;case 1111492620:return this.getBfactor100()/100;case 1111490588:return JU.C.getColixTranslucencyFractional(this.colixAtom);

case 1312817669:return this.getVolume(a,J.c.VDW.AUTO);case 1111490577:return this.getFractionalUnitCoord(!a.g.legacyJavaFloat,"X",b);case 1111490578:return this.getFractionalUnitCoord(!a.g.legacyJavaFloat,"Y",b);case 1111490579:return this.getFractionalUnitCoord(!a.g.legacyJavaFloat,"Z",b);case 1648363544:return this.getVanderwaalsRadiusFloat(a,J.c.VDW.AUTO);case 1648361473:return d=this.getVibrationVector(),null==d?0:d.length()*a.getFloat(1648361473);case 1111492626:return this.getVib("x");case 1111492627:return this.getVib("y");

case 1111492628:return this.getVib("z");case 1111490583:return this.getVib("X");case 1111490584:return this.getVib("Y");case 1111490585:return this.getVib("Z");case 1111490586:return this.getVib("O");case 1111490580:return this.getVib("1");case 1111490581:return this.getVib("2");case 1111490582:return this.getVib("3");case 1145047050:case 1145047053:case 1145045006:case 1145047052:case 1145047055:case 1145045008:case 1145047049:return a=this.atomPropertyTuple(a,d,b),null==a?-1:a.length()}return this.atomPropertyInt(d)},

"JV.Viewer,~N,JU.P3");c(b,"getVib",function(a){return this.group.chain.model.ms.getVibCoord(this.i,a)},"~S");c(b,"getNominalMass",function(){var a=this.getIsotopeNumber();return 0<a?a:JU.Elements.getNaturalIsotope(this.getElementNumber())});j(b,"getMass",function(){var a=this.getIsotopeNumber();return 0<a?a:JU.Elements.getAtomicMass(this.getElementNumber())});c(b,"atomPropertyString",function(a,d){var b;switch(d){case 1153433601:return this.getIdentity(5);case 1086324739:return b=this.altloc,"\x00"==

b?"":""+b;case 1086326786:return this.getAtomName();case 1086326785:return this.getAtomType();case 1086326788:return this.getChainIDStr();case 1086324752:return this.getCIPChirality(!0);case 1086324753:return this.getCIPChiralityRule();case 1140850705:case 1086324754:return this.getWyckoffPosition(!1);case 1086324755:return this.getWyckoffPosition(!0);case 1086324744:return this.getGroup1("?");case 1086324747:return b=this.group.getSeqcodeString(),null==b?"":b;case 1086324743:return this.getGroup1("\x00");

case 1086324742:return this.getGroup3(!1);case 1086326789:return this.getElementSymbolIso(!0);case 1086324745:return this.getIdentity(2);case 1086324746:return b=this.group.getInsertionCode(),"\x00"==b?"":""+b;case 1825200146:case 1287653388:return b=a.shm.getShapePropertyIndex(5,"label",this.i),null==b&&(b=""),b;case 1145045003:return a.getSymStatic().staticToRationalXYZ(this.getFractionalCoordPt(!a.g.legacyJavaFloat,!1,null)," ");case 1639976963:return this.group.getProteinStructureType().getBioStructureTypeName(!1);

case 1237320707:return this.group.getProteinStructureSubType().getBioStructureTypeName(!1);case 1086324749:return this.group.getStructureId();case 1086324748:return a.getHybridizationAndAxes(this.i,null,null,"d");case 1086326798:return this.getElementSymbolIso(!1);case 1088421903:return this.getSymmetryOperatorList(!0)}return""},"JV.Viewer,~N");c(b,"getWyckoffPosition",function(a){var d=this.group.chain.model.ms,b=d.getBasisAtom(this.i,!0).getSeqID();if(0!=b)return d=b>>16,b=String.fromCharCode(b&

255),(a?""+d:"")+b;var b=this.getUnitCell(),c;if(null==b||null==(c=b.getWyckoffPosition(d.vwr,this,"M")))c="0?";d.setAtomSeqID(this.i,(JU.PT.parseInt(c)<<16)+c.charAt(c.length-1).charCodeAt(0));return a?c:c.substring(c.length-1)},"~B");j(b,"getCIPChirality",function(a){var d=(this.formalChargeAndFlags&496)>>4;0==d&&(1<this.atomNumberFlags&&a)&&(d=this.group.chain.model.ms.getAtomCIPChiralityCode(this),this.formalChargeAndFlags|=(0==d?3:d)<<4);return JV.JC.getCIPChiralityName(d)},"~B");c(b,"getCIPChiralityRule",

function(){var a=0==this.getCIPChirality(!0).length?-1:(this.formalChargeAndFlags&3584)>>9;return JV.JC.getCIPRuleName(a+1)});j(b,"setCIPChirality",function(a){this.formalChargeAndFlags=this.formalChargeAndFlags&-4081|a<<4},"~N");j(b,"getCIPChiralityCode",function(){return(this.formalChargeAndFlags&496)>>4});j(b,"getInsertionCode",function(){return this.group.getInsertionCode()});c(b,"atomPropertyTuple",function(a,d,b){switch(d){case 1073742329:return JU.P3.newP(this);case 1145047050:return this.getFractionalCoordPt(!a.g.legacyJavaFloat,

!1,b);case 1145047053:return this.getFractionalCoordPt(!a.g.legacyJavaFloat,!1,b);case 1145045006:return this.group.chain.model.isJmolDataFrame?this.getFractionalCoordPt(!a.g.legacyJavaFloat,!1,b):this.getFractionalUnitCoordPt(!a.g.legacyJavaFloat,!1,b);case 1145047052:return JU.P3.new3(a.antialiased?B(this.sX/2):this.sX,a.getScreenHeight()-(a.antialiased?B(this.sY/2):this.sY),a.antialiased?B(this.sZ/2):this.sZ);case 1145047055:return this.getVibrationVector();case 1145045008:return a=this.getModulation(),

null==a?null:a.getV3();case 1145047049:return this;case 1765808134:return JU.CU.colorPtFromInt(this.group.chain.model.ms.vwr.gdata.getColorArgbOrGray(this.colixAtom),b)}return null},"JV.Viewer,~N,JU.P3");j(b,"getOffsetResidueAtom",function(a,d){return this.group.getAtomIndex(a,d)},"~S,~N");j(b,"isCrossLinked",function(a){return this.group.isCrossLinked(a.group)},"JU.Node");j(b,"getCrossLinkVector",function(a,d,b){return this.group.getCrossLinkVector(a,d,b)},"JU.Lst,~B,~B");j(b,"toString",function(){return this.getInfo()});

j(b,"findAtomsLike",function(a){return this.group.chain.model.ms.vwr.getAtomBitSet(a)},"~S");c(b,"getUnitID",function(a){var d=this.group.chain.model;return d.isBioModel?d.getUnitID(this,a):""},"~N");j(b,"getFloatProperty",function(a){a=this.group.chain.model.ms.vwr.getDataObj(a,null,1);var d=NaN;if(null!=a)try{d=a[this.i]}catch(b){if(!F(b,Exception))throw b;}return d},"~S");j(b,"modelIsRawPDB",function(){var a=this.group.chain.model;return a.isBioModel&&!a.isPdbWithMultipleBonds&&0==a.hydrogenCount});

c(b,"setSymop",function(a,d){null==this.atomSymmetry&&(this.atomSymmetry=new JU.BS);d&&this.atomSymmetry.clearAll();0<a&&this.atomSymmetry.set(a-1)},"~N,~B");j(b,"getExplicitHydrogenCount",function(){return 0});b.MAD_GLOBAL=32200});u("JM");C(["JU.V3"],"JM.AtomCollection","java.util.Arrays $.Hashtable JU.A4 $.AU $.BS $.Lst $.M3 $.Measure $.P3 $.PT J.api.Interface J.atomdata.RadiusData J.c.PAL $.VDW JM.Group JS.T JU.BSUtil $.Elements $.Logger $.Parser $.Vibration".split(" "),function(){var b=v(function(){this.at=

this.bioModelset=this.g3d=this.vwr=null;this.ac=0;this.labeler=this.pointGroup=this.trajectory=null;this.maxVanderwaalsRadius=this.maxBondingRadius=1.4E-45;this.hasBfactorRange=!1;this.bfactor100Hi=this.bfactor100Lo=0;this.haveBSClickable=this.haveBSVisible=!1;this.bsSurface=null;this.surfaceDistanceMax=this.nSurfaceAtoms=0;this.haveChirality=!1;this.bspf=null;this.canSkipLoad=this.preserveState=!0;this.haveStraightness=!1;this.aaRet=this.bsPartialCharges=this.hydrophobicities=this.bondingRadii=this.partialCharges=

this.bfactor100s=this.occupancies=this.vibrations=this.dssrData=this.atomSeqIDs=this.atomResnos=this.atomSerials=this.atomTypes=this.atomNames=this.tainted=this.surfaceDistance100s=this.atomTensors=this.atomTensorList=this.bsModulated=this.bsClickable=this.bsVisible=this.bsHidden=null;V("JM.AtomCollection.AtomSorter")||JM.AtomCollection.$AtomCollection$AtomSorter$();this.atomCapacity=0;r(this,arguments)},JM,"AtomCollection",null);c(b,"getAtom",function(a){return 0<=a&&a<this.at.length?this.at[a]:

null},"~N");c(b,"setupAC",function(){this.bsHidden=new JU.BS;this.bsVisible=new JU.BS;this.bsClickable=new JU.BS;null==JM.AtomCollection.userSettableValues&&(JM.AtomCollection.userSettableValues="atomName atomType coord element formalCharge hydrophobicity ionic occupancy partialCharge temperature valence vanderWaals vibrationVector atomNo seqID resNo chain site".$plit(" "))});c(b,"releaseModelSetAC",function(){this.ac=0;this.bfactor100s=this.occupancies=this.vibrations=this.atomSeqIDs=this.atomSerials=

this.dssrData=this.atomResnos=this.atomTypes=this.atomNames=this.tainted=this.bsSurface=this.surfaceDistance100s=this.bspf=this.g3d=this.vwr=this.at=null;this.resetPartialCharges();this.atomTensors=this.bondingRadii=null});c(b,"mergeAtomArrays",function(a){this.tainted=a.tainted;this.atomNames=a.atomNames;this.atomTypes=a.atomTypes;this.atomResnos=a.atomResnos;this.dssrData=a.dssrData;this.atomSerials=a.atomSerials;this.atomSeqIDs=a.atomSeqIDs;this.vibrations=a.vibrations;this.occupancies=a.occupancies;

this.bfactor100s=a.bfactor100s;this.bondingRadii=a.bondingRadii;this.partialCharges=a.partialCharges;this.bsPartialCharges=a.bsPartialCharges;this.atomTensors=a.atomTensors;this.atomTensorList=a.atomTensorList;this.bsModulated=a.bsModulated;this.haveStraightness=!1;this.surfaceDistance100s=null},"JM.AtomCollection");c(b,"getAtomPointVector",function(a){var d=new JU.Lst,b=this.ac;if(null!=a)for(var c=a.nextSetBit(0);0<=c&&c<b;c=a.nextSetBit(c+1))d.addLast(this.at[c]);return d},"JU.BS");c(b,"modelSetHasVibrationVectors",

function(){return null!=this.vibrations});c(b,"getAtomTypes",function(){return this.atomTypes});c(b,"getPartialCharges",function(){return this.partialCharges});c(b,"getBondingRadii",function(){return this.bondingRadii});c(b,"getBFactors",function(){return this.bfactor100s});c(b,"getHydrophobicity",function(){return this.hydrophobicities});c(b,"setBsHidden",function(a){this.bsHidden=a},"JU.BS");c(b,"isAtomHidden",function(a){return this.bsHidden.get(a)},"~N");c(b,"getLabeler",function(){return null==

this.labeler?this.labeler=J.api.Interface.getInterface("JM.LabelToken",this.vwr,"ms"):this.labeler});c(b,"getAtomInfo",function(a,d,b){return null==d?this.at[a].getInfo():this.getLabeler().formatLabel(this.vwr,this.at[a],d,b)},"~N,~S,JU.P3");c(b,"getElementName",function(a){return JU.Elements.elementNameFromNumber(this.at[a].getAtomicAndIsotopeNumber())},"~N");c(b,"getQuaternion",function(a,d){return 0>a?null:this.at[a].group.getQuaternion(d)},"~N,~S");c(b,"getFirstAtomIndexFromAtomNumber",function(a,

d){for(var b=0;b<this.ac;b++){var c=this.at[b];if(!JM.AtomCollection.isDeleted(c)&&c.getAtomNumber()==a&&d.get(c.mi))return b}return-1},"~N,JU.BS");c(b,"setFormalCharges",function(a,d){if(null!=a){this.resetPartialCharges();for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.at[b].setFormalCharge(d),this.taintAtom(b,4)}},"JU.BS,~N");c(b,"getAtomicCharges",function(){for(var a=K(this.ac,0),d=this.ac;0<=--d;)a[d]=JM.AtomCollection.isDeleted(this.at[d])?0:this.at[d].getElementNumber();return a});

c(b,"getRadiusVdwJmol",function(a){return JU.Elements.getVanderwaalsMar(a.getElementNumber(),J.c.VDW.JMOL)/1E3},"JM.Atom");c(b,"getMaxVanderwaalsRadius",function(){1.4E-45==this.maxVanderwaalsRadius&&this.findMaxRadii();return this.maxVanderwaalsRadius});c(b,"findMaxRadii",function(){for(var a,d=this.ac;0<=--d;){var b=this.at[d];if(!JM.AtomCollection.isDeleted(b)){if((a=b.getBondingRadius())>this.maxBondingRadius)this.maxBondingRadius=a;if((a=b.getVanderwaalsRadiusFloat(this.vwr,J.c.VDW.AUTO))>this.maxVanderwaalsRadius)this.maxVanderwaalsRadius=

a}}});c(b,"clearBfactorRange",function(){this.hasBfactorRange=!1});c(b,"calcBfactorRange",function(a){if(!this.hasBfactorRange){this.bfactor100Lo=2147483647;this.bfactor100Hi=-2147483648;if(null==a)for(var d=0;d<this.ac;d++)this.setBf(d);else for(d=a.nextSetBit(0);0<=d;d=a.nextSetBit(d+1))this.setBf(d);this.hasBfactorRange=!0}},"JU.BS");c(b,"setBf",function(a){JM.AtomCollection.isDeleted(this.at[a])||(a=this.at[a].getBfactor100(),a<this.bfactor100Lo?this.bfactor100Lo=a:a>this.bfactor100Hi&&(this.bfactor100Hi=

a))},"~N");c(b,"getBfactor100Lo",function(){this.hasBfactorRange||(this.vwr.g.rangeSelected?this.calcBfactorRange(this.vwr.bsA()):this.calcBfactorRange(null));return this.bfactor100Lo});c(b,"getBfactor100Hi",function(){this.getBfactor100Lo();return this.bfactor100Hi});c(b,"getSurfaceDistanceMax",function(){null==this.surfaceDistance100s&&this.calcSurfaceDistances();return this.surfaceDistanceMax});c(b,"calculateVolume",function(a,d){var b=0;if(null!=a)for(var c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+

1))b+=this.at[c].getVolume(this.vwr,d);return b},"JU.BS,J.c.VDW");c(b,"getSurfaceDistance100",function(a){if(0==this.nSurfaceAtoms)return-1;null==this.surfaceDistance100s&&this.calcSurfaceDistances();return this.surfaceDistance100s[a]},"~N");c(b,"calcSurfaceDistances",function(){this.calculateSurface(null,-1)});c(b,"calculateSurface",function(a,d){0>d&&(d=3);var b=J.api.Interface.getOption("geodesic.EnvelopeCalculation",this.vwr,"ms").set(this.vwr,this.ac,null);b.calculate(new J.atomdata.RadiusData(null,

d,J.atomdata.RadiusData.EnumType.ABSOLUTE,null),3.4028235E38,a,JU.BSUtil.copyInvert(a,this.ac),!1,!1,!1,!0);var c=b.getPoints();this.surfaceDistanceMax=0;this.bsSurface=b.getBsSurfaceClone();this.surfaceDistance100s=E(this.ac,0);this.nSurfaceAtoms=JU.BSUtil.cardinalityOf(this.bsSurface);if(0==this.nSurfaceAtoms||null==c||0==c.length)return c;for(var b=3.4028235E38==d?0:d,f=0;f<this.ac;f++)if(this.bsSurface.get(f)||JM.AtomCollection.isDeleted(this.at[f]))this.surfaceDistance100s[f]=0;else{for(var e=

3.4028235E38,h=this.at[f],k=c.length;0<=--k;)e=Math.min(Math.abs(c[k].distance(h)-b),e);e=this.surfaceDistance100s[f]=B(Math.floor(100*e));this.surfaceDistanceMax=Math.max(this.surfaceDistanceMax,e)}return c},"JU.BS,~N");c(b,"setAtomCoord2",function(a,d,b){var c=null,f=null,e=null,h=0,k=1;if(y(b,"JU.P3"))c=b;else if(y(b,"JU.Lst")){e=b;if(0==(k=e.size()))return;h=1}else if(JU.AU.isAP(b)){f=b;if(0==(k=f.length))return;h=2}else return;b=0;if(null!=a)for(var m=a.nextSetBit(0);0<=m;m=a.nextSetBit(m+1)){switch(h){case 1:if(b>=

k)return;c=e.get(b++);break;case 2:if(b>=k)return;c=f[b++]}if(null!=c)switch(d){case 1145047049:this.setAtomCoord(m,c.x,c.y,c.z);break;case 1145047050:case 1145047053:this.at[m].setFractionalCoordTo(c,!1);this.taintAtom(m,2);break;case 1145047055:this.setAtomVibrationVector(m,c)}}},"JU.BS,~N,~O");c(b,"setAtomVibrationVector",function(a,d){this.setVibrationVector(a,d);this.taintAtom(a,12)},"~N,JU.T3");c(b,"setAtomCoord",function(a,d,b,c){if(!(0>a||a>=this.ac)){var f=this.at[a];f.set(d,b,c);this.fixTrajectory(f);

this.taintAtom(a,2)}},"~N,~N,~N,~N");c(b,"fixTrajectory",function(a){this.isTrajectory(a.mi)&&this.trajectory.fixAtom(a)},"JM.Atom");c(b,"setAtomCoordRelative",function(a,d,b,c){if(!(0>a||a>=this.ac)){var f=this.at[a];f.add3(d,b,c);this.fixTrajectory(f);this.taintAtom(a,2)}},"~N,~N,~N,~N");c(b,"setAtomsCoordRelative",function(a,d,b,c){if(null!=a)for(var f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1))this.setAtomCoordRelative(f,d,b,c)},"JU.BS,~N,~N,~N");c(b,"setAPa",function(a,d,b,c,f,e,h){var k=0;if(!(null!=

e&&0==e.length||null==a)){for(var m=null!=e&&e.length==this.ac||null!=h&&h.length==this.ac,j=a.nextSetBit(0);0<=j;j=a.nextSetBit(j+1)){m&&(k=j);if(null!=e){if(k>=e.length)return;c=e[k++];if(Float.isNaN(c))continue;b=D(c)}else if(null!=h){if(k>=h.length)return;f=h[k++]}var p=this.at[j],q;switch(d){case 1086326786:this.setAtomName(j,f,!0);break;case 1086326785:this.setAtomType(j,f);break;case 1086326788:this.setChainID(j,f);break;case 1094715393:this.setAtomNumber(j,b,!0);break;case 1094713365:this.setAtomSeqID(j,

b);break;case 1111492609:case 1111492629:this.setAtomCoord(j,c,p.y,p.z);break;case 1111492610:case 1111492630:this.setAtomCoord(j,p.x,c,p.z);break;case 1111492611:case 1111492631:this.setAtomCoord(j,p.x,p.y,c);break;case 1111492626:case 1111492627:case 1111492628:this.setVibrationVector2(j,d,c);break;case 1111492612:case 1111492613:case 1111492614:case 1111492615:case 1111492616:case 1111492617:p.setFractionalCoord(d,c,!1);this.taintAtom(j,2);break;case 1094715402:case 1086326789:this.setElement(p,

b,!0);break;case 1631586315:this.resetPartialCharges();p.setFormalCharge(b);this.taintAtom(j,4);break;case 1113589786:this.setHydrophobicity(j,c);break;case 1128269825:q=2>c&&0.01<=c?100*c:c;this.setOccupancy(j,q,!0);break;case 1111492619:this.setPartialCharge(j,c,!0);break;case 1111492618:this.setBondingRadius(j,c);break;case 1111492620:this.setBFactor(j,c,!0);break;case 1094715412:this.setAtomResno(j,b);break;case 1825200146:case 1287653388:this.vwr.shm.setAtomLabel(f,j);break;case 1665140738:case 1112152075:q=

c;0>q?q=0:16<q&&(q=16.1);p.madAtom=ca(2E3*q);break;case 1113589787:this.vwr.slm.setSelectedAtom(p.i,0!=c);break;case 1094715418:p.setValence(b);this.taintAtom(j,10);break;case 1648363544:p.setRadius(c)?this.taintAtom(j,11):this.untaint(j,11);break;default:JU.Logger.error("unsettable atom property: "+JS.T.nameOf(d));return}}switch(d){case 1113589787:this.vwr.slm.setSelectedAtom(-1,!1);break;case 1665140738:case 1112152075:this.vwr.setShapeSize(0,2147483647,a)}}},"JU.BS,~N,~N,~N,~S,~A,~A");c(b,"getVibCoord",

function(a,d){var b=null,c=null;switch(d.charCodeAt(0)){case 120:case 121:case 122:c=this.getVibration(a,!1);break;default:b=this.getModulation(a),null!=b&&(c=b.getVibration(!1),null==c&&(c=b))}if(null==c&&null==b)return NaN;switch(d.charCodeAt(0)){case 120:case 88:return c.x;case 121:case 89:return c.y;case 122:case 90:return c.z;case 79:return b.getModulation("O",null,!0).floatValue();case 49:case 50:case 51:return b=b.getModulation("T",null,!0),b="1"==d?b.x:"2"==d?b.y:b.z,b-Math.floor(b);default:return NaN}},

"~N,~S");c(b,"getVibration",function(a,d){var b=null==this.vibrations?null:this.vibrations[a];return y(b,"J.api.JmolModulationSet")?b.getVibration(d):null==b&&d?new JU.Vibration:b},"~N,~B");c(b,"getModulation",function(a){a=null==this.vibrations?null:this.vibrations[a];return null!=a&&0<a.modDim?a:null},"~N");c(b,"setVibrationVector",function(a,d){if(null==d)null!=this.vibrations&&this.vibrations.length>a&&(this.vibrations[a]=null);else if(!Double.isNaN(d.x)&&!Double.isNaN(d.y)&&!Double.isNaN(d.z)){if(null==

this.vibrations||this.vibrations.length<=a)this.vibrations=Array(this.at.length);y(d,"JU.Vibration")?this.vibrations[a]=d:(null==this.vibrations[a]&&(this.vibrations[a]=new JU.Vibration),this.vibrations[a].setXYZ(d));this.at[a].setVibrationVector()}},"~N,JU.T3");c(b,"setVibrationVector2",function(a,d,b){var c=this.getVibration(a,!0);if(null!=c){switch(d){case 1111492626:c.x=b;break;case 1111492627:c.y=b;break;case 1111492628:c.z=b}this.setAtomVibrationVector(a,c)}},"~N,~N,~N");c(b,"setAtomName",function(a,

d,b){if(!b||!d.equals(this.at[a].getAtomName())){var c=this.am[this.at[a].mi].isBioModel?this.vwr.getJBR().lookupSpecialAtomID(d):0;this.at[a].atomID=c;0>=c&&(null==this.atomNames&&(this.atomNames=Array(this.at.length)),this.atomNames[a]=d);b&&this.taintAtom(a,0)}},"~N,~S,~B");c(b,"setAtomType",function(a,d){d.equals(this.at[a].getAtomType())||(null==this.atomTypes&&(this.atomTypes=Array(this.at.length)),this.atomTypes[a]=d)},"~N,~S");c(b,"setChainID",function(a,d){if(!d.equals(this.at[a].getChainIDStr())){var b=

this.at[a].getChainID(),b=this.getChainBits(b);this.at[a].group.chain.chainID=this.vwr.getChainID(d,!0);for(var c=b.nextSetBit(0);0<=c;c=b.nextSetBit(c+1))this.taintAtom(c,16)}},"~N,~S");c(b,"setAtomNumber",function(a,d,b){b&&d==this.at[a].getAtomNumber()||(null==this.atomSerials&&(this.atomSerials=E(this.at.length,0)),this.atomSerials[a]=d,b&&this.taintAtom(a,13))},"~N,~N,~B");c(b,"setElement",function(a,d,b){b&&a.getElementNumber()==d||(a.setAtomicAndIsotopeNumber(d),a.paletteID=J.c.PAL.CPK.id,

a.colixAtom=this.vwr.cm.getColixAtomPalette(a,J.c.PAL.CPK.id),this.resetPartialCharges(),b&&this.taintAtom(a.i,3))},"JM.Atom,~N,~B");c(b,"setSite",function(a,d,b){a.atomSite!=d&&(a.atomSite=d,b&&this.taintAtom(a.i,17))},"JM.Atom,~N,~B");c(b,"resetPartialCharges",function(){this.bsPartialCharges=this.partialCharges=null});c(b,"setAtomResno",function(a,d){d!=this.at[a].getResno()&&(this.at[a].group.setResno(d),null==this.atomResnos&&(this.atomResnos=E(this.at.length,0)),this.atomResnos[a]=d,this.taintAtom(a,

15))},"~N,~N");c(b,"setAtomSeqID",function(a,d){d!=this.at[a].getSeqID()&&(null==this.atomSeqIDs&&(this.atomSeqIDs=E(this.at.length,0)),this.atomSeqIDs[a]=d,this.taintAtom(a,14))},"~N,~N");c(b,"setOccupancy",function(a,d,b){if(!(b&&d==this.at[a].getOccupancy100())){if(null==this.occupancies){if(100==d)return;this.occupancies=K(this.at.length,0);for(var c=this.at.length;0<=--c;)this.occupancies[c]=100}this.occupancies[a]=d;b&&this.taintAtom(a,7)}},"~N,~N,~B");c(b,"getOccupancyFloat",function(a){return null==

this.occupancies||a>=this.occupancies.length?100:this.occupancies[a]},"~N");c(b,"setPartialCharge",function(a,d,b){if(!Float.isNaN(d)){if(null==this.partialCharges){this.bsPartialCharges=new JU.BS;if(0==d)return;this.partialCharges=K(this.at.length,0)}this.bsPartialCharges.set(a);this.partialCharges[a]=d;b&&this.taintAtom(a,8)}},"~N,~N,~B");c(b,"setBondingRadius",function(a,d){Float.isNaN(d)||d==this.at[a].getBondingRadius()||(null==this.bondingRadii?this.bondingRadii=K(this.at.length,0):this.bondingRadii.length<

this.at.length&&(this.bondingRadii=JU.AU.ensureLengthA(this.bondingRadii,this.at.length)),this.bondingRadii[a]=d,this.taintAtom(a,6))},"~N,~N");c(b,"setBFactor",function(a,d,b){if(!(Float.isNaN(d)||b&&d==this.at[a].getBfactor100())){if(null==this.bfactor100s){if(0==d)return;this.bfactor100s=W(this.at.length,0)}this.bfactor100s[a]=va(100*(-327.68>d?-327.68:327.67<d?327.67:d)+(0>d?-0.5:0.5));b&&this.taintAtom(a,9)}},"~N,~N,~B");c(b,"setHydrophobicity",function(a,d){if(!(Float.isNaN(d)||d==this.at[a].getHydrophobicity())){if(null==

this.hydrophobicities){this.hydrophobicities=K(this.at.length,0);for(var b=0;b<this.at.length;b++)this.hydrophobicities[b]=JU.Elements.getHydrophobicity(this.at[b].group.groupID)}this.hydrophobicities[a]=d;this.taintAtom(a,5)}},"~N,~N");c(b,"setAtomData",function(a,d,b,c){var f=null,e=null;switch(a){case 2:this.loadCoordinates(b,!1,!c);return;case 12:this.loadCoordinates(b,!0,!0);return;case 18:f=K(this.ac,0),e=JU.BS.newN(this.ac)}c=JU.Parser.markLines(b,";");var h=0;try{for(var k=JU.PT.parseInt(b.substring(0,

c[0]-1)),m=1;m<=k;m++){var j=JU.PT.getTokens(JU.PT.parseTrimmed(b.substring(c[m],c[m+1]-1))),p=JU.PT.parseInt(j[0])-1;if(!(0>p||p>=this.ac)){var q=this.at[p];h++;var x=j.length-1,s=JU.PT.parseFloat(j[x]);switch(a){case 18:f[p]=s;e.set(p);continue;case 0:this.setAtomName(p,j[x],!0);break;case 13:this.setAtomNumber(p,D(s),!0);break;case 15:this.setAtomResno(p,D(s));break;case 14:this.setAtomSeqID(p,D(s));break;case 1:this.setAtomType(p,j[x]);break;case 16:this.setChainID(p,j[x]);break;case 17:q.atomSite=

D(s);break;case 3:q.setAtomicAndIsotopeNumber(D(s));q.paletteID=J.c.PAL.CPK.id;q.colixAtom=this.vwr.cm.getColixAtomPalette(q,J.c.PAL.CPK.id);break;case 4:q.setFormalCharge(D(s));break;case 5:this.setHydrophobicity(p,s);break;case 6:this.setBondingRadius(p,s);break;case 8:this.setPartialCharge(p,s,!0);break;case 9:this.setBFactor(p,s,!0);break;case 10:q.setValence(D(s));break;case 11:q.setRadius(s)}this.taintAtom(p,a)}}18==a&&0<h&&this.vwr.setData(d,w(-1,[d,f,e,Integer.$valueOf(1)]),0,0,0,0,0)}catch(n){if(F(n,

Exception))JU.Logger.error("loadData error: "+n);else throw n;}},"~N,~S,~S,~B");c(b,"loadCoordinates",function(a,d,b){var c=JU.Parser.markLines(a,";"),f=d?new JU.V3:null;try{for(var e=JU.PT.parseInt(a.substring(0,c[0]-1)),h=1;h<=e;h++){var k=JU.PT.getTokens(JU.PT.parseTrimmed(a.substring(c[h],c[h+1]))),m=JU.PT.parseInt(k[0])-1,j=k[3].equalsIgnoreCase("1.4E-45")?1.4E-45:JU.PT.parseFloat(k[3]),p=k[4].equalsIgnoreCase("1.4E-45")?1.4E-45:JU.PT.parseFloat(k[4]),q=JU.PT.parseFloat(k[5]);d?(f.set(j,p,q),

this.setAtomVibrationVector(m,f)):(this.setAtomCoord(m,j,p,q),b||this.untaint(m,2))}}catch(x){if(F(x,Exception))JU.Logger.error("Frame.loadCoordinate error: "+x);else throw x;}},"~S,~B,~B");c(b,"validateBspf",function(a){null!=this.bspf&&(this.bspf.isValid=a)},"~B");c(b,"validateBspfForModel",function(a,d){null!=this.bspf&&this.bspf.validateModel(a,d)},"~N,~B");c(b,"setPreserveState",function(a){this.preserveState=a},"~B");b.getUserSettableType=c(b,"getUserSettableType",function(a){var d=0==a.indexOf("property_");

a=d?a.substring(9):a;for(var b=0;18>b;b++)if(JM.AtomCollection.userSettableValues[b].equalsIgnoreCase(a))return b;return d?18:-1},"~S");c(b,"getTaintedAtoms",function(a){return null==this.tainted?null:this.tainted[a]},"~N");c(b,"taintAtoms",function(a,d){this.canSkipLoad=!1;if(this.preserveState)for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.taintAtom(b,d)},"JU.BS,~N");c(b,"taintAtom",function(a,d){this.preserveState&&(null==this.tainted&&(this.tainted=Array(18)),null==this.tainted[d]&&(this.tainted[d]=

JU.BS.newN(this.ac)),this.tainted[d].set(a));2==d&&this.taintModelCoord(a)},"~N,~N");c(b,"taintModelCoord",function(a){a=this.am[this.at[a].mi];this.validateBspfForModel(a.trajectoryBaseIndex,!1);a.isBioModel&&a.resetDSSR(!0);this.pointGroup=null},"~N");c(b,"untaint",function(a,d){this.preserveState&&(null==this.tainted||null==this.tainted[d]||this.tainted[d].clear(a))},"~N,~N");c(b,"setTaintedAtoms",function(a,d){if(this.preserveState){if(null==a){if(null==this.tainted)return;this.tainted[d]=null;

return}null==this.tainted&&(this.tainted=Array(18));null==this.tainted[d]&&(this.tainted[d]=JU.BS.newN(this.ac));JU.BSUtil.copy2(a,this.tainted[d])}if(2==d){var b=a.nextSetBit(0);0<=b&&this.taintModelCoord(b)}},"JU.BS,~N");c(b,"unTaintAtoms",function(a,d){if(!(null==this.tainted||null==this.tainted[d])){for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.tainted[d].clear(b);0>this.tainted[d].nextSetBit(0)&&(this.tainted[d]=null)}},"JU.BS,~N");c(b,"findNearest2",function(a,d,b,c,f){for(var e=null,

h,k=this.ac;0<=--k;)if(!(null!=c&&c.get(k)||null==(h=this.at[k])))h.isClickable()&&this.isCursorOnTopOf(h,a,d,f,e)&&(e=h);b[0]=e},"~N,~N,~A,JU.BS,~N");c(b,"isCursorOnTopOf",function(a,d,b,c,f){return 1<a.sZ&&!this.g3d.isClippedZ(a.sZ)&&this.g3d.isInDisplayRange(a.sX,a.sY)&&a.isCursorOnTopOf(d,b,c,f)},"JM.Atom,~N,~N,~N,JM.Atom");c(b,"fillADa",function(a,d){a.xyz=a.atoms=this.at;a.ac=this.ac;a.atomicNumber=E(this.ac,0);var b=0!=(d&2);b&&(a.atomRadius=K(this.ac,0));for(var c=0!=(d&16),f=0;f<this.ac;f++){var e=

this.at[f];JM.AtomCollection.isDeleted(e)||!c&&0<=a.modelIndex&&e.mi!=a.firstModelIndex?(null==a.bsIgnored&&(a.bsIgnored=new JU.BS),a.bsIgnored.set(f)):(a.atomicNumber[f]=e.getElementNumber(),a.lastModelIndex=e.mi,b&&(a.atomRadius[f]=this.getWorkingRadius(e,a)))}},"J.atomdata.AtomData,~N");c(b,"getWorkingRadius",function(a,d){var b=0,c=d.radiusData;switch(c.factorType){case J.atomdata.RadiusData.EnumType.ABSOLUTE:b=c.value;break;case J.atomdata.RadiusData.EnumType.FACTOR:case J.atomdata.RadiusData.EnumType.OFFSET:switch(c.vdwType){case J.c.VDW.BONDING:b=

a.getBondingRadius();break;case J.c.VDW.ADPMAX:b=a.getADPMinMax(!0);break;case J.c.VDW.ADPMIN:b=a.getADPMinMax(!1);break;default:b=a.getVanderwaalsRadiusFloat(this.vwr,d.radiusData.vdwType)}b=c.factorType===J.atomdata.RadiusData.EnumType.FACTOR?b*c.value:b+c.value}return b+c.valueExtended},"JM.Atom,J.atomdata.AtomData");c(b,"calculateHydrogens",function(a,d,b,c){var f=256==(c&256),e=512==(c&512),h=8==(c&8),k=2048==(c&2048);c=4096==(c&4096);var m=new JU.V3,j=new JU.V3,p=Array(this.ac),q=this.vwr.slm.bsDeleted,

x,s=d[0]=0;if(null==a)return p;var n=this.vwr.getOperativeSymmetry();null!=n&&0==this.vwr.getObjectMad10(5)&&(n=null);for(var r=null==n?null:new JU.P3,u=a.nextSetBit(0);0<=u;u=a.nextSetBit(u+1))if(!(null!=q&&q.get(u))){var v=this.at[u],w=v.getElementNumber();if(!(e&&6!=w)){var y=6>=w?1.1:10>=w?1:1.3;switch(w){case 7:case 8:y=1}var B=f||k||c?v.getCovalentHydrogenCount():0;if(!(f&&0<B||k&&0==B)){var z=this.getMissingHydrogenCount(v,!1);if(!(f&&0==z)){k||(B=z);var C=this.aaRet[0];x=this.aaRet[2];var D=

this.aaRet[3]-(k?B:0);if(!(0==D&&v.isHetero())){p[u]=Array(B);z=0;if(0==D)switch(B){case 4:m.set(0.635,0.635,0.635),x=JU.P3.newP(m),x.add(v),z=JM.AtomCollection.addH(p[u],z,x,v,b,n,r);case 3:m.set(-0.635,-0.635,0.635),x=JU.P3.newP(m),x.add(v),z=JM.AtomCollection.addH(p[u],z,x,v,b,n,r);case 2:m.set(-0.635,0.635,-0.635),x=JU.P3.newP(m),x.add(v),z=JM.AtomCollection.addH(p[u],z,x,v,b,n,r);case 1:m.set(0.635,-0.635,-0.635),x=JU.P3.newP(m),x.add(v),z=JM.AtomCollection.addH(p[u],z,x,v,b,n,r)}else switch(B){case 3:this.getHybridizationAndAxes(u,

w,m,j,"sp3b",!1,!0,h,null);x=new JU.P3;x.scaleAdd2(y,m,v);z=JM.AtomCollection.addH(p[u],z,x,v,b,n,r);this.getHybridizationAndAxes(u,w,m,j,"sp3c",!1,!0,h,null);x=new JU.P3;x.scaleAdd2(y,m,v);z=JM.AtomCollection.addH(p[u],z,x,v,b,n,r);this.getHybridizationAndAxes(u,w,m,j,"sp3d",!1,!0,h,null);x=new JU.P3;x.scaleAdd2(y,m,v);z=JM.AtomCollection.addH(p[u],z,x,v,b,n,r);break;case 2:D=2==x||5==w||1==D&&4==C||7==w&&this.isAdjacentSp2(v);this.getHybridizationAndAxes(u,w,m,j,D?"sp2b":3==C?"sp3c":"lpa",!1,!0,

h,null);x=JU.P3.newP(m);x.scaleAdd2(y,m,v);z=JM.AtomCollection.addH(p[u],z,x,v,b,n,r);this.getHybridizationAndAxes(u,w,m,j,D?"sp2c":3==C?"sp3d":"lpb",!1,!0,h,null);x=JU.P3.newP(m);x.scaleAdd2(y,m,v);z=JM.AtomCollection.addH(p[u],z,x,v,b,n,r);break;case 1:switch(C-D){case 1:if(8==w&&v===v.group.getCarbonylOxygenAtom()){p[u]=null;continue}if(null!=this.getHybridizationAndAxes(u,w,m,j,2==x||5==w||6==w&&1==this.aaRet[1]||7==w&&(new Boolean((new Boolean(v.group.getNitrogenAtom()===v&0==v.getFormalCharge())).valueOf()||

this.isAdjacentSp2(v))).valueOf()?"sp2c":"sp3d",!0,!1,h,null))x=JU.P3.newP(m),x.scaleAdd2(y,m,v),z=JM.AtomCollection.addH(p[u],z,x,v,b,n,r);break;case 2:this.getHybridizationAndAxes(u,w,m,j,4==C?"sp2c":"sp2b",!1,!1,h,null);x=JU.P3.newP(m);x.scaleAdd2(y,m,v);z=JM.AtomCollection.addH(p[u],z,x,v,b,n,r);break;case 3:this.getHybridizationAndAxes(u,w,m,j,"spb",!1,!0,h,null),x=JU.P3.newP(m),x.scaleAdd2(y,m,v),z=JM.AtomCollection.addH(p[u],z,x,v,b,n,r)}}if(z<B){v=Array(z);for(w=0;w<z;w++)v[w]=p[u][w];p[u]=

v}s+=z}}}}}d[0]=s;return p},"JU.BS,~A,JU.Lst,~N");b.addH=c(b,"addH",function(a,d,b,c,f,e,h){if(null!=e&&(h.setT(b),e.toFractional(h,!1),!e.isWithinUnitCell(h,1,1,1)))return d;a[d++]=b;null!=f&&f.addLast(c);return d},"~A,~N,JU.P3,JM.Atom,JU.Lst,J.api.SymmetryInterface,JU.P3");c(b,"isAdjacentSp2",function(a){for(var d=a.bonds,b=0;b<d.length;b++)for(var c=d[b].getOtherAtom(a).bonds,f=0;f<c.length;f++)switch(c[f].getCovalentOrder()){case 2:case 3:return!0}return!1},"JM.Atom");c(b,"getMissingHydrogenCount",

function(a,d){null==this.aaRet&&(this.aaRet=E(5,0));var b=a.getTargetValence();if(0>b)return 0;var c=a.getFormalCharge(),f=a.getValence(),e=this.am[a.mi],e=e.isBioModel&&!e.isPdbWithMultipleBonds?a.group.getGroup3():null;this.aaRet[0]=b;this.aaRet[1]=c;this.aaRet[2]=0;this.aaRet[3]=a.getCovalentBondCount();this.aaRet[4]=null==e?0:f;null!=e&&0==c&&this.bioModelset.getAminoAcidValenceAndCharge(e,a.getAtomName(),this.aaRet)&&(b=this.aaRet[0],c=this.aaRet[1]);0!=c&&(b+=4==b?-Math.abs(c):c,this.aaRet[0]=

b);b-=f;return 0>b&&!d?0:b},"JM.Atom,~B");c(b,"fixFormalCharges",function(a){for(var d=0,b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1)){var c=this.at[b],f=this.getMissingHydrogenCount(c,!0);if(0!=f){var e=c.getFormalCharge(),f=e-f;c.setFormalCharge(f);this.taintAtom(b,4);JU.Logger.debugging&&JU.Logger.debug("atom "+c+" formal charge "+e+" -> "+f);d++}}return d},"JU.BS");c(b,"getHybridizationAndAxes",function(a,d,b,c,f,e,h,k,m){var j=0<f.length&&"-"==f.charAt(0)?f.substring(1):f;if(0<=f.indexOf("d")&&

!f.endsWith("sp3d"))return this.getHybridizationAndAxesD(a,b,c,j);f=this.at[a];0==d&&(d=f.getElementNumber());var p=this.getAttached(f,4,e,k),q=p.length,x=j.charAt(j.length-1).charCodeAt(0)-97;if(0>x||6<x)x=0;b.set(0,0,0);c.set(0,0,0);for(var s=Array(4),n=0;n<q;n++){var r=p[n];if(null==r){q=n;break}s[n]=JU.V3.newVsub(f,r);s[n].normalize();b.add(s[n])}0<q&&c.setT(s[0]);n=!1;a=new JU.V3;if(3<=q){2.9845130209103035>c.angle(s[1])?a.cross(c,s[1]):a.cross(c,s[2]);a.normalize();var u=new JU.V3;2.9845130209103035>

s[1].angle(s[2])?u.cross(s[1],s[2]):u.cross(c,s[2]);u.normalize();n=0.95<=Math.abs(u.dot(a))}var v=0==j.indexOf("sp3"),r=!v&&0==j.indexOf("sp2"),w=!v&&!r&&0==j.indexOf("sp"),y=0==j.indexOf("p"),z=0==j.indexOf("lp"),u=null;if(e){if(0==q)return null;if(v){if(3<x||4<q)return null}else if(r){if(2<x||3<q)return null}else if(w&&(1<x||2<q))return null;switch(q){case 1:if(1==d&&!v)return null;if(v){u="sp3";break}switch(p[0].getCovalentBondCount()){case 1:if(2!=p[0].getValence()){u="sp";break}case 2:u=w?"sp":

"sp2";break;case 3:if(!r&&!y)return null;u="sp2"}break;case 2:if(0.1>b.length()){if(0<=j.indexOf("2")||0<=j.indexOf("3"))return null;u="sp";break}u=v?"sp3":"sp2";if(0==j.indexOf("sp"))break;if(z){u="lp";break}u=j;break;default:if(n&&!k)u="sp2";else{n&&b.setT(a);if(z&&3==q){u="lp";break}u="sp3"}}if(null==u)return null;if(0==j.indexOf("p")){if("sp3"===u)return null}else if(0>j.indexOf(u))return null}if(x<q&&!j.startsWith("p")&&!j.startsWith("l"))return b.sub2(p[x],f),b.normalize(),u;switch(q){case 0:j.equals("sp3c")||

j.equals("sp2d")||j.equals("lpa")?b.set(-0.5,-0.7,1):j.equals("sp3b")||j.equals("lpb")?b.set(0.5,-0.7,-1):j.equals("sp3a")?b.set(0,1,0):b.set(0,0,1);c.set(1,0,0);break;case 1:a.setT(JM.AtomCollection.vRef);c.cross(a,b);if(v){for(n=p[0].getBondCount();0<=--n;)if(p[0].bonds[n].isCovalentNotPartial0()&&p[0].getBondedAtomIndex(n)!=f.i&&(c.sub2(p[0],p[0].bonds[n].getOtherAtom(p[0])),c.cross(b,c),0!=c.length())){c.cross(c,b);break}c.normalize();Float.isNaN(c.x)&&(c.setT(JM.AtomCollection.vRef),c.cross(c,

b));a.cross(b,c);a.normalize();b.normalize();c.scaleAdd2(2.828,c,b);3!=x&&(c.normalize(),(new JU.M3).setAA(JU.A4.new4(b.x,b.y,b.z,2.09439507*(2==x?1:-1))).rotate(c));b.setT(c);c.cross(a,b);break}a.cross(c,b);j=p[0].getCovalentBondCount();switch(j){case 3:if(m!==p[0]){this.getHybridizationAndAxes(p[0].i,0,c,a,"pz",!1,h,k,f);a.setT(c);r?(c.cross(c,b),1==x&&c.scale(-1),c.scale(JM.AtomCollection.sqrt3_2),b.scaleAdd2(0.5,b,c)):w||(a.setT(b),b.setT(c));c.cross(a,b);break}j=2;case 1:if(1==j&&2!=p[0].getValence())break;

case 2:h=p[0];c.setT(b);for(a.setT(JM.AtomCollection.vRef);null!=h&&2==h.getCovalentBondCount();){k=h.bonds;r=null;for(n=0;n<k.length;n++)if(k[n].isCovalentNotPartial0()&&(r=k[n].getOtherAtom(h),r!==f)){a.sub2(r,h);break}a.cross(a,c);if(0.1<a.length()||2!=r.getCovalentBondCount())break;f=h;h=r}w||(0.1<a.length()?(b.cross(a,c),b.normalize(),1==x&&b.scale(-1),b.scale(JM.AtomCollection.sqrt3_2),b.scaleAdd2(0.5,c,b),y&&(a.cross(b,c),b.setT(a),a.setT(c)),c.cross(a,b)):(b.setT(c),c.cross(JM.AtomCollection.vRef,

c)))}break;case 2:if(0.1>b.length()){if(!j.equals("pz")){r=p[0];(m=3==r.getCovalentBondCount())||(m=3==(r=p[1]).getCovalentBondCount());if(m){this.getHybridizationAndAxes(r.i,0,c,b,"pz",!1,h,k,null);j.equals("px")&&c.scale(-1);b.setT(s[0]);break}a.setT(JM.AtomCollection.vRef);b.cross(a,c);a.cross(b,c)}b.setT(c);c.cross(a,b);break}a.cross(b,c);if(r){c.cross(b,a);break}if(v||z){a.normalize();b.normalize();j.equals("lp")||(0==x||2==x?b.scaleAdd2(-1.2,a,b):b.scaleAdd2(1.2,a,b));c.cross(b,a);break}c.cross(b,

a);b.setT(a);0>b.z&&(b.scale(-1),c.scale(-1));break;default:if(v)break;if(!n){c.cross(b,c);break}b.setT(a);0>b.z&&h&&(b.scale(-1),c.scale(-1))}c.normalize();b.normalize();return u},"~N,~N,JU.V3,JU.V3,~S,~B,~B,~B,JU.T3");c(b,"getHybridizationAndAxesD",function(a,d,b,c){c.startsWith("sp3d2")&&(c="d2sp3"+(5==c.length?"a":c.substring(5)));c.startsWith("sp3d")&&(c="dsp3"+(4==c.length?"a":c.substring(4)));if(c.equals("d2sp3")||c.equals("dsp3"))c+="a";var f=c.startsWith("dsp3"),e=c.charAt(c.length-1).charCodeAt(0)-

97;if(null!=d&&(!f&&(5<e||!c.startsWith("d2sp3"))||f&&4<e))return null;a=this.at[a];c=this.getAttached(a,6,!0,!1);if(null==c)return null==d?null:"?";var h=c.length;if(3>h&&null!=d)return null;for(var k=e>=h,m=B(h*(h-1)/2),j=JU.AU.newInt2(m),p=E(3,0),m=E(3,m,0),q=0,x=0,s=0;s<h-1;s++)for(var n=s+1;n<h;n++){var r=JU.Measure.computeAngleABC(c[s],a,c[n],!0),r=105>r?0:150<=r?2:1;m[r][p[r]]=q;p[r]++;j[q++]=E(-1,[s,n]);0==s&&1==r&&x++}q=100*p[0]+10*p[1]+p[2];if(null==d)switch(q){default:return"";case 0:return"";

case 1:return"linear";case 100:case 10:return"bent";case 111:case 201:return"T-shaped";case 30:case 120:case 210:case 300:return 162<Math.abs(JU.Measure.computeTorsion(c[0],a,c[1],c[2],!0))?"trigonal planar":"trigonal pyramidal";case 330:return 1==x%2?"tetrahedral":"uncapped trigonal pyramid";case 60:case 150:case 240:return"tetrahedral";case 402:return"square planar";case 411:case 501:return"see-saw";case 631:return"trigonal bipyramidal";case 802:return"uncapped square pyramid";case 1203:return"octahedral"}switch(q){default:return null;

case 201:break;case 210:case 330:case 411:case 631:if(!f)return null;break;case 300:case 402:case 501:case 802:case 1203:if(f)return null}if(k)if(f)switch(p[1]){case 0:d.sub2(c[j[m[0][0]][0]],a);b.sub2(c[j[m[0][0]][1]],a);d.cross(d,b);d.normalize();4==e&&d.scale(-1);p=this.findNotAttached(h,j,m[2],p[2]);s=p.nextSetBit(0);b.sub2(c[s],a);b.normalize();b.scale(0.5);d.scaleAdd2(JM.AtomCollection.sqrt3_2,d,b);e=-1;break;case 1:4==e?(b=j[m[1][0]],d.add2(c[b[0]],c[b[1]]),d.scaleAdd2(-2,a,d),e=-1):(p=this.findNotAttached(h,

j,m[1],p[1]),e=p.nextSetBit(0));break;default:p=this.findNotAttached(h,j,m[1],p[1]),e=p.nextSetBit(0)}else{q=!1;if(4==h)switch(p[2]){case 1:p=this.findNotAttached(h,j,m[2],p[2]);s=p.nextSetBit(0);e=4==e?s:p.nextSetBit(s+1);break;default:q=!0}else{p=this.findNotAttached(h,j,m[2],p[2]);s=p.nextSetBit(0);for(n=h;n<e&&0<=s;n++)s=p.nextSetBit(s+1);-1==s?q=!0:e=s}q&&(d.sub2(c[j[m[0][0]][0]],a),b.sub2(c[j[m[0][0]][1]],a),d.cross(d,b),4==e&&d.scale(-1),e=-1)}0<=e&&d.sub2(c[e],a);k&&d.scale(-1);d.normalize();

return f?"dsp3":"d2sp3"},"~N,JU.V3,JU.V3,~S");c(b,"getAttached",function(a,d,b,c){var f=a.getCovalentBondCount();if(f>d)return null;d=Array(f);if(0<f){for(var f=a.bonds,e=0,h=0;h<f.length;h++)if(f[h].isCovalentNotPartial0()){var k=f[h].getOtherAtom(a);if(!c||1!=k.getAtomicAndIsotopeNumber())d[e++]=k}b&&!c&&java.util.Arrays.sort(d,U(JM.AtomCollection.AtomSorter,this,null))}return d},"JM.Atom,~N,~B,~B");c(b,"findNotAttached",function(a,d,b,c){var f=JU.BS.newN(a);f.setBits(0,a);for(var e=0;e<a;e++)for(var h=

0;h<c;h++){var k=d[b[h]];(k[0]==e||k[1]==e)&&f.clear(e)}return f},"~N,~A,~A,~N");c(b,"getAtomBitsMDa",function(a,d,b){var c=y(d,Integer)?d.intValue():0;switch(a){case 1086326786:case 1086326785:var f=1086326785==a,e=","+d+",";for(a=this.ac;0<=--a;)JM.AtomCollection.isDeleted(this.at[a])||(d=f?this.at[a].getAtomType():this.at[a].getAtomName(),0<=e.indexOf(","+d+",")&&b.set(a));return b;case 1094715393:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].getAtomNumber()==c&&b.set(a);

return b;case 2097155:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&0<this.at[a].getCovalentBondCount()&&b.set(a);return b;case 2097188:case 2097156:case 136314895:case 2097166:case 2097168:case 2097170:case 2097172:case 2097174:case 2097184:return this.haveBioModels?this.bioModelset.getAtomBitsBS(a,null,b):b;case 1612709900:c=1;case 1094715402:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].getElementNumber()==c&&b.set(a);return b;case 1612709894:for(a=

this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].isHetero()&&b.set(a);return b;case 1073741824:return this.getIdentifierOrNull(d);case 2097165:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].isLeadAtom()&&b.set(a);return b;case 1094713362:case 1639976963:return this.haveBioModels?this.bioModelset.getAtomBitsBS(a,d,b):b;case 1094715412:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].getResno()==c&&b.set(a);return b;case 1612709912:d=

E(2,0);for(a=this.ac;0<=--a;)if(!JM.AtomCollection.isDeleted(this.at[a]))if(c=this.at[a].group.groupID,42<=c&&45>c)b.set(a);else if(8==(f=this.at[a]).getElementNumber()&&2==f.getCovalentBondCount()){for(var c=f.bonds,h=0,k=c.length;0<=--k&&3>h;)if(c[k].isCovalentNotPartial0()&&1==(e=c[k].getOtherAtom(f)).getElementNumber())d[h++%2]=e.i;2==h&&(b.set(d[1]),b.set(d[0]),b.set(a))}return b;case 1073742355:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.isAltLoc(this.at[a].altloc,d)&&

b.set(a);return b;case 1073742356:f=d.toUpperCase();0<=f.indexOf("\\?")&&(f=JU.PT.rep(f,"\\?","\u0001"));(e=f.startsWith("?*"))&&(f=f.substring(1));for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.isAtomNameMatch(this.at[a],f,e,e)&&b.set(a);return b;case 1073742357:return JU.BSUtil.copy(this.getChainBits(c));case 1073742360:return this.getSpecName(d);case 1073742361:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].group.groupID==c&&b.set(a);return b;case 1073742362:return JU.BSUtil.copy(this.getSeqcodeBits(c,

!0));case 5:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].group.getInsCode()==c&&b.set(a);return b;case 1296041985:for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].getSymOp()==c&&b.set(a);return b}e=d.nextSetBit(0);if(0>e)return b;switch(a){case 1094717454:f=JU.BSUtil.copy(d);for(a=e;0<=a;a=f.nextSetBit(a+1))b.or(this.am[this.at[a].mi].bsAtoms),f.andNot(b);return b;case 1086326788:f=JU.BSUtil.copy(d);for(a=e;0<=a;a=f.nextSetBit(a+1))this.at[a].group.chain.setAtomBits(b),

f.andNot(b);return b;case 1086326789:f=new JU.BS;for(a=e;0<=a;a=d.nextSetBit(a+1))f.set(this.at[a].getElementNumber());for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&f.get(this.at[a].getElementNumber())&&b.set(a);return b;case 1086324742:f=JU.BSUtil.copy(d);for(a=e;0<=a;a=f.nextSetBit(a+1))this.at[a].group.setAtomBits(b),f.andNot(b);return b;case 1094713366:f=new JU.BS;for(a=e;0<=a;a=d.nextSetBit(a+1))f.set(this.at[a].atomSite);for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&

f.get(this.at[a].atomSite)&&b.set(a);return b}JU.Logger.error("MISSING getAtomBits entry for "+JS.T.nameOf(a));return b},"~N,~O,JU.BS");c(b,"getChainBits",function(a){var d=this.vwr.getBoolean(603979822);d?97<=a&&122>=a&&(a+=159):0<=a&&300>a&&(a=this.chainToUpper(a));for(var b=new JU.BS,c=JU.BS.newN(this.ac),f,e=c.nextClearBit(0);e<this.ac;e=c.nextClearBit(e+1))if(!JM.AtomCollection.isDeleted(this.at[e])){var h=this.at[e].group.chain;a==(f=h.chainID)||!d&&0<=f&&300>f&&a==this.chainToUpper(f)?(h.setAtomBits(b),

c.or(b)):h.setAtomBits(c)}return b},"~N");c(b,"chainToUpper",function(a){return 97<=a&&122>=a?a-32:256<=a&&300>a?a-191:a},"~N");c(b,"isAltLoc",function(a,d){if(null==d)return"\x00"==a;if(1!=d.length)return!1;var b=d.charAt(0);return"*"==b||"?"==b&&"\x00"!=a||a==b},"~S,~S");c(b,"getSeqcodeBits",function(a,d){var b=new JU.BS,c=JM.Group.getSeqNumberFor(a),f=2147483647!=c,e=!0,h=JM.Group.getInsertionCodeChar(a);switch(h.charCodeAt(0)){case 63:for(var k=this.ac;0<=--k;)if(!JM.AtomCollection.isDeleted(this.at[k])){var m=

this.at[k].group.seqcode;if((!f||c==JM.Group.getSeqNumberFor(m))&&0!=JM.Group.getInsertionCodeFor(m))b.set(k),e=!1}break;default:for(k=this.ac;0<=--k;)if(!JM.AtomCollection.isDeleted(this.at[k])&&(m=this.at[k].group.seqcode,a==m||!f&&a==JM.Group.getInsertionCodeFor(m)||"*"==h&&c==JM.Group.getSeqNumberFor(m)))b.set(k),e=!1}return!e||d?b:null},"~N,~B");c(b,"getIdentifierOrNull",function(a){var d=this.getSpecNameOrNull(a,!1);0<=a.indexOf("\\?")&&(a=JU.PT.rep(a,"\\?","\u0001"));return null!=d||0<a.indexOf("?")?

d:0<a.indexOf("*")?this.getSpecNameOrNull(a,!0):this.haveBioModels?this.bioModelset.getIdentifierOrNull(a):null},"~S");c(b,"getSpecName",function(a){var d=this.getSpecNameOrNull(a,!1);if(null!=d)return d;0<a.indexOf("*")&&(d=this.getSpecNameOrNull(a,!0));return null==d?new JU.BS:d},"~S");c(b,"getSpecNameOrNull",function(a,d){var b=null;a=a.toUpperCase();0<=a.indexOf("\\?")&&(a=JU.PT.rep(a,"\\?","\u0001"));var c=a.startsWith("?*");c&&(a=a.substring(1));for(var f=this.ac;0<=--f;)if(!JM.AtomCollection.isDeleted(this.at[f])){var e=

this.at[f].getGroup3(!0);if(null!=e&&0<e.length){if(JU.PT.isMatch(e,a,d,!0)){null==b&&(b=JU.BS.newN(f+1));for(b.set(f);0<=--f;)!JM.AtomCollection.isDeleted(this.at[f])&&this.at[f].getGroup3(!0).equals(e)&&b.set(f);f++}}else this.isAtomNameMatch(this.at[f],a,d,c)&&(null==b&&(b=JU.BS.newN(f+1)),b.set(f))}return b},"~S,~B");c(b,"isAtomNameMatch",function(a,d,b,c){return JU.PT.isMatch(a.getAtomName().toUpperCase(),d,b,c)},"JM.Atom,~S,~B,~B");c(b,"getAtomIndices",function(a){for(var d=0,b=E(this.ac,0),

c=a.nextSetBit(0);0<=c&&c<this.ac;c=a.nextSetBit(c+1))b[c]=++d;return b},"JU.BS");c(b,"getAtomsNearPlane",function(a,d){for(var b=new JU.BS,c=this.ac;0<=--c;){var f=this.at[c];if(!JM.AtomCollection.isDeleted(f)){var e=JU.Measure.distanceToPlane(d,f);(0<a&&-0.1<=e&&e<=a||0>a&&0.1>=e&&e>=a||0==a&&0.01>Math.abs(e))&&b.set(f.i)}}return b},"~N,JU.P4");c(b,"clearVisibleSets",function(){this.haveBSClickable=this.haveBSVisible=!1});c(b,"getAtomsInFrame",function(a){this.clearVisibleSets();a.clearAll();for(var d=

this.ac;0<=--d;)!JM.AtomCollection.isDeleted(this.at[d])&&this.at[d].isVisible(1)&&a.set(d)},"JU.BS");c(b,"getVisibleSet",function(a){if(a)this.vwr.setModelVisibility(),this.vwr.shm.finalizeAtoms(null,!0);else if(this.haveBSVisible)return this.bsVisible;this.bsVisible.clearAll();for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].checkVisible()&&this.bsVisible.set(a);null!=this.vwr.shm.bsSlabbedInternal&&this.bsVisible.andNot(this.vwr.shm.bsSlabbedInternal);this.haveBSVisible=

!0;return this.bsVisible},"~B");c(b,"getClickableSet",function(a){if(a)this.vwr.setModelVisibility();else if(this.haveBSClickable)return this.bsClickable;this.bsClickable.clearAll();for(a=this.ac;0<=--a;)!JM.AtomCollection.isDeleted(this.at[a])&&this.at[a].isClickable()&&this.bsClickable.set(a);this.haveBSClickable=!0;return this.bsClickable},"~B");c(b,"isModulated",function(a){return null!=this.bsModulated&&this.bsModulated.get(a)},"~N");c(b,"deleteModelAtoms",function(a,d,b){this.at=JU.AU.deleteElements(this.at,

a,d);this.ac=this.at.length;for(var c=a;c<this.ac;c++)this.at[c].i=c,this.at[c].mi--;null!=this.bsModulated&&JU.BSUtil.deleteBits(this.bsModulated,b);this.deleteAtomTensors(b);this.atomNames=JU.AU.deleteElements(this.atomNames,a,d);this.atomTypes=JU.AU.deleteElements(this.atomTypes,a,d);this.atomResnos=JU.AU.deleteElements(this.atomResnos,a,d);this.atomSerials=JU.AU.deleteElements(this.atomSerials,a,d);this.atomSeqIDs=JU.AU.deleteElements(this.atomSeqIDs,a,d);this.dssrData=JU.AU.deleteElements(this.dssrData,

a,d);this.bfactor100s=JU.AU.deleteElements(this.bfactor100s,a,d);this.hasBfactorRange=!1;this.occupancies=JU.AU.deleteElements(this.occupancies,a,d);this.resetPartialCharges();this.atomTensorList=JU.AU.deleteElements(this.atomTensorList,a,d);this.vibrations=JU.AU.deleteElements(this.vibrations,a,d);this.nSurfaceAtoms=0;this.surfaceDistance100s=this.bsSurface=null;if(null!=this.tainted)for(a=0;18>a;a++)JU.BSUtil.deleteBits(this.tainted[a],b)},"~N,~N,JU.BS");c(b,"getAtomIdentityInfo",function(a,d,b){d.put("_ipt",

Integer.$valueOf(a));d.put("atomIndex",Integer.$valueOf(a));d.put("atomno",Integer.$valueOf(this.at[a].getAtomNumber()));d.put("info",this.getAtomInfo(a,null,b));d.put("sym",this.at[a].getElementSymbol())},"~N,java.util.Map,JU.P3");c(b,"getAtomTensorList",function(a){return 0>a||null==this.atomTensorList||a>=this.atomTensorList.length?null:this.atomTensorList[a]},"~N");c(b,"deleteAtomTensors",function(a){if(null!=this.atomTensors){for(var d=new JU.Lst,b,c=this.atomTensors.keySet().iterator();c.hasNext()&&

((b=c.next())||1);){for(var f=this.atomTensors.get(b),e=f.size();0<=--e;){var h=f.get(e);(a.get(h.atomIndex1)||0<=h.atomIndex2&&a.get(h.atomIndex2))&&f.removeItemAt(e)}0==f.size()&&d.addLast(b)}for(e=d.size();0<=--e;)this.atomTensors.remove(d.get(e))}},"JU.BS");c(b,"setCapacity",function(a){this.atomCapacity+=a},"~N");c(b,"setAtomTensors",function(a,d){if(!(null==d||0==d.size())){null==this.atomTensors&&(this.atomTensors=new java.util.Hashtable);null==this.atomTensorList&&(this.atomTensorList=Array(this.at.length));

this.atomTensorList=JU.AU.ensureLength(this.atomTensorList,this.at.length);this.atomTensorList[a]=JM.AtomCollection.getTensorList(d);for(var b=d.size();0<=--b;){var c=d.get(b);c.atomIndex1=a;c.atomIndex2=-1;c.modelIndex=this.at[a].mi;this.addTensor(c,c.type);null!=c.altType&&this.addTensor(c,c.altType)}}},"~N,JU.Lst");c(b,"addTensor",function(a,d){d=d.toLowerCase();var b=this.atomTensors.get(d);null==b&&(this.atomTensors.put(d,b=new JU.Lst),b.ensureCapacity(this.atomCapacity));b.addLast(a)},"JU.Tensor,~S");

b.getTensorList=c(b,"getTensorList",function(a){for(var d=-1,b=!1,c=a.size(),f=c;0<=--f;){var e=a.get(f);e.forThermalEllipsoid?d=f:2==e.iType&&(b=!0)}var h=Array((0<=d||!b?0:1)+c);if(0<=d&&(h[0]=a.get(d),1==a.size()))return h;if(b){d=0;for(f=c;0<=--f;)e=a.get(f),e.forThermalEllipsoid||(h[++d]=e)}else for(f=0;f<c;f++)h[f]=a.get(f);return h},"JU.Lst");c(b,"getAtomTensor",function(a,d){var b=this.getAtomTensorList(a);if(null!=b&&null!=d){d=d.toLowerCase();for(var c=0;c<b.length;c++){var f=b[c];if(null!=

f&&(d.equals(f.type)||d.equals(f.altType)))return f}}return null},"~N,~S");c(b,"getAllAtomTensors",function(a){if(null==this.atomTensors)return null;if(null!=a)return this.atomTensors.get(a.toLowerCase());a=new JU.Lst;for(var d,b=this.atomTensors.entrySet().iterator();b.hasNext()&&((d=b.next())||1);)a.addAll(d.getValue());return a},"~S");c(b,"scaleVectorsToMax",function(a){if(null!=this.vibrations){for(var d=0,b=JU.BS.newN(this.ac),c=this.vibrations.length;0<=--c;){var f=this.getVibration(c,!1);if(null!=

f&&(-1==f.modDim||-2==f.modDim))d=Math.max(d,f.length()),b.set(c)}if(!(d==a||0==d)){d=a/d;a=!1;for(c=b.nextSetBit(0);0<=c;c=b.nextSetBit(c+1)){var f=this.getVibration(c,!1),e=this.getModulation(c);if(null==e){if(0==d)return;f.scale(d)}else e.scaleVibration(d);a||(this.taintAtom(c,12),a=!0)}this.tainted[12].or(b)}}},"~N");c(b,"getAtomsFromAtomNumberInFrame",function(a){for(var d=this.vwr.getFrameAtoms(),b=d.nextSetBit(0);0<=b;b=d.nextSetBit(b+1))this.at[b].getAtomNumber()!=a&&d.clear(b);return d},

"~N");c(b,"generateCrystalClass",function(a,d){var b=0>a||a>=this.ac?this.vwr.getOperativeSymmetry():this.at[a].getUnitCell(),c=null!=d&&Float.isNaN(d.x),b=null==b?null:b.generateCrystalClass(c?null:null!=d?d:this.at[a]);return null==b?new JU.Lst:b},"~N,JU.P3");b.isDeleted=c(b,"isDeleted",function(a){return null==a||a.isDeleted()},"JM.Atom");b.$AtomCollection$AtomSorter$=function(){var a=v(function(){Y(this,arguments);r(this,arguments)},JM.AtomCollection,"AtomSorter",null,java.util.Comparator);j(a,

"compare",function(a,b){return a.i>b.i?1:a.i<b.i?-1:0},"JM.Atom,JM.Atom")};b.sqrt3_2=Math.sqrt(3)/2;b.vRef=JU.V3.new3(3.14159,2.71828,1.41421);b.userSettableValues=null});u("JM");C(["J.api.AtomIndexIterator"],"JM.AtomIteratorWithinModel",["J.atomdata.RadiusData"],function(){var b=v(function(){this.bspf=this.cubeIterator=null;this.isZeroBased=this.hemisphereOnly=this.threadSafe=!1;this.modelIndex=2147483647;this.atomIndex=-1;this.distanceSquared=this.zeroBase=0;this.bsSelected=null;this.checkGreater=

this.isGreaterOnly=!1;this.radiusData=null;this.vdw1=0;this.isVdw=!1;this.vwr=this.atoms=null;this.iNext=0;r(this,arguments)},JM,"AtomIteratorWithinModel",null,J.api.AtomIndexIterator);c(b,"initialize",function(a,d,b,c,f,e){this.bspf=a;this.bsSelected=d;this.isGreaterOnly=b;this.isZeroBased=c;this.hemisphereOnly=f;this.threadSafe=e;this.cubeIterator=null},"J.bspt.Bspf,JU.BS,~B,~B,~B,~B");j(b,"setModel",function(a,d,b,c,f,e,h){this.threadSafe&&(d=-1-d);if(d!=this.modelIndex||null==this.cubeIterator)this.cubeIterator=

this.bspf.getCubeIterator(d),this.modelIndex=d;this.zeroBase=this.isZeroBased?b:0;if(-2147483648!=e){this.atomIndex=0>e?-1:c;if(this.isVdw=null!=h)this.radiusData=h,this.atoms=a.at,this.vwr=a.vwr,e=h.factorType===J.atomdata.RadiusData.EnumType.OFFSET?5+h.value:5*h.value,this.vdw1=this.atoms[c].getVanderwaalsRadiusFloat(this.vwr,h.vdwType);this.checkGreater=this.isGreaterOnly&&2147483647!=c;this.setCenter(f,e)}},"JM.ModelSet,~N,~N,~N,JU.T3,~N,J.atomdata.RadiusData");j(b,"setCenter",function(a,d){this.setCenter2(a,

d)},"JU.T3,~N");c(b,"setCenter2",function(a,d){null!=this.cubeIterator&&(this.cubeIterator.initialize(a,d,this.hemisphereOnly),this.distanceSquared=d*d)},"JU.T3,~N");j(b,"hasNext",function(){return this.hasNext2()});c(b,"hasNext2",function(){if(0<=this.atomIndex)for(;this.cubeIterator.hasMoreElements();){var a=this.cubeIterator.nextElement();if((this.iNext=a.i)!=this.atomIndex&&(!this.checkGreater||this.iNext>this.atomIndex)&&(null==this.bsSelected||this.bsSelected.get(this.iNext)))return!0}else if(this.cubeIterator.hasMoreElements())return a=

this.cubeIterator.nextElement(),this.iNext=a.i,!0;this.iNext=-1;return!1});j(b,"next",function(){return this.iNext-this.zeroBase});j(b,"foundDistance2",function(){return null==this.cubeIterator?-1:this.cubeIterator.foundDistance2()});j(b,"addAtoms",function(a){for(var d;this.hasNext();)if(0<=(d=this.next())){var b;if(this.isVdw){b=this.atoms[d].getVanderwaalsRadiusFloat(this.vwr,this.radiusData.vdwType)+this.vdw1;switch(this.radiusData.factorType){case J.atomdata.RadiusData.EnumType.OFFSET:b+=2*this.radiusData.value;

break;case J.atomdata.RadiusData.EnumType.FACTOR:b*=this.radiusData.value}b*=b}else b=this.distanceSquared;this.foundDistance2()<=b&&a.set(d)}},"JU.BS");j(b,"release",function(){null!=this.cubeIterator&&(this.cubeIterator.release(),this.cubeIterator=null)});j(b,"getPosition",function(){return null})});u("JM");C(["JM.AtomIteratorWithinModel"],"JM.AtomIteratorWithinModelSet",null,function(){var b=v(function(){this.center=this.bsModels=null;this.distance=0;r(this,arguments)},JM,"AtomIteratorWithinModelSet",

JM.AtomIteratorWithinModel);z(b,function(a){L(this,JM.AtomIteratorWithinModelSet,[]);this.bsModels=a},"JU.BS");j(b,"setCenter",function(a,d){this.center=a;this.distance=d;this.set(0)},"JU.T3,~N");c(b,"set",function(a){if(0>(this.modelIndex=this.bsModels.nextSetBit(a))||null==(this.cubeIterator=this.bspf.getCubeIterator(this.modelIndex)))return!1;this.setCenter2(this.center,this.distance);return!0},"~N");j(b,"hasNext",function(){return this.hasNext2()?!0:!this.set(this.modelIndex+1)?!1:this.hasNext()})});

u("JM");C(["JU.Edge","JV.JC"],"JM.Bond",["JU.C"],function(){var b=v(function(){this.atom2=this.atom1=null;this.shapeVisibilityFlags=this.colix=this.mad=0;r(this,arguments)},JM,"Bond",JU.Edge);z(b,function(a,d,b,c,f){L(this,JM.Bond,[]);this.atom1=a;this.atom2=d;this.colix=f;this.setOrder(b);this.setMad(c)},"JM.Atom,JM.Atom,~N,~N,~N");c(b,"setMad",function(a){this.mad=a;this.setShapeVisibility(0!=a)},"~N");c(b,"setShapeVisibility",function(a){0!=(this.shapeVisibilityFlags&JM.Bond.myVisibilityFlag)!=

a&&(this.atom1.addDisplayedBond(JM.Bond.myVisibilityFlag,a),this.atom2.addDisplayedBond(JM.Bond.myVisibilityFlag,a),this.shapeVisibilityFlags=a?this.shapeVisibilityFlags|JM.Bond.myVisibilityFlag:this.shapeVisibilityFlags&~JM.Bond.myVisibilityFlag)},"~B");c(b,"getIdentity",function(){return this.index+1+" "+JU.Edge.getBondOrderNumberFromOrder(this.order)+" "+this.atom1.getInfo()+" -- "+this.atom2.getInfo()+" "+this.atom1.distance(this.atom2)});j(b,"isCovalent",function(){return 0!=(this.order&1023)});

j(b,"isHydrogen",function(){return JU.Edge.isOrderH(this.order)});c(b,"isStereo",function(){return 0!=(this.order&1024)});j(b,"isPartial",function(){return 0!=(this.order&224)});c(b,"isAromatic",function(){return 0!=(this.order&512)});c(b,"getEnergy",function(){return 0});c(b,"getValence",function(){return!this.isCovalent()||33==this.order?0:this.is(515)?1:this.order&7});c(b,"deleteAtomReferences",function(){null!=this.atom1&&this.atom1.deleteBond(this);null!=this.atom2&&this.atom2.deleteBond(this);

this.atom1=this.atom2=null});c(b,"setTranslucent",function(a,d){this.colix=JU.C.getColixTranslucent3(this.colix,a,d)},"~B,~N");c(b,"setOrder",function(a){16==this.atom1.getElementNumber()&&16==this.atom2.getElementNumber()&&(a|=256);512==a&&(a=515);this.order=a|this.order&131072},"~N");j(b,"getAtomIndex1",function(){return this.atom1.i});j(b,"getAtomIndex2",function(){return this.atom2.i});j(b,"getCovalentOrder",function(){return JU.Edge.getCovalentBondOrder(this.order)});c(b,"getOtherAtom",function(a){return this.atom1===

a?this.atom2:this.atom2===a?this.atom1:null},"JM.Atom");c(b,"is",function(a){return(this.order&131071)==a},"~N");j(b,"getOtherNode",function(a){return this.atom1===a?this.atom2:this.atom2===a||null==a?this.atom1:null},"JU.SimpleNode");c(b,"setAtropisomerOptions",function(){var a,d=2147483647,b=this.atom1.bonds;for(a=0;a<b.length;a++){var c=b[a].getOtherAtom(this.atom1);if(c!==this.atom2)break}if(a<b.length){b=this.atom2.bonds;for(d=0;d<b.length&&!(c=b[d].getOtherAtom(this.atom2),c!==this.atom1);d++);

}this.order=2<a||d>=b.length||2<d?1:JU.Edge.getAtropismOrder(a+1,d+1)});j(b,"getCIPChirality",function(){return""},"~B");j(b,"setCIPChirality",function(){},"~N");j(b,"toString",function(){return this.atom1+" - "+this.atom2});j(b,"getAtom",function(a){return 1==a?this.atom2:this.atom1},"~N");c(b,"isCovalentNotPartial0",function(){return 0!=(this.order&1023)&&33!=this.order});b.myVisibilityFlag=JV.JC.getShapeVisibilityFlag(1)});u("JM");C(["JM.AtomCollection","JU.V3"],"JM.BondCollection","JU.AU $.BS $.Measure JM.Bond $.BondIteratorSelected $.BondSet $.HBond JU.C $.Edge".split(" "),

function(){var b=v(function(){this.bo=null;this.bondCount=0;this.molecules=this.freeBonds=this.numCached=null;this.defaultCovalentMad=this.moleculeCount=0;this.bsAromatic=this.bsAromaticDouble=this.bsAromaticSingle=null;this.haveHiddenBonds=!1;this.v2=this.v1=null;this.haveAtropicBonds=!1;r(this,arguments)},JM,"BondCollection",JM.AtomCollection);Q(b,function(){this.v1=new JU.V3;this.v2=new JU.V3});c(b,"setupBC",function(){this.bsAromatic=new JU.BS;this.numCached=E(5,0);this.freeBonds=Array(5);for(var a=

5;0<--a;)this.freeBonds[a]=Array(200);this.setupAC()});c(b,"releaseModelSetBC",function(){this.freeBonds=this.bo=null;this.releaseModelSetAC()});c(b,"getBondIteratorForType",function(a,d){return new JM.BondIteratorSelected(this.bo,this.bondCount,a,d,this.vwr.getBoolean(603979812))},"~N,JU.BS");c(b,"getBondIterator",function(a){return new JM.BondIteratorSelected(this.bo,this.bondCount,131071,a,!1)},"JU.BS");c(b,"getBondColix1",function(a){return JU.C.getColixInherited(this.bo[a].colix,this.bo[a].atom1.colixAtom)},

"~N");c(b,"getBondColix2",function(a){return JU.C.getColixInherited(this.bo[a].colix,this.bo[a].atom2.colixAtom)},"~N");c(b,"getBondCountInModel",function(a){for(var d=0,b=this.bondCount;0<=--b;)null!=this.bo[b]&&this.bo[b].atom1.mi==a&&d++;return d},"~N");c(b,"getBondsForSelectedAtoms",function(a,d){var b=new JU.BS,c=a.cardinality();switch(c){case 0:return b;case 1:case 2:var f=this.at[a.nextSetBit(0)],e=2==c?this.at[a.nextSetBit(f.i+1)]:null;if(1==c||d){for(c=f.getBondCount();0<=--c;)b.set(f.bonds[c].index);

if(null!=e)for(c=e.getBondCount();0<=--c;)b.set(e.bonds[c].index)}else c=f.getBond(e),null!=c&&b.set(c.index);return b}for(f=0;f<this.bondCount;++f)c=this.bo[f],null!=c&&(e=a.get(c.atom1.i),c=a.get(c.atom2.i),(d?e||c:e&&c)&&b.set(f));return b},"JU.BS,~B");c(b,"bondAtoms",function(a,d,b,c,f,e,h,k){b=this.getOrAddBond(a,d,b,c,f,e,!0);k&&(b.order|=131072,h&&(a.group=d.group,a.group.addAtoms(a.i)));return b},"JM.Atom,JM.Atom,~N,~N,JU.BS,~N,~B,~B");c(b,"getOrAddBond",function(a,d,b,c,f,e,h){if(131071==

b||65535==b)b=1;a.isBonded(d)?(a=a.getBond(d).index,h&&(this.bo[a].setOrder(b),this.bo[a].setMad(c),y(this.bo[a],"JM.HBond")&&(this.bo[a].energy=e))):(this.bondCount==this.bo.length&&(this.bo=JU.AU.arrayCopyObject(this.bo,this.bondCount+250)),a=this.setBond(this.bondCount++,this.bondMutually(a,d,b,c,e)).index);null!=f&&f.set(a);return this.bo[a]},"JM.Atom,JM.Atom,~N,~N,JU.BS,~N,~B");c(b,"setBond",function(a,d){return this.bo[d.index=a]=d},"~N,JM.Bond");c(b,"bondMutually",function(a,d,b,c,f){b=JU.Edge.isOrderH(b)?

new JM.HBond(a,d,b,c,0,f):new JM.Bond(a,d,b,c,0);this.addBondToAtom(a,b);this.addBondToAtom(d,b);return b},"JM.Atom,JM.Atom,~N,~N,~N");c(b,"addBondToAtom",function(a,d){null==a.bonds?(a.bonds=Array(1),a.bonds[0]=d):a.bonds=this.addToBonds(d,a.bonds)},"JM.Atom,JM.Bond");c(b,"addToBonds",function(a,d){var b;if(null==d)b=0<this.numCached[1]?this.freeBonds[1][--this.numCached[1]]:Array(1),b[0]=a;else{var c=d.length;b=c+1;b=5>b&&0<this.numCached[b]?this.freeBonds[b][--this.numCached[b]]:Array(b);b[c]=

a;for(var f=c;0<=--f;)b[f]=d[f];5>c&&200>this.numCached[c]&&(this.freeBonds[c][this.numCached[c]++]=d)}return b},"JM.Bond,~A");c(b,"addHBond",function(a,d,b,c){this.bondCount==this.bo.length&&(this.bo=JU.AU.arrayCopyObject(this.bo,this.bondCount+250));return this.setBond(this.bondCount++,this.bondMutually(a,d,b,1,c)).index},"JM.Atom,JM.Atom,~N,~N");c(b,"deleteAllBonds2",function(){this.vwr.setShapeProperty(1,"reset",null);for(var a=this.bondCount;0<=--a;)null!=this.bo[a]&&(this.bo[a].deleteAtomReferences(),

this.bo[a]=null);this.bondCount=0});c(b,"getDefaultMadFromOrder",function(a){return JU.Edge.isOrderH(a)?1:32768==a?B(Math.floor(2E3*this.vwr.getFloat(570425406))):this.defaultCovalentMad},"~N");c(b,"deleteConnections",function(a,d,b,c,f,e,h){var k=0>a,m=0>d,j=k||m;a=this.fixD(a,k);d=this.fixD(d,m);var p=new JU.BS,q=0,x=b|=131072;!h&&JU.Edge.isOrderH(b)&&(b=30720);if(e)e=c;else{e=new JU.BS;for(var s=c.nextSetBit(0);0<=s;s=c.nextSetBit(s+1)){var n=this.at[s];if(null!=n.bonds)for(var r=n.bonds.length;0<=

--r;)f.get(n.getBondedAtomIndex(r))&&e.set(n.bonds[r].index)}}for(s=e.nextSetBit(0);s<this.bondCount&&0<=s;s=e.nextSetBit(s+1))if(c=this.bo[s],null!=c&&this.isInRange(c.atom1,c.atom2,a,d,k,m,j)&&(h||x==(c.order&-257|131072)||0!=(b&c.order&30720)))p.set(s),q++;0<q&&this.deleteBonds(p,!1);return E(-1,[0,q])},"~N,~N,~N,JU.BS,JU.BS,~B,~B");c(b,"fixD",function(a,d){return d?-a:a*a},"~N,~B");c(b,"isInRange",function(a,d,b,c,f,e,h){var k=a.distanceSquared(d);return h?(h=Math.sqrt(k),a=a.getBondingRadius()+

d.getBondingRadius(),(f?h>=a*b:k>=b)&&(e?h<=a*c:k<=c)):k>=b&&k<=c},"JM.Atom,JM.Atom,~N,~N,~B,~B,~B");c(b,"dBb",function(a,d){if(0!=a.cardinality()){this.resetMolecules();for(var b=-1,c=a.nextSetBit(0);0<=c&&c<this.bondCount;c=a.nextSetBit(c+1)){var f=this.bo[c];if(null!=f&&a.get(c)){if(!d){var e=f.atom1.mi;e!=b&&this.am[b=e].resetBoundCount()}f.deleteAtomReferences();this.bo[c]=null}}b=this.vwr.getShapeProperty(1,"sets");if(null!=b)for(c=0;c<b.length;c++)null!=b[c]&&b[c].andNot(a);this.bsAromatic.andNot(a)}},

"JU.BS,~B");c(b,"resetAromatic",function(){for(var a=this.bondCount;0<=--a;){var d=this.bo[a];null!=d&&d.isAromatic()&&d.setOrder(515)}});c(b,"assignAromaticBondsBs",function(a,d){a||(this.bsAromatic=new JU.BS);this.bsAromaticSingle=new JU.BS;this.bsAromaticDouble=new JU.BS;for(var b=null==d,c=b?this.bondCount-1:d.nextSetBit(0),f=c;0<=f;f=b?f-1:d.nextSetBit(f+1)){var e=this.bo[f];if(null!=e)switch(this.bsAromatic.get(f)&&e.setOrder(515),e.order&131071){case 515:if(!this.assignAromaticMustBeSingle(e.atom1)&&

!this.assignAromaticMustBeSingle(e.atom2)){this.bsAromatic.set(f);break}e.order=513;case 513:this.bsAromaticSingle.set(f);break;case 514:this.bsAromaticDouble.set(f)}}for(var c=(b=null==d)?this.bondCount-1:d.nextSetBit(0),h=new JU.BS,f=c;0<=f;f=b?f-1:d.nextSetBit(f+1))if(e=this.bo[f],e.is(515)&&(!this.bsAromaticDouble.get(f)&&!this.bsAromaticSingle.get(f))&&(h.set(f),8==e.atom1.getElementNumber()||8==e.atom2.getElementNumber()))this.assignAromaticDouble(e)||this.assignAromaticSingle(e);for(f=h.nextSetBit(0);0<=

f;f=h.nextSetBit(f+1))this.assignAromaticDouble(e=this.bo[f])||this.assignAromaticSingle(e);h=new JU.BS;for(f=c;0<=f;f=b?f-1:d.nextSetBit(f+1))if(e=this.bo[f],this.bsAromaticDouble.get(f))e.is(514)||(this.bsAromatic.set(f),h.set(e.atom1.mi),e.setOrder(this.isLinear(e,this.v1,this.v2)?3:514));else if((this.bsAromaticSingle.get(f)||e.isAromatic())&&!e.is(513))this.bsAromatic.set(f),e.setOrder(513);b=this.am;for(f=h.nextSetBit(0);0<=f;f=h.nextSetBit(f+1))b[f].isBioModel&&(b[f].isPdbWithMultipleBonds=

!0);this.assignAromaticNandO(d);this.bsAromaticDouble=this.bsAromaticSingle=null},"~B,JU.BS");c(b,"isLinear",function(a,d,b){if(3==a.order)return!0;if(2!=a.atom1.getCovalentBondCount()||2!=a.atom2.getCovalentBondCount())return!1;for(var c=a.atom1.getEdges(),f=c.length;0<=-f;)if(c[f]!==a&&c[f].isCovalent()){if(175>JU.Measure.computeAngle(c[f].getOtherNode(a.atom1),a.atom1,a.atom2,d,b,!0))return!1;break}c=a.atom2.getEdges();for(f=c.length;0<=-f;)if(c[f]!==a&&c[f].isCovalent()){if(175>JU.Measure.computeAngle(c[f].getOtherNode(a.atom2),

a.atom2,a.atom1,d,b,!0))return!1;break}return!0},"JM.Bond,JU.V3,JU.V3");c(b,"assignAromaticDouble",function(a){var d=a.index;if(this.bsAromaticSingle.get(d))return!1;if(this.bsAromaticDouble.get(d))return!0;this.bsAromaticDouble.set(d);return!this.assignAromaticSingleForAtom(a.atom1,d)||!this.assignAromaticSingleForAtom(a.atom2,d)?(this.bsAromaticDouble.clear(d),!1):!0},"JM.Bond");c(b,"assignAromaticSingle",function(a){var d=a.index;if(this.bsAromaticDouble.get(d))return!1;if(this.bsAromaticSingle.get(d))return!0;

this.bsAromaticSingle.set(d);return!this.assignAromaticDoubleForAtom(a.atom1)||!this.assignAromaticDoubleForAtom(a.atom2)?(this.bsAromaticSingle.clear(d),!1):!0},"JM.Bond");c(b,"assignAromaticSingleForAtom",function(a,d){var b=a.bonds;if(null==b)return!1;for(var c=b.length;0<=--c;){var f=b[c],e=f.index;if(!(e==d||!f.isAromatic()||this.bsAromaticSingle.get(e)))if(this.bsAromaticDouble.get(e)||!this.assignAromaticSingle(f))return!1}return!0},"JM.Atom,~N");c(b,"assignAromaticDoubleForAtom",function(a){a=

a.bonds;if(null==a)return!1;for(var d=!1,b=-1,c=a.length;0<=--c;)this.bsAromaticDouble.get(a[c].index)&&(d=!0),a[c].isAromatic()&&(b=c);for(c=a.length;0<=--c;){var f=a[c],e=f.index;if(f.isAromatic()&&!this.bsAromaticDouble.get(e)&&!this.bsAromaticSingle.get(e))if(!d&&this.assignAromaticDouble(f))d=!0;else if((d||c<b)&&!this.assignAromaticSingle(f))return!1}return d},"JM.Atom");c(b,"allowAromaticBond",function(a){if(this.assignAromaticMustBeSingle(a.atom1)||this.assignAromaticMustBeSingle(a.atom2))return!1;

switch(a.getCovalentOrder()){case 1:case 2:return 3>=a.atom1.getCovalentBondCount()&&3>=a.atom2.getCovalentBondCount();default:return!1}},"JM.Bond");c(b,"assignAromaticMustBeSingle",function(a){var d=a.getElementNumber();switch(d){case 6:case 7:case 8:case 16:break;default:return!0}var b=a.getValenceAromatic(!1);switch(d){case 6:return 4==b;case 7:return a.group.getNitrogenAtom()===a||3==b&&1>a.getFormalCharge();case 8:return a.group.getCarbonylOxygenAtom()!==a&&2==b&&1>a.getFormalCharge();case 16:return 5==

a.group.groupID||2==b&&1>a.getFormalCharge()}return!1},"JM.Atom");c(b,"assignAromaticNandO",function(a){for(var d,b=null==a,c=b?this.bondCount-1:a.nextSetBit(0);0<=c;c=b?c-1:a.nextSetBit(c+1))if(d=this.bo[c],null!=d&&d.is(513)){var f,e=d.atom2,h,k=e.getElementNumber();7==k||8==k?(h=k,f=e,e=d.atom1,k=e.getElementNumber()):(f=d.atom1,h=f.getElementNumber());if(!(7!=h&&8!=h)){var m=f.getValence();if(!(0>m)){var j=f.getCovalentBondCount();f=f.getFormalCharge();switch(h){case 7:3==m&&(3==j&&1>f&&6==k&&

3==e.getValence())&&d.setOrder(514);break;case 8:1==m&&(0==f&&(14==k||16==k))&&d.setOrder(514)}}}}},"JU.BS");c(b,"getAtomBitsMDb",function(a,d){var b=new JU.BS;switch(a){default:return this.getAtomBitsMDa(a,d,b);case 1677721602:for(var c=d.nextSetBit(0);0<=c;c=d.nextSetBit(c+1))c<this.bondCount&&null!=this.bo[c]?(b.set(this.bo[c].atom1.i),b.set(this.bo[c].atom2.i)):d.clear(c);return b;case 1073742331:for(c=this.bondCount;0<=--c;)null!=this.bo[c]&&this.bo[c].isAromatic()&&(b.set(this.bo[c].atom1.i),

b.set(this.bo[c].atom2.i));return b}},"~N,~O");c(b,"removeUnnecessaryBonds",function(a,d){var b=new JU.BS,c=new JU.BS,f=a.bonds;if(null!=f){for(var e=0;e<f.length;e++)f[e].isCovalent()?1==f[e].getOtherAtom(a).getElementNumber()&&b.set(f[e].getOtherAtom(a).i):c.set(f[e].index);0<=c.nextSetBit(0)&&this.deleteBonds(c,!1);d&&b.set(a.i);0<=b.nextSetBit(0)&&this.vwr.deleteAtoms(b,!1)}},"JM.Atom,~B");c(b,"displayBonds",function(a,d){d||(this.haveHiddenBonds=!0);for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+

1))b<this.bondCount&&(null!=this.bo[b]&&0!=this.bo[b].mad)&&this.bo[b].setShapeVisibility(d)},"JM.BondSet,~B");c(b,"getAtomsConnected",function(a,d,b,c){for(var f=y(c,"JM.BondSet"),e=f?new JM.BondSet:new JU.BS,h=E(this.ac,0),k,m=30720==b,j=65535==b,p=0;p<this.bondCount;p++){var q=this.bo[p];if(null!=q&&(j||q.is(b)||m&&q.isHydrogen()))f?e.set(p):(c.get(q.atom1.i)&&(h[k=q.atom2.i]++,e.set(k)),c.get(q.atom2.i)&&(h[k=q.atom1.i]++,e.set(k)))}if(f)return e;b=0==a;for(k=this.ac;0<=--k;)c=h[k],null==this.at[k]||

c<a||c>d?e.clear(k):b&&0==c&&e.set(k);return e},"~N,~N,~N,JU.BS");c(b,"addConnectedHAtoms",function(a,d){if(null!=a.bonds)for(var b=a.bonds.length;0<=--b;){var c=a.bonds[b].getOtherAtom(a);1==c.getElementNumber()&&d.set(c.i)}},"JM.Atom,JU.BS")});u("JM");O(JM,"BondIterator");u("JM");C(["JM.BondIterator"],"JM.BondIteratorSelected",null,function(){var b=v(function(){this.bonds=null;this.iBond=this.bondType=this.bondCount=0;this.bsSelected=null;this.bondSelectionModeOr=!1;r(this,arguments)},JM,"BondIteratorSelected",

null,JM.BondIterator);z(b,function(a,d,b,c,f){this.bonds=a;this.bondCount=d;this.bondType=b;this.bsSelected=c;this.bondSelectionModeOr=f},"~A,~N,~N,JU.BS,~B");j(b,"hasNext",function(){if(131071==this.bondType)return this.iBond=this.bsSelected.nextSetBit(this.iBond),0<=this.iBond&&this.iBond<this.bondCount;for(;this.iBond<this.bondCount;++this.iBond){var a=this.bonds[this.iBond];if(!(null==a||65535!=this.bondType&&0==(a.order&this.bondType))&&!(65535==this.bondType&&32768==a.order)){var d=this.bsSelected.get(a.atom1.i),

a=this.bsSelected.get(a.atom2.i);if(!this.bondSelectionModeOr&&d&&a||this.bondSelectionModeOr&&(d||a))return!0}}return!1});j(b,"nextIndex",function(){return this.iBond});j(b,"next",function(){return this.bonds[this.iBond++]})});u("JM");C(["JU.BS"],"JM.BondSet",["JU.BSUtil"],function(){var b=v(function(){this.associatedAtoms=null;r(this,arguments)},JM,"BondSet",JU.BS);z(b,function(){L(this,JM.BondSet,[])});b.newBS=c(b,"newBS",function(a){var d=new JM.BondSet;JU.BSUtil.copy2(a,d);return d},"JU.BS");

c(b,"getAssociatedAtoms",function(a){null==this.associatedAtoms&&(this.associatedAtoms=a.getAtomIndices(a.getAtoms(1677721602,this)));return this.associatedAtoms},"JM.ModelSet")});u("JM");C(["JM.Structure"],"JM.Chain",null,function(){var b=v(function(){this.model=null;this.chainNo=this.chainID=0;this.groups=null;this.selectedGroupCount=this.groupCount=0;r(this,arguments)},JM,"Chain",null,JM.Structure);z(b,function(a,d,b){this.model=a;this.chainID=d;this.chainNo=b;this.groups=Array(16)},"JM.Model,~N,~N");

c(b,"getIDStr",function(){return 0==this.chainID?"":256>this.chainID?""+String.fromCharCode(this.chainID):this.model.ms.vwr.getChainIDStr(this.chainID)});c(b,"calcSelectedGroupsCount",function(a){for(var d=this.selectedGroupCount=0;d<this.groupCount;d++)this.groups[d].selectedIndex=this.groups[d].isSelected(a)?this.selectedGroupCount++:-1},"JU.BS");c(b,"fixIndices",function(a,d){for(var b=0;b<this.groupCount;b++)this.groups[b].fixIndices(a,d)},"~N,JU.BS");j(b,"setAtomBits",function(a){for(var d=0;d<

this.groupCount;d++)this.groups[d].setAtomBits(a)},"JU.BS");j(b,"setAtomBitsAndClear",function(a,d){for(var b=0;b<this.groupCount;b++)this.groups[b].setAtomBitsAndClear(a,d)},"JU.BS,JU.BS")});u("JM");C(["JM.Structure","java.lang.Short","JV.JC"],"JM.Group","java.util.Hashtable JU.BS $.Quat J.c.STR JU.BSUtil $.Escape $.Logger".split(" "),function(){var b=v(function(){this.chain=null;this.groupIndex=0;this.group1="\x00";this.leadAtomIndex=this.firstAtomIndex=-1;this.lastAtomIndex=0;this.bsAdded=null;

this.shapeVisibilityFlags=this.selectedIndex=this.groupID=this.seqcode=0;this.dssrNT=null;r(this,arguments)},JM,"Group",null,JM.Structure);c(b,"setGroup",function(a,d,b,c,f){this.chain=a;this.seqcode=b;this.firstAtomIndex=c;this.lastAtomIndex=f;null!=d&&0<d.length&&this.setGroupID(d);return this},"JM.Chain,~S,~N,~N,~N");c(b,"setGroupID",function(){},"~S");c(b,"isAdded",function(a){return null!=this.bsAdded&&this.bsAdded.get(a)},"~N");c(b,"addAtoms",function(a){null==this.bsAdded&&(this.bsAdded=new JU.BS);

this.bsAdded.set(a)},"~N");j(b,"setAtomBits",function(a){a.setBits(this.firstAtomIndex,this.lastAtomIndex+1);null!=this.bsAdded&&a.or(this.bsAdded)},"JU.BS");j(b,"setAtomBitsAndClear",function(a,d){a.setBits(this.firstAtomIndex,this.lastAtomIndex+1);d.clearBits(this.firstAtomIndex,this.lastAtomIndex+1);null!=this.bsAdded&&(a.or(this.bsAdded),d.andNot(this.bsAdded))},"JU.BS,JU.BS");c(b,"isSelected",function(a){var d=a.nextSetBit(this.firstAtomIndex);return 0<=d&&d<=this.lastAtomIndex||null!=this.bsAdded&&

this.bsAdded.intersects(a)},"JU.BS");c(b,"setShapeVisibility",function(a,d){this.shapeVisibilityFlags=d?this.shapeVisibilityFlags|a:this.shapeVisibilityFlags&~a},"~N,~B");c(b,"getGroup3",function(){return 1>this.groupID?"":JM.Group.group3Names[this.groupID]});c(b,"getGroup1",function(){return"\x00"==this.group1?"?":this.group1});c(b,"getBioPolymerLength",function(){return 0});c(b,"getMonomerIndex",function(){return-1});c(b,"getStructure",function(){return null});c(b,"getStrucNo",function(){return 0});

c(b,"getProteinStructureType",function(){return J.c.STR.NOT});c(b,"getProteinStructureSubType",function(){return this.getProteinStructureType()});c(b,"setProteinStructureType",function(){return-1},"J.c.STR,~N");c(b,"isProtein",function(){return 1<=this.groupID&&24>this.groupID});c(b,"isNucleic",function(){return 24<=this.groupID&&42>this.groupID});c(b,"isDna",function(){return this.isDnaByID()});c(b,"isRna",function(){return this.isRnaByID()});c(b,"isPurine",function(){return this.isPurineByID()});

c(b,"isPurineByID",function(){return this.isNucleic()&&0!=(153957&1<<this.groupID-24)||0<="AGag".indexOf(this.getGroup1())});c(b,"isPyrimidine",function(){return this.isPyrimidineByID()});c(b,"isPyrimidineByID",function(){return this.isNucleic()&&0!=(108186&1<<this.groupID-24)});c(b,"isRnaByID",function(){return this.isNucleic()&&0!=(196663&1<<this.groupID-24)});c(b,"isDnaByID",function(){return this.isNucleic()&&0!=(65480&1<<this.groupID-24)});c(b,"isCarbohydrate",function(){return!1});c(b,"getResno",

function(){return-2147483648==this.seqcode?0:this.seqcode>>8});c(b,"setResno",function(a){this.seqcode=JM.Group.getSeqcodeFor(a,this.getInsertionCode())},"~N");b.getSeqNumberFor=c(b,"getSeqNumberFor",function(a){return JM.Group.haveSequenceNumber(a)?a>>8:2147483647},"~N");b.haveSequenceNumber=c(b,"haveSequenceNumber",function(a){return 0!=(a&128)},"~N");c(b,"getSeqcodeString",function(){return JM.Group.getSeqcodeStringFor(this.seqcode)});b.getSeqcodeFor=c(b,"getSeqcodeFor",function(a,d){if(-2147483648==

a)return a;"A"<=d&&"Z">=d||("a"<=d&&"z">=d||"0"<=d&&"9">=d||"?"==d||"*"==d)||(" "!=d&&"\x00"!=d&&JU.Logger.warn("unrecognized insertionCode:"+d),d="\x00");return(2147483647==a?0:a<<8|128)+d.charCodeAt(0)},"~N,~S");b.getSeqcodeStringFor=c(b,"getSeqcodeStringFor",function(a){if(-2147483648==a)return null;var d=""+(a>>8);0!=(a&127)&&(d+="^"+String.fromCharCode(a&127));return d},"~N");c(b,"getInsertionCode",function(){return-2147483648==this.seqcode?"\x00":String.fromCharCode(this.seqcode&127)});c(b,

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c(b,"getSelectedMonomerCount",function(){return 0});c(b,"getSelectedMonomerIndex",function(){return-1});c(b,"isLeadAtom",function(){return!1},"~N");c(b,"getLeadAtomOr",function(a){var d=this.getLeadAtom();return null==d?a:d},"JM.Atom");c(b,"getLeadAtom",function(){return null});c(b,"getQuaternion",function(){return null},"~S");c(b,"getQuaternionFrame",function(a){if(3>this.lastAtomIndex-this.firstAtomIndex)return null;var d=this.firstAtomIndex;return JU.Quat.getQuaternionFrame(a[d],a[++d],a[++d])},

"~A");c(b,"setStrucNo",function(){},"~N");c(b,"getHelixData",function(a){return JU.Escape.escapeHelical(null,a,null,null,null)},"~N,~S,~N");c(b,"isWithinStructure",function(){return!1},"J.c.STR");c(b,"getProteinStructureTag",function(){return null});c(b,"getStructureId",function(){return""});c(b,"getBioPolymerIndexInModel",function(){return-1});c(b,"isCrossLinked",function(){return!1},"JM.Group");c(b,"getCrossLinkVector",function(){return!1},"JU.Lst,~B,~B");c(b,"getNitrogenAtom",function(){return null});

c(b,"getCarbonylOxygenAtom",function(){return null});c(b,"fixIndices",function(a,d){this.firstAtomIndex-=a;this.leadAtomIndex-=a;this.lastAtomIndex-=a;null!=this.bsAdded&&JU.BSUtil.deleteBits(this.bsAdded,d)},"~N,JU.BS");c(b,"getGroupInfo",function(a,d){var b=new java.util.Hashtable;b.put("groupIndex",Integer.$valueOf(a));b.put("groupID",Short.$valueOf(this.groupID));var c=this.getSeqcodeString();null!=c&&b.put("seqCode",c);b.put("_apt1",Integer.$valueOf(this.firstAtomIndex));b.put("_apt2",Integer.$valueOf(this.lastAtomIndex));

null!=this.bsAdded&&b.put("addedAtoms",this.bsAdded);b.put("atomInfo1",this.chain.model.ms.getAtomInfo(this.firstAtomIndex,null,d));b.put("atomInfo2",this.chain.model.ms.getAtomInfo(this.lastAtomIndex,null,d));b.put("visibilityFlags",Integer.$valueOf(this.shapeVisibilityFlags));return b},"~N,JU.P3");c(b,"getMinZ",function(a,d){d[0]=2147483647;for(var b=this.firstAtomIndex;b<=this.lastAtomIndex;b++)this.checkMinZ(a[b],d);if(null!=this.bsAdded)for(b=this.bsAdded.nextSetBit(0);0<=b;b=this.bsAdded.nextSetBit(b+

1))this.checkMinZ(a[b],d)},"~A,~A");c(b,"checkMinZ",function(a,d){var b=a.sZ-B(a.sD/2)-2;b<d[0]&&(d[0]=Math.max(1,b))},"JM.Atom,~A");c(b,"getGroupParameter",function(){return NaN},"~N");c(b,"getAtomIndex",function(){return-1},"~S,~N");c(b,"getBSSideChain",function(){return new JU.BS});j(b,"toString",function(){return"["+this.getGroup3()+"-"+this.getSeqcodeString()+"]"});c(b,"isNucleicMonomer",function(){return!1});b.standardGroupList=null;b.group3Names=Array(128);b.specialAtomNames=null});u("JM");

C(["JM.Bond"],"JM.HBond",["JU.Logger"],function(){var b=v(function(){this.energy=0;r(this,arguments)},JM,"HBond",JM.Bond);z(b,function(a,d,b,c,f,e){L(this,JM.HBond,[a,d,b,c,f]);this.energy=e;JU.Logger.debugging&&JU.Logger.debug("HBond energy = "+e+" #"+this.getIdentity())},"JM.Atom,JM.Atom,~N,~N,~N,~N");j(b,"getEnergy",function(){return this.energy});b.calcEnergy=c(b,"calcEnergy",function(a,d,b,c){return Math.round(-27888/a- -27888/c+-27888/b- -27888/d)},"~N,~N,~N,~N")});u("JM");C(null,"JM.LabelToken",

"java.util.Hashtable JU.AU $.PT $.SB JS.SV $.T JU.Edge JV.JC".split(" "),function(){var b=v(function(){this.data=this.key=this.text=null;this.tok=0;this.pt=-1;this.ch1="\x00";this.width=0;this.precision=2147483647;this.intAsFloat=this.zeroPad=this.alignLeft=!1;r(this,arguments)},JM,"LabelToken",null);c(b,"set",function(a,d){this.text=a;this.pt=d;return this},"~S,~N");b.isLabelPropertyTok=c(b,"isLabelPropertyTok",function(a){for(var d=JM.LabelToken.labelTokenIds.length;0<=--d;)if(JM.LabelToken.labelTokenIds[d]==

a)return!0;return!1},"~N");b.compile=c(b,"compile",function(a,d,b,c){if(null==d||0==d.length)return null;if(0>d.indexOf("%")||2>d.length)return w(-1,[(new JM.LabelToken).set(d,-1)]);for(var f=0,e=-1,h=d.length;++e<h&&0<=(e=d.indexOf("%",e));)f++;for(var f=Array(2*f+1),k,m=0,e=0;0<=(k=d.indexOf("%",e));)e!=k&&(f[m++]=(new JM.LabelToken).set(d.substring(e,k),-1)),e=f[m++]=(new JM.LabelToken).set(null,k),a.autoCalculate(e.tok,null),e=JM.LabelToken.setToken(a,d,e,h,b.charCodeAt(0),c);e<h&&(f[m++]=(new JM.LabelToken).set(d.substring(e),

-1));return f},"JV.Viewer,~S,~S,java.util.Map");c(b,"formatLabel",function(a,d,b,c){return null==b||0==b.length?null:JM.LabelToken.formatLabelAtomArray(a,d,JM.LabelToken.compile(a,b,"\x00",null),"\x00",null,c)},"JV.Viewer,JM.Atom,~S,JU.P3");b.formatLabelAtomArray=c(b,"formatLabelAtomArray",function(a,d,b,c,f,e){if(null==d)return null;var h="0"<c?null:new JU.SB;if(null!=b)for(var k=0;k<b.length;k++){var m=b[k];if(null==m)break;"0"<c&&m.ch1!=c||(0>=m.tok||null!=m.key?null!=h&&(h.append(m.text),"\x00"!=

m.ch1&&h.appendC(m.ch1)):JM.LabelToken.appendAtomTokenValue(a,d,m,h,f,e))}return null==h?null:h.toString().intern()},"JV.Viewer,JM.Atom,~A,~S,~A,JU.P3");b.getBondLabelValues=c(b,"getBondLabelValues",function(){var a=new java.util.Hashtable;a.put("#","");a.put("ORDER","");a.put("TYPE","");a.put("LENGTH",Float.$valueOf(0));a.put("ENERGY",Float.$valueOf(0));return a});b.formatLabelBond=c(b,"formatLabelBond",function(a,d,b,c,f,e){c.put("#",""+(d.index+1));c.put("ORDER",""+JU.Edge.getBondOrderNumberFromOrder(d.order));

c.put("TYPE",JU.Edge.getBondOrderNameFromOrder(d.order));c.put("LENGTH",Float.$valueOf(d.atom1.distance(d.atom2)));c.put("ENERGY",Float.$valueOf(d.getEnergy()));JM.LabelToken.setValues(b,c);JM.LabelToken.formatLabelAtomArray(a,d.atom1,b,"1",f,e);JM.LabelToken.formatLabelAtomArray(a,d.atom2,b,"2",f,e);return JM.LabelToken.getLabel(b)},"JV.Viewer,JM.Bond,~A,java.util.Map,~A,JU.P3");b.formatLabelMeasure=c(b,"formatLabelMeasure",function(a,d,b,c,f){var e=new java.util.Hashtable;e.put("#",""+(d.index+

1));e.put("VALUE",Float.$valueOf(c));e.put("UNITS",f);b=JM.LabelToken.compile(a,b,"\u0001",e);if(null==b)return"";JM.LabelToken.setValues(b,e);e=d.ms.at;d=d.countPlusIndices;for(c=d[0];1<=c;--c)0<=d[c]&&JM.LabelToken.formatLabelAtomArray(a,e[d[c]],b,String.fromCharCode(48+c),null,null);b=JM.LabelToken.getLabel(b);return null==b?"":b},"JV.Viewer,JM.Measurement,~S,~N,~S");b.setValues=c(b,"setValues",function(a,d){for(var b=0;b<a.length;b++){var c=a[b];if(null==c)break;if(null!=c.key){var f=d.get(c.key);

c.text=y(f,Float)?c.format(f.floatValue(),null,null):c.format(NaN,f,null)}}},"~A,java.util.Map");b.getLabel=c(b,"getLabel",function(a){for(var d=new JU.SB,b=0;b<a.length;b++){var c=a[b];if(null==c)break;d.append(c.text)}return d.toString()},"~A");b.setToken=c(b,"setToken",function(a,d,b,c,f,e){var h=b.pt+1;if(h>=c)return b.text="%",h;var k;"-"==d.charAt(h)&&(b.alignLeft=!0,++h);h<c&&"0"==d.charAt(h)&&(b.zeroPad=!0,++h);for(;h<c&&JU.PT.isDigit(k=d.charAt(h));)b.width=10*b.width+(k.charCodeAt(0)-48),

++h;b.precision=2147483647;var m=!1;if(h<c&&"."==d.charAt(h)){++h;if(h<c&&"-"==(k=d.charAt(h)))m=!0,++h;if(h<c&&JU.PT.isDigit(k=d.charAt(h))){++h;b.precision=k.charCodeAt(0)-48;if(h<c&&JU.PT.isDigit(k=d.charAt(h)))++h,b.precision=10*b.precision+(k.charCodeAt(0)-48);m&&(b.precision=-1-b.precision)}}if(h<c&&null!=e){var j;for(e=e.keySet().iterator();e.hasNext()&&((j=e.next())||1);)if(d.indexOf(j,h)==h)return h+(b.key=j).length}if(h<c)switch((k=d.charAt(h++)).charCodeAt(0)){case 37:return b.text="%",

h;case 91:j=d.indexOf("]",h);if(j<h){h=c;break}h=d.substring(h,j).toLowerCase();h.startsWith("property_")?(b.tok=134221834,b.data=a.getDataObj(h,null,1)):h.startsWith("validation.")?(b.tok=1073742189,b.data=a.getDataObj("property_"+h.substring(11),null,1)):h.startsWith("unitid")?(b.tok=1073741974,b.data=Integer.$valueOf(JV.JC.getUnitIDFlags(h.substring(6)))):(a=JS.T.getTokenFromName(h),null!=a&&JM.LabelToken.isLabelPropertyTok(a.tok)&&(b.tok=a.tok));h=j+1;break;case 123:j=d.indexOf("}",h);if(j<h){h=

c;break}h=d.substring(h,j);b.data=a.getDataObj(h,null,1);null==b.data?(b.data=a.getDataObj(h,null,-1),null!=b.data&&(b.data=b.data[1],"string"==typeof b.data&&(b.data=JU.PT.split(b.data,"\n")),JU.AU.isAS(b.data)||(b.data=null)),null==b.data?(b.tok=1715472409,b.data=h):b.tok=1275068418):b.tok=134221834;h=j+1;break;default:var p,q;if(h<c&&0<=(p="fuv".indexOf(k))&&0<=(q="xyz".indexOf(d.charAt(h))))b.tok=JM.LabelToken.twoCharLabelTokenIds[3*p+q],h++;else if(0<=(p="AaBbCcDEefGgIiLlMmNnOoPpQqRrSsTtUuVvWwXxxYyyZzz%%%gqW".indexOf(k)))b.tok=

JM.LabelToken.labelTokenIds[p]}b.text=d.substring(b.pt,h);if(h<c&&0!=f&&JU.PT.isDigit(k=d.charAt(h)))h++,b.ch1=k,k.charCodeAt(0)!=f&&1!=f&&(b.tok=0);return h},"JV.Viewer,~S,JM.LabelToken,~N,~N,java.util.Map");b.appendAtomTokenValue=c(b,"appendAtomTokenValue",function(a,d,b,c,f,e){var h=null,k=NaN,m=null;try{switch(b.tok){case 1153433601:h=d.atomPropertyString(a,1153433601);break;case 1094713347:h=""+(null==f?d.i:f[d.i]);break;case 1765808134:m=d.atomPropertyTuple(a,b.tok,e);break;case 1073741974:h=

d.getUnitID(b.data.intValue());break;case 134221834:case 1073742189:if(null!=b.data&&(k=b.data[d.i],1073742189==b.tok&&1!=k&&0!=k)){var j=a.getAtomValidation(b.text.substring(13,b.text.length-1),d);if(null==j)System.out.println("?? o is null ??");else if(1==j.size())k=j.get(0).floatValue();else{k=NaN;h="";a=0;for(var p=j.size();a<p;a++)h+=","+j.get(a);1<h.length&&(h=h.substring(1))}}break;case 1715472409:var q=a.ms.getInfo(d.mi,b.data),x=d.i-a.ms.am[d.mi].firstAtomIndex,j=null;if(0<=x)if(y(q,Array))var s=

q,j=x<s.length?s[x]:null;else y(q,"JU.Lst")&&(j=x<q.size()?JS.SV.oValue(q.get(x)):null);null==j?h="":y(j,Float)?k=j.floatValue():y(j,Integer)?k=j.intValue():y(j,"JU.T3")?m=j:h=j.toString();break;case 1275068418:null!=b.data&&(s=b.data,h=d.i<s.length?s[d.i]:"");break;case 1631586315:var n=d.getFormalCharge(),h=0<n?""+n+"+":0>n?""+-n+"-":"";break;case 1094717454:h=d.getModelNumberForLabel();break;case 1128269825:h=""+d.atomPropertyInt(b.tok);break;case 1665140738:k=d.atomPropertyFloat(a,b.tok,e);break;

case 1086324749:h=d.group.getStructureId();break;case 1094713367:var r=d.group.getStrucNo(),h=0>=r?"":""+r;break;case 1111490574:if(Float.isNaN(k=d.group.getGroupParameter(1111490574)))h="null";break;case 1111492626:case 1111492627:case 1111492628:case 1111490583:case 1111490584:case 1111490585:case 1111490586:k=d.atomPropertyFloat(a,b.tok,e);Float.isNaN(k)&&(h="");break;case 1073877011:h=a.getNBOAtomLabel(d);break;case 1086324747:case 1639976963:case 1237320707:h=d.atomPropertyString(a,b.tok);break;

case 1140850705:h=d.getIdentityXYZ(e,1);break;case 1086324754:h=d.getWyckoffPosition(!1);break;case 1086324755:h=d.getWyckoffPosition(!0);break;case 79:h=d.getSymmetryOperatorList(!1);break;case 81:k=d.getOccupancy100()/100;break;default:switch(b.tok&1136656384){case 1094713344:b.intAsFloat?k=d.atomPropertyInt(b.tok):h=""+d.atomPropertyInt(b.tok);break;case 1111490560:k=d.atomPropertyFloat(a,b.tok,e);break;case 1086324736:h=d.atomPropertyString(a,b.tok);break;case 1077936128:m=d.atomPropertyTuple(a,

b.tok,e);null==m&&(h="");break;default:1145045003==b.tok&&(h=d.atomPropertyString(a,1145045003))}}}catch(u){if(F(u,"IndexOutOfBoundsException"))k=NaN,m=h=null;else throw u;}h=b.format(k,h,m);null==c?b.text=h:c.append(h)},"JV.Viewer,JM.Atom,JM.LabelToken,JU.SB,~A,JU.P3");c(b,"format",function(a,d,b){return Float.isNaN(a)?null!=d?JU.PT.formatS(d,this.width,this.precision,this.alignLeft,this.zeroPad):null!=b?(0==this.width&&2147483647==this.precision&&(this.width=6,this.precision=2),JU.PT.formatF(b.x,

this.width,this.precision,!1,!1)+JU.PT.formatF(b.y,this.width,this.precision,!1,!1)+JU.PT.formatF(b.z,this.width,this.precision,!1,!1)):this.text:JU.PT.formatF(a,this.width,this.precision,this.alignLeft,this.zeroPad)},"~N,~S,JU.T3");b.labelTokenIds=E(-1,[1086324739,1086326786,1086326785,1111492620,1631586315,1086326788,1094713347,1086324746,1086326789,1111490569,1094713357,1094713361,1111492618,1094715393,1094713363,1094715402,1094717454,1086324743,1094713360,1086324742,79,1088421903,1111492619,1111490570,

81,1128269825,1094715412,1086324747,1094713366,1086326788,1111490574,1111492620,1086324745,1111490575,1648363544,1145047055,1140850705,1086324755,1111492612,1111492609,1111492629,1111492613,1111492610,1111492630,1111492614,1111492611,1111492631,1114249217,1112152066,1112150019,1112150020,1112150021,1112152070,1112152071,1112152073,1112152074,1112152076,1649022989,1112152078,1111490561,1111490562,1153433601,1094713346,1228931586,1765808134,1094713356,1111490564,1228935687,1287653388,1825200146,1111490567,

1094713359,1111490565,1111490568,1094713362,1715472409,1665140738,1113589787,1086324748,1086324744,1112152075,1639976963,1237320707,1094713367,1086324749,1086326798,1111490576,1111490577,1111490578,1111490579,1094715418,1648361473,1111492626,1111492627,1111492628,1312817669,1145045006,1145047050,1145047049,1145047053,1111492615,1111492616,1111492617,1113589786,1111490571,1111490572,1111490573,1145047052,1111490566,1111490563,1094713351,1094713365,1111490583,1111490584,1111490585,1111490586,1145045008,

1296041985,1073877011,1086324752,1086324753,1086324754,1145045003]);b.twoCharLabelTokenIds=E(-1,[1111492612,1111492613,1111492614,1111490577,1111490578,1111490579,1111492626,1111492627,1111492628])});u("JM");C(null,"JM.Measurement","JU.Measure $.PT $.SB J.atomdata.RadiusData J.c.VDW JM.LabelToken JU.Escape".split(" "),function(){var b=v(function(){this.thisID=this.ms=null;this.index=0;this.isVisible=!0;this.isTrajectory=this.isHidden=!1;this.$isValid=!0;this.colix=0;this.labelColix=-1;this.mad=0;

this.tickInfo=null;this.traceX=-2147483648;this.count=this.traceY=0;this.pts=this.countPlusIndices=null;this.value=0;this.type=this.strMeasurement=this.vwr=this.text=this.units=this.strFormat=this.property=null;this.tainted=!1;this.newUnits=this.renderArc=this.renderAxis=null;this.fixedValue=NaN;this.useDefaultLabel=this.inFront=this.isPending=!1;r(this,arguments)},JM,"Measurement",null);Q(b,function(){this.countPlusIndices=E(5,0)});c(b,"isTainted",function(){return this.tainted&&!(this.tainted=!1)});

c(b,"setM",function(a,d,b,c,f,e){this.ms=a;this.index=e;this.vwr=a.vwr;this.colix=c;this.strFormat=f;null!=d&&(this.tickInfo=d.tickInfo,this.pts=d.pts,this.mad=d.mad,this.thisID=d.thisID,this.text=d.text,this.property=d.property,this.units=d.units,null==this.property&&"+hz".equals(this.units)&&(this.property="property_J"),null!=this.thisID&&null!=this.text&&(this.labelColix=this.text.colix));null==this.pts&&(this.pts=Array(4));d=null==d?null:d.countPlusIndices;this.count=null==d?0:d[0];0<this.count&&

(System.arraycopy(d,0,this.countPlusIndices,0,this.count+1),this.isTrajectory=a.isTrajectoryMeasurement(this.countPlusIndices));this.value=(this.isPending=Float.isNaN(b))||this.isTrajectory?this.getMeasurement(null):b;this.formatMeasurement(null);return this},"JM.ModelSet,JM.Measurement,~N,~N,~S,~N");c(b,"setPoints",function(a,d,b,c){this.ms=a;this.countPlusIndices=d;this.count=d[0];this.pts=null==b?Array(4):b;this.vwr=a.vwr;this.tickInfo=c;return this},"JM.ModelSet,~A,~A,JM.TickInfo");c(b,"setCount",

function(a){this.setCountM(a)},"~N");c(b,"setCountM",function(a){this.count=this.countPlusIndices[0]=a},"~N");c(b,"getAtomIndex",function(a){return 0<a&&a<=this.count?this.countPlusIndices[a]:-1},"~N");c(b,"getAtom",function(a){a=this.countPlusIndices[a];return-1>a?this.pts[-2-a]:this.ms.at[a]},"~N");c(b,"getLastIndex",function(){return 0<this.count?this.countPlusIndices[this.count]:-1});c(b,"getString",function(){return this.strMeasurement});j(b,"toString",function(){return this.getString()});c(b,

"getStringUsing",function(a,d,b){this.vwr=a;this.value=this.getMeasurement(null);this.formatMeasurementAs(d,b,!0);return null==d?this.getInfoAsString(b):this.strMeasurement},"JV.Viewer,~S,~S");c(b,"getStringDetail",function(){return(2==this.count?"Distance":3==this.count?"Angle":"Torsion")+this.getMeasurementScript(" - ",!1)+" : "+this.value});c(b,"refresh",function(a){this.value=this.getMeasurement(a);this.isTrajectory=this.ms.isTrajectoryMeasurement(this.countPlusIndices);this.formatMeasurement(null)},

"~A");c(b,"getMeasurementScript",function(a,d){for(var b=new JU.SB,c=a.equals(" "),f=1;f<=this.count;f++)b.append(1<f?a:" ").append(this.getLabel(f,c,d));return b.toString()},"~S,~B");c(b,"formatMeasurementAs",function(a,d,b){null!=a&&0==a.length&&(a=null);if(b||!(null!=a&&0!=a.indexOf(this.countPlusIndices[0]+":")))this.strFormat=a,this.formatMeasurement(d)},"~S,~S,~B");c(b,"formatMeasurement",function(a){this.tainted=!0;switch(Float.isNaN(this.value)?0:this.count){default:this.strMeasurement=null;

break;case 2:this.strMeasurement=this.formatDistance(a);break;case 3:case 4:this.strMeasurement=this.formatAngle(this.value)}},"~S");c(b,"reformatDistanceIfSelected",function(a){if(2==this.count&&this.vwr.slm.isSelected(this.countPlusIndices[1])&&this.vwr.slm.isSelected(this.countPlusIndices[2])){var d;if(this.useDefaultLabel&&null!=this.strFormat&&0<=(d=this.strFormat.indexOf("//")))this.strFormat=this.strFormat.substring(0,d);a&&(this.units=null);this.formatMeasurement(null)}},"~B");c(b,"formatDistance",

function(a){var d=this.getLabelString();if(null==d)return"";var b=this.strFormat.indexOf("//");null==a&&(a=this.units,null==a&&(a=0<=b?this.strFormat.substring(b+2):null==this.property?this.vwr.g.measureDistanceUnits:""));0<=b&&(this.strFormat=this.strFormat.substring(0,b));this.strFormat+="//"+a;a=JM.Measurement.fixUnits(a);b=d.indexOf("//");0<=b&&(d=d.substring(0,b),0==d.length&&(d="%VALUE"));a=this.fixValue(a,0<=d.indexOf("%V"));return this.formatString(a,this.newUnits,d)},"~S");c(b,"fixValue",

function(a,d){this.checkJ(a);null!=a&&a.startsWith("+")&&(this.isPending||(this.value=Math.abs(this.value)),a=a.substring(1));this.newUnits=a;if(2!=this.count)return this.value;var b=this.value;null==a&&null!=this.property&&(a="");if(null!=a){var c=a.equals("%");if(null==this.property&&(c||a.endsWith("hz"))){var f=this.getAtomIndex(1),e=this.getAtomIndex(2);if(0<=f&&0<=e){var f=this.getAtom(1),e=this.getAtom(2),h=JM.Measurement.nmrType(a),k=!c&&1==h;this.type=c?"percent":k?"dipoleCouplingConstant":

3==h?"NOE or 3JHH":"J-CouplingConstant";3==h?(f=this.vwr.getNMRCalculation().getNOEorJHH(w(-1,[f,null,null,e]),11),null==f?(b=NaN,this.newUnits=a=""):(b=f[1],a=this.newUnits=2==f.length?"noe":"hz")):b=c?b/(f.getVanderwaalsRadiusFloat(this.vwr,J.c.VDW.AUTO)+e.getVanderwaalsRadiusFloat(this.vwr,J.c.VDW.AUTO)):k?this.vwr.getNMRCalculation().getDipolarConstantHz(f,e):this.vwr.getNMRCalculation().getIsoOrAnisoHz(!0,f,e,a,null);this.$isValid=!Float.isNaN(b);c&&(a="pm")}}return JM.Measurement.toUnits(b,

a,d)}return d?Math.round(100*b)/100:b},"~S,~B");c(b,"checkJ",function(a){null!=this.property||(null!=a||null!=this.units)||(a=this.vwr.g.measureDistanceUnits,"+hz".equals(a)&&(this.property="property_J",this.units=a))},"~S");b.nmrType=c(b,"nmrType",function(a){return 0>a.indexOf("hz")?0:a.equals("noe_hz")?3:a.startsWith("dc_")||a.equals("khz")?1:2},"~S");c(b,"formatAngle",function(a){var d=this.getLabelString();0<=d.indexOf("%V")&&(a=Math.round(10*a)/10);return this.formatString(a,"\u00b0",d)},"~N");

c(b,"getLabelString",function(){var a=this.countPlusIndices[0]+":",d=null;if(null!=this.strFormat){if(0==this.strFormat.length)return null;d=2<this.strFormat.length&&0==this.strFormat.indexOf(a)?this.strFormat:null}this.useDefaultLabel=!1;null==d&&(this.strFormat=null,d=this.vwr.getDefaultMeasurementLabel(this.countPlusIndices[0]),this.useDefaultLabel=null==this.units);0==d.indexOf(a)&&(d=d.substring(2));null==this.strFormat&&(this.strFormat=a+d);return d});c(b,"formatString",function(a,d,b){return JM.LabelToken.formatLabelMeasure(this.vwr,

this,b,a,d)},"~N,~S,~S");c(b,"sameAsPoints",function(a,d){if(this.count!=a[0])return!1;for(var b=!0,c=1;c<=this.count&&b;c++)b=this.countPlusIndices[c]==a[c];if(b)for(c=0;c<this.count&&b;c++)null!=d[c]&&(b=0.01>this.pts[c].distance(d[c]));if(b)return!0;switch(this.count){default:return!0;case 2:return this.sameAsIJ(a,d,1,2)&&this.sameAsIJ(a,d,2,1);case 3:return this.sameAsIJ(a,d,1,3)&&this.sameAsIJ(a,d,2,2)&&this.sameAsIJ(a,d,3,1);case 4:return this.sameAsIJ(a,d,1,4)&&this.sameAsIJ(a,d,2,3)&&this.sameAsIJ(a,

d,3,2)&&this.sameAsIJ(a,d,4,1)}},"~A,~A");c(b,"sameAsIJ",function(a,d,b,c){b=this.countPlusIndices[b];a=a[c];return 0<=b||0<=a?b==a:0.01>this.pts[-2-b].distance(d[-2-a])},"~A,~A,~N,~N");c(b,"sameAs",function(a,d){return this.sameAsIJ(this.countPlusIndices,this.pts,a,d)},"~N,~N");c(b,"getPropMeasurement",function(a){if(null==this.countPlusIndices||2!=this.count)return NaN;for(var d=this.count;0<=--d;)if(0>this.countPlusIndices[d+1])return NaN;try{var b=null==a?this.getAtom(1):a[0],c=null==a?this.getAtom(2):

a[1],f=this.vwr.getDataObj(this.property,null,2),e=b.i,h=c.i;return null==f||h>=f.length||e>=f.length?NaN:f[e][h]}catch(k){return NaN}},"~A");c(b,"getMeasurement",function(a){this.checkJ(null);if(!Float.isNaN(this.fixedValue))return this.fixedValue;if(null!=this.property)return this.getPropMeasurement(a);if(null==this.countPlusIndices||2>this.count)return NaN;for(var d=this.count;0<=--d;)if(-1==this.countPlusIndices[d+1])return NaN;var d=null==a?this.getAtom(1):a[0],b=null==a?this.getAtom(2):a[1],

c;switch(this.count){case 2:return d.distance(b);case 3:return c=null==a?this.getAtom(3):a[2],JU.Measure.computeAngleABC(d,b,c,!0);case 4:return c=null==a?this.getAtom(3):a[2],a=null==a?this.getAtom(4):a[3],JU.Measure.computeTorsion(d,b,c,a,!0);default:return NaN}},"~A");c(b,"getLabel",function(a,d,b){var c=this.countPlusIndices[a];return 0>c?(b?"modelIndex "+this.getAtom(a).mi+" ":"")+JU.Escape.eP(this.getAtom(a)):d?"({"+c+"})":this.vwr.getAtomInfo(c)},"~N,~B,~B");c(b,"setModelIndex",function(a){if(null!=

this.pts)for(var d=0;d<this.count;d++)null!=this.pts[d]&&(this.pts[d].mi=a)},"~N");c(b,"isValid",function(){return!(this.sameAs(1,2)||2<this.count&&this.sameAs(1,3)||4==this.count&&this.sameAs(2,4))});b.find=c(b,"find",function(a,d){for(var b=d.countPlusIndices,c=d.pts,f=a.size();0<=--f;)if(a.get(f).sameAsPoints(b,c))return f;return-1},"JU.Lst,JM.Measurement");c(b,"isConnected",function(a,d){for(var b=-1,c=1;c<=d;c++){var f=this.getAtomIndex(c);if(!(0>f)){if(0<=b&&!a[f].isBonded(a[b]))return!1;b=

f}}return!0},"~A,~N");c(b,"getInfoAsString",function(a){var d=this.fixValue(a,!0);a=new JU.SB;a.append(2==this.count?null!=this.property?this.property:null==this.type?"distance":this.type:3==this.count?"angle":"dihedral");a.append(" \t").appendF(d);a.append(" \t").append(JU.PT.esc(this.strMeasurement));for(d=1;d<=this.count;d++)a.append(" \t").append(this.getLabel(d,!1,!1));null!=this.thisID&&a.append(" \t").append(this.thisID);return a.toString()},"~S");c(b,"isInRange",function(a,d){if(a.factorType===

J.atomdata.RadiusData.EnumType.FACTOR){var b=this.getAtom(1),c=this.getAtom(2),b=(b.getVanderwaalsRadiusFloat(this.vwr,a.vdwType)+c.getVanderwaalsRadiusFloat(this.vwr,a.vdwType))*a.value;return d<=b}return 3.4028235E38==a.values[0]||d>=a.values[0]&&d<=a.values[1]},"J.atomdata.RadiusData,~N");c(b,"isIntramolecular",function(a,d){for(var b=-1,c=1;c<=d;c++){var f=this.getAtomIndex(c);if(!(0>f))if(f=a[f].getMoleculeNumber(!1),0>b)b=f;else if(f!=b)return!1}return!0},"~A,~N");c(b,"isMin",function(a){var d=

this.getAtom(1),b=this.getAtom(2),c=D(100*b.distanceSquared(d)),d=d.getAtomName(),b=b.getAtomName(),b=0>d.compareTo(b)?d+b:b+d;a=a.get(b);return null!=a&&c==a.intValue()},"java.util.Map");b.isUnits=c(b,"isUnits",function(a){return JU.PT.isOneOf((a.startsWith("+")?a.substring(1):a).toLowerCase(),";nm;nanometers;pm;picometers;angstroms;angstroms;ang;\u00c5;au;vanderwaals;vdw;%;noe;")||0>a.indexOf(" ")&&a.endsWith("hz")},"~S");b.toUnits=c(b,"toUnits",function(a,d,b){return Float.isNaN(a)?NaN:d.equals("hz")?

b?Math.round(10*a)/10:a:d.equals("nm")?b?Math.round(100*a)/1E3:a/10:d.equals("pm")?b?Math.round(1E3*a)/10:100*a:d.equals("au")?b?Math.round(1E3*(a/0.5291772))/1E3:a/0.5291772:d.endsWith("khz")?b?Math.round(a/10)/100:a/1E3:b?Math.round(100*a)/100:a},"~N,~S,~B");b.fromUnits=c(b,"fromUnits",function(a,d){return d.equals("nm")?10*a:d.equals("pm")?a/100:d.equals("au")?0.5291772*a:d.equals("\u00c5")?a:0},"~N,~S");b.fixUnits=c(b,"fixUnits",function(a){var d=a.endsWith("s")?a.substring(0,a.length-1):a;return d.equals("nanometer")?

"nm":d.equals("bohr")||d.equals("atomicunits")||d.equals("atomic")?"au":d.equals("picometer")?"pm":d.equals("\u00e5")||d.equals("angstrom")||d.equals("a")||d.equals("ang")?"\u00c5":d.equals("vanderwaal")||d.equals("vdw")?"%":a},"~S");c(b,"getDistanceFormatForState",function(){return this.useDefaultLabel?null:this.strFormat});c(b,"setFromMD",function(a){null!=a.thisID&&(this.thisID=a.thisID,this.mad=a.mad,0!=a.colix&&(this.colix=a.colix),this.strFormat=a.strFormat,this.text=a.text);this.units="default".equals(a.units)?

null:a.units;this.property=a.property;this.fixedValue=a.fixedValue;0!=a.colix&&(this.colix=a.colix);0!=a.mad&&(this.mad=a.mad);null!=a.strFormat&&(this.strFormat=(null==this.strFormat?a.strFormat:this.strFormat.substring(0,2))+a.strFormat.substring(2));null!=a.text&&(null==this.text?this.text=a.text:(null!=a.text.font&&(this.text.setFont(a.text.font,!1),this.text.fontScale=a.text.font.fontSize/a.text.font.fontSizeNominal),this.text.text=null,0!=a.text.align&&(this.text.align=a.text.align),0!=a.colix&&

(this.labelColix=this.text.colix=a.text.colix)));this.formatMeasurement(null)},"JM.MeasurementData,~B")});u("JM");C(["J.api.JmolMeasurementClient"],"JM.MeasurementData",["JU.Lst","JM.Measurement"],function(){var b=v(function(){this.points=this.measurements=this.measurementStrings=this.bsSelected=this.client=null;this.mustNotBeConnected=this.mustBeConnected=!1;this.tickInfo=null;this.tokAction=12290;this.note=this.property=this.strFormat=this.radiusData=null;this.isAll=!1;this.colix=0;this.intramolecular=

null;this.mad=0;this.units=this.text=this.thisID=null;this.fixedValue=0;this.ms=this.minArray=this.atoms=null;this.allowSelf=!1;this.vwr=null;this.iFirstAtom=0;this.justOneModel=!0;this.htMin=null;r(this,arguments)},JM,"MeasurementData",null,J.api.JmolMeasurementClient);c(b,"init",function(a,d,b){this.vwr=d;this.points=b;this.thisID=a;return this},"~S,JV.Viewer,JU.Lst");c(b,"setModelSet",function(a){this.ms=a;return this},"JM.ModelSet");c(b,"set",function(a,d,b,c,f,e,h,k,m,j,p,q,x,s,n,r){this.ms=

this.vwr.ms;this.tokAction=a;2<=this.points.size()&&(y(this.points.get(0),"JU.BS")&&y(this.points.get(1),"JU.BS"))&&(this.justOneModel=this.vwr.ms.getModelBS(this.points.get(0),!1).equals(this.vwr.ms.getModelBS(this.points.get(1),!1)));this.bsSelected=r;this.htMin=d;this.radiusData=b;this.property=c;this.strFormat=f;this.units=e;this.tickInfo=h;this.mustBeConnected=k;this.mustNotBeConnected=m;this.intramolecular=j;this.isAll=p;this.mad=q;this.colix=x;this.text=s;this.fixedValue=n;return this},"~N,java.util.Map,J.atomdata.RadiusData,~S,~S,~S,JM.TickInfo,~B,~B,Boolean,~B,~N,~N,JM.Text,~N,JU.BS");

c(b,"processNextMeasure",function(a,d){var b=d.getMeasurement(null);if(!(null!=this.htMin&&!d.isMin(this.htMin)||null!=this.radiusData&&!d.isInRange(this.radiusData,b)))if(null==this.measurementStrings&&null==this.measurements){var c=this.minArray[this.iFirstAtom];d.value=b;b=d.fixValue(this.units,!1);this.minArray[this.iFirstAtom]=-Infinity==1/c?b:Math.min(c,b)}else null!=this.measurementStrings?this.measurementStrings.addLast(d.getStringUsing(this.vwr,this.strFormat,this.units)):this.measurements.addLast(Float.$valueOf(d.getMeasurement(null)))},

"JM.MeasurementData,JM.Measurement");c(b,"getMeasurements",function(a,d){if(d){this.minArray=K(this.points.get(0).cardinality(),0);for(var b=0;b<this.minArray.length;b++)this.minArray[b]=-0;this.define(null,this.ms);return this.minArray}if(a)return this.allowSelf=!0,this.measurements=new JU.Lst,this.define(null,this.ms),this.measurements;this.measurementStrings=new JU.Lst;this.define(null,this.ms);return this.measurementStrings},"~B,~B");c(b,"define",function(a,d){this.client=null==a?this:a;this.atoms=

d.at;var b=this.points.size();if(!(2>b)){var c=-1,f=Array(4),e=E(5,0),h=(new JM.Measurement).setPoints(d,e,f,null);h.setCount(b);h.property=this.property;h.strFormat=this.strFormat;h.units=this.units;h.fixedValue=this.fixedValue;for(var k=-1,m=0;m<b;m++){var j=this.points.get(m);if(y(j,"JU.BS")){k=j.cardinality();if(0==k)return;1<k&&(c=0);k=m;0==m&&(this.iFirstAtom=0);e[m+1]=j.nextSetBit(0)}else f[m]=j,e[m+1]=-2-m}this.nextMeasure(0,k,h,c)}},"J.api.JmolMeasurementClient,JM.ModelSet");c(b,"nextMeasure",

function(a,d,b,c){if(a>d)(this.allowSelf&&!this.mustBeConnected&&!this.mustNotBeConnected||b.isValid())&&((!this.mustBeConnected||b.isConnected(this.atoms,a))&&(!this.mustNotBeConnected||!b.isConnected(this.atoms,a))&&(null==this.intramolecular||b.isIntramolecular(this.atoms,a)==this.intramolecular.booleanValue()))&&this.client.processNextMeasure(this,b);else{var f=this.points.get(a),e=b.countPlusIndices,h=0==a?2147483647:e[a];if(0>h)this.nextMeasure(a+1,d,b,c);else{for(var k=!1,m=f.nextSetBit(0),

j=0;0<=m;m=f.nextSetBit(m+1),j++)if(m!=h||this.allowSelf){var p=this.atoms[m].mi;if(0<=c&&this.justOneModel)if(0==a)c=p;else if(c!=p)continue;e[a+1]=m;0==a&&(this.iFirstAtom=j);k=!0;this.nextMeasure(a+1,d,b,c)}k||this.nextMeasure(a+1,d,b,c)}}},"~N,~N,JM.Measurement,~N")});u("JM");C(["JM.Measurement"],"JM.MeasurementPending",null,function(){var b=v(function(){this.haveModified=this.haveTarget=!1;this.numSet=0;this.lastIndex=-1;r(this,arguments)},JM,"MeasurementPending",JM.Measurement);c(b,"set",function(a){return this.setM(a,

null,NaN,0,null,0)},"JM.ModelSet");c(b,"checkPoint",function(a){for(var d=1;d<=this.numSet;d++)if(this.countPlusIndices[d]==-1-d&&0.01>this.pts[d-1].distance(a))return!1;return!0},"JU.Point3fi");c(b,"getIndexOf",function(a){for(var d=1;d<=this.numSet;d++)if(this.countPlusIndices[d]==a)return d;return 0},"~N");j(b,"setCount",function(a){this.setCountM(a);this.numSet=a},"~N");c(b,"addPoint",function(a,d,b){this.haveModified=a!=this.lastIndex;this.lastIndex=a;if(null==d){if(0<this.getIndexOf(a))return b&&

(this.numSet=this.count),this.count;this.haveTarget=0<=a;if(!this.haveTarget)return this.count=this.numSet;this.count=this.numSet+1;this.countPlusIndices[this.count]=a}else{if(!this.checkPoint(d))return b&&(this.numSet=this.count),this.count;a=this.numSet;this.haveModified=this.haveTarget=!0;this.count=this.numSet+1;this.pts[a]=d;this.countPlusIndices[this.count]=-2-a}this.countPlusIndices[0]=this.count;b&&(this.numSet=this.count);this.value=this.getMeasurement(null);this.strFormat=null;this.formatMeasurement(null);

return this.count},"~N,JU.Point3fi,~B")});u("JM");C(null,"JM.Model","java.util.Hashtable JU.AU $.BS $.SB JU.BSUtil JV.FileManager".split(" "),function(){var b=v(function(){this.mat4=this.ms=null;this.fileIndex=this.modelIndex=0;this.isModelKit=this.isPdbWithMultipleBonds=this.isBioModel=!1;this.translation=this.dataFrames=this.biosymmetry=this.properties=this.auxiliaryInfo=this.orientation=this.dssrCache=this.simpleCage=this.chains=null;this.dataSourceFrame=-1;this.loadState="";this.loadScript=null;

this.isTrajectory=this.isJmolDataFrame=this.structureTainted=this.hasRasmolHBonds=!1;this.act=this.insertionCount=this.altLocCount=this.trajectoryBaseIndex=0;this.bondCount=-1;this.chainCount=0;this.groupCount=-1;this.firstMoleculeIndex=this.firstAtomIndex=this.biosymmetryCount=this.moleculeCount=this.hydrogenCount=0;this.bsAtomsDeleted=this.bsAtoms=null;this.frameDelay=this.defaultRotationRadius=0;this.selectedTrajectory=-1;this.bsCheck=this.pdbID=this.jmolFrameType=this.jmolData=null;this.hasChirality=

!1;this.isOrderly=!0;this.bsAsymmetricUnit=null;r(this,arguments)},JM,"Model",null);z(b,function(){this.setupArrays()});c(b,"setupArrays",function(){this.chains=Array(8);this.loadScript=new JU.SB;this.bsAtoms=new JU.BS;this.bsAtomsDeleted=new JU.BS});c(b,"set",function(a,d,b,c,f,e){this.ms=a;this.dataSourceFrame=this.modelIndex=d;this.trajectoryBaseIndex=(this.isTrajectory=0<=b)?b:d;null==e&&(e=new java.util.Hashtable);this.auxiliaryInfo=e;a=e.get("biosymmetryCount");null!=a&&(this.biosymmetryCount=

a.intValue(),this.biosymmetry=e.get("biosymmetry"));a=e.get("fileName");null!=a&&e.put("fileName",JV.FileManager.stripTypePrefix(a));this.properties=f;null==c?this.jmolFrameType="modelSet":(this.jmolData=c,this.isJmolDataFrame=!0,e.put("jmolData",c),e.put("title",c),this.jmolFrameType=0<=c.indexOf("ramachandran")?"ramachandran":0<=c.indexOf("quaternion")?"quaternion":"data");return this},"JM.ModelSet,~N,~N,~S,java.util.Properties,java.util.Map");c(b,"getTrueAtomCount",function(){return JU.BSUtil.andNot(this.bsAtoms,

this.bsAtomsDeleted).cardinality()});c(b,"isContainedIn",function(a){null==this.bsCheck&&(this.bsCheck=new JU.BS);this.bsCheck.clearAll();this.bsCheck.or(a);a=JU.BSUtil.andNot(this.bsAtoms,this.bsAtomsDeleted);this.bsCheck.and(a);return this.bsCheck.equals(a)},"JU.BS");c(b,"resetBoundCount",function(){this.bondCount=-1});c(b,"getBondCount",function(){if(0<=this.bondCount)return this.bondCount;var a=this.ms.bo;this.bondCount=0;for(var d=this.ms.bondCount;0<=--d;)null!=a[d]&&a[d].atom1.mi==this.modelIndex&&

this.bondCount++;return this.bondCount});c(b,"getChainCount",function(a){if(1<this.chainCount&&!a)for(a=0;a<this.chainCount;a++)if(0==this.chains[a].chainID)return this.chainCount-1;return this.chainCount},"~B");c(b,"calcSelectedGroupsCount",function(a){for(var d=this.chainCount;0<=--d;)this.chains[d].calcSelectedGroupsCount(a)},"JU.BS");c(b,"getGroupCount",function(){if(0>this.groupCount){this.groupCount=0;for(var a=this.chainCount;0<=--a;)this.groupCount+=this.chains[a].groupCount}return this.groupCount});

c(b,"getChainAt",function(a){return a<this.chainCount?this.chains[a]:null},"~N");c(b,"getChain",function(a){for(var d=this.chainCount;0<=--d;){var b=this.chains[d];if(b.chainID==a)return b}return null},"~N");c(b,"resetDSSR",function(a){this.dssrCache=null;a&&this.auxiliaryInfo.remove("dssr")},"~B");c(b,"fixIndices",function(a,d,b){this.fixIndicesM(a,d,b)},"~N,~N,JU.BS");c(b,"fixIndicesM",function(a,d,b){this.dataSourceFrame>a&&this.dataSourceFrame--;this.trajectoryBaseIndex>a&&this.trajectoryBaseIndex--;

this.firstAtomIndex-=d;for(a=0;a<this.chainCount;a++)this.chains[a].fixIndices(d,b);JU.BSUtil.deleteBits(this.bsAtoms,b);JU.BSUtil.deleteBits(this.bsAtomsDeleted,b)},"~N,~N,JU.BS");c(b,"freeze",function(){this.freezeM();return!1});c(b,"freezeM",function(){for(var a=0;a<this.chainCount;a++)if(0==this.chains[a].groupCount){for(var d=a+1;d<this.chainCount;d++)this.chains[d-1]=this.chains[d];this.chainCount--}this.chains=JU.AU.arrayCopyObject(this.chains,this.chainCount);this.groupCount=-1;this.getGroupCount();

for(a=0;a<this.chainCount;++a)this.chains[a].groups=JU.AU.arrayCopyObject(this.chains[a].groups,this.chains[a].groupCount)});c(b,"setSimpleCage",function(a){null!=(this.simpleCage=a)&&this.auxiliaryInfo.put("unitCellParams",a.getUnitCellParams())},"J.api.SymmetryInterface")});u("JM");C(["java.util.Hashtable","JU.BS"],"JM.ModelLoader","java.util.Arrays JU.AU $.Lst $.P3 $.PT $.SB $.V3 J.api.Interface JM.AtomCollection $.Chain $.Group $.Model $.ModelSet JS.T JU.BSUtil $.Elements $.JmolMolecule $.Logger JV.JC".split(" "),

function(){var b=v(function(){this.modelSet0=this.ms=this.vwr=null;this.appendNew=this.merging=!1;this.specialAtomIndexes=this.group3Counts=this.group3Lists=this.jmolData=null;this.doAddPDBHydrogens=this.doMinimize=this.isPyMOLsession=this.isTrajectory=this.isMutate=this.isMOL2D=this.is2D=this.someModelsAreModulated=this.someModelsHaveUnitcells=!1;this.groups=this.jbr=this.fileHeader=null;this.groupCount=0;this.modulationTUV=null;this.noH=!1;this.firstAtomIndexes=this.seqcodes=this.group3Of=this.chainOf=

this.htAtomMap=null;this.iModel=0;this.model=null;this.currentChainID=0;this.isNewChain=!1;this.currentChain=null;this.currentGroupSequenceNumber=0;this.currentGroupInsertionCode="\x00";this.nullGroup=this.currentGroup3=null;this.adapterTrajectoryCount=this.adapterModelCount=this.baseTrajectoryCount=this.baseGroupIndex=this.baseAtomIndex=this.baseModelCount=this.baseModelIndex=0;this.modulationOn=this.noAutoBond=!1;this.$mergeGroups=this.appendToModelIndex=this.htGroup1=null;this.iChain=0;this.vStereo=

null;this.lastModel=-1;this.structuresDefinedInFile=null;this.stereodir=1;r(this,arguments)},JM,"ModelLoader",null);Q(b,function(){this.htAtomMap=new java.util.Hashtable;this.structuresDefinedInFile=new JU.BS});z(b,function(a,d,b,c,f,e){this.vwr=a;this.ms=new JM.ModelSet(a,d);var h=a.getModelAdapter();this.modelSet0=f;(this.merging=null!=f&&(0<f.ac||null!=f.vwr.getOperativeSymmetry()))?this.ms.canSkipLoad=!1:a.resetShapes(!1);this.ms.preserveState=a.getPreserveState();this.ms.showRebondTimes=a.getBoolean(603979934);

null==e?(this.initializeInfo(d,null),this.createModelSet(null,null,null),a.setStringProperty("_fileType","")):(this.ms.preserveState||(this.ms.canSkipLoad=!1),d=h.getAtomSetCollectionAuxiliaryInfo(c),d.put("loadScript",b),this.initializeInfo(h.getFileTypeName(c).toLowerCase().intern(),d),this.createModelSet(h,c,e),null!=d.get("lowPrecision")&&a.setBooleanPropertyTok("doublePrecision",603979831,!1),null!=this.jbr&&this.jbr.setLoader(null),this.jbr=null)},"JV.Viewer,~S,JU.SB,~O,JM.ModelSet,JU.BS");

c(b,"initializeInfo",function(a,d){this.ms.g3d=this.vwr.gdata;this.ms.modelSetTypeName=a;this.ms.isXYZ="xyz"===a;this.ms.msInfo=d;this.ms.modelSetProperties=this.ms.getInfoM("properties");this.ms.haveBioModels=this.ms.getMSInfoB(JV.JC.getBoolName(4));this.isMutate=this.ms.getMSInfoB("isMutate");this.ms.haveBioModels&&(this.jbr=this.vwr.getJBR().setLoader(this));this.jmolData=0==this.adapterModelCount?this.ms.getInfoM("jmolData"):null;this.fileHeader=this.ms.getInfoM("fileHeader");var b=this.ms.getInfoM("trajectorySteps");

if(this.isTrajectory=null!=b)this.ms.trajectory=this.newTrajectory(this.ms,b);this.isPyMOLsession=this.ms.getMSInfoB("isPyMOL");this.doAddPDBHydrogens=null!=this.jbr&&!this.isTrajectory&&!this.isPyMOLsession&&!this.ms.getMSInfoB("pdbNoHydrogens")&&(this.ms.getMSInfoB("pdbAddHydrogens")||this.vwr.getBoolean(603979894));null!=d&&(d.remove("pdbNoHydrogens"),d.remove("pdbAddHydrogens"),d.remove("trajectorySteps"),this.isTrajectory&&(this.ms.vibrationSteps=d.remove("vibrationSteps")),d.containsKey("highPrecision")&&

this.vwr.setBooleanProperty("legacyJavaFloat",!0));this.htGroup1=this.ms.getInfoM("htGroup1");b=this.ms.getInfoM("modulationOn");null!=b&&(this.modulationOn=!0,this.modulationTUV=b===Boolean.TRUE?null:b);this.noAutoBond=this.ms.getMSInfoB("noAutoBond");this.noH=this.ms.getMSInfoB("noHydrogen");this.doMinimize=((this.is2D=this.ms.getMSInfoB("is2D"))&&!this.noH||this.ms.getMSInfoB("minimize3D"))&&this.ms.getMSInfoB("doMinimize");this.adapterTrajectoryCount=this.isTrajectory?this.ms.trajectory.steps.size():

0;this.ms.someModelsHaveSymmetry=this.ms.getMSInfoB(JV.JC.getBoolName(1));this.someModelsHaveUnitcells=this.ms.getMSInfoB(JV.JC.getBoolName(2));this.someModelsAreModulated=this.ms.getMSInfoB(JV.JC.getBoolName(9));this.ms.someModelsHaveFractionalCoordinates=this.ms.getMSInfoB(JV.JC.getBoolName(1));this.merging&&(this.ms.haveBioModels=(new Boolean(this.ms.haveBioModels|this.modelSet0.haveBioModels)).valueOf(),this.ms.bioModelset=this.modelSet0.bioModelset,null!=this.ms.bioModelset&&this.ms.bioModelset.set(this.vwr,

this.ms),this.ms.someModelsHaveSymmetry=(new Boolean(this.ms.someModelsHaveSymmetry|this.modelSet0.getMSInfoB(JV.JC.getBoolName(1)))).valueOf(),this.someModelsHaveUnitcells=(new Boolean(this.someModelsHaveUnitcells|this.modelSet0.getMSInfoB(JV.JC.getBoolName(2)))).valueOf(),this.ms.someModelsHaveFractionalCoordinates=(new Boolean(this.ms.someModelsHaveFractionalCoordinates|this.modelSet0.getMSInfoB(JV.JC.getBoolName(0)))).valueOf(),this.ms.someModelsHaveAromaticBonds=(new Boolean(this.ms.someModelsHaveAromaticBonds|

this.modelSet0.someModelsHaveAromaticBonds)).valueOf(),this.ms.msInfo.put(JV.JC.getBoolName(1),Boolean.$valueOf(this.ms.someModelsHaveSymmetry)),this.ms.msInfo.put(JV.JC.getBoolName(2),Boolean.$valueOf(this.someModelsHaveUnitcells)),this.ms.msInfo.put(JV.JC.getBoolName(0),Boolean.$valueOf(this.ms.someModelsHaveFractionalCoordinates)),this.ms.msInfo.put(JV.JC.getBoolName(8),Boolean.$valueOf(this.ms.someModelsHaveAromaticBonds)))},"~S,java.util.Map");c(b,"newTrajectory",function(a,d){return J.api.Interface.getInterface("JM.Trajectory",

this.vwr,"load").set(this.vwr,a,d)},"JM.ModelSet,JU.Lst");c(b,"getGroup3",function(a){return a>=this.group3Of.length?null:this.group3Of[a]},"~N");c(b,"getFirstAtomIndex",function(a){return this.firstAtomIndexes[a]},"~N");c(b,"getAtomCount",function(){return this.ms.ac});c(b,"createModelSet",function(a,d,b){var c=null==a?0:a.getAtomCount(d,-1);0<c&&JU.Logger.info("reading "+c+" atoms");this.adapterModelCount=null==a?1:a.getAtomSetCount(d);this.appendToModelIndex=null==this.ms.msInfo?null:this.ms.msInfo.get("appendToModelIndex");

this.appendNew=!this.isMutate&&(!this.merging||null==a||1<this.adapterModelCount||this.isTrajectory||this.vwr.getBoolean(603979792)&&null==this.appendToModelIndex);this.htAtomMap.clear();this.chainOf=Array(32);this.group3Of=Array(32);this.seqcodes=E(32,0);this.firstAtomIndexes=E(32,0);this.currentChainID=2147483647;this.currentChain=null;this.currentGroupInsertionCode="\uffff";this.currentGroup3="xxxxx";this.iModel=-1;this.model=null;this.merging&&this.mergeTrajAndVib(this.modelSet0,this.ms);this.initializeAtomBondModelCounts(c);

!this.noH&&(null!=b&&(this.doMinimize||this.is2D))&&b.setBits(this.baseAtomIndex,this.baseAtomIndex+a.getAtomCount(d,0));if(null==a)this.setModelNameNumberProperties(0,-1,"",1,null,null,null);else{0<this.adapterModelCount&&(JU.Logger.info("ModelSet: haveSymmetry:"+this.ms.someModelsHaveSymmetry+" haveUnitcells:"+this.someModelsHaveUnitcells+" haveFractionalCoord:"+this.ms.someModelsHaveFractionalCoordinates),JU.Logger.info(this.adapterModelCount+" model"+(1==this.ms.mc?"":"s")+' in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.'));

b=this.ms.getInfoM("defaultOrientationQuaternion");null!=b&&(JU.Logger.info("defaultOrientationQuaternion = "+b),JU.Logger.info('Use "set autoLoadOrientation TRUE" before loading or "restore orientation DEFAULT" after loading to view this orientation.'));this.iterateOverAllNewModels(a,d);b=a.getBondIterator(d);c=null!=b;this.iterateOverAllNewAtoms(a,d,c);var f=this.vwr.getMadBond();c&&(this.ms.defaultCovalentMad=null==this.jmolData?f:0,this.iterateOverAllNewBonds(b));this.ms.defaultCovalentMad=f;

this.merging&&!this.appendNew&&(b=a.getAtomSetAuxiliaryInfo(d,0),this.ms.setInfo(this.baseModelIndex,"initialAtomCount",b.get("initialAtomCount")),this.ms.setInfo(this.baseModelIndex,"initialBondCount",b.get("initialBondCount")));this.initializeUnitCellAndSymmetry();this.initializeBonding()}this.finalizeGroupBuild();this.is2D&&this.doMinimize&&this.setupMinimization();this.doAddPDBHydrogens&&this.jbr.finalizeHydrogens();null!=a&&(this.ms.calculatePolymers(this.groups,this.groupCount,this.baseGroupIndex,

null),null!=this.jbr&&this.jbr.iterateOverAllNewStructures(a,d));this.setDefaultRendering(this.vwr.getInt(553648170));var e=this.vwr.rd;b=this.ms.ac;c=this.ms.at;for(f=this.baseAtomIndex;f<b;f++)c[f].setMadAtom(this.vwr,e);e=this.ms.am;for(f=e[this.baseModelIndex].firstAtomIndex;f<b;f++)null!=c[f]&&e[c[f].mi].bsAtoms.set(f);this.freeze();this.finalizeShapes();this.vwr.setModelSet(this.ms);this.setAtomProperties();null!=a&&a.finish(d);null!=this.modelSet0&&this.modelSet0.releaseModelSet();this.modelSet0=

null},"J.api.JmolAdapter,~O,JU.BS");c(b,"mergeTrajAndVib",function(a,d){this.baseModelCount=a.mc;this.baseTrajectoryCount=0;null==a.trajectory&&this.isTrajectory&&this.newTrajectory(a,new JU.Lst);if(!(null==a.trajectory||0==a.mc)){this.baseTrajectoryCount=a.mc;for(var b=a.trajectory.steps.size(),c=b;c<this.baseTrajectoryCount;c++)a.trajectory.steps.addLast(null);if(this.isTrajectory){if(null==a.vibrationSteps){a.vibrationSteps=new JU.Lst;for(c=b;0<=--c;)a.vibrationSteps.addLast(null)}b=d.trajectory.steps.size();

for(c=0;c<b;c++)a.trajectory.steps.addLast(d.trajectory.steps.get(c)),a.vibrationSteps.addLast(null==d.vibrationSteps?null:d.vibrationSteps.get(c))}else d.trajectory=this.newTrajectory(d,null);d.vibrationSteps=a.vibrationSteps;d.trajectory.steps=a.trajectory.steps;a.trajectory=null}},"JM.ModelSet,JM.ModelSet");c(b,"setDefaultRendering",function(a){if(!this.isPyMOLsession){for(var d=new JU.SB,b=this.ms.mc,c=this.ms.am,f=this.baseModelIndex;f<b;f++)c[f].isBioModel&&c[f].getDefaultLargePDBRendering(d,

a);0!=d.length()&&(d.append("select *;"),a=this.ms.getInfoM("jmolscript"),null==a&&(a=""),d.append(a),this.ms.msInfo.put("jmolscript",d.toString()))}},"~N");c(b,"setAtomProperties",function(){for(var a=this.ms.mc,d=this.baseModelIndex;d<a;d++){var b=this.ms.getInfo(d,"atomProperties");null!=this.jmolData&&this.addJmolDataProperties(this.ms.am[d],this.ms.getInfo(d,"jmolDataProperties"));var c=this.ms.getInfo(d,"groupPropertyList");this.ms.am[d].isBioModel&&null!=this.ms.getInfo(d,"dssr")&&this.vwr.getAnnotationParser(!0).setGroup1(this.ms,

d);if(null!=b){for(var f,b=b.entrySet().iterator();b.hasNext()&&((f=b.next())||1);){var e=f.getKey(),h=f.getValue(),k=this.ms.getModelAtomBitSetIncludingDeleted(d,!0);if(this.doAddPDBHydrogens)var m=null!=c&&JU.PT.isOneOf(e,c),h=this.jbr.fixPropertyValue(k,h,m);e="property_"+e.toLowerCase();JU.Logger.info("creating "+e+" for model "+this.ms.getModelName(d));this.vwr.setData(e,w(-1,[e,h,k,Integer.$valueOf(-1),Boolean.FALSE,f]),this.ms.ac,0,0,2147483647,0)}this.ms.setInfo(d,"atomProperties",null)}}});

c(b,"initializeAtomBondModelCounts",function(a){var d=this.adapterTrajectoryCount;if(this.merging){if(this.appendNew)this.baseModelIndex=this.baseModelCount,this.ms.mc=this.baseModelCount+this.adapterModelCount;else{this.baseModelIndex=null==this.appendToModelIndex?this.vwr.am.cmi:this.appendToModelIndex.intValue();if(0>this.baseModelIndex||this.baseModelIndex>=this.baseModelCount)this.baseModelIndex=this.baseModelCount-1;this.ms.mc=this.baseModelCount}this.ms.ac=this.baseAtomIndex=this.modelSet0.ac;

this.ms.bondCount=this.modelSet0.bondCount;this.$mergeGroups=this.modelSet0.getGroups();this.groupCount=this.baseGroupIndex=this.$mergeGroups.length;this.ms.mergeModelArrays(this.modelSet0);this.ms.growAtomArrays(this.ms.ac+a)}else this.ms.mc=this.adapterModelCount,this.ms.ac=0,this.ms.bondCount=0,this.ms.at=Array(a),this.ms.bo=Array(250+a);this.doAddPDBHydrogens&&this.jbr.initializeHydrogenAddition();1<d&&(this.ms.mc+=d-1);this.ms.am=JU.AU.arrayCopyObject(this.ms.am,this.ms.mc);this.ms.modelFileNumbers=

JU.AU.arrayCopyI(this.ms.modelFileNumbers,this.ms.mc);this.ms.modelNumbers=JU.AU.arrayCopyI(this.ms.modelNumbers,this.ms.mc);this.ms.modelNumbersForAtomLabel=JU.AU.arrayCopyS(this.ms.modelNumbersForAtomLabel,this.ms.mc);this.ms.modelNames=JU.AU.arrayCopyS(this.ms.modelNames,this.ms.mc);this.ms.frameTitles=JU.AU.arrayCopyS(this.ms.frameTitles,this.ms.mc);if(this.merging)for(a=0;a<this.modelSet0.mc;a++)(this.ms.am[a]=this.modelSet0.am[a]).ms=this.ms},"~N");c(b,"mergeGroups",function(){var a=this.modelSet0.getModelSetAuxiliaryInfo(null),

d=a.get("group3Lists"),a=a.get("group3Counts"),b=null==d?0:d.length;if(null!=d){for(var c=0;c<this.baseModelCount;c++)c<b&&(this.group3Lists[c+1]=d[c+1],this.group3Counts[c+1]=a[c+1]),this.structuresDefinedInFile.set(c);this.group3Lists[0]=d[0];this.group3Counts[0]=a[0]}!this.appendNew&&this.ms.haveBioModels&&this.structuresDefinedInFile.clear(this.baseModelIndex)});c(b,"iterateOverAllNewModels",function(a,d){this.group3Lists=Array(this.ms.mc+1);this.group3Counts=JU.AU.newInt2(this.ms.mc+1);this.structuresDefinedInFile=

new JU.BS;this.merging&&this.mergeGroups();for(var b=this.isTrajectory?this.baseTrajectoryCount:-1,c=this.baseModelIndex,f=0;f<this.adapterModelCount;++f,++c){var e=a.getAtomSetNumber(d,f),h=a.getAtomSetName(d,f),k=a.getAtomSetAuxiliaryInfo(d,f);k.containsKey("modelID")&&k.put("modelID0",k.get("modelID"));var m=k.get("modelProperties");if(!this.merging||this.appendNew){var j=k.get("fileType");this.vwr.setStringProperty("_fileType",j);this.vwr.fm.setFileType(j)}null==h&&(h=null!=this.jmolData&&2<this.jmolData.indexOf(";")?

this.jmolData.substring(this.jmolData.indexOf(":")+2,this.jmolData.indexOf(";")):this.appendNew?""+e%1E6:"");this.setModelNameNumberProperties(c,b,h,e,m,k,this.jmolData)}b=this.ms.am[null==this.appendToModelIndex?this.baseModelIndex:this.ms.mc-1];this.vwr.setSmilesString(this.ms.msInfo.get("smilesString"));f=this.ms.msInfo.remove("loadState");e=this.ms.msInfo.remove("loadScript");if(0>e.indexOf("Viewer.AddHydrogens")||!b.isModelKit){h=JU.PT.split(f,"\n");k=new JU.SB;for(f=0;f<h.length;f++)m=b.loadState.indexOf(h[f]),

(0>m||m!=b.loadState.lastIndexOf(h[f]))&&k.append(h[f]).appendC("\n");b.loadState+=b.loadScript.toString()+k.toString();b.loadScript=new JU.SB;if(0<=e.indexOf("load append ")||0<=e.indexOf('data "append '))e.insert(0,";var anew = appendNew;"),e.append(";set appendNew anew");b.loadScript.append(" ").appendSB(e).append(";\n")}if(this.isTrajectory){f=this.ms.mc-c+1;JU.Logger.info(f+" trajectory steps read");this.ms.setInfo(this.baseModelCount,"trajectoryStepCount",Integer.$valueOf(f));b=this.adapterModelCount;

for(f=c;f<this.ms.mc;f++,b++)this.ms.am[f]=this.ms.am[this.baseModelCount],this.ms.modelNumbers[f]=a.getAtomSetNumber(d,b),this.ms.modelNames[f]=a.getAtomSetName(d,b),this.structuresDefinedInFile.set(f)}this.finalizeModels(this.baseModelCount)},"J.api.JmolAdapter,~O");c(b,"setModelNameNumberProperties",function(a,d,b,c,f,e,h){if(this.appendNew){var k=null!=e&&Boolean.TRUE===e.get(JV.JC.getBoolName(4));this.ms.am[a]=k?this.jbr.getBioModel(a,d,h,f,e):(new JM.Model).set(this.ms,a,d,h,f,e);this.ms.modelNumbers[a]=

c;this.ms.modelNames[a]=b;k&&this.jbr.setGroupLists(a)}else d=e.get("PDB_CONECT_firstAtom_count_max"),null!=d&&this.ms.setInfo(a,"PDB_CONECT_firstAtom_count_max",d);d=this.ms.am;c=this.ms.at;d[a].bsAtoms.set(c.length+1);d[a].bsAtoms.clear(c.length+1);c=this.ms.getInfo(a,"altLocs");d[a].altLocCount=null==c?0:c.length;null!=c&&(c=c.toCharArray(),java.util.Arrays.sort(c),c=String.valueOf(c),this.ms.setInfo(a,"altLocs",c));c=this.ms.getInfo(a,"insertionCodes");d[a].insertionCount=null==c?0:c.length;b=

null!=this.ms.modelSetName&&this.ms.modelSetName.startsWith("Jmol Model Kit")||b.startsWith("Jmol Model Kit")||"Jme".equals(this.ms.getInfo(a,"fileType"))&&this.is2D;d[a].isModelKit=b},"~N,~N,~S,~N,java.util.Properties,java.util.Map,~S");c(b,"finalizeModels",function(a){var d=this.ms.mc;if(d!=a){var b,c=0,f=-1,e=this.ms.modelNumbers,h=this.ms.modelNames;if(this.isTrajectory)for(var k=a;++k<this.ms.mc;)e[k]=e[k-1]+1;if(0<a){if(1E6>e[0])for(k=0;k<a;k++)0==h[k].length&&(h[k]=""+e[k]),e[k]+=1E6,this.ms.modelNumbersForAtomLabel[k]=

"1."+(k+1);var m=e[a-1],m=m-m%1E6;1E6>e[a]&&(m+=1E6);for(k=a;k<d;k++)e[k]+=m}for(var j=this.ms.am,k=a;k<d;++k)if(this.ms.setInfo(k,"fileType",this.ms.modelSetTypeName),null!=this.fileHeader&&this.ms.setInfo(k,"fileHeader",this.fileHeader),m=B(e[k]/1E6),m!=f&&(c=0,f=m),c++,0==m?(b=""+this.ms.getModelNumber(k),m=1):b=m+"."+c,this.ms.modelNumbersForAtomLabel[k]=b,j[k].fileIndex=m-1,this.ms.modelFileNumbers[k]=1E6*m+c,null==h[k]||0==h[k].length)h[k]=b;if(this.merging)for(k=0;k<a;k++)j[k].ms=this.ms;for(k=

0;k<d;k++)this.ms.setInfo(k,"modelName",h[k]),this.ms.setInfo(k,"modelNumber",Integer.$valueOf(e[k]%1E6)),this.ms.setInfo(k,"modelFileNumber",Integer.$valueOf(this.ms.modelFileNumbers[k])),this.ms.setInfo(k,"modelNumberDotted",this.ms.getModelNumberDotted(k)),a=this.ms.getInfo(k,"altLocs"),null!=a&&JU.Logger.info("model "+this.ms.getModelNumberDotted(k)+" alternative locations: "+a)}},"~N");c(b,"iterateOverAllNewAtoms",function(a,d,b){var c=-1,f=0,e=!1,h=!1,k=a.getAtomIterator(d),m=a.getAtomCount(d,

-1);this.ms.setCapacity(a.getAtomCount(d,-1));d=0;var j=this.ms.am;0<this.ms.mc&&(this.nullGroup=(new JM.Group).setGroup(new JM.Chain(this.ms.am[this.baseModelIndex],32,0),"",0,-1,-1));for(;k.hasNext();){d++;var p=k.getAtomSetIndex()+this.baseModelIndex;p!=c&&(this.iChain=0,this.iModel=p,this.model=j[p],c=this.model.bsAtoms,this.merging&&(!this.appendNew&&null!=this.vwr.getOperativeSymmetry())&&(f=this.getAtomSiteBase(c)),this.currentChainID=2147483647,this.isNewChain=!0,c.set(this.ms.ac+m),c.clearAll(),

this.model.isOrderly=null==this.appendToModelIndex,e=this.model.isBioModel,c=p,h=e&&this.doAddPDBHydrogens,null!=this.jbr&&this.jbr.setHaveHsAlready(!1));var p=k.getGroup3(),q=k.getChainID();this.checkNewGroup(a,q,p,k.getSequenceNumber(),k.getInsertionCode(),h,!1);q=k.getElementNumber();h&&1==JU.Elements.getElementNumber(q)&&this.jbr.setHaveHsAlready(!0);var x=k.getAtomName(),s=h?this.getPdbCharge(p,x):k.getFormalCharge(),p=this.addAtom(e,k,x,q,f,s,p);b&&this.htAtomMap.put(k.getUniqueID(),p)}0<this.groupCount&&

h&&this.jbr.addImplicitHydrogenAtoms(a,this.groupCount-1,this.isNewChain?1:0);c=-1;a=null;b=this.ms.at;for(f=j[0].firstAtomIndex=0;f<this.ms.ac;f++)null!=b[f]&&b[f].mi>c&&(c=b[f].mi,k=j[c],k.firstAtomIndex=f,k.isOrderly=k.act==k.bsAtoms.length()-f,k=this.ms.getDefaultVdwType(c),k!==a&&(JU.Logger.info("Default Van der Waals type for model set to "+k.getVdwLabel()),a=k));JU.Logger.info(d+" atoms created")},"J.api.JmolAdapter,~O,~B");c(b,"getAtomSiteBase",function(a){for(var d=0,b=a.nextSetBit(0);0<=

b;b=a.nextSetBit(b+1)){var c=this.ms.at[b];!JM.AtomCollection.isDeleted(c)&&c.atomSite>d&&(d=c.atomSite)}return d},"JU.BS");c(b,"addJmolDataProperties",function(a,d){if(null!=d)for(var b=a.bsAtoms,c=b.cardinality(),f,e=d.entrySet().iterator();e.hasNext()&&((f=e.next())||1);){var h=f.getKey(),k=f.getValue();if(k.length!=c)break;var j=h.startsWith("property_")?1715472409:JS.T.getTokFromName(h);switch(j){default:if(JS.T.tokAttr(j,2048)){this.vwr.setAtomProperty(b,j,0,0,null,k,null);break}case 1111492629:case 1111492630:case 1111492631:h=

"property_"+h;case 1715472409:this.vwr.setData(h,w(-1,[h,k,b,Integer.$valueOf(1)]),0,0,0,0,0)}}},"JM.Model,java.util.Map");c(b,"getPdbCharge",function(a,d){return a.equals("ARG")&&d.equals("NH1")||a.equals("LYS")&&d.equals("NZ")||a.equals("HIS")&&d.equals("ND1")?1:0},"~S,~S");c(b,"addAtom",function(a,d,b,c,f,e,h){var k=d.getSymmetry(),j=d.getAtomSite()+f,A=d.getPartialCharge(),p=d.getTensors(),q=d.getOccupancy(),x=d.getBfactor(),s=d.getXYZ(),n=d.getIsHetero(),r=0>d.getPart(),u=d.getSerial(),v=d.getSeqID(),

w=d.getVib();f=d.getAltLoc();var y=d.getRadius();d=d.getBondRadius();var z=0,B=null;if(null!=b){var C;if(0<=(C=b.indexOf("\x00")))B=b.substring(C+1),b=b.substring(0,C);a&&(0<=b.indexOf("*")&&(b=b.$replace("*","'")),z=this.vwr.getJBR().lookupSpecialAtomID(b),2==z&&"CA".equalsIgnoreCase(h)&&(z=0))}a=this.ms.addAtom(this.iModel,this.nullGroup,c,b,B,u,v,j,s,y,w,e,A,q,x,p,n,r,z,k,d);a.altloc=f;return a},"~B,J.api.JmolAdapterAtomIterator,~S,~N,~N,~N,~S");c(b,"checkNewGroup",function(a,d,b,c,f,e,h){d!=this.currentChainID&&

(this.currentChainID=d,this.currentChain=this.getOrAllocateChain(this.model,d),this.currentGroupInsertionCode="\uffff",this.currentGroupSequenceNumber=-1,this.currentGroup3="xxxx",this.isNewChain=!0);d=null==b?null:b.intern();if(c!=this.currentGroupSequenceNumber||f!=this.currentGroupInsertionCode||d!==this.currentGroup3){0<this.groupCount&&e&&(this.jbr.addImplicitHydrogenAtoms(a,this.groupCount-1,this.isNewChain&&!h?1:0),this.jbr.setHaveHsAlready(!1));this.currentGroupSequenceNumber=c;this.currentGroupInsertionCode=

f;for(this.currentGroup3=d;this.groupCount>=this.group3Of.length;)this.chainOf=JU.AU.doubleLength(this.chainOf),this.group3Of=JU.AU.doubleLengthS(this.group3Of),this.seqcodes=JU.AU.doubleLengthI(this.seqcodes),this.firstAtomIndexes=JU.AU.doubleLengthI(this.firstAtomIndexes);this.firstAtomIndexes[this.groupCount]=this.ms.ac;this.chainOf[this.groupCount]=this.currentChain;this.group3Of[this.groupCount]=b;this.seqcodes[this.groupCount]=JM.Group.getSeqcodeFor(c,f);++this.groupCount}},"J.api.JmolAdapter,~N,~S,~N,~S,~B,~B");

c(b,"getOrAllocateChain",function(a,d){var b=a.getChain(d);if(null!=b)return b;a.chainCount==a.chains.length&&(a.chains=0==a.chainCount?Array(2):JU.AU.doubleLength(a.chains));return a.chains[a.chainCount++]=new JM.Chain(a,d,0==d||32==d?0:++this.iChain)},"JM.Model,~N");c(b,"iterateOverAllNewBonds",function(a){for(var d=this.isMutate&&!this.vwr.getBoolean(603979894),b=!1;a.hasNext();){var c=a.getEncodedOrder(),f=d?1:c,e=this.bondAtoms(a.getAtomUniqueID1(),a.getAtomUniqueID2(),f);null!=e&&(1<f&&(1025!=

f&&1041!=f)&&(b=!0),f=a.getRadius(),0<f&&e.setMad(ca(2E3*f)),f=a.getColix(),0<=f&&(e.colix=f),e.order|=c&98304)}b&&(this.ms.someModelsHaveSymmetry&&!this.vwr.getBoolean(603979794))&&JU.Logger.info('ModelSet: use "set appletSymmetryToBonds TRUE " to apply the file-based multiple bonds to symmetry-generated atoms.')},"J.api.JmolAdapterBondIterator");c(b,"bondAtoms",function(a,d,b){var c=this.htAtomMap.get(a);if(null==c)return JU.Logger.error("bondAtoms cannot find atomUid1?:"+a),null;a=this.htAtomMap.get(d);

if(null==a)return JU.Logger.error("bondAtoms cannot find atomUid2?:"+d),null;if(c.isBonded(a))return null;1025==b||1041==b?(d=c.getModelIndex(),d!=this.lastModel&&(this.lastModel=d,d=this.ms.getModelAuxiliaryInfo(d),this.isMOL2D=this.is2D||null!=d&&"2D".equals(d.get("dimension"))),b=this.ms.bondMutually(c,a,this.isMOL2D?b:513,this.ms.getDefaultMadFromOrder(1),0),this.isMOL2D&&(null==this.vStereo&&(this.vStereo=new JU.Lst),this.vStereo.addLast(b))):(b=this.ms.bondMutually(c,a,b,this.ms.getDefaultMadFromOrder(b),

0),b.isAromatic()&&(this.ms.someModelsHaveAromaticBonds=!0));this.ms.bondCount==this.ms.bo.length&&(this.ms.bo=JU.AU.arrayCopyObject(this.ms.bo,this.ms.bondCount+250));this.ms.setBond(this.ms.bondCount++,b);return b},"~O,~O,~N");c(b,"initializeUnitCellAndSymmetry",function(){this.someModelsAreModulated&&null==this.ms.bsModulated&&(this.ms.bsModulated=new JU.BS);var a=null!=this.modelSet0&&null!=this.modelSet0.unitCells;if(this.someModelsHaveUnitcells||a){this.ms.unitCells=Array(this.ms.mc);this.ms.haveUnitCells=

!0;for(var d=0,b=0;d<this.ms.mc;d++)if(a&&d<this.baseModelCount)this.ms.unitCells[d]=this.modelSet0.unitCells[d];else if(null!=this.ms.getModelAuxiliaryInfo(d).get("spaceGroupIndex")){this.ms.unitCells[d]=J.api.Interface.getSymmetry(this.vwr,"file");var c=null;if(this.isTrajectory){var f=this.ms.getInfoM("unitCells");null!=f&&(c=f.get(b++))}this.ms.unitCells[d].setSymmetryInfoFromFile(this.ms,d,c)}}if(this.appendNew&&this.ms.someModelsHaveSymmetry){this.ms.getAtoms(1088421903,null);a=this.ms.at;d=

this.baseAtomIndex;b=-1;for(c=0;d<this.ms.ac;d++){if(a[d].mi!=b){b=a[d].mi;c=this.baseAtomIndex+this.ms.getInfoI(b,"presymmetryAtomIndex");if(0>c)break;f=this.ms.getInfoI(b,"presymmetryAtomCount");this.ms.am[b].auxiliaryInfo.put("presymmetryAtomIndex",Integer.$valueOf(c));this.ms.setInfo(b,"asymmetricUnit",this.ms.am[b].bsAsymmetricUnit=JU.BSUtil.newBitSet2(c,c+f));c+=f}d>=c&&this.ms.bsSymmetry.set(d)}}if(this.appendNew&&this.ms.someModelsHaveFractionalCoordinates){a=this.ms.at;b=-1;c=null;f=!1;for(d=

this.baseAtomIndex;d<this.ms.ac;d++)if(a[d].mi!=b&&(b=a[d].mi,c=this.ms.getUnitCell(b),f=null!=c&&c.getCoordinatesAreFractional()),f){var e=null==this.ms.getModulation(d)?c:a[d].getUnitCell();e.toCartesian(e.toSupercell(a[d]),!1)}for(d=this.baseModelIndex;d<this.ms.mc;d++)this.ms.isTrajectory(d)&&this.ms.trajectory.setUnitCell(d)}});c(b,"initializeBonding",function(){var a=this.ms.mc,d=this.ms.am,b=0,c=this.ms.getInfoM("bsExcludeBonding");null==c&&(c=null==this.ms.getInfoM(JV.JC.getBoolName(3))?null:

new JU.BS,null!=c&&this.ms.setPdbConectBonding(this.baseAtomIndex,this.baseModelIndex,c));var f=this.vwr.getBoolean(603979794),e=this.vwr.getBoolean(603979798),h=this.vwr.getBoolean(603979848),k=null,j=!1;if(!this.noAutoBond)for(var A=this.baseModelIndex;A<a;A++){var b=d[A].bsAtoms.cardinality(),p=this.ms.getInfoI(A,"initialBondCount"),q=d[A].isBioModel;0>p&&(p=this.ms.bondCount);if(h||e&&(0==p||q&&null==this.jmolData&&(this.ms.getMSInfoB("havePDBHeaderName")||p<B(b/2))||this.ms.getInfoB(A,"hasSymmetry")&&

!f&&!this.ms.getInfoB(A,"hasBonds")))if(j=!0,this.merging||1<a)null==k&&(k=JU.BS.newN(this.ms.ac)),(A==this.baseModelIndex||!this.isTrajectory)&&k.or(d[A].bsAtoms)}this.modulationOn&&this.ms.setModulation(null,!0,this.modulationTUV,!1);j?(this.ms.autoBondBs4(k,k,c,null,this.ms.defaultCovalentMad,this.vwr.getBoolean(603979872),null),JU.Logger.info("ModelSet: autobonding; use autobond=false to not generate bonds automatically")):JU.Logger.info("ModelSet: not autobonding; use forceAutobond=true to force automatic bond creation")});

c(b,"finalizeGroupBuild",function(){this.groups=Array(this.groupCount);if(this.merging)for(var a=0;a<this.$mergeGroups.length;a++)(this.groups[a]=this.$mergeGroups[a]).chain.model.ms=this.ms;for(a=this.baseGroupIndex;a<this.groupCount;++a)this.distinguishAndPropagateGroup(a,this.chainOf[a],this.group3Of[a],this.seqcodes[a],this.firstAtomIndexes[a],(a==this.groupCount-1?this.ms.ac:this.firstAtomIndexes[a+1])-1);if(null!=this.group3Lists){this.ms.msInfo.put("group3Lists",this.group3Lists);this.ms.msInfo.put("group3Counts",

this.group3Counts);for(a=0;a<this.group3Counts.length;a++)null==this.group3Counts[a]&&(this.group3Counts[a]=E(0,0))}});c(b,"distinguishAndPropagateGroup",function(a,d,b,c,f,e){if(e<f)throw new NullPointerException;var h=null==b||null==this.jbr?null:this.jbr.distinguishAndPropagateGroup(d,b,c,f,e,this.specialAtomIndexes,this.ms.at);null==h?(h=(new JM.Group).setGroup(d,b,c,f,e),null!=this.jbr&&(h.groupID=this.jbr.getGroupID(b)),c="o>"):c=h.isProtein()?"p>":h.isNucleic()?"n>":h.isCarbohydrate()?"c>":

"o>";null!=b&&(this.countGroup(this.ms.at[f].mi,c,b),h.isNucleic()&&(b=null==this.htGroup1?null:this.htGroup1.get(b),null!=b&&(h.group1=b.charAt(0))));this.addGroup(d,h);this.groups[a]=h;h.groupIndex=a;for(a=e+1;--a>=f;)this.ms.at[a].group=h},"~N,JM.Chain,~S,~N,~N,~N");c(b,"addGroup",function(a,d){a.groupCount==a.groups.length&&(a.groups=JU.AU.doubleLength(a.groups));a.groups[a.groupCount++]=d},"JM.Chain,JM.Group");c(b,"countGroup",function(a,d,b){var c=a+1;if(!(null==this.group3Lists||null==this.group3Lists[c])){var f=

(b+" ").substring(0,3),e=this.group3Lists[c].indexOf(f);0>e&&(this.group3Lists[c]+=",["+f+"]",e=this.group3Lists[c].indexOf(f),this.group3Counts[c]=JU.AU.arrayCopyI(this.group3Counts[c],this.group3Counts[c].length+10));this.group3Counts[c][B(e/6)]++;e=this.group3Lists[c].indexOf(",["+f);0<=e&&(this.group3Lists[c]=this.group3Lists[c].substring(0,e)+d+this.group3Lists[c].substring(e+2));0<=a&&this.countGroup(-1,d,b)}},"~N,~S,~S");c(b,"freeze",function(){this.htAtomMap.clear();this.ms.ac<this.ms.at.length&&

this.ms.growAtomArrays(this.ms.ac);this.ms.bondCount<this.ms.bo.length&&(this.ms.bo=JU.AU.arrayCopyObject(this.ms.bo,this.ms.bondCount));for(var a=5;0<--a;){this.ms.numCached[a]=0;for(var d=this.ms.freeBonds[a],b=d.length;0<=--b;)d[b]=null}this.ms.setAtomNamesAndNumbers(0,this.baseAtomIndex,this.modelSet0,!1);this.findElementsPresent();this.ms.resetMolecules();this.currentChain=this.model=null;!this.ms.haveBioModels||this.isPyMOLsession||this.isMutate?this.ms.freezeModels():(a=this.vwr.getBoolean(603979826),

a=this.ms.calculateStructuresAllExcept(this.structuresDefinedInFile,a,!1,!0,!0,a,1405E3<=JV.JC.versionInt&&null==this.ms.getInfoM("DSSP1")?2:1),0<a.length&&JU.Logger.info(a))});c(b,"findElementsPresent",function(){this.ms.elementsPresent=Array(this.ms.mc);for(var a=0;a<this.ms.mc;a++)this.ms.elementsPresent[a]=JU.BS.newN(64);for(a=this.ms.ac;0<=--a;){var d=this.ms.at[a];if(null!=d){var b=d.getAtomicAndIsotopeNumber();b>=JU.Elements.elementNumberMax&&(b=JU.Elements.elementNumberMax+JU.Elements.altElementIndexFromNumber(b));

this.ms.elementsPresent[d.mi].set(b)}}});c(b,"setupMinimization",function(){this.initialize2DMin();var a=new JU.V3;if(null!=this.vStereo){var d=this.vStereo.size();a:for(;0<=--d;)for(var b=this.vStereo.get(d),c=b.atom1,f=c.bonds,e=c.getBondCount();0<=--e;){var h=f[e];if(h!==b&&(h=h.getOtherAtom(c),a.sub2(h,c),0.1>Math.abs(a.x))){1025==b.order==0>a.y&&(this.stereodir=-1);break a}}}this.set2dZ(a);if(null!=this.vStereo){a=JU.BSUtil.newBitSet2(this.baseAtomIndex,this.vwr.ms.ac);for(d=this.vStereo.size();0<=

--d;){b=this.vStereo.get(d);c=1025==b.order?3:-3;b.order=1;6>b.atom1.getBondCount()&&(b.atom2.z!=b.atom1.z&&0>c==b.atom2.z<b.atom1.z)&&(c/=3);f=JU.JmolMolecule.getBranchBitSet(this.ms.at,b.atom2.i,a,null,b.atom1.i,!1,!0);f.set(b.atom2.i);for(e=f.nextSetBit(0);0<=e;e=f.nextSetBit(e+1))this.ms.at[e].z+=c;b.atom2.x=(b.atom1.x+b.atom2.x)/2;b.atom2.y=(b.atom1.y+b.atom2.y)/2}this.vStereo=null}this.is2D=!1});c(b,"initialize2DMin",function(){for(var a=0,d=0,b=-1,c=this.baseAtomIndex,f=this.vwr.ms.ac,e=c;e<

f;e++){var h=this.ms.at[e],k=h.getModelIndex();k!=b&&(b=k,this.ms.setInfo(k,"dimension","3D"));k=h.bonds;if(null!=k)for(var j=k.length;0<=--j;)if(null!=k[j]){var A=k[j].getOtherAtom(h);1!=A.getAtomNumber()&&A.getIndex()>e&&(a+=A.distance(h),d++)}}if(0!=d){a=1.45/(a/d);for(e=c;e<f;e++)this.ms.at[e].scale(a)}});c(b,"set2dZ",function(a){var d=this.baseAtomIndex,b=this.vwr.ms.ac,c=JU.BS.newN(b),f=new JU.BS,e=JU.V3.new3(0,1,0),h=new JU.V3,k=new JU.BS;for(k.setBits(d,b);d<b;d++)!c.get(d)&&!f.get(d)&&(f=

this.getBranch2dZ(d,-1,k,f,a,e,h,this.stereodir),c.or(f))},"JU.V3");c(b,"getBranch2dZ",function(a,d,b,c,f,e,h,k){c=JU.BS.newN(this.ms.ac);if(0>a)return c;b=JU.BSUtil.copy(b);0<=d&&b.clear(d);JM.ModelLoader.setBranch2dZ(this.ms.at[a],c,b,f,e,h,k);return c},"~N,~N,JU.BS,JU.BS,JU.V3,JU.V3,JU.V3,~N");b.setBranch2dZ=c(b,"setBranch2dZ",function(a,d,b,c,f,e,h){var k=a.i;if(b.get(k)&&(b.clear(k),d.set(k),null!=a.bonds))for(k=a.bonds.length;0<=--k;){var j=a.bonds[k];j.isHydrogen()||(j=j.getOtherAtom(a),JM.ModelLoader.setAtom2dZ(a,

j,c,f,e,h),JM.ModelLoader.setBranch2dZ(j,d,b,c,f,e,h))}},"JM.Atom,JU.BS,JU.BS,JU.V3,JU.V3,JU.V3,~N");b.setAtom2dZ=c(b,"setAtom2dZ",function(a,d,b,c,f,e){b.sub2(d,a);b.z=0;b.normalize();f.cross(c,b);b=Math.acos(b.dot(c));e=0.4*-e*Math.sin(4*b);d.z=a.z+e},"JM.Atom,JM.Atom,JU.V3,JU.V3,JU.V3,~N");c(b,"finalizeShapes",function(){this.ms.sm=this.vwr.shm;this.ms.sm.setModelSet(this.ms);this.ms.setBsHidden(this.vwr.slm.getHiddenSet());this.merging||this.ms.sm.resetShapes(!1);this.ms.sm.loadDefaultShapes(this.ms);

this.ms.someModelsHaveAromaticBonds&&this.vwr.getBoolean(603979944)&&this.ms.assignAromaticBondsBs(!1,null);this.merging&&1==this.baseModelCount&&this.ms.sm.setShapePropertyBs(6,"clearModelIndex",null,null)});c(b,"undeleteAtom",function(a){this.ms.at[a].valence=0},"~N");b.createAtomDataSet=c(b,"createAtomDataSet",function(a,d,b,c,f){if(null==c)return null;var e=a.getModelAdapter(),h=new JU.P3,k=d.at,j=a.getFloat(570425363);if(null!=d.unitCells)for(var A=f.nextSetBit(0);0<=A;A=f.nextSetBit(A+1))if(null!=

k[A].atomSymmetry){j=-j;break}for(var A=-1,p=0,q=JU.BSUtil.cardinalityOf(f)==a.ms.ac,x=e.getAtomIterator(c);x.hasNext();){var s=x.getXYZ();if(!Float.isNaN(s.x+s.y+s.z))if(1145047049==b){A=f.nextSetBit(A+1);if(0>A)break;p++;JU.Logger.debugging&&JU.Logger.debug("atomIndex = "+A+": "+k[A]+" --\x3e ("+s.x+","+s.y+","+s.z);d.setAtomCoord(A,s.x,s.y,s.z)}else{h.setT(s);s=JU.BS.newN(d.ac);d.getAtomsWithin(j,h,s,-1);s.and(f);if(q)if(p=JU.BSUtil.cardinalityOf(s),0==p){JU.Logger.warn("createAtomDataSet: no atom found at position "+

h);continue}else 1<p&&JU.Logger.debugging&&JU.Logger.debug("createAtomDataSet: "+p+" atoms found at position "+h);switch(b){case 1145047055:var n=x.getVib();if(null==n)continue;JU.Logger.debugging&&JU.Logger.debug("xyz: "+h+" vib: "+n);d.setAtomCoords(s,1145047055,n);break;case 1128269825:d.setAtomProperty(s,b,0,x.getOccupancy(),null,null,null);break;case 1111492619:d.setAtomProperty(s,b,0,x.getPartialCharge(),null,null,null);break;case 1111492620:d.setAtomProperty(s,b,0,x.getBfactor(),null,null,

null)}}}switch(b){case 1145047055:d=e.getAtomSetName(c,0);JU.Logger.info("_vibrationName = "+d);a.setStringProperty("_vibrationName",d);break;case 1145047049:if(JU.Logger.info(p+" atom positions read"),d.recalculateLeadMidpointsAndWingVectors(-1),p==d.ac)return"boundbox {*};reset"}return null},"JV.Viewer,JM.ModelSet,~N,~O,JU.BS")});u("JM");C(["JM.BondCollection"],"JM.ModelSet","java.util.Hashtable JU.A4 $.AU $.BS $.Lst $.M3 $.M4 $.Measure $.P3 $.P4 $.PT $.Quat $.SB $.V3 J.api.Interface J.atomdata.RadiusData J.bspt.Bspf J.c.PAL $.VDW JM.Atom $.AtomIteratorWithinModel $.AtomIteratorWithinModelSet $.HBond $.Model $.StateScript JS.ScriptCompiler JU.BSUtil $.BoxInfo $.Edge $.Elements $.Escape $.JmolMolecule $.Logger JV.JC".split(" "),

function(){var b=v(function(){this.haveBioModels=!1;this.am=this.modelSetName=this.bsSymmetry=null;this.mc=0;this.unitCells=null;this.haveUnitCells=!1;this.elementsPresent=this.frameTitles=this.modelNames=this.modelNumbersForAtomLabel=this.modelFileNumbers=this.modelNumbers=this.closest=null;this.isXYZ=!1;this.msInfo=this.modelSetProperties=null;this.isBbcageDefault=this.someModelsHaveFractionalCoordinates=this.someModelsHaveAromaticBonds=this.someModelsHaveSymmetry=!1;this.stateScripts=this.boxInfo=

this.bboxAtoms=this.bboxModels=null;this.thisStateModel=0;this.selectedMolecules=this.vibrationSteps=null;this.showRebondTimes=!0;this.sm=this.bsAll=null;this.proteinStructureTainted=!1;this.defaultBBox=this.vTemp=this.mat4t=this.mat4=this.matInv=this.matTemp=this.ptTemp2=this.ptTemp1=this.ptTemp=this.vOrientations=this.htPeaks=null;this.echoShapeActive=this.haveJmolDataFrames=!1;this.translations=this.modelSetTypeName=null;this.maxBondWarned=!1;r(this,arguments)},JM,"ModelSet",JM.BondCollection);

z(b,function(a,d){L(this,JM.ModelSet,[]);this.vwr=a;this.modelSetName=d;this.selectedMolecules=new JU.BS;this.stateScripts=new JU.Lst;this.boxInfo=new JU.BoxInfo;this.boxInfo.addBoundBoxPoint(JU.P3.new3(-10,-10,-10));this.boxInfo.addBoundBoxPoint(JU.P3.new3(10,10,10));this.am=Array(1);this.modelNumbers=E(1,0);this.modelFileNumbers=E(1,0);this.modelNumbersForAtomLabel=Array(1);this.modelNames=Array(1);this.frameTitles=Array(1);this.closest=Array(1);this.ptTemp=new JU.P3;this.ptTemp1=new JU.P3;this.ptTemp2=

new JU.P3;this.matTemp=new JU.M3;this.matInv=new JU.M3;this.mat4=new JU.M4;this.mat4t=new JU.M4;this.vTemp=new JU.V3;this.setupBC()},"JV.Viewer,~S");c(b,"getBoxInfo",function(){return this.boxInfo});c(b,"releaseModelSet",function(){this.am=null;this.mc=0;this.unitCells=this.bsAll=this.bsSymmetry=this.am=this.closest[0]=null;this.releaseModelSetBC()});c(b,"getEchoStateActive",function(){return this.echoShapeActive});c(b,"setEchoStateActive",function(a){this.echoShapeActive=a},"~B");c(b,"getModelSetTypeName",

function(){return this.modelSetTypeName});c(b,"getModelNumberIndex",function(a,d,b){if(d){for(d=0;d<this.mc;d++)if(this.modelNumbers[d]==a||1E6>a&&this.modelNumbers[d]==1E6+a)return d;return-1}if(1E6>a)return a;for(d=0;d<this.mc;d++)if(this.modelFileNumbers[d]==a)return b&&this.isTrajectory(d)&&this.setTrajectory(d),d;return-1},"~N,~B,~B");c(b,"getModelDataBaseName",function(a){for(var d=0;d<this.mc;d++)if(a.equals(this.am[d].bsAtoms))return this.getInfo(d,"dbName");return null},"JU.BS");c(b,"setTrajectory",

function(a){0<=a&&(this.isTrajectory(a)&&this.at[this.am[a].firstAtomIndex].mi!=a)&&this.trajectory.setModel(a)},"~N");c(b,"getBitSetTrajectories",function(){return null==this.trajectory?null:this.trajectory.getModelsSelected()});c(b,"setTrajectoryBs",function(a){if(null!=this.trajectory)for(var d=0;d<this.mc;d++)a.get(d)&&this.setTrajectory(d)},"JU.BS");c(b,"morphTrajectories",function(a,d,b){0<=a&&(0<=d&&this.isTrajectory(a)&&this.isTrajectory(d))&&this.trajectory.morph(a,d,b)},"~N,~N,~N");c(b,

"getTranslation",function(a){return null==this.translations||a>=this.translations.length?null:this.translations[a]},"~N");c(b,"translateModel",function(a,d){if(null==d){var b=this.getTranslation(a);null!=b&&(d=JU.P3.newP(b),d.scale(-1),this.translateModel(a,d),this.translations[a]=null)}else{if(null==this.translations||this.translations.length<=a)this.translations=Array(this.mc);null==this.translations[a]&&(this.translations[a]=new JU.P3);this.translations[a].add(d);for(var b=this.am[a].bsAtoms,c=

b.nextSetBit(0);0<=c;c=b.nextSetBit(c+1))this.at[c].add(d)}},"~N,JU.T3");c(b,"getFrameOffsets",function(a,d){if(null==a){if(d)for(var b=this.mc;0<=--b;){var c=this.am[b];!c.isJmolDataFrame&&!c.isTrajectory&&this.translateModel(c.modelIndex,null)}return null}if(0>a.nextSetBit(0))return null;if(d){for(var f=JU.BSUtil.copy(a),e=null,h=new JU.P3,b=0;b<this.mc;b++){c=this.am[b];if(!c.isJmolDataFrame&&!c.isTrajectory){var k=f.nextSetBit(0);c.bsAtoms.get(k)&&(null==e?e=JU.P3.newP(this.at[k]):(h.sub2(e,this.at[k]),

this.translateModel(b,h)))}f.andNot(c.bsAtoms)}return null}f=Array(this.mc);for(b=this.mc;0<=--b;)f[b]=new JU.P3;for(var h=e=0,k=null,j=null!=this.trajectory&&this.trajectory.steps.size()==this.mc,A=j?this.mc:1,c=0;c<A;c++){j&&this.setTrajectory(c);for(b=0;b<=this.ac;b++)if(!(b<this.ac&&JM.AtomCollection.isDeleted(this.at[b]))){if(b==this.ac||this.at[b].mi!=e){0<h&&(k.scale(-1/h),0!=e&&k.sub(f[0]),h=0);if(b==this.ac)break;e=this.at[b].mi;k=f[e]}a.get(b)&&(k.add(this.at[b]),h++)}}f[0].set(0,0,0);return f},

"JU.BS,~B");c(b,"getAtoms",function(a,d){switch(a){default:return JU.BSUtil.andNot(this.getAtomBitsMaybeDeleted(a,d),this.vwr.slm.bsDeleted);case 1073742358:var b=d.intValue(),c=this.getModelNumberIndex(b,!0,!0);return 0>c&&0<b?new JU.BS:this.vwr.getModelUndeletedAtomsBitSet(c);case 1275203608:return b=w(-1,[null,null,null]),this.vwr.shm.getShapePropertyData(21,"getCenters",b),null==b[1]?new JU.BS:b[1]}},"~N,~O");c(b,"findNearestAtomIndex",function(a,d,b,c){if(0==this.ac)return-1;this.closest[0]=

null;this.g3d.isAntialiased()&&(a<<=1,d<<=1);this.findNearest2(a,d,this.closest,b,c);this.sm.findNearestShapeAtomIndex(a,d,this.closest,b);a=null==this.closest[0]?-1:this.closest[0].i;this.closest[0]=null;return a},"~N,~N,JU.BS,~N");c(b,"calculatePointGroup",function(a){return this.calculatePointGroupForFirstModel(a,!1,!1,null,0,0,null,null,null)},"JU.BS");c(b,"getPointGroupInfo",function(a){return this.calculatePointGroupForFirstModel(a,!1,!0,null,0,0,null,null,null)},"JU.BS");c(b,"getPointGroupAsString",

function(a,d,b,c,f,e,h){return this.calculatePointGroupForFirstModel(a,!0,!1,d,b,c,f,e,h)},"JU.BS,~S,~N,~N,~A,JU.P3,~S");c(b,"calculatePointGroupForFirstModel",function(a,d,b,c,f,e,h,k,j){var A=this.pointGroup,p=J.api.Interface.getSymmetry(this.vwr,"ms"),q=null,x=!1,s=!1,n=!1,r=null!=h,u=this.vwr.am.cmi;if(!r)if(h=null==a?-1:a.nextSetBit(0),0>u&&0<=h&&(u=this.at[h].mi),0>u&&(u=this.vwr.getVisibleFramesBitSet().nextSetBit(0),a=null),q=this.vwr.getModelUndeletedAtomsBitSet(u),n=null!=a&&q.cardinality()!=

a.cardinality(),null!=a&&q.and(a),h=q.nextSetBit(0),0>h&&(q=this.vwr.getModelUndeletedAtomsBitSet(u),h=q.nextSetBit(0)),s=this.vwr.shm.getShapePropertyIndex(18,"mad",h),x=null!=s&&0!=s.intValue()||this.vwr.tm.vibrationOn,s=null!=c&&0<=c.toUpperCase().indexOf(":POLY")){A=w(-1,[Integer.$valueOf(h),null]);this.vwr.shm.getShapePropertyData(21,"points",A);h=A[1];if(null==h)return null;q=null;x=!1;A=null}else h=this.at;var v;if(null!=c&&0<=(v=c.indexOf(":")))c=c.substring(0,v);if(null!=c&&0<=(v=c.indexOf(".")))f=

JU.PT.parseInt(c.substring(v+1)),0>f&&(f=0),c=c.substring(0,v);A=p.setPointGroup(this.vwr,A,k,h,q,x,r?0:this.vwr.getFloat(570425382),this.vwr.getFloat(570425384),null==q?h.length:q.cardinality(),n);!s&&!r&&(this.pointGroup=A);if(!d&&!b)return A.getPointGroupName();d=A.getPointGroupInfo(u,j,b,c,f,e);return b?d:(1<this.mc?"frame "+this.getModelNumberDotted(u)+"; ":"")+d},"JU.BS,~B,~B,~S,~N,~N,~A,JU.P3,~S");c(b,"getDefaultStructure",function(a,d){return this.haveBioModels?this.bioModelset.getAllDefaultStructures(a,

d):""},"JU.BS,JU.BS");c(b,"deleteModelBonds",function(a){a=this.getModelAtomBitSetIncludingDeleted(a,!1);this.makeConnections(0,3.4028235E38,131071,12291,a,a,null,!1,!1,0)},"~N");c(b,"makeConnections",function(a,d,b,c,f,e,h,k,j,A){this.moleculeCount=0;var p=1073741852==c&&2048!=b?new JU.SB:null;a=this.makeConnections2(a,d,b,c,f,e,h,k,j,A,p);null!=p&&this.addStateScript(p.toString(),null,null,null,null,!1,!0);return a},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");c(b,"setPdbConectBonding",function(a,

d,b){for(var c=this.vwr.getMadBond();d<this.mc;d++){var f=this.getInfo(d,"PDB_CONECT_bonds");if(null!=f){var e=f.size();this.setInfo(d,"initialBondCount",Integer.$valueOf(e));var h=this.getInfo(d,"PDB_CONECT_firstAtom_count_max"),k=h[0]+a,j=k+h[1];j>this.atomSerials.length&&(j=this.atomSerials.length);for(var h=h[2],A=E(h+1,0),p=k;p<j;p++)if(0<(k=this.atomSerials[p]))A[k]=p+1;for(j=0;j<e;j++){var k=f.get(j),p=k[0],q=k[1],k=k[2];if(!(0>p||0>q||p>h||q>h))if(p=A[p]-1,q=A[q]-1,!(0>p||0>q)){var x=this.at[p],

s=this.at[q];null!=b&&(x.isHetero()&&b.set(p),s.isHetero()&&b.set(q));if(x.altloc==s.altloc||"\x00"==x.altloc||"\x00"==s.altloc)this.getOrAddBond(x,s,k,2048==k?1:c,null,0,!1)}}}}},"~N,~N,JU.BS");c(b,"deleteAllBonds",function(){this.moleculeCount=0;for(var a=this.stateScripts.size();0<=--a;)this.stateScripts.get(a).isConnect()&&this.stateScripts.removeItemAt(a);this.deleteAllBonds2()});c(b,"includeAllRelatedFrames",function(a){for(var d=0,b=0;b<this.mc;b++){var c=this.isTrajectory(b),f=c&&a.get(d=

this.am[b].trajectoryBaseIndex);if(a.get(b)){if(c&&!f){a.set(d);this.includeAllRelatedFrames(a);break}}else(c||this.isJmolDataFrameForModel(b)&&a.get(this.am[b].dataSourceFrame))&&a.set(b)}},"JU.BS");c(b,"deleteModels",function(a){this.includeAllRelatedFrames(a);var d=a.cardinality();if(0==d)return null;this.moleculeCount=0;null!=this.msInfo&&this.msInfo.remove("models");for(var b=new JU.BS,c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1))this.clearDataFrameReference(c),b.or(this.am[c].bsAtoms);var f;if(d==

this.mc)return f=this.getModelAtomBitSetIncludingDeleted(-1,!0),this.vwr.zap(!0,!1,!1),f;this.validateBspf(!1);f=new JU.BS;for(var e=!0,h=!1,k=new JU.BS,j=b.nextSetBit(0),c=0;c<this.mc;c++)b=this.am[c],c<this.mc-1&&(e=(new Boolean(e&(b.isOrderly||b.bsAtoms.length()<=j))).valueOf()),a.get(c)?(0<=b.fileIndex&&k.set(b.fileIndex),f.or(this.getModelAtomBitSetIncludingDeleted(c,!1))):0<=b.fileIndex&&k.get(b.fileIndex)&&(h=!0);if(!e||h)return this.vwr.deleteAtoms(f,!1),null;d=Array(this.mc-d);e=this.am;

for(h=c=0;c<this.mc;c++)a.get(c)||(b=this.am[c],b.modelIndex=h,d[h++]=b);this.am=d;b=this.mc;k=this.getBondsForSelectedAtoms(f,!0);this.deleteBonds(k,!0);for(h=c=0;c<b;c++)if(a.get(c)){var A=e[c],j=A.act;if(0!=j){var p=A.bsAtoms,A=A.firstAtomIndex;JU.BSUtil.deleteBits(this.bsSymmetry,p);this.deleteModel(h,p,k);this.deleteModelAtoms(A,j,p);this.vwr.deleteModelAtoms(h,A,j,p);for(var q=b;--q>c;)e[q].fixIndices(h,j,p);this.vwr.shm.deleteShapeAtoms(w(-1,[d,this.at,E(-1,[h,A,j])]),p);this.mc--}}else h++;

this.haveBioModels=!1;for(c=this.mc;0<=--c;)this.am[c].isBioModel&&(this.haveBioModels=!0,this.bioModelset.set(this.vwr,this));this.validateBspf(!1);this.bsAll=null;this.resetMolecules();this.isBbcageDefault=!1;this.calcBoundBoxDimensions(null,1);return f},"JU.BS");c(b,"resetMolecules",function(){this.molecules=this.bsAll=null;this.moleculeCount=0;this.resetChirality()});c(b,"resetChirality",function(){if(this.haveChirality)for(var a=-1,d=this.ac;0<=--d;){var b=this.at[d];null!=b&&(b.setCIPChirality(0),

b.mi!=a&&b.mi<this.am.length&&(this.am[a=b.mi].hasChirality=!1))}});c(b,"deleteModel",function(a,d,b){if(!(0>a)){this.modelNumbers=JU.AU.deleteElements(this.modelNumbers,a,1);this.modelFileNumbers=JU.AU.deleteElements(this.modelFileNumbers,a,1);this.modelNumbersForAtomLabel=JU.AU.deleteElements(this.modelNumbersForAtomLabel,a,1);this.modelNames=JU.AU.deleteElements(this.modelNames,a,1);this.frameTitles=JU.AU.deleteElements(this.frameTitles,a,1);this.thisStateModel=-1;var c=this.getInfoM("group3Lists"),

f=this.getInfoM("group3Counts"),e=a+1;if(null!=c&&null!=c[e])for(var h=B(c[e].length/6);0<=--h;)0<f[e][h]&&(f[0][h]-=f[e][h],0==f[0][h]&&(c[0]=c[0].substring(0,6*h)+",["+c[0].substring(6*h+2)));null!=c&&(this.msInfo.put("group3Lists",JU.AU.deleteElements(c,a,1)),this.msInfo.put("group3Counts",JU.AU.deleteElements(f,a,1)));null!=this.unitCells&&(this.unitCells=JU.AU.deleteElements(this.unitCells,a,1));for(h=this.stateScripts.size();0<=--h;)this.stateScripts.get(h).deleteAtoms(a,b,d)||this.stateScripts.removeItemAt(h)}},

"~N,JU.BS,JU.BS");c(b,"setAtomProperty",function(a,d,b,c,f,e,h){switch(d){case 1114249217:case 1112152066:case 1112152071:case 1112152073:case 1112152074:case 1649022989:case 1112152078:if(4<c&&(c=4),null!=e){b=K(this.ac,0);try{var k=a.nextSetBit(0);for(f=0;0<=k;k=a.nextSetBit(k+1))b[k]=e[f++]}catch(j){if(F(j,Exception))return;throw j;}e=b}case 1112152070:case 1112152076:k=null;b=0;null==e?(16<c&&(c=16.1),0>c&&(c=0),b=B(Math.floor(2E3*c))):k=new J.atomdata.RadiusData(e,0,null,null);this.sm.setShapeSizeBs(JV.JC.shapeTokenIndex(d),

b,k,a);return}this.setAPm(a,d,b,c,f,e,h)},"JU.BS,~N,~N,~N,~S,~A,~A");c(b,"getFileData",function(a){if(0>a)return"";var d=this.getInfo(a,"fileData");if(null!=d)return d;if(!this.getInfoB(a,"isCIF"))return this.getPDBHeader(a);d=this.vwr.getCifData(a);this.setInfo(a,"fileData",d);return d},"~N");c(b,"addHydrogens",function(a,d){var b=a.get(0).mi,c=new JU.BS;if(this.isTrajectory(b)||1<this.am[b].getGroupCount())return c;this.growAtomArrays(this.ac+d.length);var f=this.vwr.rd,e=this.getDefaultMadFromOrder(1);

this.am[b].resetDSSR(!1);for(var h=0,k=this.am[b].act+1;h<a.size();h++,k++){var j=a.get(h),A=this.addAtom(b,j.group,1,"H"+k,null,k,j.getSeqID(),k,d[h],NaN,null,0,0,100,NaN,null,!1,!1,0,null,NaN);A.setMadAtom(this.vwr,f);c.set(A.i);this.bondAtoms(j,A,1,e,null,0,!1,!1)}this.sm.loadDefaultShapes(this);return c},"JU.Lst,~A");c(b,"mergeModelArrays",function(a){this.at=a.at;this.bo=a.bo;this.stateScripts=a.stateScripts;this.proteinStructureTainted=a.proteinStructureTainted;this.thisStateModel=-1;this.bsSymmetry=

a.bsSymmetry;this.modelFileNumbers=a.modelFileNumbers;this.modelNumbersForAtomLabel=a.modelNumbersForAtomLabel;this.modelNames=a.modelNames;this.modelNumbers=a.modelNumbers;this.frameTitles=a.frameTitles;this.haveChirality=a.haveChirality;this.boxInfo.setBoundBox(a.boxInfo.bbCorner0,a.boxInfo.bbCorner1,!0,1);null!=this.msInfo&&this.msInfo.remove("models");this.mergeAtomArrays(a)},"JM.ModelSet");c(b,"getUnitCell",function(a){var d=-2147483648==a;d&&(a=this.vwr.am.cmi);if(0>a||a>=this.mc)return null;

this.isTrajectory(a)&&(a=this.am[a].trajectoryBaseIndex);var b=this.am[a].simpleCage,c=null;null!=this.unitCells&&(a<this.unitCells.length&&null!=this.unitCells[a]&&this.unitCells[a].haveUnitCell())&&(c=this.unitCells[a]);if(null!=c&&d)return null==b?this.setModelCagePts(a,c.getUnitCellVectors(),"cage"):b;if(null==c||null!=b&&!c.isSymmetryCell(b))c=b;return c},"~N");c(b,"setModelCagePts",function(a,d,b){if(0>a&&0>(a=this.vwr.am.cmi))return null;var c=this.vwr.getSymTemp();try{return this.setModelCage(a,

null==d?null:c.getUnitCell(d,!1,b))}catch(f){if(F(f,Exception))return f.printStackTrace(),null;throw f;}},"~N,~A,~S");c(b,"getModelName",function(a){return 1>this.mc?"":0<=a?this.modelNames[a]:this.modelNumbersForAtomLabel[-1-a]},"~N");c(b,"getModelTitle",function(a){return this.getInfo(a,"title")},"~N");c(b,"getModelFileName",function(a){return this.getInfo(a,"fileName")},"~N");c(b,"getModelFileType",function(a){return this.getInfo(a,"fileType")},"~N");c(b,"setFrameTitle",function(a,d){if("string"==

typeof d)for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.frameTitles[b]=d;else for(var b=a.nextSetBit(0),c=0;0<=b;b=a.nextSetBit(b+1))c<d.length&&(this.frameTitles[b]=d[c++])},"JU.BS,~O");c(b,"getFrameTitle",function(a){return 0<=a&&a<this.mc?this.frameTitles[a]:""},"~N");c(b,"getModelNumberForAtomLabel",function(a){return this.modelNumbersForAtomLabel[a]},"~N");c(b,"getGroups",function(){for(var a=0,d=0;d<this.mc;d++)a+=this.am[d].getGroupCount();for(var a=Array(a),b=d=0;d<this.mc;d++)for(var c=

0;c<this.am[d].chainCount;c++)for(var f=0;f<this.am[d].chains[c].groupCount;f++)a[b]=this.am[d].chains[c].groups[f],a[b].groupIndex=b,b++;return a});c(b,"setCrystallographicDefaults",function(){return!this.haveBioModels&&(this.someModelsHaveSymmetry&&this.someModelsHaveFractionalCoordinates||null!=this.getUnitCell(this.vwr.am.cmi))});c(b,"getBoundBoxCenter",function(a){return this.isJmolDataFrameForModel(a)?new JU.P3:(null==this.getDefaultBoundBox()?this.boxInfo:this.defaultBBox).getBoundBoxCenter()},

"~N");c(b,"getBoundBoxCornerVector",function(){return this.boxInfo.getBoundBoxCornerVector()});c(b,"getBBoxVertices",function(){return this.boxInfo.getBoundBoxVertices()});c(b,"setBoundBox",function(a,d,b,c){0==c&&null!=this.msInfo&&(this.msInfo.remove("boundbox"),this.defaultBBox=null,this.isBbcageDefault=!1,this.calcBoundBoxDimensions(null,c=1));this.isBbcageDefault=!1;this.bboxAtoms=this.bboxModels=null;this.boxInfo.setBoundBox(a,d,b,c)},"JU.T3,JU.T3,~B,~N");c(b,"getBoundBoxCommand",function(a){if(!a&&

null!=this.bboxAtoms)return"boundbox "+JU.Escape.eBS(this.bboxAtoms);this.ptTemp.setT(this.boxInfo.getBoundBoxCenter());var d=this.boxInfo.getBoundBoxCornerVector();a=a?"boundbox "+JU.Escape.eP(this.ptTemp)+" "+JU.Escape.eP(d)+"\n#or\n":"";this.ptTemp.sub(d);a+="boundbox corners "+JU.Escape.eP(this.ptTemp)+" ";this.ptTemp.scaleAdd2(2,d,this.ptTemp);d=Math.abs(8*d.x*d.y*d.z);return a+=JU.Escape.eP(this.ptTemp)+" # volume = "+d},"~B");c(b,"findAtomsInRectangle",function(a){for(var d=this.vwr.getVisibleFramesBitSet(),

b=new JU.BS,c=this.ac;0<=--c;){var f=this.at[c];JM.AtomCollection.isDeleted(f)||(d.get(f.mi)?f.checkVisible()&&a.contains(f.sX,f.sY)&&b.set(c):c=this.am[f.mi].firstAtomIndex)}return b},"JU.Rectangle");c(b,"getDefaultVdwType",function(a){return!this.am[a].isBioModel?J.c.VDW.AUTO_BABEL:0==this.am[a].hydrogenCount?J.c.VDW.AUTO_JMOL:J.c.VDW.AUTO_BABEL},"~N");c(b,"setRotationRadius",function(a,d){return this.isJmolDataFrameForModel(a)?(this.am[a].defaultRotationRadius=d,!1):!0},"~N,~N");c(b,"calcRotationRadius",

function(a,d,b){if(this.isJmolDataFrameForModel(a))return a=this.am[a].defaultRotationRadius,0==a?10:a;if(b&&null!=this.getDefaultBoundBox())return 1.2*(this.defaultBBox.getMaxDim()/2);if(0==this.ac)return 10;a=-2;b=0;for(var c=this.ac;0<=--c;){var f=this.at[c];if(!JM.AtomCollection.isDeleted(f))if(this.isJmolDataFrameForAtom(f)){for(a=f.mi;0<=c&&null!=this.at[c]&&this.at[c].mi==a;)c--;c++}else{if(f.mi!=a){a=f.mi;var e=this.am[a].isBioModel?null:this.getUnitCell(a);if(null!=e)for(var h=e.getUnitCellVerticesNoOffset(),

e=e.getCartesianOffset(),k=0;8>k;k++)this.ptTemp.setT(h[k]),this.ptTemp.add(e),b=Math.max(b,d.distance(this.ptTemp))}f=d.distance(f)+this.getRadiusVdwJmol(f);f>b&&(b=f)}}return 0==b?10:b},"~N,JU.P3,~B");c(b,"calcBoundBoxDimensions",function(a,d){null!=a&&0>a.nextSetBit(0)&&(a=null);if(!(null==a&&this.isBbcageDefault||0==this.ac)){if(null==this.getDefaultBoundBox())this.bboxModels=this.getModelBS(this.bboxAtoms=JU.BSUtil.copy(a),!1),this.calcAtomsMinMax(a,this.boxInfo)==this.ac&&(this.isBbcageDefault=

!0),null==a&&null!=this.unitCells&&this.calcUnitCellMinMax();else{var b=this.defaultBBox.getBoundBoxVertices();this.boxInfo.reset();for(var c=0;8>c;c++)this.boxInfo.addBoundBoxPoint(b[c])}this.boxInfo.setBbcage(d)}},"JU.BS,~N");c(b,"getDefaultBoundBox",function(){var a=this.getInfoM("boundbox");null==a?this.defaultBBox=null:(null==this.defaultBBox&&(this.defaultBBox=new JU.BoxInfo),this.defaultBBox.setBoundBoxFromOABC(a));return this.defaultBBox});c(b,"getBoxInfo",function(a,d){if(null==a)return this.boxInfo;

b=b.getCartesianOffset(),f=0;8>f;f++)a.add2(b,c[f]),this.boxInfo.addBoundBoxPoint(a)}});c(b,"calcRotationRadiusBs",function(a){for(var d=this.getAtomSetCenter(a),b=0,c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1)){var f=this.at[c],f=d.distance(f)+this.getRadiusVdwJmol(f);f>b&&(b=f)}return 0==b?10:b},"JU.BS");c(b,"getCenterAndPoints",function(a,d){for(var b,c,f=d?1:0,e=a.size();0<=--e;){var h=a.get(e);b=h[0];y(h[1],"JU.BS")?(c=h[1],f+=Math.min(b.cardinality(),c.cardinality())):f+=Math.min(b.cardinality(),

h[1].length)}var k=w(2,f,null);d&&(k[0][0]=new JU.P3,k[1][0]=new JU.P3);for(e=a.size();0<=--e;)if(h=a.get(e),b=h[0],y(h[1],"JU.BS")){c=h[1];for(var h=b.nextSetBit(0),j=c.nextSetBit(0);0<=h&&0<=j;h=b.nextSetBit(h+1),j=c.nextSetBit(j+1))k[0][--f]=this.at[h],k[1][f]=this.at[j],d&&(k[0][0].add(this.at[h]),k[1][0].add(this.at[j]))}else{c=h[1];h=b.nextSetBit(0);for(j=0;0<=h&&j<c.length;h=b.nextSetBit(h+1),j++)k[0][--f]=this.at[h],k[1][f]=c[j],d&&(k[0][0].add(this.at[h]),k[1][0].add(c[j]))}d&&(k[0][0].scale(1/

(k[0].length-1)),k[1][0].scale(1/(k[1].length-1)));return k},"JU.Lst,~B");c(b,"getAtomSetCenter",function(a){for(var d=new JU.P3,b=0,c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1))this.isJmolDataFrameForAtom(this.at[c])||(b++,d.add(this.at[c]));1<b&&d.scale(1/b);return d},"JU.BS");c(b,"getAverageAtomPoint",function(){return this.getAtomSetCenter(this.vwr.bsA())});c(b,"setAPm",function(a,d,b,c,f,e,h){this.setAPa(a,d,b,c,f,e,h);switch(d){case 1094715418:case 1631586315:this.vwr.getBoolean(603979944)&&this.assignAromaticBondsBs(!0,

null)}},"JU.BS,~N,~N,~N,~S,~A,~A");c(b,"addStateScript",function(a,d,b,c,f,e,h){var k=this.vwr.am.cmi;e?(this.thisStateModel!=k&&(a="frame "+(0>k?"all #"+k:this.getModelNumberDotted(k))+";\n "+a),this.thisStateModel=k):this.thisStateModel=-1;a=new JM.StateScript(this.thisStateModel,a,d,b,c,f,h);a.isValid()&&this.stateScripts.addLast(a);return a},"~S,JU.BS,JU.BS,JU.BS,~S,~B,~B");c(b,"freezeModels",function(){this.haveBioModels=!1;for(var a=this.mc;0<=--a;)this.haveBioModels=(new Boolean(this.haveBioModels|

this.am[a].freeze())).valueOf()});c(b,"getStructureList",function(){return this.vwr.getStructureList()});c(b,"getInfoM",function(a){return null==this.msInfo?null:this.msInfo.get(a)},"~S");c(b,"getMSInfoB",function(a){a=this.getInfoM(a);return y(a,Boolean)&&a.booleanValue()},"~S");c(b,"isTrajectory",function(a){return this.am[a].isTrajectory},"~N");c(b,"isTrajectorySubFrame",function(a){return this.am[a].trajectoryBaseIndex!=a},"~N");c(b,"isTrajectoryMeasurement",function(a){return null!=this.trajectory&&

this.trajectory.hasMeasure(a)},"~A");c(b,"getModelBS",function(a,d){var b=new JU.BS,c=0,f=null==a;d=(new Boolean(d&null!=this.trajectory)).valueOf();for(var e=f?0:a.nextSetBit(0);0<=e&&e<this.ac;e=f?e+1:a.nextSetBit(e+1))JM.AtomCollection.isDeleted(this.at[e])||(b.set(c=this.at[e].mi),d&&this.trajectory.getModelBS(c,b),c=this.am[c],c.isOrderly&&(e=c.firstAtomIndex+c.act-1));return b},"JU.BS,~B");c(b,"getIterativeModels",function(a){for(var d=new JU.BS,b=0;b<this.mc;b++)if(a||!this.isJmolDataFrameForModel(b))this.isTrajectorySubFrame(b)||

d.set(b);return d},"~B");c(b,"fillAtomData",function(a,d){if(0!=(d&4)){this.getMolecules();a.bsMolecules=Array(this.molecules.length);a.atomMolecule=E(this.ac,0);for(var b,c=0;c<this.molecules.length;c++){b=a.bsMolecules[c]=this.molecules[c].atomList;for(var f=b.nextSetBit(0);0<=f;f=b.nextSetBit(f+1))a.atomMolecule[f]=c}}0!=(d&8)?(b=E(1,0),a.hAtomRadius=this.vwr.getVanderwaalsMar(1)/1E3,a.hAtoms=this.calculateHydrogens(a.bsSelected,b,null,512),a.hydrogenAtomCount=b[0]):(a.firstAtomIndex=0>a.modelIndex?

null==a.bsSelected?0:Math.max(0,a.bsSelected.nextSetBit(0)):this.am[a.modelIndex].firstAtomIndex,a.lastModelIndex=a.firstModelIndex=0==this.ac?0:this.at[a.firstAtomIndex].mi,a.modelName=this.getModelNumberDotted(a.firstModelIndex),this.fillADa(a,d))},"J.atomdata.AtomData,~N");c(b,"getModelNumberDotted",function(a){return 1>this.mc||a>=this.mc||0>a?"":JU.Escape.escapeModelFileNumber(this.modelFileNumbers[a])},"~N");c(b,"getModelNumber",function(a){return this.modelNumbers[2147483647==a?this.mc-1:a]},

"~N");c(b,"getModelProperty",function(a,d){var b=this.am[a].properties;return null==b?null:b.getProperty(d)},"~N,~S");c(b,"getModelAuxiliaryInfo",function(a){return 0>a?null:this.am[a].auxiliaryInfo},"~N");c(b,"setInfo",function(a,d,b){0<=a&&a<this.mc&&(null==b?this.am[a].auxiliaryInfo.remove(d):this.am[a].auxiliaryInfo.put(d,b))},"~N,~O,~O");c(b,"getInfo",function(a,d){return 0>a?null:this.am[a].auxiliaryInfo.get(d)},"~N,~S");c(b,"getInfoB",function(a,d){var b=this.am[a].auxiliaryInfo;return null!=

b&&b.containsKey(d)&&b.get(d).booleanValue()},"~N,~S");c(b,"getInfoI",function(a,d){var b=this.am[a].auxiliaryInfo;return null!=b&&b.containsKey(d)?b.get(d).intValue():-2147483648},"~N,~S");c(b,"getInsertionCountInModel",function(a){return this.am[a].insertionCount},"~N");b.modelFileNumberFromFloat=c(b,"modelFileNumberFromFloat",function(a){var d=B(Math.floor(a));for(a=B(Math.floor(1E4*(a-d+1E-5)));0!=a&&0==a%10;)a/=10;return 1E6*d+a},"~N");c(b,"getChainCountInModelWater",function(a,d){if(0>a){for(var b=

0,c=this.mc;0<=--c;)b+=this.am[c].getChainCount(d);return b}return this.am[a].getChainCount(d)},"~N,~B");c(b,"getGroupCountInModel",function(a){if(0>a){a=0;for(var d=this.mc;0<=--d;)a+=this.am[d].getGroupCount();return a}return this.am[a].getGroupCount()},"~N");c(b,"calcSelectedGroupsCount",function(){for(var a=this.vwr.bsA(),d=this.mc;0<=--d;)this.am[d].calcSelectedGroupsCount(a)});c(b,"isJmolDataFrameForModel",function(a){return this.haveJmolDataFrames&&null!=this.am&&0<=a&&a<this.mc&&this.am[a].isJmolDataFrame},

"~N");c(b,"isJmolDataFrameForAtom",function(a){return this.haveJmolDataFrames&&this.am[a.mi].isJmolDataFrame},"JM.Atom");c(b,"setJmolDataFrame",function(a,d,b){this.haveJmolDataFrames=!0;var c=this.am[null==a?this.am[b].dataSourceFrame:d];null==a&&(a=this.am[b].jmolFrameType);0<=d&&(null==c.dataFrames&&(c.dataFrames=new java.util.Hashtable),this.am[b].dataSourceFrame=d,this.am[b].jmolFrameType=a,c.dataFrames.put(a,Integer.$valueOf(b)));a.startsWith("quaternion")&&0>a.indexOf("deriv")&&(a=a.substring(0,

a.indexOf(" ")),c.dataFrames.put(a,Integer.$valueOf(b)))},"~S,~N,~N");c(b,"getJmolDataFrameIndex",function(a,d){if(null==this.am[a].dataFrames)return-1;var b=this.am[a].dataFrames.get(d);return null==b?-1:b.intValue()},"~N,~S");c(b,"clearDataFrameReference",function(a){for(var d=0;d<this.mc;d++){var b=this.am[d].dataFrames;if(null!=b)for(b=b.values().iterator();b.hasNext();)b.next().intValue()==a&&b.remove()}},"~N");c(b,"getJmolFrameType",function(a){return 0<=a&&a<this.mc?this.am[a].jmolFrameType:

"modelSet"},"~N");c(b,"getJmolDataSourceFrame",function(a){return 0<=a&&a<this.mc?this.am[a].dataSourceFrame:-1},"~N");c(b,"saveModelOrientation",function(a,d){this.am[a].orientation=d},"~N,JM.Orientation");c(b,"getModelOrientation",function(a){return this.am[a].orientation},"~N");c(b,"getPDBHeader",function(a){return this.am[a].isBioModel?this.am[a].getFullPDBHeader():this.getFileHeader(a)},"~N");c(b,"getFileHeader",function(a){if(0>a)return"";if(this.am[a].isBioModel)return this.getPDBHeader(a);

a=this.getInfo(a,"fileHeader");null==a&&(a=this.modelSetName);return null!=a?a:"no header information found"},"~N");c(b,"getAltLocCountInModel",function(a){return this.am[a].altLocCount},"~N");c(b,"getAltLocIndexInModel",function(a,d){if("\x00"==d)return 0;var b=this.getAltLocListInModel(a);return 0==b.length?0:b.indexOf(d)+1},"~N,~S");c(b,"getInsertionCodeIndexInModel",function(a,d){if("\x00"==d)return 0;var b=this.getInsertionListInModel(a);return 0==b.length?0:b.indexOf(d)+1},"~N,~S");c(b,"getAltLocListInModel",

function(a){a=this.getInfo(a,"altLocs");return null==a?"":a},"~N");c(b,"getInsertionListInModel",function(a){a=this.getInfo(a,"insertionCodes");return null==a?"":a},"~N");c(b,"getModelSymmetryCount",function(a){return 0<this.am[a].biosymmetryCount?this.am[a].biosymmetryCount:null==this.unitCells||null==this.unitCells[a]?0:this.unitCells[a].getSpaceGroupOperationCount()},"~N");c(b,"getModelCellRange",function(a){return null==this.unitCells?null:this.unitCells[a].getCellRange()},"~N");c(b,"getLastVibrationVector",

function(a,d){if(null!=this.vibrations&&a<this.vwr.ms.mc)for(var b,c=0>a||this.isTrajectory(a)||a>=this.mc-1?this.ac:this.am[a+1].firstAtomIndex,f=0>=a?0:this.am[a].firstAtomIndex;--c>=f;)if((0>a||!JM.AtomCollection.isDeleted(this.at[c])&&this.at[c].mi==a)&&((1275072532==d||0==d)&&null!=(b=this.getModulation(c))||(4166==d||0==d)&&null!=(b=this.getVibration(c,!1)))&&b.isNonzero())return c;return-1},"~N,~N");c(b,"getModulationList",function(a,d,b){var c=new JU.Lst;if(null!=this.vibrations)for(var f=

a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1))y(this.vibrations[f],"J.api.JmolModulationSet")?c.addLast(this.vibrations[f].getModulation(d,b,!1)):c.addLast(Float.$valueOf("O"==d?NaN:-1));return c},"JU.BS,~S,JU.P3");c(b,"getElementsPresentBitSet",function(a){if(0<=a)return this.elementsPresent[a];a=new JU.BS;for(var d=0;d<this.mc;d++)a.or(this.elementsPresent[d]);return a},"~N");c(b,"getMoleculeIndex",function(a,d){0==this.moleculeCount&&this.getMolecules();for(var b=0;b<this.moleculeCount;b++)if(this.molecules[b].atomList.get(a))return d?

this.molecules[b].indexInModel:b;return 0},"~N,~B");c(b,"getMoleculeBitSet",function(a){0==this.moleculeCount&&this.getMolecules();var d=JU.BSUtil.copy(a);a=JU.BSUtil.copy(a);for(var b=0,c=new JU.BS;0<=(b=a.length()-1);)c=this.getMoleculeBitSetForAtom(b),null==c?(a.clear(b),d.clear(b)):(a.andNot(c),d.or(c));return d},"JU.BS");c(b,"getMoleculeBitSetForAtom",function(a){0==this.moleculeCount&&this.getMolecules();for(var d=0;d<this.moleculeCount;d++)if(this.molecules[d].atomList.get(a))return this.molecules[d].atomList;

return null},"~N");c(b,"getModelDipole",function(a){if(0>a)return null;var d=this.getInfo(a,"dipole");null==d&&(d=this.getInfo(a,"DIPOLE_VEC"));return d},"~N");c(b,"calculateMolecularDipole",function(a,d){if(null!=d){var b=d.nextSetBit(0);if(0>b)return null;a=this.at[b].mi}if(0>a)return null;var c=b=0,f=0,e=0,h=new JU.V3,k=new JU.V3;null==d&&(d=this.getModelAtomBitSetIncludingDeleted(-1,!1));this.vwr.getOrCalcPartialCharges(this.am[a].bsAtoms,null);for(var j=d.nextSetBit(0);0<=j;j=d.nextSetBit(j+

1))if(!(JM.AtomCollection.isDeleted(this.at[j])||this.at[j].mi!=a)){var A=this.partialCharges[j];0>A?(c++,e+=A,k.scaleAdd2(A,this.at[j],k)):0<A&&(b++,f+=A,h.scaleAdd2(A,this.at[j],h))}if(0.015<Math.abs(f+e))return JU.Logger.info("Dipole calculation requires balanced charges: "+f+" "+e),null;if(0==c||0==b)return null;h.add(k);h.scale(4.8);return h},"~N,JU.BS");c(b,"getMoleculeCountInModel",function(a){var d=0;0==this.moleculeCount&&this.getMolecules();if(0>a)return this.moleculeCount;for(var b=0;b<

this.mc;b++)a==b&&(d+=this.am[b].moleculeCount);return d},"~N");c(b,"calcSelectedMoleculesCount",function(){var a=this.vwr.bsA();0==this.moleculeCount&&this.getMolecules();this.selectedMolecules.xor(this.selectedMolecules);for(var d=new JU.BS,b=0;b<this.moleculeCount;b++)JU.BSUtil.copy2(a,d),d.and(this.molecules[b].atomList),0<d.length()&&this.selectedMolecules.set(b)});c(b,"setCentroid",function(a,d){var b=this.getNotInCentroid(a,d);null!=b&&0<=b.nextSetBit(0)&&this.vwr.deleteAtoms(b,!1)},"JU.BS,~A");

c(b,"getNotInCentroid",function(a,d){var b=a.nextSetBit(0);if(0>b)return null;b=this.getUnitCell(this.at[b].mi);return null==b?null:b.notInCentroid(this,a,d)},"JU.BS,~A");c(b,"getMolecules",function(){if(0<this.moleculeCount)return this.molecules;null==this.molecules&&(this.molecules=Array(4));this.moleculeCount=0;for(var a=null,d=Array(this.mc),b=null,c=0;c<this.mc;c++)d[c]=this.vwr.getModelUndeletedAtomsBitSet(c),a=this.am[c],a.moleculeCount=0,b=a.isBioModel?a.getBioBranches(b):null;this.molecules=

JU.JmolMolecule.getMolecules(this.at,d,b,null);for(c=this.moleculeCount=this.molecules.length;0<=--c;)a=this.am[this.molecules[c].modelIndex],a.firstMoleculeIndex=c,a.moleculeCount++;return this.molecules});c(b,"initializeBspf",function(){if(!(null!=this.bspf&&this.bspf.isValid)){this.showRebondTimes&&JU.Logger.startTimer("build bspf");var a=new J.bspt.Bspf(3);JU.Logger.debugging&&JU.Logger.debug("sequential bspt order");for(var d=JU.BS.newN(this.mc),b=this.ac;0<=--b;){var c=this.at[b];!JM.AtomCollection.isDeleted(c)&&

!this.isTrajectorySubFrame(c.mi)&&(a.addTuple(this.am[c.mi].trajectoryBaseIndex,c),d.set(c.mi))}this.showRebondTimes&&(JU.Logger.checkTimer("build bspf",!1),a.stats());for(b=d.nextSetBit(0);0<=b;b=d.nextSetBit(b+1))a.validateModel(b,!0);a.isValid=!0;this.bspf=a}});c(b,"initializeBspt",function(a){this.initializeBspf();this.bspf.isInitializedIndex(a)||this.bspf.initialize(a,this.at,this.vwr.getModelUndeletedAtomsBitSet(a))},"~N");c(b,"setIteratorForPoint",function(a,d,b,c){0>d?a.setCenter(b,c):(this.initializeBspt(d),

a.setModel(this,d,this.am[d].firstAtomIndex,2147483647,b,c,null))},"J.api.AtomIndexIterator,~N,JU.T3,~N");c(b,"setIteratorForAtom",function(a,d,b,c,f){0>d&&(d=this.at[b].mi);d=this.am[d].trajectoryBaseIndex;this.initializeBspt(d);a.setModel(this,d,this.am[d].firstAtomIndex,b,this.at[b],c,f)},"J.api.AtomIndexIterator,~N,~N,~N,J.atomdata.RadiusData");c(b,"getSelectedAtomIterator",function(a,d,b,c,f){this.initializeBspf();if(f){f=this.getModelBS(a,!1);for(var e=f.nextSetBit(0);0<=e;e=f.nextSetBit(e+

1))this.initializeBspt(e);f=new JM.AtomIteratorWithinModelSet(f)}else f=new JM.AtomIteratorWithinModel;f.initialize(this.bspf,a,d,b,c,this.vwr.isParallel());return f},"JU.BS,~B,~B,~B,~B");j(b,"getBondCountInModel",function(a){return 0>a?this.bondCount:this.am[a].getBondCount()},"~N");c(b,"getAtomCountInModel",function(a){return 0>a?this.ac:this.am[a].act},"~N");c(b,"getModelAtomBitSetIncludingDeletedBs",function(a){var d=new JU.BS;null==a&&null==this.bsAll&&(this.bsAll=JU.BSUtil.setAll(this.ac));

if(null==a)d.or(this.bsAll);else for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))d.or(this.getModelAtomBitSetIncludingDeleted(b,!1));return d},"JU.BS");c(b,"getModelAtomBitSetIncludingDeleted",function(a,d){var b=0>a?this.bsAll:this.am[a].bsAtoms;null==b&&(b=this.bsAll=JU.BSUtil.setAll(this.ac));return d?JU.BSUtil.copy(b):b},"~N,~B");c(b,"getAtomBitsMaybeDeleted",function(a,d){var b;switch(a){default:return this.getAtomBitsMDa(a,d,new JU.BS);case 1073741925:case 1073742189:case 1111490587:case 1073742128:case 1073741863:case 1086324744:return b=

new JU.BS,this.haveBioModels?this.bioModelset.getAtomBitsStr(a,d,b):b;case 1677721602:case 1073742331:return this.getAtomBitsMDb(a,d);case 1812599299:var c=this.getBoxInfo(d,1);b=this.getAtomsWithin(c.getBoundBoxCornerVector().length()+1E-4,c.getBoundBoxCenter(),null,-1);for(var f=b.nextSetBit(0);0<=f;f=b.nextSetBit(f+1))c.isWithin(this.at[f])||b.clear(f);return b;case 1094713350:b=JU.BSUtil.newBitSet2(0,this.ac);f=d;c=E(-1,[D(f.x)-1,D(f.y)-1,D(f.z)-1,D(f.x),D(f.y),D(f.z),0]);for(f=this.mc;0<=--f;){var e=

this.getUnitCell(f);null==e?JU.BSUtil.andNot(b,this.am[f].bsAtoms):b.andNot(e.notInCentroid(this,this.am[f].bsAtoms,c))}return b;case 1094713360:return this.getMoleculeBitSet(d);case 1073742363:return this.getSelectCodeRange(d);case 2097196:b=JU.BS.newN(this.ac);c=-1;e=0;for(f=this.ac;0<=--f;){var h=this.at[f];if(!JM.AtomCollection.isDeleted(h)){var k=h.atomSymmetry;if(null!=k){if(h.mi!=c){c=h.mi;if(null==this.getModelCellRange(c))continue;e=this.getModelSymmetryCount(c)}for(var h=0,j=e;0<=--j;)if(k.get(j)&&

1<++h){b.set(f);break}}}}return b;case 1088421903:return JU.BSUtil.copy(null==this.bsSymmetry?this.bsSymmetry=JU.BS.newN(this.ac):this.bsSymmetry);case 1814695966:if("unitcell".equals(d))d=JU.P3.new3(1,1,1);else{b=new JU.BS;e=y(d,"J.api.SymmetryInterface")?d:this.vwr.getCurrentUnitCell();if(null==e)return b;e=e.getUnitCellMultiplied();for(f=this.ac;0<=--f;)null!=this.at[f]&&(this.ptTemp1.setT(this.at[f]),e.toFractional(this.ptTemp1,!1),e.checkPeriodic(this.ptTemp1)&&b.set(f));return b}case 1094713349:b=

new JU.BS;c=d;e=this.vwr.getSymTemp();System.out.println("MS test within");k=-1;for(f=this.ac;0<=--f;)JM.AtomCollection.isDeleted(this.at[f])||(h=this.at[f].getModelIndex(),k!=h&&(k=h,e=this.getUnitCell(k)),null!=e&&(this.ptTemp.setT(this.at[f]),e.toFractional(this.ptTemp,!1),e.isWithinUnitCell(this.ptTemp,c.x,c.y,c.z)&&b.set(f)));System.out.println("MS test within"+b);return b}},"~N,~O");c(b,"getSelectCodeRange",function(a){var d=new JU.BS,b=a[0],c=a[1];a=a[2];var f=this.vwr.getBoolean(603979822);

0<=a&&(300>a&&!f)&&(a=this.chainToUpper(a));for(var e=this.mc;0<=--e;)if(this.am[e].isBioModel)for(var h=this.am[e],k,j=h.chainCount;0<=--j;){var A=h.chains[j];if(-1==a||a==(k=A.chainID)||!f&&0<k&&300>k&&a==this.chainToUpper(k))for(var p=A.groups,A=A.groupCount,q=0;0<=q;)q=JM.ModelSet.selectSeqcodeRange(p,A,q,b,c,d)}return d},"~A");b.selectSeqcodeRange=c(b,"selectSeqcodeRange",function(a,d,b,c,f,e){var h,k,j,A=!1;for(k=b;k<d&&a[k].seqcode!=c;k++);if(k==d){if(0<b)return-1;A=!0;j=2147483647;for(var p=

d;0<=--p;)if((h=a[p].seqcode)>c&&h-c<j)k=p,j=h-c;if(2147483647==j)return-1}if(2147483647==f)c=d-1,A=!0;else{for(c=k;c<d&&a[c].seqcode!=f;c++);if(c==d){if(0<b)return-1;A=!0;j=2147483647;for(p=k;p<d;p++)if((h=a[p].seqcode)<f&&f-h<j)c=p,j=f-h;if(2147483647==j)return-1}}for(p=k;p<=c;++p)a[p].setAtomBits(e);return A?-1:c+1},"~A,~N,~N,~N,~N,JU.BS");c(b,"getAtomsWithinRadius",function(a,d,b,c,f){var e=new JU.BS;d=JU.BSUtil.andNot(d,this.vwr.slm.bsDeleted);var h=this.getSelectedAtomIterator(f,!1,!1,!1,!1);

if(b){b=!this.vwr.g.legacyJavaFloat;var k=new JU.P3;f=null==f?JU.BSUtil.newBitSet2(0,this.mc):this.getModelBS(f,!1);f.and(this.getIterativeModels(!1));for(var j=d.nextSetBit(0);0<=j;j=d.nextSetBit(j+1))for(var A=f.nextSetBit(0);0<=A;A=f.nextSetBit(A+1))0>a?this.getAtomsWithin(a,this.at[j].getFractionalUnitCoordPt(b,!0,k),e,A):(this.setIteratorForAtom(h,A,j,a,c),h.addAtoms(e))}else{null==f&&e.or(d);for(j=d.nextSetBit(0);0<=j;j=d.nextSetBit(j+1))0>a?this.getAtomsWithin(a,this.at[j],e,this.at[j].mi):

(this.setIteratorForAtom(h,-1,j,a,c),h.addAtoms(e))}h.release();return e},"~N,JU.BS,~B,J.atomdata.RadiusData,JU.BS");c(b,"getAtomsWithin",function(a,d,b,c){null==b&&(b=new JU.BS);if(0>a){a=-a;for(var f=this.ac;0<=--f;){var e=this.at[f];JM.AtomCollection.isDeleted(e)||0<=c&&e.mi!=c||!b.get(f)&&e.getFractionalUnitDistance(d,this.ptTemp1,this.ptTemp2)<=a&&b.set(e.i)}return b}for(var e=this.getSelectedAtomIterator(null,!1,!1,!1,!1),h=0<=c?JU.BSUtil.newAndSetBit(c):this.getIterativeModels(!0),k=h.nextSetBit(0);0<=

k;k=h.nextSetBit(k+1))f=this.am[k].bsAtoms.nextSetBit(0),0>f||(this.setIteratorForAtom(e,c,f,-1,null),e.setCenter(d,a),e.addAtoms(b));e.release();return b},"~N,JU.T3,JU.BS,~N");c(b,"deleteBonds",function(a,d){if(!d)for(var b=new JU.BS,c=new JU.BS,f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1)){var e=this.bo[f];if(null!=e){var h=e.atom1;this.am[h.mi].isModelKit||(b.clearAll(),c.clearAll(),b.set(h.i),c.set(e.getAtomIndex2()),this.addStateScript("connect ",null,b,c,"delete",!1,!0))}}this.dBb(a,d)},"JU.BS,~B");

c(b,"makeConnections2",function(a,d,b,c,f,e,h,k,j,A,p){null==h&&(h=new JU.BS);var q=65535==b,x=131071==b,s=65537==b;x&&(b=1);var n=JU.Edge.isOrderH(b),r=!1,u=!1,v=!1,w=!1;switch(c){case 12291:return this.deleteConnections(a,d,b,f,e,k,x);case 603979872:case 1073741852:if(515!=b){if(k){a=f;f=new JU.BS;e=new JU.BS;for(var y=a.nextSetBit(0);0<=y;y=a.nextSetBit(y+1))null!=this.bo[y]&&(f.set(this.bo[y].atom1.i),e.set(this.bo[y].atom2.i))}return E(-1,[n?this.autoHbond(f,e,!1):this.autoBondBs4(f,e,null,h,

this.vwr.getMadBond(),603979872==c,p),0])}u=w=!0;break;case 1086324745:r=u=!0;break;case 1073742025:u=!0;break;case 1073741904:v=!0}c=!r&&!q;this.defaultCovalentMad=this.vwr.getMadBond();p=0>a;var x=0>d,z=p||x,B=!k||0.1!=a||1E8!=d;B&&(a=this.fixD(a,p),d=this.fixD(d,x));var C=this.getDefaultMadFromOrder(b),D=0,H=0,I=null,K=null,L=null,O="\x00",P=b|131072,Q=65535!=b&&0!=(b&512);try{for(y=f.nextSetBit(0);0<=y;y=f.nextSetBit(y+1)){if(k){I=this.bo[y];if(null==I)continue;K=I.atom1;L=I.atom2}else{K=this.at[y];

if(K.isDeleted())continue;O=this.isModulated(y)?"\x00":K.altloc}for(var R=k?0:e.nextSetBit(0);0<=R;R=e.nextSetBit(R+1)){if(k)R=2147483646;else{if(R==y)continue;L=this.at[R];if(null==L||K.mi!=L.mi||L.isDeleted())continue;if("\x00"!=O&&O!=L.altloc&&"\x00"!=L.altloc)continue;I=K.getBond(L)}if(!(null==I?u:v)&&!(B&&!this.isInRange(K,L,a,d,p,x,z)||Q&&null!=I&&!this.allowAromaticBond(I)))if(null==I)h.set(this.bondAtoms(K,L,b,C,h,A,j,!0).index),D++;else if(c&&(I.setOrder(b),s&&(this.haveAtropicBonds=!0,I.setAtropisomerOptions()),

this.bsAromatic.clear(I.index)),q||b==I.order||P==I.order||n&&I.isHydrogen())h.set(I.index),H++}}}catch(T){if(!F(T,Exception))throw T;}w&&this.assignAromaticBondsBs(!0,h);r||this.sm.setShapeSizeBs(1,-2147483648,null,h);return E(-1,[D,H])},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N,JU.SB");c(b,"autoBondBs4",function(a,d,b,c,f,e,h){if(e)return this.autoBond_Pre_11_9_24(a,d,b,c,f);if(0==this.ac)return 0;0==f&&(f=1);1.4E-45==this.maxBondingRadius&&this.findMaxRadii();e=this.vwr.getFloat(570425348);var k=

this.vwr.getFloat(570425364),k=k*k,j=0;this.showRebondTimes&&JU.Logger.startTimer("autobond");var A=-1,p=null==a,q,x;p?(x=0,q=null):(a.equals(d)?q=a:(q=JU.BSUtil.copy(a),q.or(d)),x=q.nextSetBit(0));for(var s=this.getSelectedAtomIterator(null,!1,!1,!0,!1),n=!1;0<=x&&x<this.ac;x=p?x+1:q.nextSetBit(x+1)){var r=p||a.get(x),u=p||d.get(x),v=this.at[x];if(!JM.AtomCollection.isDeleted(v)){var w=v.mi;if(w!=A){A=w;if(this.isJmolDataFrameForModel(w)){x=this.am[w].firstAtomIndex+this.am[w].act-1;continue}n=this.getInfoB(w,

"autoBondUsingOccupation")}w=v.getBondingRadius();if(0!=w){var y=v.getFormalCharge(),z=0!=y;z&&(y=Math.signum(y));var B=null!=b&&b.get(x);for(this.setIteratorForAtom(s,-1,x,w+this.maxBondingRadius+e,null);s.hasNext();){var C=this.at[s.next()];if(!C.isDeleted()){var D=C.i,E=p||a.get(D),F=p||d.get(D);!E&&!F||(!(r&&F||u&&E)||B&&b.get(D)||n&&null!=this.occupancies&&50>this.occupancies[x]!=50>this.occupancies[D]||z&&Math.signum(C.getFormalCharge())==y)||(E=this.isBondable(w,C.getBondingRadius(),s.foundDistance2(),

k,e)?1:0,0<E&&this.autoBondCheck(v,C,E,f,c)&&(j++,null!=h&&h.append("connect ({"+x+"}) ({"+D+"});")))}}s.release()}}}this.showRebondTimes&&JU.Logger.checkTimer("autoBond",!1);return j},"JU.BS,JU.BS,JU.BS,JU.BS,~N,~B,JU.SB");c(b,"isBondable",function(a,d,b,c,f){if(0==a||0==d||b<c)return!1;a=a+d+f;return b<=a*a},"~N,~N,~N,~N,~N");c(b,"autoBondCheck",function(a,d,b,c,f){if(20<a.getCurrentBondCount()||20<d.getCurrentBondCount())return this.maxBondWarned||JU.Logger.warn("maximum auto bond count reached"),

this.maxBondWarned=!0,!1;var e=a.getFormalCharge();if(0!=e){var h=d.getFormalCharge();if(0>e&&0>h||0<e&&0<h)return!1}if(a.altloc!=d.altloc&&"\x00"!=a.altloc&&"\x00"!=d.altloc&&null==this.getModulation(a.i))return!1;this.getOrAddBond(a,d,b,c,f,0,!1);return!0},"JM.Atom,JM.Atom,~N,~N,JU.BS");c(b,"autoBond_Pre_11_9_24",function(a,d,b,c,f){if(0==this.ac)return 0;0==f&&(f=1);1.4E-45==this.maxBondingRadius&&this.findMaxRadii();var e=this.vwr.getFloat(570425348),h=this.vwr.getFloat(570425364),h=h*h,k=0;this.initializeBspf();

for(var j=-1,A=this.ac;0<=--A;){var p=this.at[A];if(!JM.AtomCollection.isDeleted(p)){var q=null==a||a.get(A),x=null==d||d.get(A);if((q||x)&&!p.isDeleted()){var s=p.mi;if(s!=j&&(j=s,this.isJmolDataFrameForModel(s))){for(;0<=--A&&!(JM.AtomCollection.isDeleted(this.at[A])||this.at[A].mi!=s););A++;continue}var n=p.getBondingRadius();if(0!=n){var r=n+this.maxBondingRadius+e;this.initializeBspt(s);s=this.bspf.getCubeIterator(s);for(s.initialize(p,r,!0);s.hasMoreElements();)if(r=s.nextElement(),!(r===p||

r.isDeleted())){var u=r.i,v=null==a||a.get(u),w=null==d||d.get(u);if(!(!v&&!w||null!=b&&b.get(u)&&b.get(A)))if(q&&w||x&&v)u=this.isBondable(n,r.getBondingRadius(),s.foundDistance2(),h,e)?1:0,0<u&&this.autoBondCheck(p,r,u,f,c)&&k++}s.release()}}}}return k},"JU.BS,JU.BS,JU.BS,JU.BS,~N");c(b,"autoHbond",function(a,d,b){if(b){for(var c=this.getModelBS(a,!1),f=c.nextSetBit(0);0<=f&&b;f=c.nextSetBit(f+1))b=!this.am[f].hasRasmolHBonds;if(b)return 0}b=!1;for(f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1))if(1==

this.at[f].getElementNumber()){b=!0;break}c=new JU.BS;f=this.vwr.getBoolean(603979853);if(null==d||f&&!b)return JU.Logger.info((null==d?"DSSP/DSSR ":"RasMol")+" pseudo-hbond calculation"),this.calcRasmolHydrogenBonds(a,d,null,!1,2147483647,!1,c),-c.cardinality();JU.Logger.info(b?"Standard Hbond calculation":"Jmol pseudo-hbond calculation");var e=null;if(!b){e=new JU.BS;for(f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1))switch(this.at[f].atomID){case 64:case 4:case 14:case 15:case 16:case 17:e.set(f)}}var h,

k;b?(h=this.vwr.getFloat(570425361),k=1):(h=this.vwr.getFloat(570425360),k=JM.ModelSet.hbondMinRasmol*JM.ModelSet.hbondMinRasmol);var j=h*h,A=3.141592653589793*this.vwr.getFloat(570425359)/180,p=0,q=0;this.showRebondTimes&&JU.Logger.debugging&&JU.Logger.startTimer("hbond");var x=null,s=null;d=this.getSelectedAtomIterator(d,!1,!1,!1,!1);for(f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1)){var n=this.at[f],r=n.getElementNumber(),u=1==r;if(!(u?!b:b||7!=r&&8!=r)){if(u){r=!1;x=n.bonds;if(null==x)continue;for(var v=

!1,s=0;!v&&s<x.length;s++)v=x[s].getOtherAtom(n).getElementNumber(),v=7==v||8==v;if(!v)continue}else r=e.get(f);for(this.setIteratorForAtom(d,-1,n.i,h,null);d.hasNext();)if(v=this.at[d.next()],x=v.getElementNumber(),!(v===n||(u?1==x:7!=x&&8!=x)||(q=d.foundDistance2())<k||q>j||r&&e.get(v.i)||n.isBonded(v)))if(this.v1.sub2(n,v),null!=(s=JM.ModelSet.checkMinAttachedAngle(n,A,this.v1,this.v2,b)))if(this.v1.scale(-1),null!=(x=JM.ModelSet.checkMinAttachedAngle(v,A,this.v1,this.v2,b))){var w=0,y;u&&!Float.isNaN(x.x)&&

!Float.isNaN(s.x)?(y=4096,w=JM.HBond.calcEnergy(Math.sqrt(q),x.distance(n),x.distance(s),v.distance(s))/1E3):y=2048;c.set(this.addHBond(n,v,y,w));p++}}}d.release();this.sm.setShapeSizeBs(1,-2147483648,null,c);this.showRebondTimes&&JU.Logger.checkTimer("hbond",!1);return b?p:-p},"JU.BS,JU.BS,~B");b.checkMinAttachedAngle=c(b,"checkMinAttachedAngle",function(a,d,b,c,f){var e=a.bonds,h=!0,k=null;if(null!=e&&0<e.length)for(var j=3.4028235E38,A=e.length;0<=--A;)if(e[A].isCovalent()){var h=!1,p=e[A].getOtherAtom(a);

if(f||1!=p.getElementNumber()){c.sub2(a,p);var q=c.angle(b);if(q<d)return null;q<j&&(k=p,j=q)}}return h?JU.P3.new3(NaN,0,0):k},"JM.Atom,~N,JU.V3,JU.V3,~B");c(b,"setStructureIndexes",function(){for(var a,d=0,b=-1,c=-1,f=-1,e=0;e<this.ac;e++)if(!JM.AtomCollection.isDeleted(this.at[e])){if((c=this.at[e].mi)!=f)d=0,f=c,b=-1;if((a=this.at[e].group.getStrucNo())!=b&&0!=a)this.at[e].group.setStrucNo(++d),b=d}});c(b,"getModelInfoAsString",function(){var a=(new JU.SB).append('<models count="');a.appendI(this.mc).append('" modelSetHasVibrationVectors="').append(this.modelSetHasVibrationVectors()+

'">\n<properties>');if(null!=this.modelSetProperties){for(var d=this.modelSetProperties.propertyNames();d.hasMoreElements();){var b=d.nextElement();a.append('\n <property name="').append(b).append('" value=').append(JU.PT.esc(this.modelSetProperties.getProperty(b))).append(" />")}a.append("\n</properties>")}for(d=0;d<this.mc;++d)a.append('\n<model index="').appendI(d).append('" n="').append(this.getModelNumberDotted(d)).append('" id=').append(JU.PT.esc(""+this.getInfo(d,"modelID"))),b=this.vwr.getJDXBaseModelIndex(d),

b!=d&&a.append(" baseModelId=").append(JU.PT.esc(this.getInfo(b,"jdxModelID"))),a.append(" name=").append(JU.PT.esc(this.getModelName(d))).append(" title=").append(JU.PT.esc(this.getModelTitle(d))).append(' hasVibrationVectors="').appendB(this.vwr.modelHasVibrationVectors(d)).append('" />');a.append("\n</models>");return a.toString()});c(b,"getSymmetryInfoAsString",function(){for(var a=(new JU.SB).append("Symmetry Information:"),d=0;d<this.mc;++d){a.append("\nmodel #").append(this.getModelNumberDotted(d)).append("; name=").append(this.getModelName(d)).append("\n");

var b=this.getUnitCell(d);a.append(null==b?"no symmetry information":b.getSymmetryInfoStr())}return a.toString()});c(b,"createModels",function(a){a=this.mc+a;var d=JU.AU.arrayCopyObject(this.am,a);this.validateBspf(!1);this.modelNumbers=JU.AU.arrayCopyI(this.modelNumbers,a);this.modelFileNumbers=JU.AU.arrayCopyI(this.modelFileNumbers,a);this.modelNumbersForAtomLabel=JU.AU.arrayCopyS(this.modelNumbersForAtomLabel,a);this.modelNames=JU.AU.arrayCopyS(this.modelNames,a);this.frameTitles=JU.AU.arrayCopyS(this.frameTitles,

a);for(var b=B(this.modelFileNumbers[this.mc-1]/1E6)+1,c=this.mc,f=0;c<a;c++)this.modelNumbers[c]=c+this.mc,this.modelFileNumbers[c]=1E6*b+ ++f,this.modelNumbersForAtomLabel[c]=this.modelNames[c]=b+"."+f;this.thisStateModel=-1;b=this.getInfoM("group3Lists");null!=b&&(c=this.getInfoM("group3Counts"),b=JU.AU.arrayCopyS(b,a),c=JU.AU.arrayCopyII(c,a),this.msInfo.put("group3Lists",b),this.msInfo.put("group3Counts",c));this.unitCells=null==this.unitCells?Array(a):JU.AU.arrayCopyObject(this.unitCells,a);

for(c=this.mc;c<a;c++)d[c]=(new JM.Model).set(this,c,-1,null,null,null),d[c].loadState=" model create #"+c+";";this.am=d;this.mc=a;this.vwr.setAnimationRange(-1,-1)},"~N");c(b,"deleteAtoms",function(a){if(null!=a){for(var d=this.getModelBS(a,!1),b=new JU.BS,c=a.nextSetBit(0);0<=c&&c<this.ac;c=a.nextSetBit(c+1))JM.AtomCollection.isDeleted(this.at[c])||this.at[c].$delete(b);for(var f=JU.BSUtil.copy(a),c=0;c<this.mc;c++){var e=this.am[c];e.resetDSSR(!1);e.bsAtomsDeleted.or(a);e.bsAtomsDeleted.and(e.bsAtoms);

null!=e.bsAsymmetricUnit&&e.bsAsymmetricUnit.andNot(a);d.get(e.modelIndex)&&this.updateBasisFromSite(e.modelIndex);a=JU.BSUtil.andNot(e.bsAtoms,e.bsAtomsDeleted);e.firstAtomIndex=a.nextSetBit(0);e.act=a.cardinality();e.isOrderly=e.act==e.bsAtoms.length()-e.firstAtomIndex}this.dBb(b,!1);this.vwr.shm.notifyAtoms("atomsDeleted",w(-1,[f,d]));this.validateBspf(!1)}},"JU.BS");c(b,"clearDB",function(a){this.getModelAuxiliaryInfo(this.at[a].mi).remove("dbName")},"~N");c(b,"adjustAtomArrays",function(a,d,

b){this.ac=b;for(var c=d;c<b;c++){this.at[c]=this.at[a[c]];this.at[c].i=c;var f=this.am[this.at[c].mi];f.firstAtomIndex==a[c]&&(f.firstAtomIndex=c);f.bsAtoms.set(c)}if(null!=this.vibrations)for(c=d;c<b;c++)this.vibrations[c]=this.vibrations[a[c]];if(null!=this.atomTensorList)for(c=d;c<b;c++)if(f=this.atomTensorList[c]=this.atomTensorList[a[c]],null!=f)for(var e=f.length;0<=--e;){var h=f[e];null!=h&&(h.atomIndex1=c)}if(null!=this.atomNames)for(c=d;c<b;c++)this.atomNames[c]=this.atomNames[a[c]];if(null!=

this.atomTypes)for(c=d;c<b;c++)this.atomTypes[c]=this.atomTypes[a[c]];if(null!=this.atomResnos)for(c=d;c<b;c++)this.atomResnos[c]=this.atomResnos[a[c]];if(null!=this.atomSerials)for(c=d;c<b;c++)this.atomSerials[c]=this.atomSerials[a[c]];if(null!=this.atomSeqIDs)for(c=d;c<b;c++)this.atomSeqIDs[c]=this.atomSeqIDs[a[c]];if(null!=this.bfactor100s)for(c=d;c<b;c++)this.bfactor100s[c]=this.bfactor100s[a[c]];if(null!=this.occupancies)for(c=d;c<b;c++)this.occupancies[c]=this.occupancies[a[c]];if(null!=this.partialCharges)for(c=

d;c<b;c++)this.partialCharges[c]=this.partialCharges[a[c]]},"~A,~N,~N");c(b,"growAtomArrays",function(a){this.at=JU.AU.arrayCopyObject(this.at,a);null!=this.vibrations&&(this.vibrations=JU.AU.arrayCopyObject(this.vibrations,a));null!=this.occupancies&&(this.occupancies=JU.AU.arrayCopyF(this.occupancies,a));null!=this.bfactor100s&&(this.bfactor100s=JU.AU.arrayCopyShort(this.bfactor100s,a));null!=this.partialCharges&&(this.partialCharges=JU.AU.arrayCopyF(this.partialCharges,a));null!=this.atomTensorList&&

(this.atomTensorList=JU.AU.arrayCopyObject(this.atomTensorList,a));null!=this.atomNames&&(this.atomNames=JU.AU.arrayCopyS(this.atomNames,a));null!=this.atomTypes&&(this.atomTypes=JU.AU.arrayCopyS(this.atomTypes,a));null!=this.atomResnos&&(this.atomResnos=JU.AU.arrayCopyI(this.atomResnos,a));null!=this.atomSerials&&(this.atomSerials=JU.AU.arrayCopyI(this.atomSerials,a));null!=this.atomSeqIDs&&(this.atomSeqIDs=JU.AU.arrayCopyI(this.atomSeqIDs,a))},"~N");c(b,"addAtom",function(a,d,b,c,f,e,h,k,j,A,p,

q,x,s,n,r,u,v,w,y,z){k=(new JM.Atom).setAtom(a,this.ac,j,A,y,k,b,q,u,!1);this.am[a].act++;this.am[a].bsAtoms.set(this.ac);JU.Elements.isElement(b,1)&&this.am[a].hydrogenCount++;this.ac>=this.at.length&&this.growAtomArrays(this.ac+100);this.at[this.ac]=k;this.setBFactor(this.ac,n,!1);this.setOccupancy(this.ac,s,!1);this.setPartialCharge(this.ac,x,!1);null!=r&&this.setAtomTensors(this.ac,r);k.group=d;k.colixAtom=this.vwr.cm.getColixAtomPalette(k,J.c.PAL.CPK.id);v&&k.setTranslucent(!0,0.5);null!=c&&

(null!=f&&(null==this.atomTypes&&(this.atomTypes=Array(this.at.length)),this.atomTypes[this.ac]=f),k.atomID=w,0==w&&(null==this.atomNames&&(this.atomNames=Array(this.at.length)),this.atomNames[this.ac]=c.intern()));-2147483648!=e&&(null==this.atomSerials&&(this.atomSerials=E(this.at.length,0)),this.atomSerials[this.ac]=e);0!=h&&(null==this.atomSeqIDs&&(this.atomSeqIDs=E(this.at.length,0)),this.atomSeqIDs[this.ac]=h);null!=p&&this.setVibrationVector(this.ac,p);Float.isNaN(z)||this.setBondingRadius(this.ac,

z);this.ac++;return k},"~N,JM.Group,~N,~S,~S,~N,~N,~N,JU.P3,~N,JU.V3,~N,~N,~N,~N,JU.Lst,~B,~B,~N,JU.BS,~N");c(b,"getInlineData",function(a){var d=null;if(0<=a)d=this.am[a].loadScript;else for(a=this.mc;0<=--a&&!(0<(d=this.am[a].loadScript).length()););a=d.lastIndexOf('data "');if(0>a)return d=JU.PT.getQuotedStringAt(d.toString(),0),JS.ScriptCompiler.unescapeString(d,0,d.length);a=d.indexOf2('"',a+7);var b=d.lastIndexOf('end "');return b<a||0>a?null:d.substring2(a+2,b)},"~N");c(b,"isAtomPDB",function(a){return 0<=

a&&this.am[this.at[a].mi].isBioModel},"~N");c(b,"setAtomNamesAndNumbers",function(a,d,b,c){var f=-1;if(c){for(;a<this.ac&&JM.AtomCollection.isDeleted(this.at[a]);)a++;if(a>=this.ac)return;f=this.at[a].mi;a=this.am[f].firstAtomIndex}null==this.atomSerials&&(this.atomSerials=E(this.ac,0));null==this.atomNames&&(this.atomNames=Array(this.ac));for(var e=this.isXYZ&&this.vwr.getBoolean(603979978),h=2147483647,k=1;a<this.ac;++a){var j=this.at[a];if(!JM.AtomCollection.isDeleted(j)){if(j.mi!=h){if(c&&2147483647!=

h&&j.mi!=f)continue;h=j.mi;k=e?0:1}var A=this.atomSerials[a];if(a>=-d){if(0==A||c)this.atomSerials[a]=a<d?b.atomSerials[a]:k;if(null==this.atomNames[a]||c)this.atomNames[a]=(j.getElementSymbol()+this.atomSerials[a]).intern()}else A>k&&(k=A),c&&(this.atomNames[a]=(j.getElementSymbol()+A).intern());(!this.am[h].isModelKit||0<j.getElementNumber())&&k++}}},"~N,~N,JM.AtomCollection,~B");c(b,"connect",function(a){this.resetMolecules();for(var d=new JU.BS,b=0;b<a.length;b++){var c=a[b];if(!(null==c||2>c.length)){var f=

D(c[0]),e=0>f;e&&(f=-1-f);var h=D(c[1]);if(!(0>h||f>=this.ac||h>=this.ac)){var k=2<c.length?D(c[2]):1;0>k&&(k&=65535);var j=3<c.length?ca(1E3*a[b][3]):this.getDefaultMadFromOrder(k);0==k||0==j&&32768!=k&&!JU.Edge.isOrderH(k)?(c=this.at[f].getBond(this.at[h]),null!=c&&d.set(c.index)):this.bondAtoms(this.at[f],this.at[h],k,j,null,4<c.length?c[4]:0,e,!0)}}}0<=d.nextSetBit(0)&&this.deleteBonds(d,!1)},"~A");c(b,"setFrameDelayMs",function(a,d){for(var b=d.nextSetBit(0);0<=b;b=d.nextSetBit(b+1))this.am[this.am[b].trajectoryBaseIndex].frameDelay=

a},"~N,JU.BS");c(b,"getFrameDelayMs",function(a){return a<this.am.length&&0<=a?this.am[this.am[a].trajectoryBaseIndex].frameDelay:0},"~N");c(b,"getModelIndexFromId",function(a){var d=0<=a.indexOf("#"),b=a.toLowerCase().endsWith(".basemodel");b&&(a=a.substring(0,a.length-10));for(var c=-1,f=null,e=0;e<this.mc;e++){var h=this.getInfo(e,"modelID"),k=a.startsWith("~")?"~"+this.getModelNumberDotted(e):null;if(!(null==k&&null==h&&null==(h=this.getModelTitle(e)))){d&&(f=this.getModelFileName(e),f.endsWith("#molfile")?

h=f:(f+="#",h=f+h));if(a.equalsIgnoreCase(h)||a.equalsIgnoreCase(k))return b?this.vwr.getJDXBaseModelIndex(e):e;null!=f&&a.startsWith(f)&&(c=-2)}}return null==f&&!d?-2:c},"~S");c(b,"getModelSetAuxiliaryInfo",function(a){var d=this.msInfo;null==d&&(d=new java.util.Hashtable);if(null!=a||!d.containsKey("models")){for(var b=new JU.Lst,c=0;c<this.mc;++c)if(null==a||a.get(c)){var f=this.getModelAuxiliaryInfo(c);f.put("modelIndex",Integer.$valueOf(c));b.addLast(f)}d.put("models",b)}return d},"JU.BS");c(b,

"getDihedralMap",function(a){for(var d=new JU.Lst,b=a.length,c=null,f=null,e=null,h=null,k=b-1;0<=--k;)for(var j=b;--j>k;)if(c=this.at[a[k]],f=this.at[a[j]],c.isBonded(f))for(var A=b;0<=--A;)if(A!=k&&A!=j&&(e=this.at[a[A]]).isBonded(c))for(var p=b;0<=--p;)if(p!=k&&p!=j&&p!=A&&(h=this.at[a[p]]).isBonded(f)){var q=E(4,0);q[0]=e.i;q[1]=c.i;q[2]=f.i;q[3]=h.i;d.addLast(q)}b=d.size();a=JU.AU.newInt2(b);for(k=b;0<=--k;)a[b-k-1]=d.get(k);return a},"~A");c(b,"setModulation",function(a,d,b,c){if(null==this.bsModulated)if(d)this.bsModulated=

new JU.BS;else if(null==a)return;null==a&&(a=this.getModelAtomBitSetIncludingDeleted(-1,!1));for(var f=this.vwr.getFloat(1275072532),e=!1,h=a.nextSetBit(0);0<=h;h=a.nextSetBit(h+1)){var k=this.getModulation(h);null!=k&&(k.setModTQ(this.at[h],d,b,c,f),null!=this.bsModulated&&this.bsModulated.setBitTo(h,d),e=!0)}e||(this.bsModulated=null)},"JU.BS,~B,JU.P3,~B");c(b,"getBoundBoxOrientation",function(a,d,b){var c=0,f=0,e=0,h=null,k=null,j=d.nextSetBit(0),A=0;if(0<=j){if(null==this.vOrientations){for(var p=

0,h=new JU.P4,A=Array(3375),c=-7;7>=c;c++)for(f=-7;7>=f;f++)for(e=0;14>=e;e++,p++)1<(A[p]=JU.V3.new3(c/7,f/7,e/14)).length()&&--p;this.vOrientations=Array(p);for(c=p;0<=--c;)h.set4(A[c].x,A[c].y,A[c].z,0),this.vOrientations[c]=JU.Quat.newP4(h);for(c=p;0<=--c;)p=Math.sqrt(1-A[c].lengthSquared()),Float.isNaN(p)&&(p=0),h.set4(A[c].x,A[c].y,A[c].z,p),this.vOrientations[c]=JU.Quat.newP4(h)}var p=new JU.P3,A=3.4028235E38,e=null,q=new JU.BoxInfo;q.setMargin(1312817669==a?0:0.1);for(c=this.vOrientations.length;0<=

--c;){h=this.vOrientations[c];q.reset();if(null==b)for(f=j;0<=f;f=d.nextSetBit(f+1)){var x=h.transform2(this.at[f],p);q.addBoundBoxPoint(x)}else for(f=b.length;0<=--f;)q.addBoundBoxPoint(h.transform2(b[f],p));switch(a){default:case 1312817669:case 1073741864:case 1814695966:f=(q.bbCorner1.x-q.bbCorner0.x)*(q.bbCorner1.y-q.bbCorner0.y)*(q.bbCorner1.z-q.bbCorner0.z);break;case 1111492629:f=q.bbCorner1.x-q.bbCorner0.x;break;case 1111492630:f=q.bbCorner1.y-q.bbCorner0.y;break;case 1111492631:f=q.bbCorner1.z-

q.bbCorner0.z}f<A&&(k=h,e=q,q=new JU.BoxInfo,q.setMargin(0.1),A=f)}switch(a){default:return k;case 1814695966:a=e.getBoundBoxVertices();a=w(-1,[a[0],a[4],a[2],a[1]]);k=k.inv();for(c=0;4>c;c++)k.transform2(a[c],a[c]),0<c&&a[c].sub(a[0]);return a;case 1312817669:case 1073741864:h=JU.Quat.newQ(k),c=e.bbCorner1.x-e.bbCorner0.x,f=e.bbCorner1.y-e.bbCorner0.y,e=e.bbCorner1.z-e.bbCorner0.z,c<f&&(p.set(0,0,1),h=JU.Quat.newVA(p,90).mulQ(h),k=c,c=f,f=k),f<e&&(e>c&&(p.set(0,1,0),h=JU.Quat.newVA(p,90).mulQ(h),

k=c,c=e,e=k),p.set(1,0,0),h=JU.Quat.newVA(p,90).mulQ(h),k=f,f=e,e=k)}}return 1312817669==a?A+"\t{"+c+" "+f+" "+e+"}\t"+d:1814695966==a?null:null==h||0==h.getTheta()?new JU.Quat:h},"~N,JU.BS,~A");c(b,"getUnitCellForAtom",function(a){if(0>a||a>this.ac||null==this.at[a])return null;if(null!=this.bsModulated){var d=this.getModulation(a),d=null==d?null:d.getSubSystemUnitCell();if(null!=d)return d}return this.getUnitCell(this.at[a].mi)},"~N");c(b,"clearCache",function(){for(var a=this.mc;0<=--a;)this.am[a].resetDSSR(!1)});

c(b,"getSymMatrices",function(a){var d=this.getModelSymmetryCount(a);if(0==d)return null;var b=Array(d),c=this.am[a].biosymmetry;null==c&&(c=this.getUnitCell(a));for(a=d;0<=--a;)b[a]=c.getSpaceGroupOperation(a);return b},"~N");c(b,"getSymmetryInvariant",function(a){a=this.getBasisAtom(a,!0);return null==a?E(0,0):this.getUnitCellForAtom(a.i).getInvariantSymops(a,null)},"~N");c(b,"getBsBranches",function(a){for(var d=B(a.length/6),b=Array(d),c=new java.util.Hashtable,f=0,e=0;f<d;f++,e+=6)if(!(1>Math.abs(a[e+

5]-a[e+4]))){var h=D(a[e+1]),k=D(a[e+2]),j=""+h+"_"+k;if(!c.containsKey(j)){c.put(j,Boolean.TRUE);for(var j=this.vwr.getBranchBitSet(k,h,!0),A=this.at[h].bonds,h=this.at[h],p=0;p<A.length;p++){var q=A[p];if(q.isCovalent()&&(q=q.getOtherAtom(h).i,q!=k&&j.get(q))){j=null;break}}b[f]=j}}return b},"~A");c(b,"recalculatePositionDependentQuantities",function(a,d){null!=this.vwr.shm.getShape(21)&&this.vwr.shm.getShapePropertyData(21,"move",w(-1,[a,d]));this.haveStraightness&&this.calculateStraightnessAll();

this.recalculateLeadMidpointsAndWingVectors(-1);for(var b=this.getModelBS(a,!1),c=b.nextSetBit(0);0<=c;c=b.nextSetBit(c+1))if(this.sm.notifyAtomPositionsChanged(c,a,d),null!=d){var f=this.am[c];f.isContainedIn(a)&&(null==f.mat4&&(f.mat4=JU.M4.newM4(null)),f.mat4.mul2(d,f.mat4))}},"JU.BS,JU.M4");c(b,"moveAtoms",function(a,d,b,c,f,e,h,k){if(null!=a){for(d=f.nextSetBit(0);0<=d;d=f.nextSetBit(d+1))a.rotTrans(this.at[d]),this.taintAtom(d,2);this.mat4.setM4(a);c=null}else if(k)h||(this.matInv.setM3(b),

this.matInv.invert(),this.matInv.rotate(c));else{null==d?this.matTemp.setM3(b):(this.ptTemp.set(0,0,0),this.matInv.setM3(b),this.matInv.invert(),this.matTemp.mul2(d,b),this.matTemp.mul2(this.matInv,this.matTemp));h?(this.vTemp.setT(e),this.mat4.setIdentity(),this.mat4.setTranslation(this.vTemp),this.mat4t.setToM3(this.matTemp),this.mat4.mul(this.mat4t),this.mat4t.setIdentity(),this.vTemp.scale(-1),this.mat4t.setTranslation(this.vTemp),this.mat4.mul(this.mat4t)):this.mat4.setToM3(this.matTemp);for(d=

f.nextSetBit(0);0<=d;d=f.nextSetBit(d+1))h?this.mat4.rotTrans(this.at[d]):(this.ptTemp.add(this.at[d]),this.mat4.rotTrans(this.at[d]),this.ptTemp.sub(this.at[d])),this.taintAtom(d,2);h||(this.ptTemp.scale(1/f.cardinality()),null==c&&(c=new JU.V3),c.add(this.ptTemp))}if(null!=c){for(d=f.nextSetBit(0);0<=d;d=f.nextSetBit(d+1))this.at[d].add(c),this.taintAtom(d,2);k||(this.mat4t.setIdentity(),this.mat4t.setTranslation(c),this.mat4.mul2(this.mat4t,this.mat4))}this.recalculatePositionDependentQuantities(f,

this.mat4)},"JU.M4,JU.M3,JU.M3,JU.V3,JU.BS,JU.P3,~B,~B");c(b,"setDihedrals",function(a,d,b){var c=B(a.length/6);1<b&&(b=1);for(var f=0,e=0;f<c;f++,e+=6){var h=d[f];if(!(null==h||h.isEmpty())){var k=this.at[D(a[e+1])],j=JU.V3.newVsub(this.at[D(a[e+2])],k),j=JU.A4.newVA(j,-((a[e+5]-a[e+4])*b)/57.29577951308232);this.matTemp.setAA(j);this.ptTemp.setT(k);for(k=h.nextSetBit(0);0<=k;k=h.nextSetBit(k+1))this.at[k].sub(this.ptTemp),this.matTemp.rotate(this.at[k]),this.at[k].add(this.ptTemp),this.taintAtom(k,

2)}}},"~A,~A,~N");c(b,"setAtomCoordsRelative",function(a,d){this.setAtomsCoordRelative(d,a.x,a.y,a.z);this.mat4.setIdentity();this.vTemp.setT(a);this.mat4.setTranslation(this.vTemp);this.recalculatePositionDependentQuantities(d,this.mat4)},"JU.T3,JU.BS");c(b,"setAtomCoords",function(a,d,b){this.setAtomCoord2(a,d,b);switch(d){case 1111492626:case 1111492627:case 1111492628:case 1145047055:break;default:this.recalculatePositionDependentQuantities(a,null)}},"JU.BS,~N,~O");c(b,"invertSelected",function(a,

d,b,c){this.resetChirality();if(null!=a)for(var f=c.nextSetBit(0);0<=f;f=c.nextSetBit(f+1)){var e=2*(a.x-this.at[f].x);b=2*(a.y-this.at[f].y);var h=2*(a.z-this.at[f].z);this.setAtomCoordRelative(f,e,b,h)}else if(null!=d){a=JU.V3.new3(d.x,d.y,d.z);a.normalize();for(var k=Math.sqrt(d.x*d.x+d.y*d.y+d.z*d.z),f=c.nextSetBit(0);0<=f;f=c.nextSetBit(f+1))h=2*-JU.Measure.distanceToPlaneD(d,k,this.at[f]),e=a.x*h,b=a.y*h,h*=a.z,this.setAtomCoordRelative(f,e,b,h)}else if(0<=b&&(d=this.at[b],a=d.bonds,null!=a)){e=

new JU.BS;h=new JU.Lst;k=this.vwr.getModelUndeletedAtomsBitSet(d.mi);for(f=0;f<a.length;f++){var j=a[f].getOtherAtom(d);c.get(j.i)?e.or(JU.JmolMolecule.getBranchBitSet(this.at,j.i,k,null,b,!0,!0)):h.addLast(j)}0!=h.size()&&(a=JU.Measure.getCenterAndPoints(h)[0],c=JU.V3.newVsub(d,a),c=JU.Quat.newVA(c,180),this.moveAtoms(null,null,c.getMatrix(),null,e,d,!0,!1))}},"JU.P3,JU.P4,~N,JU.BS");c(b,"getCellWeights",function(a){var d=null,b=a.nextSetBit(0),c=-1,f;if(0<=b&&null!=(f=this.getUnitCell(c=this.at[b].mi))){f=

f.getUnitCellMultiplied();this.getModelAtomBitSetIncludingDeleted(c,!0).and(a);for(var d=K(a.cardinality(),0),e=new JU.P3,h=0;0<=b;b=a.nextSetBit(b+1))c=this.at[b],e.setT(c),f.toFractional(e,!1),f.unitize(e),d[h++]=f.getCellWeight(e)}return d},"JU.BS");c(b,"getAtomGroupQuaternions",function(a,d,b){var c=0,f=new JU.Lst;a=JU.BSUtil.copy(a);for(var e=new JU.BS,h=a.nextSetBit(0);0<=h&&c<d;h=a.nextSetBit(h+1)){var k=this.at[h].group;k.setAtomBits(e);a.andNot(e);var j=k.getQuaternion(b);if(null==j&&(this.am[this.at[h].mi].isBioModel||

(j=k.getQuaternionFrame(this.at)),null==j))continue;c++;f.addLast(j)}return f.toArray(Array(f.size()))},"JU.BS,~N,~S");c(b,"getConformation",function(a,d,b,c){for(var f=new JU.BS,e=this.mc;0<=--e;)if(!(0<=a&&e!=a)){var h=this.am[e],k=this.vwr.getModelUndeletedAtomsBitSet(a);null!=c&&k.and(c);if(!(0>k.nextSetBit(0)))if(d>h.altLocCount)1==d&&f.or(k);else{if(this.am[e].isBioModel){if(-1E3>d){var h=1E3+d,j=this.getAltLocListInModel(e);-32!=h&&0>j.indexOf(String.fromCharCode(-h))&&(h=-2147483648)}else 0>

d?(j=this.getAltLocListInModel(e),h=-1-d,h=h>=j.length?-2147483648:-j.charAt(h).charCodeAt(0)):h=d;if(-2147483648==h)continue;this.am[e].getConformation(h,b,k,f)}else{var A=this.getAltLocCountInModel(e),j=this.getAltLocListInModel(e),p=new JU.BS;if(-1E3>d)var q=String.fromCharCode(-1E3-d),h=j.indexOf(q);else if(0>d)if(h=-d,q=this.vwr.getDataObj("property_part",k,1),null==q)h-=1;else{for(var x=0,s=k.nextSetBit(0);0<=s;s=k.nextSetBit(s+1)){var n=q[x++];0!=n&&(n!=h&&n!=-h)&&k.clear(s)}f.or(k);h=-1}else h=

d-1;if(0>h||h>=A)continue;for(q=A;0<=--q;)q!=h&&k.andNot(this.getAtomBitsMDa(1073742355,j.substring(q,q+1),p))}f.or(k)}}return f},"~N,~N,~B,JU.BS");c(b,"getSequenceBits",function(a,d,b){return this.haveBioModels?this.bioModelset.getAllSequenceBits(a,d,b):b},"~S,JU.BS,JU.BS");c(b,"getBioPolymerCountInModel",function(a){return this.haveBioModels?this.bioModelset.getBioPolymerCountInModel(a):0},"~N");c(b,"getPolymerPointsAndVectors",function(a,d,b,c){this.haveBioModels&&this.bioModelset.getAllPolymerPointsAndVectors(a,

d,b,c)},"JU.BS,JU.Lst,~B,~N");c(b,"recalculateLeadMidpointsAndWingVectors",function(a){this.haveBioModels&&this.bioModelset.recalculatePoints(a)},"~N");c(b,"calcRasmolHydrogenBonds",function(a,d,b,c,f,e,h){this.haveBioModels&&this.bioModelset.calcAllRasmolHydrogenBonds(a,d,b,c,f,e,h,2)},"JU.BS,JU.BS,JU.Lst,~B,~N,~B,JU.BS");c(b,"calculateStraightnessAll",function(){this.haveBioModels&&!this.haveStraightness&&this.bioModelset.calculateStraightnessAll()});c(b,"calculateStruts",function(a,d){return this.haveBioModels?

this.bioModelset.calculateStruts(a,d):0},"JU.BS,JU.BS");c(b,"getGroupsWithin",function(a,d){return this.haveBioModels?this.bioModelset.getGroupsWithinAll(a,d):new JU.BS},"~N,JU.BS");c(b,"getProteinStructureState",function(a,d){return this.haveBioModels?this.bioModelset.getFullProteinStructureState(a,d):""},"JU.BS,~N");c(b,"calculateStructures",function(a,d,b,c,f,e){return this.haveBioModels?this.bioModelset.calculateAllStuctures(a,d,b,c,f,e):""},"JU.BS,~B,~B,~B,~B,~N");c(b,"calculateStructuresAllExcept",

function(a,d,b,c,f,e,h){this.freezeModels();return this.haveBioModels?this.bioModelset.calculateAllStructuresExcept(a,d,b,c,f,e,h):""},"JU.BS,~B,~B,~B,~B,~B,~N");c(b,"recalculatePolymers",function(a){this.bioModelset.recalculateAllPolymers(a,this.getGroups())},"JU.BS");c(b,"calculatePolymers",function(a,d,b,c){null!=this.bioModelset&&this.bioModelset.calculateAllPolymers(a,d,b,c)},"~A,~N,~N,JU.BS");c(b,"calcSelectedMonomersCount",function(){this.haveBioModels&&this.bioModelset.calcSelectedMonomersCount()});

c(b,"setProteinType",function(a,d){this.haveBioModels&&this.bioModelset.setAllProteinType(a,d)},"JU.BS,J.c.STR");c(b,"setStructureList",function(a){this.haveBioModels&&this.bioModelset.setAllStructureList(a)},"java.util.Map");c(b,"setConformation",function(a){this.haveBioModels&&this.bioModelset.setAllConformation(a);return JU.BSUtil.copy(a)},"JU.BS");c(b,"getHeteroList",function(a){a=this.haveBioModels?this.bioModelset.getAllHeteroList(a):null;return null==a?this.getInfoM("hetNames"):a},"~N");c(b,

"getUnitCellPointsWithin",function(a,d,b,c){var f=new JU.Lst,e=null,h=null;c&&(e=new java.util.Hashtable,h=new JU.Lst,e.put("atoms",h),e.put("points",f));var k=null==d?-1:d.nextSetBit(0);d=this.vwr.getModelUndeletedAtomsBitSet(0>k?this.vwr.am.cmi:this.at[k].mi);0>k&&(k=d.nextSetBit(0));if(0<=k){var j=this.getUnitCellForAtom(k);if(null!=j){d=j.getIterator(this.vwr,this.at[k],d,a);for(null!=b&&d.setCenter(b,a);d.hasNext();)k=d.next(),b=d.getPosition(),f.addLast(b),c&&h.addLast(Integer.$valueOf(k))}}return c?

e:f},"~N,JU.BS,JU.P3,~B");c(b,"calculateDssrProperty",function(a){if(null!=a){if(null==this.dssrData||this.dssrData.length<this.ac)this.dssrData=K(this.ac,0);for(var d=0;d<this.ac;d++)this.dssrData[d]=NaN;for(d=this.mc;0<=--d;)this.am[d].isBioModel&&this.am[d].getAtomicDSSRData(this.dssrData,a)}},"~S");c(b,"getAtomicDSSRData",function(a){return null==this.dssrData||this.dssrData.length<=a?NaN:this.dssrData[a]},"~N");c(b,"getAtomCIPChiralityCode",function(a){this.haveChirality=!0;var d=this.am[a.mi];

d.hasChirality||(this.calculateChiralityForAtoms(d.bsAtoms,!1),d.hasChirality=!0);return a.getCIPChiralityCode()},"JM.Atom");c(b,"calculateChiralityForAtoms",function(a,d){this.haveChirality=!0;for(var b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.at[b].setCIPChirality(0);J.api.Interface.getSymmetry(this.vwr,"ms").calculateCIPChiralityForAtoms(this.vwr,a);if(!d)return null;for(var c="",b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))c+=this.at[b].getCIPChirality(!1);return c},"JU.BS,~B");c(b,"getPointTransf",

function(a,d,b,c){this.isTrajectory(0<=a?a:d.mi)?this.trajectory.getFractional(d,c):c.setT(d);null!=b&&b.transform2(c,c)},"~N,JM.Atom,JU.Quat,JU.P3");c(b,"getSymmetryEquivAtoms",function(a,d,b){a=JU.BS.copy(a);var c=JU.BS.copy(a),f=a.nextSetBit(0);null==d&&(d=this.getUnitCellForAtom(f));if(null!=d){null==b&&(b=this.vwr.getModelUndeletedAtomsBitSet(this.at[f].mi));d=JU.BSUtil.copy(b);for(b=a.nextSetBit(0);0<=b;b=a.nextSetBit(b+1))this.getSymmetryEquivAtomsForAtom(b,a,d,c)}return c},"JU.BS,J.api.SymmetryInterface,JU.BS");

c(b,"getSymmetryEquivAtomsForAtom",function(a,d,b,c){a=this.at[a].getAtomSite();if(0<a)for(var f=b.nextSetBit(0);0<=f;f=b.nextSetBit(f+1))this.at[f].getAtomSite()==a&&(c.set(f),null!=d&&(d.clear(f),b.clear(f)))},"~N,JU.BS,JU.BS,JU.BS");c(b,"setSpaceGroup",function(a,d,b){null==this.unitCells&&(this.unitCells=Array(this.mc));this.unitCells[a]=d;this.haveUnitCells=!0;var c=1==d.getSpaceGroupOperationCount(),f=d.getFinalOperationCount();if(null!=b){var e=b.isEmpty(),h=this.vwr.getModelUndeletedAtomsBitSet(a);

e?b=JU.BSUtil.copy(h):this.setAsymmetricUnit(a,h,b,!c);1<f&&this.setModelCage(a,null);if(0<(null==this.atomSeqIDs?0:this.atomSeqIDs.length))for(var k=h.nextSetBit(0);0<=k;k=h.nextSetBit(k+1))this.atomSeqIDs[k]=0;if(c)this.fixP1AtomSites(d,h);else{for(var j=null!=this.occupancies,A=d.getSymmetryOperations(),p=new JU.P3,q=new JU.P3,n=new JU.P3,s=0,r=b.nextSetBit(0);0<=r;r=b.nextSetBit(r+1)){k=this.at[r];q.setT(k);d.toFractional(q,!1);d.unitize(q);e&&this.setSite(k,++s,!0);s=k.atomSite;h.clear(r);var u=

j?this.occupancies[r]:0,k=h.nextSetBit(e?r+1:0);a:for(;0<=k;k=h.nextSetBit(k+1)){var v=this.at[k];if(!(v.atomNumberFlags!=v.atomNumberFlags||j&&u!=this.occupancies[k])){p.setT(v);d.toFractional(p,!1);d.unitize(p);for(var w=0;w<f;w++)if(n.setT(q),A[w].rotTrans(n),d.unitize(n),1.96E-6>n.distanceSquared(p)){this.setSite(v,s,!0);h.clear(k);b.clear(k);continue a}}}}h.isEmpty()||System.err.println("Model basis atoms not found for "+h);e&&this.setAsymmetricUnit(a,null,b,!c)}}this.setInfo(a,"unitCellParams",

d.getUnitCellParams());this.setInfo(a,"spaceGroupAssigned",Boolean.TRUE);this.setInfo(a,"spaceGroup",d.getUnitCellDisplayName());this.setInfo(a,"spaceGroupInfo",null);this.setInfo(a,"symmetryOperations",d.getSymopList(!1));null!=this.am[a].simpleCage&&(d.getUnitCell(this.am[a].simpleCage.getUnitCellVectors(),!1,null),this.setInfo(a,"unitCellParams",d.getUnitCellParams()));this.setModelCage(a,null)},"~N,J.api.SymmetryInterface,JU.BS");c(b,"setAsymmetricUnit",function(a,d,b,c){null==d&&(d=this.vwr.getModelUndeletedAtomsBitSet(a));

this.am[a].bsAsymmetricUnit=b;null==this.bsSymmetry&&(this.bsSymmetry=JU.BS.newN(this.ac));this.bsSymmetry.or(d);this.bsSymmetry.andNot(b);if(c){a=0;for(c=d.nextSetBit(0);0<=c;c=d.nextSetBit(c+1)){var f=b.get(c);this.at[c].setSymop(f?1:0,!1);f&&this.setSite(this.at[c],++a,!1)}d.andNot(b)}},"~N,JU.BS,JU.BS,~B");c(b,"setModelCage",function(a,d){0<=a&&a<this.mc&&(this.am[a].setSimpleCage(d),this.haveUnitCells=!0);return d},"~N,J.api.SymmetryInterface");c(b,"fixP1AtomSites",function(a,d){if(!(null==a||

1!=a.getSpaceGroupOperationCount()))for(var b=d.cardinality(),b=Array(b),c=0,f=a.getPrecision(),f=f*f,e=d.nextSetBit(0);0<=e;e=d.nextSetBit(e+1)){var h=this.at[e],k=new JU.A4;k.setT(h);a.toFractional(k,!1);a.unitize(k);for(var j=!1,A=0;A<c;A++){var p=b[A];if(h.atomNumberFlags==p.angle&&p.distanceSquared(k)<f){j=!0;this.setSite(h,A+1,!0);break}}j||(k.angle=h.atomNumberFlags,b[c]=k,this.setSite(h,++c,!0))}},"J.api.SymmetryInterface,JU.BS");c(b,"getBasisAtom",function(a,d){var b=this.at[a];if(!d||null!=

this.getUnitCellForAtom(a)){var c=b.atomSite;if(0<c){var f=this.am[b.mi].bsAsymmetricUnit;if(null!=f)for(var e=f.nextSetBit(0);0<=e;e=f.nextSetBit(e+1))if(this.at[e].atomSite==c)return this.at[e]}}return b},"~N,~B");c(b,"updateBasisFromSite",function(a){if(null!=this.getUnitCell(a)){var d=this.am[a].bsAsymmetricUnit;if(null!=d){d.clearAll();var b=new JU.BS;a=this.am[a].bsAtoms;for(var c=E(this.ac,0),f=0,e=a.nextSetBit(0);0<=e;e=a.nextSetBit(e+1))if(!JM.AtomCollection.isDeleted(this.at[e])){var h=

this.at[e].atomSite;if(!b.get(h)){b.set(h);if(h>=c.length)continue;c[h]=++f;d.set(e)}this.setSite(this.at[e],-1,!1);this.setSite(this.at[e],c[h],!0)}null==this.bsSymmetry&&(this.bsSymmetry=JU.BS.newN(this.ac));this.bsSymmetry.or(a);this.bsSymmetry.andNot(d)}}},"~N");c(b,"getConnectingAtoms",function(a,d){for(var b=new JU.BS,c=new JU.BS,f=a.nextSetBit(0);0<=f;f=a.nextSetBit(f+1))for(var e=this.at[f],h=e.bonds,k=0,j=e.getBondCount();0<=--j;)if(h[j].isCovalent()&&!a.get(k=h[j].getOtherAtom(e).i))b.set(f),

c.set(k);a.or(c);d.or(c);return b},"JU.BS,JU.BS");c(b,"saveAtomPositions",function(){for(var a=Array(this.at.length),d=a.length;0<=--d;){var b=this.at[d];JM.AtomCollection.isDeleted(b)||(a[d]=JU.P3.newP(b))}return a});c(b,"restoreAtomPositions",function(a){for(var d=a.length;0<=--d;){var b=this.at[d];JM.AtomCollection.isDeleted(b)||b.setT(a[d])}},"~A");c(b,"clearUnitCell",function(a){if(null!=this.unitCells){if(0>a)for(a=0;a<this.mc;a++)this.clearUnitCell(a);else if(this.am[a].simpleCage=null,a<this.unitCells.length){this.unitCells[a]=

null;for(a=this.getModelAuxiliaryInfo(a).entrySet().iterator();a.hasNext();)JV.JC.isSpaceGroupInfoKey(a.next().getKey())&&a.remove();if(1<this.mc)return}this.unitCells=null;this.haveUnitCells=!1}},"~N");c(b,"fixDeletedBonds",function(a){var d=new JU.BS;if(null==this.bo)return a;for(var b=0,c=0;b<this.bondCount;b++)null!=this.bo[b]&&(0<=c&&d.setBitTo(b,a.get(c)),c++);return d},"JU.BS");b.hbondMinRasmol=2.5});u("JM");C(["JU.M3","$.P3"],"JM.Orientation",["JU.PT","JU.Escape"],function(){var b=v(function(){this.rotationMatrix=

this.saveName=null;this.rotationRadius=this.zoom=this.yTrans=this.xTrans=0;this.navCenter=this.center=null;this.cameraY=this.cameraX=this.cameraDepth=this.navDepth=this.yNav=this.xNav=NaN;this.navigationMode=this.windowCenteredFlag=!1;this.vwr=this.pymolView=this.moveToText=null;r(this,arguments)},JM,"Orientation",null);Q(b,function(){this.rotationMatrix=new JU.M3;this.center=new JU.P3;this.navCenter=new JU.P3});z(b,function(a,d,b){this.vwr=a;null!=b?(this.pymolView=b,this.moveToText="moveTo -1.0 PyMOL "+

JU.Escape.eAF(b)):(a.finalizeTransformParameters(),d?(d=a.ms.getInfoM("defaultOrientationMatrix"),null==d?this.rotationMatrix.setScale(1):this.rotationMatrix.setM3(d)):a.tm.getRotation(this.rotationMatrix),this.xTrans=a.tm.getTranslationXPercent(),this.yTrans=a.tm.getTranslationYPercent(),this.zoom=a.tm.getZoomSetting(),this.center.setT(a.tm.fixedRotationCenter),this.windowCenteredFlag=a.tm.isWindowCentered(),this.rotationRadius=a.getFloat(570425388),this.navigationMode=a.getBoolean(603979889),this.moveToText=

a.tm.getMoveToText(-1,!1),this.navigationMode&&(this.xNav=a.tm.getNavigationOffsetPercent("X"),this.yNav=a.tm.getNavigationOffsetPercent("Y"),this.navDepth=a.tm.navigationDepthPercent,this.navCenter=JU.P3.newP(a.tm.navigationCenter)),0!=a.tm.camera.z&&(this.cameraDepth=a.tm.getCameraDepth(),this.cameraX=a.tm.camera.x,this.cameraY=a.tm.camera.y))},"JV.Viewer,~B,~A");c(b,"getMoveToText",function(a){return a?" "+this.moveToText+"\n save orientation "+JU.PT.esc(this.saveName.substring(12))+";\n":this.moveToText},

"~B");c(b,"restore",function(a,d){d?(this.vwr.setBooleanProperty("windowCentered",this.windowCenteredFlag),this.vwr.setBooleanProperty("navigationMode",this.navigationMode),null==this.pymolView?this.vwr.moveTo(this.vwr.eval,a,this.center,null,NaN,this.rotationMatrix,this.zoom,this.xTrans,this.yTrans,this.rotationRadius,this.navCenter,this.xNav,this.yNav,this.navDepth,this.cameraDepth,this.cameraX,this.cameraY):this.vwr.tm.moveToPyMOL(this.vwr.eval,a,this.pymolView)):this.vwr.tm.setRotation(this.rotationMatrix);

return!0},"~N,~B")});u("JM");C(null,"JM.StateScript",["JU.SB","JU.BSUtil","$.Escape"],function(){var b=v(function(){this.modelIndex=0;this.script2=this.script1=this.bsAtoms2=this.bsAtoms1=this.bsBonds=null;this.inDefinedStateBlock=!1;r(this,arguments)},JM,"StateScript",null);z(b,function(a,d,b,c,f,e,h){this.modelIndex=a;this.script1=d;this.bsBonds=JU.BSUtil.copy(b);this.bsAtoms1=JU.BSUtil.copy(c);this.bsAtoms2=JU.BSUtil.copy(f);this.script2=e;this.inDefinedStateBlock=h},"~N,~S,JU.BS,JU.BS,JU.BS,~S,~B");

c(b,"isValid",function(){return null!=this.script1&&0<this.script1.length&&(null==this.bsBonds||0<=this.bsBonds.nextSetBit(0))&&(null==this.bsAtoms1||0<=this.bsAtoms1.nextSetBit(0))&&(null==this.bsAtoms2||0<=this.bsAtoms2.nextSetBit(0))});j(b,"toString",function(){if(!this.isValid())return"";var a=JU.SB.newS(this.script1);null!=this.bsBonds&&a.append(" ").append(JU.Escape.eBond(this.bsBonds));null!=this.bsAtoms1&&a.append(" ").append(JU.Escape.eBS(this.bsAtoms1));null!=this.bsAtoms2&&a.append(" ").append(JU.Escape.eBS(this.bsAtoms2));

null!=this.script2&&a.append(" ").append(this.script2);a=a.toString();a.endsWith(";")||(a+=";");return a});c(b,"isConnect",function(){return 0<=this.script1.indexOf("connect")});c(b,"deleteAtoms",function(a,d,b){if(a==this.modelIndex)return!1;if(a>this.modelIndex)return!0;JU.BSUtil.deleteBits(this.bsBonds,d);JU.BSUtil.deleteBits(this.bsAtoms1,b);JU.BSUtil.deleteBits(this.bsAtoms2,b);return this.isValid()},"~N,JU.BS,JU.BS");c(b,"setModelIndex",function(a){this.modelIndex=a},"~N")});u("JM");O(JM,"Structure");

u("JM");n=v(function(){this.id="";this.type=" ";this.scale=this.tickLabelFormats=this.ticks=null;this.first=0;this.signFactor=1;this.reference=null;r(this,arguments)},JM,"TickInfo",null);z(n,function(b){this.ticks=b},"JU.P3");u("JU");C(["JU.P3","$.V3"],"JU.BoxInfo",["java.util.Hashtable","JU.Measure","$.P4","JU.Point3fi"],function(){var b=v(function(){this.bbVertices=this.bbVector=this.bbCenter=this.bbCorner1=this.bbCorner0=null;this.isScaleSet=!1;this.margin=0;r(this,arguments)},JU,"BoxInfo",null);

Q(b,function(){this.bbCorner0=new JU.P3;this.bbCorner1=new JU.P3;this.bbCenter=new JU.P3;this.bbVector=new JU.V3;this.bbVertices=Array(8);for(var a=0;8>a;a++)JU.BoxInfo.unitBboxPoints[a]=JU.P3.new3(-1,-1,-1),JU.BoxInfo.unitBboxPoints[a].scaleAdd2(2,JU.BoxInfo.unitCubePoints[a],JU.BoxInfo.unitBboxPoints[a])});z(b,function(){for(var a=8;0<=--a;)this.bbVertices[a]=new JU.Point3fi;this.reset()});c(b,"reset",function(){this.isScaleSet=!1;this.bbCorner0.set(3.4028235E38,3.4028235E38,3.4028235E38);this.bbCorner1.set(-3.4028235E38,

-3.4028235E38,-3.4028235E38)});b.scaleBox=c(b,"scaleBox",function(a,d){if(!(0==d||1==d)){for(var b=new JU.P3,c=new JU.V3,f=0;8>f;f++)b.add(a[f]);b.scale(0.125);for(f=0;8>f;f++)c.sub2(a[f],b),c.scale(d),a[f].add2(b,c)}},"~A,~N");b.getVerticesFromOABC=c(b,"getVerticesFromOABC",function(a){for(var d=Array(8),b=0;7>=b;b++)d[b]=JU.P3.newP(a[0]),4==(b&4)&&d[b].add(a[1]),2==(b&2)&&d[b].add(a[2]),1==(b&1)&&d[b].add(a[3]);return d},"~A");b.getCanonicalCopy=c(b,"getCanonicalCopy",function(a,d){for(var b=Array(8),

c=0;8>c;c++)b[JU.BoxInfo.toCanonical[c]]=JU.P3.newP(a[c]);JU.BoxInfo.scaleBox(b,d);return b},"~A,~N");b.toOABC=c(b,"toOABC",function(a,d){var b=JU.P3.newP(a[0]),c=JU.P3.newP(a[4]),f=JU.P3.newP(a[2]),e=JU.P3.newP(a[1]);c.sub(b);f.sub(b);e.sub(b);null!=d&&b.add(d);return w(-1,[b,c,f,e])},"~A,JU.T3");c(b,"getBoundBoxCenter",function(){this.isScaleSet||this.setBbcage(1);return this.bbCenter});c(b,"getBoundBoxCornerVector",function(){this.isScaleSet||this.setBbcage(1);return this.bbVector});c(b,"getBoundBoxPoints",

function(a){this.isScaleSet||this.setBbcage(1);return a?w(-1,[this.bbCenter,JU.P3.newP(this.bbVector),this.bbCorner0,this.bbCorner1]):w(-1,[this.bbCorner0,this.bbCorner1])},"~B");c(b,"getBoundBoxVertices",function(){this.isScaleSet||this.setBbcage(1);return this.bbVertices});c(b,"setBoundBoxFromOABC",function(a){for(var d=JU.P3.newP(a[0]),b=new JU.P3,c=0;4>c;c++)b.add(a[c]);this.setBoundBox(d,b,!0,1)},"~A");c(b,"setBoundBox",function(a,d,b,c){if(null!=a){if(0==c)return;if(b){if(0==a.distance(d))return;

this.bbCorner0.set(Math.min(a.x,d.x),Math.min(a.y,d.y),Math.min(a.z,d.z));this.bbCorner1.set(Math.max(a.x,d.x),Math.max(a.y,d.y),Math.max(a.z,d.z))}else{if(0==d.x||0==d.y&&0==d.z)return;this.bbCorner0.set(a.x-d.x,a.y-d.y,a.z-d.z);this.bbCorner1.set(a.x+d.x,a.y+d.y,a.z+d.z)}}this.setBbcage(c)},"JU.T3,JU.T3,~B,~N");c(b,"setMargin",function(a){this.margin=a},"~N");c(b,"addBoundBoxPoint",function(a){this.isScaleSet=!1;JU.BoxInfo.addPoint(a,this.bbCorner0,this.bbCorner1,this.margin)},"JU.T3");b.addPoint=

c(b,"addPoint",function(a,d,b,c){a.x-c<d.x&&(d.x=a.x-c);a.x+c>b.x&&(b.x=a.x+c);a.y-c<d.y&&(d.y=a.y-c);a.y+c>b.y&&(b.y=a.y+c);a.z-c<d.z&&(d.z=a.z-c);a.z+c>b.z&&(b.z=a.z+c)},"JU.T3,JU.T3,JU.T3,~N");b.addPointXYZ=c(b,"addPointXYZ",function(a,d,b,c,f,e){a-e<c.x&&(c.x=a-e);a+e>f.x&&(f.x=a+e);d-e<c.y&&(c.y=d-e);d+e>f.y&&(f.y=d+e);b-e<c.z&&(c.z=b-e);b+e>f.z&&(f.z=b+e)},"~N,~N,~N,JU.P3,JU.P3,~N");c(b,"setBbcage",function(a){this.isScaleSet=!0;this.bbCenter.add2(this.bbCorner0,this.bbCorner1);this.bbCenter.scale(0.5);

this.bbVector.sub2(this.bbCorner1,this.bbCenter);0<a?this.bbVector.scale(a):(this.bbVector.x-=a/2,this.bbVector.y-=a/2,this.bbVector.z-=a/2);for(var d=8;0<=--d;){var b=this.bbVertices[d];b.setT(JU.BoxInfo.unitBboxPoints[d]);b.x*=this.bbVector.x;b.y*=this.bbVector.y;b.z*=this.bbVector.z;b.add(this.bbCenter)}1!=a&&(this.bbCorner0.setT(this.bbVertices[0]),this.bbCorner1.setT(this.bbVertices[7]))},"~N");c(b,"isWithin",function(a){this.isScaleSet||this.setBbcage(1);return a.x>=this.bbCorner0.x&&a.x<=this.bbCorner1.x&&

a.y>=this.bbCorner0.y&&a.y<=this.bbCorner1.y&&a.z>=this.bbCorner0.z&&a.z<=this.bbCorner1.z},"JU.P3");c(b,"getMaxDim",function(){return 2*this.bbVector.length()});c(b,"getInfo",function(a){var d=Double.$valueOf(Math.abs(8*this.bbVector.x*this.bbVector.y*this.bbVector.z));if("volume".equals(a))return d;var b=JU.P3.newP(this.bbCenter);return"center".equals(a)?b:null==a||"info".equals(a)?(a=new java.util.Hashtable,a.put("center",b),b=JU.V3.newVsub(this.bbCorner1,this.bbCorner0),a.put("dimensions",b),

a.put("girth",Double.$valueOf(b.x+b.y+b.z)),a.put("area",Double.$valueOf(2*(b.x*b.y+b.x*b.z+b.z*b.y))),a.put("volume",d),a):null},"~S");j(b,"toString",function(){return""+this.bbCorner0+this.bbCorner1});b.getBoxFacesFromOABC=c(b,"getBoxFacesFromOABC",function(a){var d=Array(6),b=new JU.V3,c=new JU.V3,f=new JU.P3,e=new JU.P3,h=new JU.P3;a=null==a?JU.BoxInfo.unitCubePoints:JU.BoxInfo.getVerticesFromOABC(a);for(var k=0;6>k;k++)f.setT(a[JU.BoxInfo.facePoints[k][0]]),e.setT(a[JU.BoxInfo.facePoints[k][1]]),

h.setT(a[JU.BoxInfo.facePoints[k][2]]),d[k]=JU.Measure.getPlaneThroughPoints(f,e,h,b,c,new JU.P4);return d},"~A");b.bbcageTickEdges=T(-1,"z\x00\x00yx\x00\x00\x00\x00\x00\x00\x00".split(""));b.uccageTickEdges=T(-1,"zyx\x00\x00\x00\x00\x00\x00\x00\x00\x00".split(""));b.edges=P(-1,[0,1,0,2,0,4,1,3,1,5,2,3,2,6,3,7,4,5,4,6,5,7,6,7]);b.faceOrder=E(-1,[0,3,5,2,1,4]);b.facePoints=w(-1,[E(-1,[4,0,6]),E(-1,[4,6,5]),E(-1,[5,7,1]),E(-1,[1,3,0]),E(-1,[6,2,7]),E(-1,[1,0,5]),E(-1,[0,2,6]),E(-1,[6,7,5]),E(-1,[7,

3,1]),E(-1,[3,2,0]),E(-1,[2,3,7]),E(-1,[0,4,5])]);b.unitCubePoints=w(-1,[JU.P3.new3(0,0,0),JU.P3.new3(0,0,1),JU.P3.new3(0,1,0),JU.P3.new3(0,1,1),JU.P3.new3(1,0,0),JU.P3.new3(1,0,1),JU.P3.new3(1,1,0),JU.P3.new3(1,1,1)]);b.toCanonical=E(-1,[0,3,4,7,1,2,5,6]);b.unitBboxPoints=Array(8)});u("JU");C(["JU.BS"],"JU.BSUtil",null,function(){var b=H(JU,"BSUtil",null);b.newAndSetBit=c(b,"newAndSetBit",function(a){var d=JU.BS.newN(a+1);d.set(a);return d},"~N");b.areEqual=c(b,"areEqual",function(a,d){return null==

a||null==d?null==a&&null==d:a.equals(d)},"JU.BS,JU.BS");b.haveCommon=c(b,"haveCommon",function(a,d){return null==a||null==d?!1:a.intersects(d)},"JU.BS,JU.BS");b.cardinalityOf=c(b,"cardinalityOf",function(a){return null==a?0:a.cardinality()},"JU.BS");b.newBitSet2=c(b,"newBitSet2",function(a,d){var b=JU.BS.newN(d);b.setBits(a,d);return b},"~N,~N");b.setAll=c(b,"setAll",function(a){var d=JU.BS.newN(a);d.setBits(0,a);return d},"~N");b.andNot=c(b,"andNot",function(a,d){null!=d&&null!=a&&a.andNot(d);return a},

"JU.BS,JU.BS");b.copy=c(b,"copy",function(a){return null==a?null:a.clone()},"JU.BS");b.copy2=c(b,"copy2",function(a,d){if(null==a||null==d)return null;d.clearAll();d.or(a);return d},"JU.BS,JU.BS");b.copyInvert=c(b,"copyInvert",function(a,d){return null==a?null:JU.BSUtil.andNot(JU.BSUtil.setAll(d),a)},"JU.BS,~N");b.invertInPlace=c(b,"invertInPlace",function(a,d){return JU.BSUtil.copy2(JU.BSUtil.copyInvert(a,d),a)},"JU.BS,~N");b.toggleInPlace=c(b,"toggleInPlace",function(a,d){a.equals(d)?a.clearAll():

0==JU.BSUtil.andNot(JU.BSUtil.copy(d),a).length()?JU.BSUtil.andNot(a,d):a.or(d);return a},"JU.BS,JU.BS");b.deleteBits=c(b,"deleteBits",function(a,d){if(null==a||null==d)return a;var b=d.nextSetBit(0);if(0>b)return a;var c=a.length(),f=Math.min(c,d.length()),e;for(e=d.nextClearBit(b);e<f&&0<=e;e=d.nextClearBit(e+1))a.setBitTo(b++,a.get(e));for(e=f;e<c;e++)a.setBitTo(b++,a.get(e));b<c&&a.clearBits(b,c);return a},"JU.BS,JU.BS");b.shiftBits=c(b,"shiftBits",function(a,d,b,c){if(!(null==a||null==d)){for(var f=

d.length(),e=JU.BS.newN(f),h=!1,k=!1,j=b,A=0,p=0;A<f&&p<c;A++)d.get(A)?(k&&e.set(A),j=b,h=!1):a.get(p++)?(e.set(A),j&&(j=!1,k=h=!0)):j&&!h&&(k=!1);a.clearAll();a.or(e)}},"JU.BS,JU.BS,~B,~N");b.offset=c(b,"offset",function(a,d,b){if(null!=a){for(var c=JU.BS.newN(a.length()+b),f=a.nextSetBit(0);f>=d;f=a.nextSetBit(f+1))c.set(f+b);JU.BSUtil.copy2(c,a)}},"JU.BS,~N,~N");b.setMapBitSet=c(b,"setMapBitSet",function(a,d,b,c){var f;a.containsKey(c)?f=a.get(c):a.put(c,f=new JU.BS);f.setBits(d,b+1)},"java.util.Map,~N,~N,~S");

b.emptySet=new JU.BS});u("JU");C(["JU.Int2IntHash"],"JU.C","JU.AU $.CU $.PT $.SB J.c.PAL JU.Escape $.Logger".split(" "),function(){var b=H(JU,"C",null);b.getColix=c(b,"getColix",function(a){if(0==a)return 0;a|=4278190080;var b=JU.C.colixHash.get(a);return(0<b?b:JU.C.allocateColix(a,!1))|0},"~N");b.allocateColix=c(b,"allocateColix",function(a,b){var c;if(b)c=2047;else{if(-74566==a)return 3;for(c=JU.C.colixMax;4<=--c;)if((a&16777215)==(JU.C.argbs[c]&16777215))return c;c=JU.C.colixMax}if(c>=JU.C.argbs.length){var f=

b?c+1:2*JU.C.colixMax;2048<f&&(f=2048);JU.C.argbs=JU.AU.arrayCopyI(JU.C.argbs,f);null!=JU.C.argbsGreyscale&&(JU.C.argbsGreyscale=JU.AU.arrayCopyI(JU.C.argbsGreyscale,f))}JU.C.argbs[c]=a;null!=JU.C.argbsGreyscale&&(JU.C.argbsGreyscale[c]=JU.CU.toFFGGGfromRGB(a));JU.C.colixHash.put(a,c);return 2047>c?JU.C.colixMax++:JU.C.colixMax},"~N,~B");b.setLastGrey=c(b,"setLastGrey",function(a){JU.C.calcArgbsGreyscale();JU.C.argbsGreyscale[2047]=JU.CU.toFFGGGfromRGB(a)},"~N");b.calcArgbsGreyscale=c(b,"calcArgbsGreyscale",

function(){if(null==JU.C.argbsGreyscale){for(var a=E(JU.C.argbs.length,0),b=JU.C.argbs.length;4<=--b;)a[b]=JU.CU.toFFGGGfromRGB(JU.C.argbs[b]);JU.C.argbsGreyscale=a}});b.getArgbGreyscale=c(b,"getArgbGreyscale",function(a){null==JU.C.argbsGreyscale&&JU.C.calcArgbsGreyscale();return JU.C.argbsGreyscale[a&-30721]},"~N");b.getColixO=c(b,"getColixO",function(a){if(null==a)return 0;if(y(a,"J.c.PAL"))return a===J.c.PAL.NONE?0:2;if(y(a,Integer))return JU.C.getColix(a.intValue());if("string"==typeof a)return JU.C.getColixS(a);

if(y(a,Byte))return 0==a.byteValue()?0:2;JU.Logger.debugging&&JU.Logger.debug("?? getColix("+a+")");return 22},"~O");b.getTranslucentFlag=c(b,"getTranslucentFlag",function(a){return 0==a?0:0>a?30720:Float.isNaN(a)||255<=a||1==a?16384:(B(Math.floor(1>a?256*a:15<=a?a:9>=a?B(Math.floor(a-1))<<5:256))>>5&15)<<11},"~N");b.isColixLastAvailable=c(b,"isColixLastAvailable",function(a){return 0<a&&2047==(a&2047)},"~N");b.getArgb=c(b,"getArgb",function(a){return JU.C.argbs[a&-30721]},"~N");b.isColixColorInherited=

c(b,"isColixColorInherited",function(a){switch(a){case 0:case 1:return!0;default:return 1==(a&-30721)}},"~N");b.getColixInherited=c(b,"getColixInherited",function(a,b){switch(a){case 0:return b;case 1:return b&-30721;default:return 1==(a&-30721)?b&-30721|a&30720:a}},"~N,~N");b.renderPass2=c(b,"renderPass2",function(a){a&=30720;return 0!=a&&30720!=a},"~N");b.isColixTranslucent=c(b,"isColixTranslucent",function(a){return 0!=(a&30720)},"~N");b.getChangeableColixIndex=c(b,"getChangeableColixIndex",function(a){return 0<=

a?-1:a&2047},"~N");b.getColixTranslucent3=c(b,"getColixTranslucent3",function(a,b,c){a&=-30721;0==a&&(a=1);return b?a|JU.C.getTranslucentFlag(c):a},"~N,~B,~N");b.copyColixTranslucency=c(b,"copyColixTranslucency",function(a,b){return JU.C.getColixTranslucent3(b,JU.C.isColixTranslucent(a),JU.C.getColixTranslucencyLevel(a))},"~N,~N");b.getColixTranslucencyFractional=c(b,"getColixTranslucencyFractional",function(a){a=JU.C.getColixTranslucencyLevel(a);return-1==a?0.5:0==a?0:255==a?1:a/256},"~N");b.getColixTranslucencyLabel=

c(b,"getColixTranslucencyLabel",function(a){return"translucent "+(30720==(a&30720)?-1:JU.C.getColixTranslucencyFractional(a))},"~N");b.getColixTranslucencyLevel=c(b,"getColixTranslucencyLevel",function(a){a=a>>11&15;switch(a){case 0:return 0;case 1:case 2:case 3:case 4:case 5:case 6:case 7:return a<<5;case 15:return-1;default:return 255}},"~N");b.isTransparent=c(b,"isTransparent",function(a){return 16384==(a&30720)},"~N");b.getColixS=c(b,"getColixS",function(a){var b=JU.CU.getArgbFromString(a);return 0!=

b?JU.C.getColix(b):"none".equalsIgnoreCase(a)?0:"opaque".equalsIgnoreCase(a)?1:2},"~S");b.getColixArray=c(b,"getColixArray",function(a){if(null==a||0==a.length)return null;a=JU.PT.getTokens(a);for(var b=W(a.length,0),c=0;c<a.length;c++)if(b[c]=JU.C.getColix(JU.CU.getArgbFromString(a[c])),0==b[c])return null;return b},"~S");b.getHexCode=c(b,"getHexCode",function(a){return JU.Escape.escapeColor(JU.C.getArgb(a))},"~N");b.getHexCodes=c(b,"getHexCodes",function(a){if(null==a)return null;for(var b=new JU.SB,

c=0;c<a.length;c++)b.append(0==c?"":" ").append(JU.C.getHexCode(a[c]));return b.toString()},"~A");b.getColixTranslucent=c(b,"getColixTranslucent",function(a){var b=a>>24&255;return 255==b?JU.C.getColix(a):JU.C.getColixTranslucent3(JU.C.getColix(a),!0,b/255)},"~N");b.getBgContrast=c(b,"getBgContrast",function(a){return 128>(JU.CU.toFFGGGfromRGB(a)&255)?8:4},"~N");b.colixMax=4;b.argbs=E(128,0);JU.C.argbs[3]=-74566;b.argbsGreyscale=null;b.colixHash=new JU.Int2IntHash(256);for(var b=E(-1,[4278190080,

4294944E3,4294951115,4278190335,4294967295,4278255615,4294901760,4278222848,4286611584,4290822336,4278255360,4286578688,4278190208,4286611456,4286578816,4278222976,4294902015,4294967040,4294928820,4294956800]),a=0;a<b.length;++a)JU.C.getColix(b[a])});u("JU");C(null,"JU.ColorEncoder","java.util.Hashtable JU.AU $.CU $.Lst $.PT $.Rdr J.c.PAL JU.C $.Escape $.Logger JV.FileManager $.JC".split(" "),function(){var b=v(function(){this.argbsNucleic=this.argbsAmino=this.argbsShapely=this.argbsRwb=this.argbsRoygb=

this.argbsCpk=this.paletteFriendly=this.paletteWB=this.paletteBW=this.vwr=null;this.ihalf=0;this.schemes=null;this.currentPalette=0;this.currentSegmentCount=1;this.isTranslucent=!1;this.hi=this.lo=0;this.isReversed=!1;this.thisScale=this.userScale=null;this.thisName="scheme";this.isColorIndex=!1;this.ce=null;r(this,arguments)},JU,"ColorEncoder",null);Q(b,function(){this.userScale=E(-1,[-8355712]);this.thisScale=E(-1,[-8355712])});z(b,function(a,d){null==a?(this.vwr=d,this.schemes=new java.util.Hashtable,

this.argbsCpk=J.c.PAL.argbsCpk,this.argbsRoygb=JV.JC.argbsRoygbScale,this.argbsRwb=JV.JC.argbsRwbScale,this.argbsAmino=this.argbsNucleic=this.argbsShapely=null,this.ihalf=B(JV.JC.argbsRoygbScale.length/3),this.ce=this):(this.ce=a,this.vwr=a.vwr,this.schemes=a.schemes)},"JU.ColorEncoder,JV.Viewer");c(b,"clearCache",function(){this.schemes.clear()});b.getSchemeIndex=c(b,"getSchemeIndex",function(a){for(var d=0;d<JU.ColorEncoder.colorSchemes.length;d++)if(JU.ColorEncoder.colorSchemes[d].equalsIgnoreCase(a))return 16<=

d?d-16:13>d?d:-d;return-1},"~S");b.fixName=c(b,"fixName",function(a){if(a.equalsIgnoreCase("byelement"))return"byelement_jmol";var d=JU.ColorEncoder.getSchemeIndex(a);return 0<=d?JU.ColorEncoder.colorSchemes[d]:0<=a.indexOf("/")?a:a.toLowerCase()},"~S");c(b,"makeColorScheme",function(a,d,b){a=JU.ColorEncoder.fixName(a);if(null==d){this.schemes.remove(a);a=this.createColorScheme(a,!1,b);if(b)switch(a){case 2147483647:return 0;case 12:this.paletteFriendly=this.getPaletteAC();break;case 10:this.paletteBW=

this.getPaletteBW();break;case 11:this.paletteWB=this.getPaletteWB();break;case 0:case 1:this.argbsRoygb=JV.JC.argbsRoygbScale;break;case 6:case 7:this.argbsRwb=JV.JC.argbsRwbScale;break;case 2:this.argbsCpk=J.c.PAL.argbsCpk;break;case 3:JU.ColorEncoder.getRasmolScale();break;case 17:this.getNucleic();break;case 5:this.getAmino();break;case 4:this.getShapely()}return a}this.schemes.put(a,d);this.setThisScheme(a,d);a=this.createColorScheme(a,!1,b);if(b)switch(a){case 10:this.paletteBW=this.thisScale;

break;case 11:this.paletteWB=this.thisScale;break;case 0:case 1:this.argbsRoygb=this.thisScale;this.ihalf=B(this.argbsRoygb.length/3);break;case 6:case 7:this.argbsRwb=this.thisScale;break;case 2:this.argbsCpk=this.thisScale;break;case 5:this.argbsAmino=this.thisScale;break;case 17:this.argbsNucleic=this.thisScale;break;case 4:this.argbsShapely=this.thisScale}return-1},"~S,~A,~B");c(b,"getShapely",function(){return null==this.argbsShapely?this.argbsShapely=this.vwr.getJBR().getArgbs(1073742144):this.argbsShapely});

c(b,"getAmino",function(){return null==this.argbsAmino?this.argbsAmino=this.vwr.getJBR().getArgbs(2097154):this.argbsAmino});c(b,"getNucleic",function(){return null==this.argbsNucleic?this.argbsNucleic=this.vwr.getJBR().getArgbs(2097166):this.argbsNucleic});c(b,"createColorScheme",function(a,d,b){if(a.equalsIgnoreCase("inherit"))return 15;var c=a.lastIndexOf("="),f=a.indexOf("/"),e=Math.max(c,a.indexOf("[")),c=JU.ColorEncoder.fixName(a),h=JU.ColorEncoder.getSchemeIndex(c);if(-1==h&&(0>e||0<f)){b=

a;f=this.schemes.get(c);if(null==f)try{var k="~"==b.charAt(1);k&&(b=b.substring(1));for(c=null;;){if(0>b.indexOf("/")){0>b.indexOf(".")&&(b+=".lut.txt");var j=Array(1);try{JU.Logger.info("ColorEncoder opening colorschemes/"+b),JU.Rdr.readAllAsString(JV.FileManager.getBufferedReaderForResource(this.vwr,new JU.C,"JU/","colorschemes/"+b),-1,!1,j,0)}catch(A){if(F(A,"java.io.IOException")){JU.Logger.info("ColorEncoder "+A);break}else throw A;}b=j[0]}else{b=JU.PT.rep(b," ","%20");JU.Logger.info("ColorEncoder opening "+

b);var p=this.vwr.fm.getFileAsBytes(b,null);if("string"==typeof p){JU.Logger.info("ColorEncoder "+p);break}c=p;JU.Logger.info("ColorEncoder read "+c.length+" bytes");var j=0,q=c.length;if(800==q||802==q)j=32;if(768==q-j||770==q-j)for(var f=E(256,0),q=256+j,n=0;256>n;n++)f[n]=JU.CU.rgb(c[n+j]&255,c[n+j+256]&255,c[n+j+512]&255);else b=String.instantialize(c)}if(null==f)for(var s=JU.PT.split(b.trim(),"\n"),q=s.length,f=E(q,0),r=0<q&&0>s[0].indexOf("."),n=0;n<q;n++){var u=JU.PT.getTokens(s[n]);if(3>u.length){f=

null;break}var v=u.length;f[n]=r?JU.CU.rgb(JU.PT.parseInt(u[v-3]),JU.PT.parseInt(u[v-2]),JU.PT.parseInt(u[v-1])):JU.CU.colorTriadToFFRGB(JU.PT.parseFloat(u[v-3]),JU.PT.parseFloat(u[v-2]),JU.PT.parseFloat(u[v-1]))}if(null!=f&&k){n=0;q=f.length-1;for(k=q+1>>1;n<k;n++){var w=f[n];f[n]=f[q-n];f[q-n]=w}}break}}catch(y){if(F(y,Exception))JU.Logger.info("ColorEncoder "+y),f=null;else throw y;}null==f&&(f=E(-1,[-1]));this.schemes.put(a,f);this.setThisScheme(a,f);return-1}if(0<=e){a=a.toLowerCase();c=JU.PT.replaceAllCharacters(a.substring(0,

e)," =","");0<c.length&&(b=!0);q=0;a.length>e+1&&!a.contains("[")&&(a="["+a.substring(e+1).trim()+"]",a=JU.PT.rep(a.$replace("\n"," ")," "," "),a=JU.PT.rep(a,", ",",").$replace(" ",","),a=JU.PT.rep(a,",","]["));for(e=-1;0<=(e=a.indexOf("[",e+1));)q++;if(0==q)return this.makeColorScheme(c,null,b);f=E(q,0);for(q=0;0<=(e=a.indexOf("[",e+1));){n=a.indexOf("]",e);0>n&&(n=a.length-1);w=JU.CU.getArgbFromString(a.substring(e,n+1));0==w&&(w=JU.CU.getArgbFromString(a.substring(e+1,n).trim()));if(0==w)return JU.Logger.error("error in color value: "+

a.substring(e,n+1)),0;f[q++]=w}return c.equals("user")?(this.setUserScale(f),-13):this.makeColorScheme(c,f,b)}f=this.schemes.get(c);return null!=f?(this.setThisScheme(c,f),h):-1!=h?h:d?0:2147483647},"~S,~B,~B");c(b,"setUserScale",function(a){this.ce.userScale=a;this.makeColorScheme("user",a,!1)},"~A");c(b,"getColorSchemeArray",function(a){switch(a){case -1:return this.thisScale;case 0:return this.ce.argbsRoygb;case 1:return JU.AU.arrayCopyRangeRevI(this.ce.argbsRoygb,0,-1);case 8:return JU.AU.arrayCopyRangeI(this.ce.argbsRoygb,

0,this.ce.ihalf);case 9:var d=JU.AU.arrayCopyRangeI(this.ce.argbsRoygb,this.ce.argbsRoygb.length-2*this.ce.ihalf,-1);a=E(this.ce.ihalf,0);for(var b=a.length,c=d.length;0<=--b&&0<=--c;)a[b]=d[c--];return a;case 12:return this.getPaletteAC();case 10:return this.getPaletteBW();case 11:return this.getPaletteWB();case 6:return this.ce.argbsRwb;case 7:return JU.AU.arrayCopyRangeRevI(this.ce.argbsRwb,0,-1);case 2:return this.ce.argbsCpk;case 3:return JU.ColorEncoder.getRasmolScale();case 4:return this.ce.getShapely();

case 17:return this.ce.getNucleic();case 5:return this.ce.getAmino();case -13:return this.ce.userScale;case -14:return JU.AU.arrayCopyRangeRevI(this.ce.userScale,0,-1);default:return null}},"~N");c(b,"getColorIndexFromPalette",function(a,d,b,c,f){c=JU.C.getColix(this.getArgbFromPalette(a,d,b,c));f&&(a=(b-a)/(b-d),1<a?a=1:0.125>a&&(a=0.125),c=JU.C.getColixTranslucent3(c,!0,a));return c},"~N,~N,~N,~N,~B");c(b,"getPaletteColorCount",function(a){switch(a){case -1:return this.thisScale.length;case 10:case 11:return this.getPaletteBW().length;

case 0:case 1:return this.ce.argbsRoygb.length;case 8:case 9:return this.ce.ihalf;case 6:case 7:return this.ce.argbsRwb.length;case -13:case -14:return this.ce.userScale.length;case 2:return this.ce.argbsCpk.length;case 3:return JU.ColorEncoder.getRasmolScale().length;case 4:return this.ce.getShapely().length;case 17:return this.ce.getNucleic().length;case 5:return this.ce.getAmino().length;case 12:return this.getPaletteAC().length;default:return 0}},"~N");c(b,"getArgbFromPalette",function(a,d,b,

c){if(Float.isNaN(a))return-8355712;var f=this.getPaletteColorCount(c);switch(c){case -1:return this.isColorIndex&&(d=0,b=this.thisScale.length),this.thisScale[JU.ColorEncoder.quantize4(a,d,b,f)];case 10:return this.getPaletteBW()[JU.ColorEncoder.quantize4(a,d,b,f)];case 11:return this.getPaletteWB()[JU.ColorEncoder.quantize4(a,d,b,f)];case 0:return this.ce.argbsRoygb[JU.ColorEncoder.quantize4(a,d,b,f)];case 1:return this.ce.argbsRoygb[JU.ColorEncoder.quantize4(-a,-b,-d,f)];case 8:return this.ce.argbsRoygb[JU.ColorEncoder.quantize4(a,

d,b,f)];case 9:return this.ce.argbsRoygb[this.ce.ihalf+2*JU.ColorEncoder.quantize4(a,d,b,f)];case 6:return this.ce.argbsRwb[JU.ColorEncoder.quantize4(a,d,b,f)];case 7:return this.ce.argbsRwb[JU.ColorEncoder.quantize4(-a,-b,-d,f)];case -13:return 0==this.ce.userScale.length?-8355712:this.ce.userScale[JU.ColorEncoder.quantize4(a,d,b,f)];case -14:return 0==this.ce.userScale.length?-8355712:this.ce.userScale[JU.ColorEncoder.quantize4(-a,-b,-d,f)];case 2:return this.ce.argbsCpk[JU.ColorEncoder.colorIndex(a,

f)];case 3:return JU.ColorEncoder.getRasmolScale()[JU.ColorEncoder.colorIndex(a,f)];case 4:return this.ce.getShapely()[JU.ColorEncoder.colorIndex(a,f)];case 5:return this.ce.getAmino()[JU.ColorEncoder.colorIndex(a,f)];case 17:return this.ce.getNucleic()[JU.ColorEncoder.colorIndex(a-24+2,f)];case 12:return this.getPaletteAC()[JU.ColorEncoder.colorIndexRepeat(a,f)];default:return-8355712}},"~N,~N,~N,~N");c(b,"setThisScheme",function(a,d){this.thisName=a;this.thisScale=d;a.equals("user")&&(this.userScale=

d);this.isColorIndex=0==a.indexOf("byelement")||0==a.indexOf("byresidue")},"~S,~A");c(b,"getArgb",function(a){return this.isReversed?this.getArgbFromPalette(-a,-this.hi,-this.lo,this.currentPalette):this.getArgbFromPalette(a,this.lo,this.hi,this.currentPalette)},"~N");c(b,"getArgbMinMax",function(a,d,b){return this.isReversed?this.getArgbFromPalette(-a,-b,-d,this.currentPalette):this.getArgbFromPalette(a,d,b,this.currentPalette)},"~N,~N,~N");c(b,"getColorIndex",function(a){return this.isReversed?

this.getColorIndexFromPalette(-a,-this.hi,-this.lo,this.currentPalette,this.isTranslucent):this.getColorIndexFromPalette(a,this.lo,this.hi,this.currentPalette,this.isTranslucent)},"~N");c(b,"getColorKey",function(){for(var a=new java.util.Hashtable,d=this.getPaletteColorCount(this.currentPalette),b=new JU.Lst,c=K(d+1,0),f=(this.hi-this.lo)/d,e=f*(this.isReversed?-0.5:0.5),h=0;h<d;h++)c[h]=this.isReversed?this.hi-h*f:this.lo+h*f,b.addLast(JU.CU.colorPtFromInt(this.getArgb(c[h]+e),null));c[d]=this.isReversed?

this.lo:this.hi;a.put("values",c);a.put("colors",b);a.put("min",Float.$valueOf(this.lo));a.put("max",Float.$valueOf(this.hi));a.put("reversed",Boolean.$valueOf(this.isReversed));a.put("name",this.getCurrentColorSchemeName());return a});c(b,"getColorScheme",function(){return(this.isTranslucent?"translucent ":"")+(0>this.currentPalette?JU.ColorEncoder.getColorSchemeList(this.getColorSchemeArray(this.currentPalette)):this.getColorSchemeName(this.currentPalette))});c(b,"setColorScheme",function(a,d){this.isTranslucent=

d;null!=a&&(this.currentPalette=this.createColorScheme(a,!0,!1))},"~S,~B");c(b,"setRange",function(a,d,b){3.4028235E38==d&&(a=1,d=this.getPaletteColorCount(this.currentPalette)+1);this.lo=Math.min(a,d);this.hi=Math.max(a,d);this.isReversed=b},"~N,~N,~B");c(b,"getCurrentColorSchemeName",function(){return this.getColorSchemeName(this.currentPalette)});c(b,"getColorSchemeName",function(a){var d=Math.abs(a);return-1==a?this.thisName:d<JU.ColorEncoder.colorSchemes.length&&0<=d?JU.ColorEncoder.colorSchemes[d]:

null},"~N");b.getColorSchemeList=c(b,"getColorSchemeList",function(a){if(null==a)return"";for(var d="",b=0;b<a.length;b++)d+=(0==b?"":" ")+JU.Escape.escapeColor(a[b]);return d},"~A");b.getRasmolScale=c(b,"getRasmolScale",function(){if(null!=JU.ColorEncoder.rasmolScale)return JU.ColorEncoder.rasmolScale;JU.ColorEncoder.rasmolScale=E(J.c.PAL.argbsCpk.length,0);for(var a=J.c.PAL.argbsCpkRasmol[0]|4278190080,d=JU.ColorEncoder.rasmolScale.length;0<=--d;)JU.ColorEncoder.rasmolScale[d]=a;for(d=J.c.PAL.argbsCpkRasmol.length;0<=

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this.textY=0;this.currentFont=this.graphicsForMetrics=this.vwr=this.shader=null;this.argbNoisyDn=this.argbNoisyUp=0;this.transformedVectors=null;r(this,arguments)},JU,"GData",null,J.api.JmolGraphicsInterface);Q(b,function(){this.changeableColixMap=W(16,0);this.transformedVectors=Array(JU.GData.normixCount)});z(b,function(){this.shader=new JU.Shader});c(b,"initialize",function(a,b){this.vwr=a;this.apiPlatform=b},"JV.Viewer,J.api.GenericPlatform");c(b,"setDepth",function(a){this.depth=0>a?0:a},"~N");

j(b,"setSlab",function(a){this.slab=Math.max(0,a)},"~N");j(b,"setSlabAndZShade",function(a,b){this.setSlab(a);this.setDepth(b)},"~N,~N,~N,~N,~N");c(b,"setAmbientOcclusion",function(a){this.ambientOcclusion=a},"~N");j(b,"isAntialiased",function(){return this.antialiasThisFrame});c(b,"getChangeableColix",function(a,b){a>=this.changeableColixMap.length&&(this.changeableColixMap=JU.AU.arrayCopyShort(this.changeableColixMap,a+16));0==this.changeableColixMap[a]&&(this.changeableColixMap[a]=JU.C.getColix(b));

return a|-32768},"~N,~N");c(b,"changeColixArgb",function(a,b){a<this.changeableColixMap.length&&0!=this.changeableColixMap[a]&&(this.changeableColixMap[a]=JU.C.getColix(b))},"~N,~N");c(b,"getColorArgbOrGray",function(a){if(3==a)return JU.C.getArgb(this.contrastColix);0>a&&(a=this.changeableColixMap[a&2047]);return this.inGreyscaleMode?JU.C.getArgbGreyscale(a):JU.C.getArgb(a)},"~N");c(b,"getShades",function(a){0>a&&(a=this.changeableColixMap[a&2047]);return this.inGreyscaleMode?this.shader.getShadesG(a):

this.shader.getShades(a)},"~N");c(b,"setGreyscaleMode",function(a){this.inGreyscaleMode=a},"~B");c(b,"getSpecularPower",function(){return this.shader.specularPower});c(b,"setSpecularPower",function(a){0>a?this.setSpecularExponent(-a):this.shader.specularPower!=a&&(this.shader.specularPower=a,this.shader.intenseFraction=a/100,this.shader.flushCaches())},"~N");c(b,"getSpecularPercent",function(){return this.shader.specularPercent});c(b,"setSpecularPercent",function(a){this.shader.specularPercent!=a&&

(this.shader.specularPercent=a,this.shader.specularFactor=a/100,this.shader.flushCaches())},"~N");c(b,"getSpecularExponent",function(){return this.shader.specularExponent});c(b,"setSpecularExponent",function(a){this.shader.specularExponent!=a&&(this.shader.specularExponent=a,this.shader.phongExponent=B(Math.pow(2,a)),this.shader.usePhongExponent=!1,this.shader.flushCaches())},"~N");c(b,"getPhongExponent",function(){return this.shader.phongExponent});c(b,"setPhongExponent",function(a){this.shader.phongExponent==

a&&this.shader.usePhongExponent||(this.shader.phongExponent=a,a=Math.log(a)/Math.log(2),this.shader.usePhongExponent=a!=D(a),this.shader.usePhongExponent||(this.shader.specularExponent=D(a)),this.shader.flushCaches())},"~N");c(b,"getDiffusePercent",function(){return this.shader.diffusePercent});c(b,"setDiffusePercent",function(a){this.shader.diffusePercent!=a&&(this.shader.diffusePercent=a,this.shader.diffuseFactor=a/100,this.shader.flushCaches())},"~N");c(b,"getAmbientPercent",function(){return this.shader.ambientPercent});

c(b,"setAmbientPercent",function(a){this.shader.ambientPercent!=a&&(this.shader.ambientPercent=a,this.shader.ambientFraction=a/100,this.shader.flushCaches())},"~N");c(b,"getSpecular",function(){return this.shader.specularOn});c(b,"setSpecular",function(a){this.shader.specularOn!=a&&(this.shader.specularOn=a,this.shader.flushCaches())},"~B");c(b,"setCel",function(a){this.shader.setCel(a,this.shader.celPower,this.bgcolor)},"~B");c(b,"getCel",function(){return this.shader.celOn});c(b,"getCelPower",function(){return this.shader.celPower});

c(b,"setCelPower",function(a){this.shader.setCel(this.shader.celOn||0==this.shader.celPower,a,this.bgcolor)},"~N");c(b,"getLightSource",function(){return this.shader.lightSource});c(b,"isClipped3",function(a,b,c){return 0>a||a>=this.width||0>b||b>=this.height||c<this.slab||c>this.depth},"~N,~N,~N");c(b,"isClipped",function(a,b){return 0>a||a>=this.width||0>b||b>=this.height},"~N,~N");j(b,"isInDisplayRange",function(a,b){return a>=this.displayMinX&&a<this.displayMaxX&&b>=this.displayMinY&&b<this.displayMaxY},

"~N,~N");j(b,"isClippedXY",function(a,b,c){a=a+1>>1;return b<-a||b>=this.width+a||c<-a||c>=this.height+a},"~N,~N,~N");c(b,"isClippedZ",function(a){return-2147483648!=a&&(a<this.slab||a>this.depth)},"~N");c(b,"clipCode3",function(a,b,c){var l=0;0>a?l|=a<this.displayMinX2?-1:8:a>=this.width&&(l|=a>this.displayMaxX2?-1:4);0>b?l|=b<this.displayMinY2?-1:2:b>=this.height&&(l|=b>this.displayMaxY2?-1:1);c<this.slab?l|=32:c>this.depth&&(l|=16);return l},"~N,~N,~N");c(b,"clipCode",function(a){var b=0;a<this.slab?

b|=32:a>this.depth&&(b|=16);return b},"~N");c(b,"getFont3D",function(a){return JU.Font.createFont3D(0,0,a,a,0,this.apiPlatform,this.graphicsForMetrics)},"~N");c(b,"getFont3DFS",function(a,b){return JU.Font.createFont3D(JU.Font.getFontFaceID(a),0,b,b,0,this.apiPlatform,this.graphicsForMetrics)},"~S,~N");c(b,"getFontFidFS",function(a,b){return this.getFont3DFSS(a,"Bold",b).fid},"~S,~N");c(b,"getFont3DFSS",function(a,b,c){b=JU.Font.getFontStyleID(b);0>b&&(b=0);return JU.Font.createFont3D(JU.Font.getFontFaceID(a),

b,c,c,0,this.apiPlatform,this.graphicsForMetrics)},"~S,~S,~N");c(b,"getFont3DScaled",function(a,b){var c=a.fontSizeNominal*b;return c==a.fontSize?a:JU.Font.createFont3D(a.idFontFace,a.idFontStyle,c,a.fontSizeNominal,a.fontSizeAngstroms,this.apiPlatform,this.graphicsForMetrics)},"JU.Font,~N");c(b,"getFontFidI",function(a){return this.getFont3D(a).fid},"~N");c(b,"getFont3DCurrent",function(){return this.currentFont});c(b,"setFont",function(){},"JU.Font");c(b,"setFontBold",function(a,b){this.setFont(this.getFont3DFSS(a,

"Bold",b))},"~S,~N");c(b,"setBackgroundTransparent",function(){},"~B");c(b,"setBackgroundArgb",function(a){this.bgcolor=a;this.setCel(this.shader.celOn)},"~N");c(b,"setBackgroundImage",function(a){this.backgroundImage=a},"~O");c(b,"setWindowParameters",function(a,b,c){this.setWinParams(a,b,c)},"~N,~N,~B");c(b,"setWinParams",function(a,b,c){this.newWindowWidth=a;this.newWindowHeight=b;this.newAntialiasing=c},"~N,~N,~B");c(b,"setNewWindowParametersForExport",function(){this.windowWidth=this.newWindowWidth;

this.windowHeight=this.newWindowHeight;this.setWidthHeight(!1)});c(b,"setWidthHeight",function(a){this.width=this.windowWidth;this.height=this.windowHeight;a&&(this.width<<=1,this.height<<=1);this.xLast=this.width-1;this.yLast=this.height-1;this.displayMinX=-(this.width>>1);this.displayMaxX=this.width-this.displayMinX;this.displayMinY=-(this.height>>1);this.displayMaxY=this.height-this.displayMinY;this.displayMinX2=this.displayMinX<<2;this.displayMaxX2=this.displayMaxX<<2;this.displayMinY2=this.displayMinY<<

2;this.displayMaxY2=this.displayMaxY<<2;this.ht3=3*this.height;this.bufferSize=this.width*this.height},"~B");c(b,"beginRendering",function(){},"JU.M3,~B,~B,~B");c(b,"endRendering",function(){});c(b,"snapshotAnaglyphChannelBytes",function(){});c(b,"getScreenImage",function(){return null},"~B");c(b,"releaseScreenImage",function(){});c(b,"applyAnaglygh",function(){},"J.c.STER,~A");c(b,"setPass2",function(){return!1},"~B");c(b,"destroy",function(){});c(b,"clearFontCache",function(){});c(b,"drawQuadrilateralBits",

function(a,b,c,l,f,e){a.drawLineBits(b,b,c,l);a.drawLineBits(b,b,l,f);a.drawLineBits(b,b,f,e);a.drawLineBits(b,b,e,c)},"J.api.JmolRendererInterface,~N,JU.P3,JU.P3,JU.P3,JU.P3");c(b,"drawTriangleBits",function(a,b,c,l,f,e,h,k){1==(k&1)&&a.drawLineBits(c,f,b,l);2==(k&2)&&a.drawLineBits(f,h,l,e);4==(k&4)&&a.drawLineBits(h,c,e,b)},"J.api.JmolRendererInterface,JU.P3,~N,JU.P3,~N,JU.P3,~N,~N");c(b,"plotImage",function(){},"~N,~N,~N,~O,J.api.JmolRendererInterface,~N,~N,~N");c(b,"plotText",function(){},"~N,~N,~N,~N,~N,~S,JU.Font,J.api.JmolRendererInterface");

c(b,"renderBackground",function(){},"J.api.JmolRendererInterface");c(b,"setColor",function(a){this.argbCurrent=this.argbNoisyUp=this.argbNoisyDn=a},"~N");c(b,"setC",function(){return!0},"~N");c(b,"isDirectedTowardsCamera",function(a){return 0>a||0<this.transformedVectors[a].z},"~N");b.roundInt=c(b,"roundInt",function(a){return a},"~N");c(b,"clear",function(){});j(b,"renderAllStrings",function(){},"~O");c(b,"addRenderer",function(){},"~N");b.getHermiteList=c(b,"getHermiteList",function(a,b,c,l,f,e,

h,k,j,A){var p=j+1;j-=1;var q=c.x,n=c.y,s=c.z,r=l.x,u=l.y;l=l.z;var v=(r-b.x)*a/8,w=(u-b.y)*a/8;b=(l-b.z)*a/8;var y=(f.x-q)*a/8,z=(f.y-n)*a/8,B=(f.z-s)*a/8,C=(e.x-r)*a/8,D=(e.y-u)*a/8;a=(e.z-l)*a/8;h[k]=c;for(c=0;c<p;c++){var E=c/j;c==p-1&&(q=r,n=u,s=l,r=f.x,u=f.y,l=f.z,v=y,w=z,b=B,y=C,z=D,B=a,E-=1);var F=E*E,H=F*E;e=2*H-3*F+1;var I=-2*H+3*F,E=H-2*F+E,K=H-F,F=e*q+I*r+E*v+K*y,H=e*n+I*u+E*w+K*z;e=e*s+I*l+E*b+K*B;h[k+c]=A?JU.P3.new3(F,H,e):JU.V3.new3(F,H,e)}},"~N,JU.T3,JU.T3,JU.T3,JU.T3,JU.T3,~A,~N,~N,~B");

c(b,"setTextPosition",function(a){this.textY=a},"~N");c(b,"getTextPosition",function(){return this.textY});c(b,"getTransformedVertexVectors",function(){return this.transformedVectors});j(b,"drawLinePixels",function(){},"JU.P3i,JU.P3i,~N,~N");b.normixCount=JU.Normix.getNormixCount()});u("JU");C(["javajs.api.JSInterface","J.api.JmolAppletInterface","$.JmolStatusListener"],"JU.GenericApplet","java.net.URL java.util.Hashtable JU.Lst $.PT $.SB J.awtjs2d.Platform J.c.CBK J.i18n.GT JU.Logger $.Parser JV.JC $.Viewer".split(" "),

function(){var b=v(function(){this.documentBase=this.codeBase=null;this.isSigned=!1;this.language=null;this.doTranslate=!0;this.mayScript=this.isStereoSlave=this.haveDocumentAccess=!1;this.vwrOptions=this.b$=this.viewer=this.gRight=this.statusTextarea=this.statusText=this.statusForm=this.fullName=this.htmlName=null;this.haveNotifiedError=!1;this.appletObject=null;this.loading=!1;this.htParams=this.outputBuffer=this.syncId=null;r(this,arguments)},JU,"GenericApplet",null,[javajs.api.JSInterface,J.api.JmolAppletInterface,

J.api.JmolStatusListener]);c(b,"setStereoGraphics",function(a){return a?vwr.apiPlatform.context:null},"~B");j(b,"processMouseEvent",function(a,b,c,l,f){return this.viewer.processMouseEvent(a,b,c,l,f)},"~N,~N,~N,~N,~N");j(b,"processKeyEvent",function(a){this.viewer.processKeyEvent(a)},"~O");j(b,"setDisplay",function(a){this.viewer.setDisplay(a)},"~O");j(b,"setStatusDragDropped",function(a,b,c,l,f){return this.viewer.setStatusDragDropped(a,b,c,l,f)},"~N,~N,~N,~S,~A");j(b,"startHoverWatcher",function(a){this.viewer.startHoverWatcher(a)},

"~B");j(b,"update",function(){this.viewer.updateJS()});j(b,"openFileAsyncSpecial",function(a,b){this.viewer.openFileAsyncSpecial(a,b)},"~S,~N");j(b,"openFileAsyncSpecialType",function(a,b,c){this.viewer.openFileAsyncSpecialType(a,b,c)},"~S,~N,~S");j(b,"processTwoPointGesture",function(a){this.viewer.processTwoPointGesture(a)},"~A");j(b,"setScreenDimension",function(a,b){this.viewer.setScreenDimension(a,b)},"~N,~N");c(b,"resizeDisplay",function(a,b){J.awtjs2d.Platform.Jmol().resizeApplet(this.viewer.html5Applet,

E(-1,[a,b]))},"~N,~N");c(b,"init",function(a){this.b$=new java.util.Hashtable;null==JU.GenericApplet.htRegistry&&(JU.GenericApplet.htRegistry=new java.util.Hashtable);this.appletObject=a;this.htmlName=JU.PT.split(""+this.getJmolParameter("name"),"_object")[0];this.syncId=this.getJmolParameter("syncId");this.fullName=this.htmlName+"__"+this.syncId+"__";System.out.println("Jmol JavaScript applet "+this.fullName+" initializing");a=this.getValue("logLevel",this.getBooleanValue("debug",!1)?"5":"4").charAt(0).charCodeAt(0)-

48;4!=a&&System.out.println("setting logLevel="+a+' -- To change, use script "set logLevel [0-5]"');JU.Logger.setLogLevel(a);J.i18n.GT.ignoreApplicationBundle();this.initOptions();JU.GenericApplet.checkIn(this.fullName,this.appletObject);this.initApplication()},"~O");c(b,"initApplication",function(){this.vwrOptions.put("applet",Boolean.TRUE);null==this.getJmolParameter("statusListener")&&this.vwrOptions.put("statusListener",this);this.language=this.getJmolParameter("language");null!=this.language&&

this.vwrOptions.put("language",this.language);this.viewer=new JV.Viewer(this.vwrOptions);this.viewer.pushHoldRepaint();var a=this.getValueLowerCase("emulate","jmol");this.setStringProperty("defaults",a.equals("chime")?"RasMol":"Jmol");this.setStringProperty("backgroundColor",this.getValue("bgcolor",this.getValue("boxbgcolor","black")));this.viewer.setBooleanProperty("frank",!0);this.loading=!0;for(var b,a=0,c=J.c.CBK.values();a<c.length&&((b=c[a])||1);a++){var l=b.name(),f=this.getValue(l+"Callback",

null);if(null!=f)if("string"==typeof f)this.setStringProperty(l+"Callback",f);else{var e=null,e="Info."+f.name;this.setStringProperty(l+"Callback",e);this.setCallback(l,f)}}this.loading=!1;null!=this.language&&System.out.print("requested language="+this.language+"; ");this.doTranslate=!"none".equals(this.language)&&this.getBooleanValue("doTranslate",!0);this.language=J.i18n.GT.getLanguage();System.out.println("language="+this.language);if(null==this.b$.get(J.c.CBK.SCRIPT)&&null==this.b$.get(J.c.CBK.ERROR)&&

(null!=this.b$.get(J.c.CBK.MESSAGE)||null!=this.statusForm||null!=this.statusText))this.doTranslate&&null==this.getValue("doTranslate",null)&&(this.doTranslate=!1,JU.Logger.warn("Note -- Presence of message callback disables disable translation; to enable message translation use jmolSetTranslation(true) prior to jmolApplet()")),this.doTranslate&&JU.Logger.warn("Note -- Automatic language translation may affect parsing of message callbacks messages; use scriptCallback or errorCallback to process errors");

this.doTranslate||(J.i18n.GT.setDoTranslate(!1),JU.Logger.warn("Note -- language translation disabled"));this.getBooleanValue("popupMenu",!0)||this.viewer.getProperty("DATA_API","disablePopupMenu",null);b=this.getJmolParameter("menuFile");null!=b&&this.viewer.setMenu(b,!0);b=this.getValue("script","");a=this.getValue("loadInline",null);if(null==a){if(null!=(a=this.getValue("load",null)))b='load "'+a+'";'+b;a=null}this.viewer.popHoldRepaint("applet init");null!=a&&null!=this.viewer.loadInline(a)&&

(b="");0<b.length&&this.scriptProcessor(b,null,1);this.viewer.notifyStatusReady(!0)});j(b,"destroy",function(){this.gRight=null;this.viewer.notifyStatusReady(!1);this.viewer=null;JU.GenericApplet.checkOut(this.fullName)});c(b,"getBooleanValue",function(a,b){var c=this.getValue(a,b?"true":"");return c.equalsIgnoreCase("true")||c.equalsIgnoreCase("on")||c.equalsIgnoreCase("yes")},"~S,~B");c(b,"getValue",function(a,b){var c=this.getJmolParameter(a);System.out.println("Jmol getValue "+a+" "+c);return null==

c?b:c},"~S,~S");c(b,"getValueLowerCase",function(a,b){var c=this.getValue(a,b);null!=c&&(c=c.trim().toLowerCase(),0==c.length&&(c=null));return c},"~S,~S");c(b,"setStringProperty",function(a,b){null!=b&&(JU.Logger.info(a+' = "'+b+'"'),this.viewer.setStringProperty(a,b))},"~S,~S");c(b,"scriptProcessor",function(a,b,c){if(null==a||0==a.length)return"";switch(c){case 0:return a=this.viewer.scriptCheck(a),"string"==typeof a?a:"";case 1:return null!=b?this.viewer.scriptWaitStatus(a,b).toString():this.viewer.scriptWait(a);

default:return this.viewer.script(a)}},"~S,~S,~N");j(b,"register",function(a,b){JU.GenericApplet.checkIn(a,b)},"~S,J.api.JmolSyncInterface");j(b,"getJSpecViewProperty",function(){return null},"~S");c(b,"syncScript",function(a){this.viewer.syncScript(a,"~",0)},"~S");j(b,"handleEvent",function(a){return null==this.viewer?!1:this.viewer.processMouseEvent(a.id,a.x,a.y,a.modifiers,a.when)},"java.awt.Event");j(b,"getAppletInfo",function(){return J.i18n.GT.o(J.i18n.GT.$("Jmol Applet version {0} {1}.\n\nAn OpenScience project.\n\nSee http://www.jmol.org for more information"),

w(-1,[JV.JC.version,JV.JC.date]))+"\nhtmlName = "+JU.PT.esc(this.htmlName)+"\nsyncId = "+JU.PT.esc(this.syncId)+"\ndocumentBase = "+JU.PT.esc(this.documentBase)+"\ncodeBase = "+JU.PT.esc(this.codeBase)});j(b,"script",function(a){this.scriptNoWait(a)},"~S");j(b,"scriptCheck",function(a){return null==a||0==a.length?"":this.scriptProcessor(a,null,0)},"~S");j(b,"scriptNoWait",function(a){return null==a||0==a.length?"":this.scriptProcessor(a,null,2)},"~S");c(b,"scriptWait",function(a){return this.scriptWait(a,

null)},"~S");c(b,"scriptWait",function(a,b){if(null==a||0==a.length)return"";this.outputBuffer=null;return this.scriptProcessor(a,b,1)},"~S,~S");j(b,"scriptWaitOutput",function(a){if(null==a||0==a.length)return"";this.outputBuffer=new JU.SB;this.viewer.scriptWaitStatus(a,"");a=null==this.outputBuffer?"":this.outputBuffer.toString();this.outputBuffer=null;return a},"~S");j(b,"getModelIndexFromId",function(a){return this.viewer.getModelIndexFromId(a)},"~S");c(b,"getProperty",function(a){return this.viewer.getProperty(null,

a,"")},"~S");c(b,"getProperty",function(a,b){b||(b="");return this.viewer.getProperty(null,a,b)},"~S,~S");c(b,"getPropertyAsString",function(a){return this.viewer.getProperty("readable",a,"").toString()},"~S");c(b,"getPropertyAsString",function(a,b){b||(b="");return this.viewer.getProperty("readable",a,b).toString()},"~S,~S");c(b,"getPropertyAsJSON",function(a){return this.viewer.getProperty("JSON",a,"").toString()},"~S");c(b,"getPropertyAsJSON",function(a,b){b||(b="");return this.viewer.getProperty("JSON",

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b.htTiming=new java.util.Hashtable});u("JU");O(JU,"LoggerInterface");u("JU");C(["JU.V3"],"JU.Measure","javajs.api.Interface JU.Lst $.M3 $.P3 $.P4 $.Quat".split(" "),function(){var b=H(JU,"Measure",null);b.computeAngle=c(b,"computeAngle",function(a,b,c,l,f,e){l.sub2(a,b);f.sub2(c,b);a=l.angle(f);return e?a/0.017453292:a},"JU.T3,JU.T3,JU.T3,JU.V3,JU.V3,~B");b.computeAngleABC=c(b,"computeAngleABC",function(a,b,c,l){var f=new JU.V3,e=new JU.V3;return JU.Measure.computeAngle(a,b,c,f,e,l)},"JU.T3,JU.T3,JU.T3,~B");

b.computeTorsion=c(b,"computeTorsion",function(a,b,c,l,f){if(1E-10>a.distanceSquared(b))return 0;var e=a.x-b.x,h=a.y-b.y;a=a.z-b.z;var k=c.x-b.x,j=c.y-b.y,A=c.z-b.z,p=c.x-l.x,q=c.y-l.y,n=c.z-l.z;l=h*A-a*j;b=a*k-e*A;var s=e*j-h*k;c=j*n-A*q;A=A*p-k*n;k=k*q-j*p;p=1/(c*c+A*A+k*k);j=Math.sqrt(1/(l*l+b*b+s*s));p=Math.sqrt(p);l=(l*c+b*A+s*k)*j*p;1<l&&(l=1);-1>l&&(l=-1);l=Math.acos(l);e=e*c+h*A+a*k;h=Math.abs(e);l=0<e/h?l:-l;return f?l/0.017453292:l},"JU.T3,JU.T3,JU.T3,JU.T3,~B");b.getPlaneThroughPoints=

c(b,"getPlaneThroughPoints",function(a,b,c,l,f,e){null==l&&(l=new JU.V3);null==f&&(f=new JU.V3);a=JU.Measure.getNormalThroughPoints(a,b,c,l,f);e.set4(l.x,l.y,l.z,a);return e},"JU.T3,JU.T3,JU.T3,JU.V3,JU.V3,JU.P4");b.getPlaneThroughPoint=c(b,"getPlaneThroughPoint",function(a,b,c){c.set4(b.x,b.y,b.z,-b.dot(a))},"JU.T3,JU.V3,JU.P4");b.distanceToPlane=c(b,"distanceToPlane",function(a,b){return null==a?NaN:(a.dot(b)+a.w)/Math.sqrt(a.dot(a))},"JU.P4,JU.T3");b.directedDistanceToPlane=c(b,"directedDistanceToPlane",

function(a,b,c){a=b.dot(a)+b.w;c=b.dot(c)+b.w;return Math.signum(c)*a/Math.sqrt(b.dot(b))},"JU.P3,JU.P4,JU.P3");b.distanceToPlaneD=c(b,"distanceToPlaneD",function(a,b,c){return null==a?NaN:(a.dot(c)+a.w)/b},"JU.P4,~N,JU.P3");b.distanceToPlaneV=c(b,"distanceToPlaneV",function(a,b,c){return null==a?NaN:(a.dot(c)+b)/Math.sqrt(a.dot(a))},"JU.V3,~N,JU.P3");b.calcNormalizedNormal=c(b,"calcNormalizedNormal",function(a,b,c,l,f){f.sub2(b,a);l.sub2(c,a);l.cross(f,l);l.normalize()},"JU.T3,JU.T3,JU.T3,JU.T3,JU.T3");

b.getDirectedNormalThroughPoints=c(b,"getDirectedNormalThroughPoints",function(a,b,c,l,f,e){b=JU.Measure.getNormalThroughPoints(a,b,c,f,e);null!=l&&(c=JU.P3.newP(a),c.add(f),e=c.distance(l),c.sub2(a,f),e>c.distance(l)&&(f.scale(-1),b=-b));return b},"JU.T3,JU.T3,JU.T3,JU.T3,JU.V3,JU.V3");b.getNormalThroughPoints=c(b,"getNormalThroughPoints",function(a,b,c,l,f){JU.Measure.calcNormalizedNormal(a,b,c,l,f);f.setT(a);return-f.dot(l)},"JU.T3,JU.T3,JU.T3,JU.T3,JU.T3");b.getPlaneProjection=c(b,"getPlaneProjection",

function(a,b,c,l){var f=JU.Measure.distanceToPlane(b,a);l.set(b.x,b.y,b.z);l.normalize();0<f&&l.scale(-1);c.scaleAdd2(Math.abs(f),l,a);return f},"JU.T3,JU.P4,JU.T3,JU.V3");b.getNormalFromCenter=c(b,"getNormalFromCenter",function(a,b,c,l,f,e,h){b=JU.Measure.getNormalThroughPoints(b,c,l,e,h);a=0<JU.Measure.distanceToPlaneV(e,b,a);a==f&&e.scale(-1);return!a},"JU.P3,JU.P3,JU.P3,JU.P3,~B,JU.V3,JU.V3");b.getNormalToLine=c(b,"getNormalToLine",function(a,b,c){c.sub2(a,b);c.cross(c,JU.Measure.axisY);c.normalize();

Float.isNaN(c.x)&&c.set(1,0,0)},"JU.P3,JU.P3,JU.V3");b.getBisectingPlane=c(b,"getBisectingPlane",function(a,b,c,l,f){c.scaleAdd2(0.5,b,a);l.setT(b);l.normalize();JU.Measure.getPlaneThroughPoint(c,l,f)},"JU.P3,JU.V3,JU.T3,JU.V3,JU.P4");b.projectOntoAxis=c(b,"projectOntoAxis",function(a,b,c,l){l.sub2(a,b);var f=l.dot(c);a.scaleAdd2(f,c,b);l.sub2(a,b);return f},"JU.P3,JU.P3,JU.V3,JU.V3");b.calcBestAxisThroughPoints=c(b,"calcBestAxisThroughPoints",function(a,b,c,l,f,e){c.setT(a[0]);l.sub2(a[b-1],c);l.normalize();

JU.Measure.calcAveragePointN(a,b,c);for(var h=0;h++<e&&0.001<JU.Measure.findAxis(a,b,c,l,f););a=JU.P3.newP(a[0]);JU.Measure.projectOntoAxis(a,c,l,f);c.setT(a)},"~A,~N,JU.P3,JU.V3,JU.V3,~N");b.findAxis=c(b,"findAxis",function(a,b,c,l,f){for(var e=new JU.V3,h=new JU.V3,k=new JU.P3,j=new JU.P3,A=JU.V3.newV(l),p=0;0<=--b;)k.setT(a[b]),j.setT(k),JU.Measure.projectOntoAxis(j,c,l,f),h.sub2(k,j),h.cross(f,h),e.add(h),p+=f.lengthSquared();a=JU.V3.newV(e);a.scale(1/p);h.cross(a,l);l.add(h);l.normalize();h.sub2(l,

A);return h.length()},"~A,~N,JU.P3,JU.V3,JU.V3");b.calcAveragePoint=c(b,"calcAveragePoint",function(a,b,c){c.set((a.x+b.x)/2,(a.y+b.y)/2,(a.z+b.z)/2)},"JU.P3,JU.P3,JU.P3");b.calcAveragePointN=c(b,"calcAveragePointN",function(a,b,c){c.setT(a[0]);for(var l=1;l<b;l++)c.add(a[l]);c.scale(1/b)},"~A,~N,JU.P3");b.transformPoints=c(b,"transformPoints",function(a,b,c){for(var l=new JU.Lst,f=0;f<a.size();f++){var e=JU.P3.newP(a.get(f));e.sub(c);b.rotTrans(e);e.add(c);l.addLast(e)}return l},"JU.Lst,JU.M4,JU.P3");

b.isInTetrahedron=c(b,"isInTetrahedron",function(a,b,c,l,f,e,h,k,j){var A=0<=JU.Measure.distanceToPlane(JU.Measure.getPlaneThroughPoints(l,f,b,h,k,e),a);if(A!=0<=JU.Measure.distanceToPlane(JU.Measure.getPlaneThroughPoints(b,f,c,h,k,e),a)||A!=0<=JU.Measure.distanceToPlane(JU.Measure.getPlaneThroughPoints(c,f,l,h,k,e),a))return!1;a=JU.Measure.distanceToPlane(JU.Measure.getPlaneThroughPoints(b,c,l,h,k,e),a);if(j)return A==0<=a;f=JU.Measure.distanceToPlane(e,f);return 0>=f*a||Math.abs(f)>Math.abs(a)},

"JU.P3,JU.P3,JU.P3,JU.P3,JU.P3,JU.P4,JU.V3,JU.V3,~B");b.getIntersectionPP=c(b,"getIntersectionPP",function(a,b){var c=a.x,l=a.y,f=a.z,e=a.w,h=b.x,k=b.y,j=b.z,A=b.w,p=JU.V3.new3(c,l,f),q=JU.V3.new3(h,k,j),n=new JU.V3;n.cross(p,q);var p=Math.abs(n.x),q=Math.abs(n.y),s=Math.abs(n.z);switch(p>q?p>s?1:3:q>s?2:3){case 1:p=0;q=l*j-k*f;if(0.01>Math.abs(q))return null;f=(f*A-j*e)/q;c=(k*e-A*l)/q;break;case 2:q=c*j-h*f;if(0.01>Math.abs(q))return null;p=(f*A-j*e)/q;f=0;c=(h*e-A*c)/q;break;default:q=c*k-h*l;

if(0.01>Math.abs(q))return null;p=(l*A-k*e)/q;f=(h*e-A*c)/q;c=0}l=new JU.Lst;l.addLast(JU.P3.new3(p,f,c));n.normalize();l.addLast(n);return l},"JU.P4,JU.P4");b.getIntersection=c(b,"getIntersection",function(a,b,c,l,f,e){JU.Measure.getPlaneProjection(a,c,l,f);f.set(c.x,c.y,c.z);f.normalize();null==b&&(b=JU.V3.newV(f));c=b.dot(f);if(0.01>Math.abs(c))return null;e.sub2(l,a);l.scaleAdd2(e.dot(f)/c,b,a);return l},"JU.P3,JU.V3,JU.P4,JU.P3,JU.V3,JU.V3");b.calculateQuaternionRotation=c(b,"calculateQuaternionRotation",

function(a,b){b[1]=NaN;var c=new JU.Quat,l=a[0],f=a[1],e=l.length-1;if(2>e||l.length!=f.length)return c;for(var h=0,k=0,j=0,n=0,p=0,q=0,r=0,s=0,u=0,v=new JU.P3,w=new JU.P3,y=l[0],z=f[0],e=e+1;1<=--e;)v.sub2(l[e],y),w.sub2(f[e],z),h+=v.x*w.x,k+=v.x*w.y,j+=v.x*w.z,n+=v.y*w.x,p+=v.y*w.y,q+=v.y*w.z,r+=v.z*w.x,s+=v.z*w.y,u+=v.z*w.z;b[0]=JU.Measure.getRmsd(a,c);c=R(4,4,0);c[0][0]=h+p+u;c[0][1]=c[1][0]=q-s;c[0][2]=c[2][0]=r-j;c[0][3]=c[3][0]=k-n;c[1][1]=h-p-u;c[1][2]=c[2][1]=k+n;c[1][3]=c[3][1]=r+j;c[2][2]=

-h+p-u;c[2][3]=c[3][2]=q+s;c[3][3]=-h-p+u;h=javajs.api.Interface.getInterface("JU.Eigen").setM(c).getEigenvectorsFloatTransposed()[3];c=JU.Quat.newP4(JU.P4.new4(h[1],h[2],h[3],h[0]));b[1]=JU.Measure.getRmsd(a,c);return c},"~A,~A");b.getTransformMatrix4=c(b,"getTransformMatrix4",function(a,b,c,l){a=JU.Measure.getCenterAndPoints(a);var f=JU.Measure.getCenterAndPoints(b);b=K(2,0);var e=JU.Measure.calculateQuaternionRotation(w(-1,[a,f]),b).getMatrix();null==l?e.rotate(a[0]):l.setT(a[0]);l=JU.V3.newVsub(f[0],

a[0]);c.setMV(e,l);return b[1]},"JU.Lst,JU.Lst,JU.M4,JU.P3");b.getCenterAndPoints=c(b,"getCenterAndPoints",function(a){var b=a.size(),c=Array(b+1);c[0]=new JU.P3;if(0<b){for(var l=0;l<b;l++)c[0].add(c[l+1]=a.get(l));c[0].scale(1/b)}return c},"JU.Lst");b.getRmsd=c(b,"getRmsd",function(a,b){for(var c=0,l=a[0],f=a[1],e=l[0],h=f[0],k=l.length-1,j=new JU.P3,n=k+1;1<=--n;)j.sub2(l[n],e),b.transform2(j,j).add(h),c+=j.distanceSquared(f[n]);return Math.sqrt(c/k)},"~A,JU.Quat");b.getBestLineThroughPoints=c(b,

"getBestLineThroughPoints",function(a,b){0>=b&&(b=a.length);if(2>=b)return a;var c=new JU.P3,l=new JU.V3,f=new JU.V3;JU.Measure.calcBestAxisThroughPoints(a,b,c,l,f,8);return JU.Measure.getProjectedLineSegment(a,b,c,l,f)},"~A,~N");b.getProjectedLineSegment=c(b,"getProjectedLineSegment",function(a,b,c,l,f){null==f&&(f=new JU.V3);for(var e=b=null,h,k=3.4028235E38,j=-3.4028235E38,n=0;n<a.length;n++){JU.Measure.projectOntoAxis(h=JU.P3.newP(a[n]),c,l,f);var p=l.dot(f);p<k&&(k=p,b=h);p>j&&(j=p,e=h)}return w(-1,

[b,e])},"~A,~N,JU.P3,JU.V3,JU.V3");b.isInTriangle=c(b,"isInTriangle",function(a,b,c,l,f,e,h){f.sub2(l,b);e.sub2(c,b);h.sub2(a,b);a=f.dot(f);b=f.dot(e);f=f.dot(h);c=e.dot(e);e=e.dot(h);h=1/(a*c-b*b);c=(c*f-b*e)*h;e=(a*e-b*f)*h;return 0<=c&&0<=e&&1>=c+e},"JU.P3,JU.P3,JU.P3,JU.P3,JU.V3,JU.V3,JU.V3");b.calcBestPlaneThroughPoints=c(b,"calcBestPlaneThroughPoints",function(a,b,c){0>=b&&(b=a.length);if(3==b)return JU.Measure.getPlaneThroughPoints(a[0],a[1],a[2],null,null,c),0;var l=c,f=new JU.P4,e=JU.Measure.calcPlaneForMode(a,

b,c,"z");if(1E-6>e)return e;var h=JU.Measure.calcPlaneForMode(a,b,f,"y");h<e&&(e=h,l=f,f=c);1E-6<=e&&(h=JU.Measure.calcPlaneForMode(a,b,f,"x"),h<e&&(e=h,l=f));l!==c&&(c.setT(l),c.w=l.w);return e},"~A,~N,JU.P4");b.calcPlaneForMode=c(b,"calcPlaneForMode",function(a,b,c,l){for(var f=R(b,3,0),e=R(3,b,0),h=R(3,b,0),k=R(3,3,0),j=R(b,0),n=b;0<=--n;){var p=a[n];f[n][0]=e[0][n]="x"==l?p.z:p.x;f[n][1]=e[1][n]="y"==l?p.z:p.y;f[n][2]=e[2][n]=1;j[n]=-("y"==l?p.y:"x"==l?p.x:p.z)}for(var q=new JU.M3,n=3;0<=--n;)for(p=

3;0<=--p;){for(var r=0,s=b;0<=--s;)r+=e[n][s]*f[s][p];q.set33(n,p,r)}q.invert();for(n=3;0<=--n;)for(p=3;0<=--p;)k[n][p]=q.get33(n,p);for(n=3;0<=--n;)for(s=b;0<=--s;){r=0;for(p=3;0<=--p;)r+=k[n][p]*e[p][s];h[n][s]=r}switch(l.charCodeAt(0)){case 120:c.x=1;break;case 121:c.y=1;break;case 122:c.z=1}n=1;for(p=3;0<=--p;){f=0;for(s=b;0<=--s;)f+=h[p][s]*j[s];switch(p){case 0:n+=f*f;"x"==l?c.z=f:c.x=f;break;case 1:n+=f*f;"y"==l?c.z=f:c.y=f;break;case 2:c.w=f}}l=Math.sqrt(n);c.scale4((0<1/c.w?1:-1)/l);for(n=

l=0;n<b;n++)r=JU.Measure.distanceToPlane(c,a[n]),l+=r*r;return Math.sqrt(l/b)},"~A,~N,JU.P4,~S");b.rndPt=c(b,"rndPt",function(){return JU.P3.new3(20*Math.random(),20*Math.random(),20*Math.random())});b.testRnd=c(b,"testRnd",function(){var a=JU.P4.new4(20*Math.random(),20*Math.random(),20*Math.random(),20*Math.random());a.scale4(1/a.length());System.out.println("\n==========\n ");System.out.println("plane is "+a);for(var b=new JU.P3,c=new JU.V3,l=Array(4),f=0;f<l.length;f++){l[f]=new JU.P3;var e=JU.Measure.rndPt();

JU.Measure.getPlaneProjection(e,a,b,c);l[f].setT(b);e=0.1*Math.random();l[f].scaleAdd2(e,c,b);System.out.println(l[f]+" d="+e)}a=new JU.P4;l=JU.Measure.calcBestPlaneThroughPoints(l,-1,a);System.out.println("found "+a+" rmsd = "+l)});b.test=c(b,"test",function(){for(var a=0;10>a;a++)JU.Measure.testRnd();System.exit(0)});b.getPointsOnPlane=c(b,"getPointsOnPlane",function(a,b){for(var c=new JU.Lst,l=a.length;0<=--l;)0.001>Math.abs(JU.Measure.distanceToPlane(b,a[l]))&&c.addLast(a[l]);return c},"~A,JU.P4");

b.getLatticePoints=c(b,"getLatticePoints",function(a,b,c,l){a.addLast(new JU.P3);b=0==b?1:Math.abs(b);c=0==c?1:Math.abs(c);l=0==l?1:Math.abs(l);for(var f=a.size(),e=-b;e<=b;e++)for(var h=-c;h<=c;h++)for(var k=-l;k<=l;k++)for(var j=0;j<f;j++){var n=JU.P3.new3(e,h,k);n.add(a.get(j));a.addLast(n)}for(j=f;0<=--j;)a.removeItemAt(0);return a},"JU.Lst,~N,~N,~N");b.computeHelicalAxis=c(b,"computeHelicalAxis",function(a,b,c){var l=new JU.V3;l.sub2(b,a);var f=c.getTheta(),e=c.getNormal(),h=l.dot(e);1E-4>Math.abs(h)&&

(h=0);var k=new JU.V3;k.cross(l,e);0!=k.dot(k)&&k.normalize();var j=new JU.V3,n=JU.V3.newV(e);0==h&&(h=1.4E-45);n.scale(h);j.sub2(n,l);j.scale(0.5);k.scale(0==f?0:j.length()/Math.tan(3.141592653589793*(f/2/180)));l=JU.V3.newV(k);0!=f&&l.add(j);j=JU.P3.newP(a);j.sub(l);1.4E-45!=h&&e.scale(h);k=JU.P3.newP(j);k.add(e);f=JU.Measure.computeTorsion(a,j,k,b,!0);if(Float.isNaN(f)||1E-4>l.length())f=c.getThetaDirectedV(e);a=Math.abs(0==f?0:360/f);h=Math.abs(1.4E-45==h?0:e.length()*(0==f?1:360/f));return w(-1,

[j,e,l,JU.P3.new3(f,h,a),k])},"JU.P3,JU.P3,JU.Quat");b.axisY=JU.V3.new3(0,1,0)});u("JU");C(null,"JU.MeshSurface","JU.AU $.P3 J.api.Interface JU.BoxInfo $.C $.Geodesic $.TempArray".split(" "),function(){var b=v(function(){this.meshType=this.oabc=this.slicer=this.vwr=null;this.vc=0;this.surfaceAtoms=this.vertexSource=this.vvs=this.vs=null;this.pc=0;this.pis=null;this.haveQuads=this.isDrawPolygon=this.colorsExplicit=!1;this.colixBack=this.colix=0;this.isColorSolid=!0;this.normalsTemp=this.normals=this.vcs=

this.pcs=this.altVertices=this.offset=null;this.normixCount=this.normalCount=0;this.vertexSets=this.surfaceSet=this.mat4=this.bsPolygons=null;this.nSets=0;this.dataOnly=!1;this.vertexCount0=this.polygonCount0=this.iC=this.iB=this.iA=this.lastColix=this.lastColor=0;this.bsSlabGhost=this.bsSlabDisplay=null;this.slabColix=this.slabMeshType=0;this.slabOptions=this.bsDisplay=null;this.mergePolygonCount0=this.mergeVertexCount0=0;this.isMerged=!1;r(this,arguments)},JU,"MeshSurface",null);c(b,"getMeshSlicer",

function(){return null==this.slicer?this.slicer=J.api.Interface.getInterface("JU.MeshSlicer",this.vwr,"script").set(this):this.slicer});b.newMesh=c(b,"newMesh",function(a,b,c,l,f,e){var h=new JU.MeshSurface;h.pis=l;a?h.altVertices=b:h.vs=b;h.vc=0==c?b.length:c;h.normals=f;h.normalCount=0==e&&null!=f?f.length:e;return h},"~B,~A,~N,~A,~A,~N");c(b,"getVertices",function(){return null==this.altVertices?this.vs:this.altVertices});c(b,"getFaces",function(){return this.pis});c(b,"setColix",function(a){this.colix=

a},"~N");c(b,"setColixBack",function(a){this.colixBack=a},"~N");c(b,"addV",function(a,b){0==this.vc?this.vs=Array(25):this.vc==this.vs.length&&(this.vs=JU.AU.doubleLength(this.vs));this.vs[this.vc]=b?JU.P3.newP(a):a;return this.vc++},"JU.T3,~B");c(b,"addTriangle",function(a,b,c){this.addPolygon(E(-1,[a,b,c]),null)},"~N,~N,~N");c(b,"addQuad",function(a,b,c,l){this.haveQuads=!0;this.addPolygon(E(-1,[a,b,c,l]),null)},"~N,~N,~N,~N");c(b,"setPolygonCount",function(a){this.pc=a;if(!(0>a)&&(null==this.pis||

a>this.pis.length))this.pis=JU.AU.newInt2(a)},"~N");c(b,"addVCVal",function(a,b,c){0==this.vc?this.vvs=K(25,0):this.vc>=this.vvs.length&&(this.vvs=JU.AU.doubleLengthF(this.vvs));this.vvs[this.vc]=b;return this.addV(a,c)},"JU.T3,~N,~B");c(b,"addTriangleCheck",function(a,b,c,l,f,e){return null==this.vs||null!=this.vvs&&(Float.isNaN(this.vvs[a])||Float.isNaN(this.vvs[b])||Float.isNaN(this.vvs[c]))||Float.isNaN(this.vs[a].x)||Float.isNaN(this.vs[b].x)||Float.isNaN(this.vs[c].x)?-1:this.addPolygonV3(a,

b,c,l,f,e,null)},"~N,~N,~N,~N,~N,~N");c(b,"addPolygonV3",function(a,b,c,l,f,e,h){return this.dataOnly?this.addPolygon(E(-1,[a,b,c,l]),h):this.addPolygonC(E(-1,[a,b,c,l,f]),e,h,0>f)},"~N,~N,~N,~N,~N,~N,JU.BS");c(b,"addPolygonC",function(a,b,c,l){if(0!=b){if(null==this.pcs||0==this.pc)this.lastColor=0;l?this.colorsExplicit=!0:(null==this.pcs?this.pcs=W(25,0):this.pc>=this.pcs.length&&(this.pcs=JU.AU.doubleLengthShort(this.pcs)),this.pcs[this.pc]=l?2047:b==this.lastColor?this.lastColix:this.lastColix=

JU.C.getColix(this.lastColor=b))}return this.addPolygon(a,c)},"~A,~N,JU.BS,~B");c(b,"addPolygon",function(a,b){var c=this.pc;0==c?this.pis=JU.AU.newInt2(25):c==this.pis.length&&(this.pis=JU.AU.doubleLength(this.pis));null!=b&&b.set(c);this.pis[this.pc++]=a;return c},"~A,JU.BS");c(b,"invalidatePolygons",function(){for(var a=this.pc;--a>=this.mergePolygonCount0;)if((null==this.bsSlabDisplay||this.bsSlabDisplay.get(a))&&null==this.setABC(a))this.pis[a]=null});c(b,"setABC",function(a){if(null!=this.bsSlabDisplay&&

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this.bsSlabGhost&&1073742018==this.slabMeshType?"mesh":null});c(b,"resetSlab",function(){null!=this.slicer&&this.slicer.slabPolygons(JU.TempArray.getSlabObjectType(1073742333,null,!1,null),!1)});c(b,"slabPolygonsList",function(a,b){this.getMeshSlicer();for(var c=0;c<a.size()&&this.slicer.slabPolygons(a.get(c),b);c++);},"JU.Lst,~B");c(b,"slabBrillouin",function(){},"~A");c(b,"getResolution",function(){return 0});b.getSphereData=c(b,"getSphereData",function(a){JU.Geodesic.createGeodesic(a);var b=JU.Geodesic.getVertexCount(a),

c=JU.Geodesic.getFaceVertexes(a),l=B(c.length/3);a=JU.AU.newInt2(l);for(var f=0,e=0;f<l;f++)a[f]=E(-1,[c[e++],c[e++],c[e++]]);c=Array(b);for(f=0;f<b;f++)c[f]=JU.Geodesic.getVertexVector(f);return JU.MeshSurface.newMesh(!0,c,0,a,c,0)},"~N");c(b,"setBox",function(a,b){a.set(3.4028235E38,3.4028235E38,3.4028235E38);b.set(-3.4028235E38,-3.4028235E38,-3.4028235E38);for(var c=0;c<this.vc;c++){var l=this.vs[c];Float.isNaN(l.x)||JU.BoxInfo.addPoint(l,a,b,0)}},"JU.P3,JU.P3");c(b,"setBoundingBox",function(){},

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function(){return JU.BS.newN(JU.Normix.getNormixCount())});b.getVertexVectors=c(b,"getVertexVectors",function(){null==JU.Normix.vertexVectors&&(JU.Normix.vertexVectors=JU.Geodesic.getVertexVectors());return JU.Normix.vertexVectors});b.setInverseNormixes=c(b,"setInverseNormixes",function(){if(null==JU.Normix.inverseNormixes){JU.Normix.getNormixCount();JU.Normix.getVertexVectors();JU.Normix.inverseNormixes=W(JU.Normix.normixCount,0);for(var a=new JU.BS,b=JU.Normix.normixCount;0<=--b;){var c=JU.Normix.vertexVectors[b];

JU.Normix.inverseNormixes[b]=JU.Normix.getNormix(-c.x,-c.y,-c.z,3,a)}}});b.getInverseNormix=c(b,"getInverseNormix",function(a){return JU.Normix.inverseNormixes[a]},"~N");b.getNeighborVertexArrays=c(b,"getNeighborVertexArrays",function(){null==JU.Normix.neighborVertexesArrays&&(JU.Normix.neighborVertexesArrays=JU.Geodesic.getNeighborVertexesArrays());return JU.Normix.neighborVertexesArrays});b.getNormixV=c(b,"getNormixV",function(a,b){return JU.Normix.getNormix(a.x,a.y,a.z,3,b)},"JU.V3,JU.BS");b.get2SidedNormix=

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a.$replace(";",0>a.indexOf("\n")?"\n":" ");a=JU.PT.trim(a,"\n \t");a=JU.PT.rep(a,"\n ","\n");return a=JU.PT.rep(a,"\n\n","\n")},"~S");b.markLines=c(b,"markLines",function(a,b){for(var c=0,l=a.length;0<=--l;)a.charAt(l)==b&&c++;for(var l=E(c+1,0),f=c=0;0<=(f=a.indexOf(b,f));)l[c++]=++f;l[c]=a.length;return l},"~S,~S")});u("JU");C(["JU.P3"],"JU.Point3fi",null,function(){var b=v(function(){this.mi=-1;this.sZ=this.sY=this.sX=this.i=0;this.sD=-1;r(this,arguments)},JU,"Point3fi",JU.P3,Cloneable);c(b,"copy",

function(){try{return this.clone()}catch(a){if(F(a,"CloneNotSupportedException"))return null;throw a;}})});u("JU");n=v(function(){this.height=this.width=this.y=this.x=0;r(this,arguments)},JU,"Rectangle",null);c(n,"contains",function(b,a){return b>=this.x&&a>=this.y&&b-this.x<this.width&&a-this.y<this.height},"~N,~N");u("JU");C(null,"JU.Rgb16",["JU.SB"],function(){var b=v(function(){this.b=this.g=this.r=0;r(this,arguments)},JU,"Rgb16",null);b.newI=c(b,"newI",function(a){var b=new JU.Rgb16;b.setInt(a);

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null;this.ellipsoidShades=null});c(b,"setLastColix",function(a,b){JU.C.allocateColix(a,!0);this.checkShades(2047);b&&JU.C.setLastGrey(a);this.ashades[2047]=this.getShades2(a,!1)},"~N,~B");c(b,"getShades",function(a){this.checkShades(JU.C.colixMax);a&=-30721;var b=this.ashades[a];null==b&&(b=this.ashades[a]=this.getShades2(JU.C.argbs[a],!1));return b},"~N");c(b,"getShadesG",function(a){this.checkShades(JU.C.colixMax);a&=-30721;null==this.ashadesGreyscale&&(this.ashadesGreyscale=JU.AU.newInt2(this.ashades.length));

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function(a,b,c,l){b=B(Math.floor(16128*this.getShadeF(a/l,b/l,c/l)));a=b>>8;if(!this.useLight)return a;(b&255)>this.nextRandom8Bit()&&++a;b=this.seed&65535;21845>b&&0<a?--a:43690<b&&63>a&&++a;return a},"~N,~N,~N,~N");c(b,"calcSphereShading",function(){for(var a=-127.5,b=0;256>b;++a,++b)for(var c=-127.5,l=a*a,f=0;256>f;++c,++f){var e=0,h=16900-l-c*c;0<h&&(e=Math.sqrt(h),e=this.getShadeN(a,c,e,130));this.sphereShadeIndexes[(f<<8)+b]=e}});c(b,"nextRandom8Bit",function(){var a=this.seed;this.seed=a=(a<<

16)+(a<<1)+a&2147483647;return a>>23});c(b,"getEllipsoidShade",function(a,b,c,l,f){var e=f.m00*a+f.m01*b+f.m02*c+f.m03,h=f.m10*a+f.m11*b+f.m12*c+f.m13;a=f.m20*a+f.m21*b+f.m22*c+f.m23;l=Math.min(l/2,45)/Math.sqrt(e*e+h*h+a*a);e=D(-e*l);h=D(-h*l);l=D(a*l);if(a=-20>e||20<=e||-20>h||20<=h||0>l||40<=l){for(;0==e%2&&0==h%2&&0==l%2&&0<e+h+l;)e>>=1,h>>=1,l>>=1;a=-20>e||20<=e||-20>h||20<=h||0>l||40<=l}a?this.nOut++:this.nIn++;return a?this.getShadeIndex(e,h,l):this.ellipsoidShades[e+20][h+20][l]},"~N,~N,~N,~N,JU.M4");

c(b,"createEllipsoidShades",function(){this.ellipsoidShades=P(40,40,40,0);for(var a=0;40>a;a++)for(var b=0;40>b;b++)for(var c=0;40>c;c++)this.ellipsoidShades[a][b][c]=this.getShadeIndex(a-20,b-20,c)})});u("JU");C(["JV.Viewer"],"JU.SimpleUnitCell","JU.AU $.M4 $.P3 $.P4 $.PT $.V3 JU.Escape".split(" "),function(){var b=v(function(){this.unitCellParams=null;this.slop=0;this.matrixFtoCNoOffset=this.matrixCtoFNoOffset=this.matrixFractionalToCartesian=this.matrixCartesianToFractional=null;this.volume=0;

this.dimension=3;this.fractionalOrigin=null;this.c_=this.b_=this.a_=this.cB_=this.cA_=this.sinGamma=this.cosGamma=this.sinBeta=this.cosBeta=this.sinAlpha=this.cosAlpha=this.gamma=this.beta=this.alpha=this.c=this.b=this.a=this.nc=this.nb=this.na=0;r(this,arguments)},JU,"SimpleUnitCell",null);Q(b,function(){this.slop=JV.Viewer.isHighPrecision?1E-12:1E-4});z(b,function(){this.fractionalOrigin=new JU.P3});c(b,"getPrecision",function(){return this.slop});c(b,"setPrecision",function(a){this.unitCellParams[26]=

this.slop=!Float.isNaN(a)?a:!Float.isNaN(this.unitCellParams[26])?this.unitCellParams[26]:JV.Viewer.isHighPrecision?1E-12:1E-4},"~N");c(b,"isSupercell",function(){return 1<this.na||1<this.nb||1<this.nc});b.isValid=c(b,"isValid",function(a){return null!=a&&(0<a[0]||14<a.length&&!Float.isNaN(a[14]))},"~A");b.newA=c(b,"newA",function(a){var b=new JU.SimpleUnitCell;b.init(a);return b},"~A");b.getDimensionFromParams=c(b,"getDimensionFromParams",function(a){return 0>=a[0]?3:0>a[1]?1:0>a[2]?2:3},"~A");c(b,

"init",function(a){null==a&&(a=K(-1,[1,1,1,90,90,90]));if(JU.SimpleUnitCell.isValid(a)){this.unitCellParams=JU.SimpleUnitCell.newParams(a,NaN);var b=!1;this.dimension=JU.SimpleUnitCell.getDimensionFromParams(a);this.a=a[0];this.b=a[1];this.c=a[2];this.alpha=a[3];this.beta=a[4];this.gamma=a[5];-1==this.gamma&&0<this.c&&(b=!0,this.gamma=120);26<a.length&&(Float.isNaN(a[26])?a[26]=this.slop:this.slop=a[26]);var c=this.na=Math.max(1,24<a.length&&!Float.isNaN(a[22])?D(a[22]):1),l=this.nb=Math.max(1,24<

a.length&&!Float.isNaN(a[23])?D(a[23]):1),f=this.nc=Math.max(1,24<a.length&&!Float.isNaN(a[24])?D(a[24]):1);if(25<a.length&&!Float.isNaN(a[25])){var e=a[25];0<e&&(c*=e,l*=e,f*=e)}else c=l=f=1;if(0>=this.a&&0>=this.c){var e=JU.SimpleUnitCell.newV(a,6),h=JU.SimpleUnitCell.newV(a,9),k=JU.SimpleUnitCell.newV(a,12);this.setABC(e,h,k);0>this.c&&(a=JU.AU.arrayCopyF(a,-1),0>this.b&&(h.set(0,0,1),h.cross(h,e),0.001>h.length()&&h.set(0,1,0),h.normalize(),a[9]=h.x,a[10]=h.y,a[11]=h.z),0>this.c&&(k.cross(e,h),

k.normalize(),a[12]=k.x,a[13]=k.y,a[14]=k.z))}this.a*=c;0>=this.b?this.b=this.c=1:0>=this.c?(this.c=1,this.b*=l):(this.b*=l,this.c*=f);this.setCellParams();if(21<a.length&&!Float.isNaN(a[21])){b=K(16,0);for(e=0;16>e;e++){switch(e%4){case 0:h=c;break;case 1:h=l;break;case 2:h=f;break;default:h=1}b[e]=a[6+e]*h}this.matrixCartesianToFractional=JU.M4.newA16(b);this.matrixCartesianToFractional.getTranslation(this.fractionalOrigin);this.matrixFractionalToCartesian=JU.M4.newM4(this.matrixCartesianToFractional).invert();

1==a[0]&&this.setParamsFromMatrix()}else 14<a.length&&!Float.isNaN(a[14])?(e=this.matrixFractionalToCartesian=new JU.M4,e.setColumn4(0,a[6]*c,a[7]*c,a[8]*c,0),e.setColumn4(1,a[9]*l,a[10]*l,a[11]*l,0),e.setColumn4(2,a[12]*f,a[13]*f,a[14]*f,0),17<a.length&&!Float.isNaN(a[17])?e.setColumn4(3,a[15],a[16],a[17],1):e.setColumn4(3,0,0,0,1)):(e=this.matrixFractionalToCartesian=new JU.M4,b?(e.setColumn4(0,-this.b*this.cosGamma,-this.b*this.sinGamma,0,0),e.setColumn4(1,-this.b*this.cosGamma,this.b*this.sinGamma,

0,0)):(e.setColumn4(0,this.a,0,0,0),e.setColumn4(1,this.b*this.cosGamma,this.b*this.sinGamma,0,0)),e.setColumn4(2,this.c*this.cosBeta,this.c*(this.cosAlpha-this.cosBeta*this.cosGamma)/this.sinGamma,this.volume/(this.a*this.b*this.sinGamma),0),e.setColumn4(3,0,0,0,1)),this.matrixCartesianToFractional=JU.M4.newM4(this.matrixFractionalToCartesian).invert();this.matrixCtoFNoOffset=this.matrixCartesianToFractional;this.matrixFtoCNoOffset=this.matrixFractionalToCartesian}},"~A");b.newV=c(b,"newV",function(a,

b){return JU.V3.new3(a[b++],a[b++],a[b])},"~A,~N");b.newParams=c(b,"newParams",function(a,b){for(var c=K(27,0),l=a.length,f=0;27>f;f++)c[f]=f<l?a[f]:NaN;27>l&&(c[26]=b);return c},"~A,~N");b.addVectors=c(b,"addVectors",function(a){for(var b=JU.SimpleUnitCell.newA(a).matrixFractionalToCartesian,c=0;9>c;c++)a[6+c]=b.getElement(c%3,B(c/3))},"~A");c(b,"setParamsFromMatrix",function(){var a=JU.V3.new3(1,0,0),b=JU.V3.new3(0,1,0),c=JU.V3.new3(0,0,1);this.matrixFractionalToCartesian.rotate(a);this.matrixFractionalToCartesian.rotate(b);

this.matrixFractionalToCartesian.rotate(c);this.setABC(a,b,c);this.setCellParams()});c(b,"setABC",function(a,b,c){JU.SimpleUnitCell.fillParams(a,b,c,this.unitCellParams);a=this.unitCellParams;this.a=a[0];this.b=a[1];this.c=a[2];this.alpha=a[3];this.beta=a[4];this.gamma=a[5]},"JU.V3,JU.V3,JU.V3");b.fillParams=c(b,"fillParams",function(a,b,c,l){null==a&&(a=JU.SimpleUnitCell.newV(l,6),b=JU.SimpleUnitCell.newV(l,9),c=JU.SimpleUnitCell.newV(l,12));var f=a.length(),e=b.length(),h=c.length();0!=f&&(0==e?

e=h=-1:0==h&&(h=-1),l[0]=f,l[1]=e,l[2]=h,l[3]=0>e||0>h?90:b.angle(c)/0.017453292519943295,l[4]=0>h?90:a.angle(c)/0.017453292519943295,l[5]=0>e?90:a.angle(b)/0.017453292519943295)},"JU.V3,JU.V3,JU.V3,~A");c(b,"setCellParams",function(){this.cosAlpha=Math.cos(0.017453292519943295*this.alpha);this.sinAlpha=Math.sin(0.017453292519943295*this.alpha);this.cosBeta=Math.cos(0.017453292519943295*this.beta);this.sinBeta=Math.sin(0.017453292519943295*this.beta);this.cosGamma=Math.cos(0.017453292519943295*this.gamma);

this.sinGamma=Math.sin(0.017453292519943295*this.gamma);var a=Math.sqrt(this.sinAlpha*this.sinAlpha+this.sinBeta*this.sinBeta+this.sinGamma*this.sinGamma+2*this.cosAlpha*this.cosBeta*this.cosGamma-2);this.volume=this.a*this.b*this.c*a;this.cA_=(this.cosAlpha-this.cosBeta*this.cosGamma)/this.sinGamma;this.cB_=a/this.sinGamma;this.a_=this.b*this.c*this.sinAlpha/this.volume;this.b_=this.a*this.c*this.sinBeta/this.volume;this.c_=this.a*this.b*this.sinGamma/this.volume});c(b,"getFractionalOrigin",function(){return this.fractionalOrigin});

c(b,"toSupercell",function(a){a.x/=this.na;a.y/=this.nb;a.z/=this.nc;return a},"JU.P3");c(b,"toCartesian",function(a,b){null!=this.matrixFractionalToCartesian&&(b?this.matrixFtoCNoOffset:this.matrixFractionalToCartesian).rotTrans(a)},"JU.T3,~B");c(b,"toFractionalM",function(a){null!=this.matrixCartesianToFractional&&(a.mul(this.matrixFractionalToCartesian),a.mul2(this.matrixCartesianToFractional,a))},"JU.M4");c(b,"toFractional",function(a,b){null!=this.matrixCartesianToFractional&&(b?this.matrixCtoFNoOffset:

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this.volume])},"~B");c(b,"getInfo",function(a){switch(a){case 0:return this.a;case 1:return this.b;case 2:return this.c;case 3:return this.alpha;case 4:return this.beta;case 5:return this.gamma;case 6:return this.dimension;case 7:return JU.SimpleUnitCell.isHexagonal(this.unitCellParams)?1:0;case 8:return JU.SimpleUnitCell.isRhombohedral(this.unitCellParams)?1:0}return NaN},"~N");b.getReciprocal=c(b,"getReciprocal",function(a,b,c){var l=4==a.length?1:0,f=Array(4);f[0]=1==l?JU.P3.newP(a[0]):new JU.P3;

0==c&&(c=6.283185307179586);for(var e=0;3>e;e++){var h=f[e+1]=new JU.P3;h.cross(a[(e+1)%3+l],a[(e+2)%3+l]);var k=a[e+l].dot(h);-1==c&&(c=Math.sqrt(k));h.scale(c/k)}if(null==b)return f;for(e=0;4>e;e++)b[e]=f[e];return b},"~A,~A,~N");b.setAbc=c(b,"setAbc",function(a,b,c){if(null!=a&&(null==b&&(b=K(6,0)),a=JU.PT.split(a.$replace(",","="),"="),12<=a.length))for(var l=0;6>l;l++)b[l]=JU.PT.parseFloat(a[2*l+1]);return null==c?null:JU.SimpleUnitCell.setAbcFromParams(b,c)},"~S,~A,~A");b.setAbcFromParams=c(b,

"setAbcFromParams",function(a,b){var c=JU.SimpleUnitCell.newA(a).getUnitCellAsArray(!0);b[1].set(c[0],c[1],c[2]);b[2].set(c[3],c[4],c[5]);b[3].set(c[6],c[7],c[8]);return b},"~A,~A");c(b,"unitizeDim",function(a,b){switch(a){case 3:b.z=JU.SimpleUnitCell.unitizeX(b.z,this.slop);case 2:b.y=JU.SimpleUnitCell.unitizeX(b.y,this.slop);case 1:b.x=JU.SimpleUnitCell.unitizeX(b.x,this.slop)}},"~N,JU.T3");b.unitizeDimRnd=c(b,"unitizeDimRnd",function(a,b,c){switch(a){case 3:b.z=JU.SimpleUnitCell.unitizeXRnd(b.z,

c);case 2:b.y=JU.SimpleUnitCell.unitizeXRnd(b.y,c);case 1:b.x=JU.SimpleUnitCell.unitizeXRnd(b.x,c)}},"~N,JU.T3,~N");b.unitizeX=c(b,"unitizeX",function(a,b){a-=Math.floor(a);if(a>1-b||a<b)a=0;return a},"~N,~N");b.unitizeXRnd=c(b,"unitizeXRnd",function(a,b){a-=Math.floor(a);if(a>1-b||a<b)a=0;return a},"~N,~N");c(b,"twelfthsOf",function(a){if(0==a)return 0;a=Math.abs(12*a);var b=Math.round(a);return 12>=b&&Math.abs(a-b)<12*this.slop?b:-1},"~N");c(b,"twelfthify",function(a){switch(this.dimension){case 3:a.z=

this.setTwelfths(a.z);case 2:a.y=this.setTwelfths(a.y);case 1:a.x=this.setTwelfths(a.x)}},"JU.P3");c(b,"setTwelfths",function(a){var b=this.twelfthsOf(a);return 0<=b?b/12*(0>a?-1:1):a},"~N");b.ijkToPoint3f=c(b,"ijkToPoint3f",function(a,b,c,l){var f=1E9<a?1E3:1E6<a?100:10,e=f*f;c-=0<=c?B(5*f/10):c;b.x=B(a/e)%f+c;b.y=B(a%e/f)+c;b.z=(0==l?a%f:(-500==c?B(l/f):l)%f)+c},"~N,JU.P3,~N,~N");b.ptToIJK=c(b,"ptToIJK",function(a,b){return 5>=a.x&&5>=a.y&&5>=a.z?JU.P4.new4(555,100*(a.x+4)+10*(a.y+4)+a.z+4,b,0):

JU.P4.new4(1500500500,1500500500+1E6*a.x+1E3*a.y+a.z,b,1500500+a.z)},"JU.T3,~N");b.escapeMultiplier=c(b,"escapeMultiplier",function(a){if(y(a,"JU.P4")){var b=1E3*B(Math.floor(a.x/1E3))+B(Math.floor(a.w/1E3))-1E3,c=1E3*B(Math.floor(a.y/1E3))+B(Math.floor(a.w))%1E3;return"{"+b+" "+c+" "+a.z+"}"}return JU.Escape.eP(a)},"JU.T3");b.setMinMaxLatticeParameters=c(b,"setMinMaxLatticeParameters",function(a,b,c,l){if(c.x<=c.y&&555<=c.y){var f=new JU.P3;JU.SimpleUnitCell.ijkToPoint3f(c.x,f,0,l);b.x=D(f.x);b.y=

D(f.y);b.z=D(f.z);JU.SimpleUnitCell.ijkToPoint3f(c.y,f,1,l);c.x=D(f.x);c.y=D(f.y);c.z=D(f.z)}switch(a){case 1:b.y=0,c.y=1;case 2:b.z=0,c.z=1}},"~N,JU.P3i,JU.P3i,~N");b.isHexagonal=c(b,"isHexagonal",function(a){return JU.SimpleUnitCell.approx0(a[0]-a[1])&&JU.SimpleUnitCell.approx0(a[3]-90)&&JU.SimpleUnitCell.approx0(a[4]-90)&&(JU.SimpleUnitCell.approx0(a[5]-120)||-1==a[5])},"~A");b.isRhombohedral=c(b,"isRhombohedral",function(a){return JU.SimpleUnitCell.approx0(a[0]-a[1])&&JU.SimpleUnitCell.approx0(a[1]-

a[2])&&!JU.SimpleUnitCell.approx0(a[3]-90)&&JU.SimpleUnitCell.approx0(a[3]-a[4])&&JU.SimpleUnitCell.approx0(a[4]-a[5])},"~A");b.approx0=c(b,"approx0",function(a){return 0.001>Math.abs(a)},"~N");b.getCellRange=c(b,"getCellRange",function(a,b){var c=y(a,"JU.T4")?D(a.w):0;JU.SimpleUnitCell.ijkToPoint3f(D(a.x),b[0],0,c);JU.SimpleUnitCell.ijkToPoint3f(D(a.y),b[1],1,c);0>a.z&&(b[0].scale(-1/a.z),b[1].scale(-1/a.z));return c},"JU.T3,~A");j(b,"toString",function(){return"["+this.a+" "+this.b+" "+this.c+" "+

this.alpha+" "+this.beta+" "+this.gamma+"]"});b.parseCalc=c(b,"parseCalc",function(a,b,c){var l;l=JU.PT.parseFloatStrict(c);if(!Double.isNaN(l))return l;c=c.toLowerCase();if(null!=b&&0<=c.indexOf("(")){l=JU.PT.split(c,"(");for(var f=l.length-1;0<=--f;){for(var e=l[f],h=null,k=b.length;0<=--k;)if(e.endsWith(b[k])){h=b[k];break}null==h&&(System.err.println("Unrecognized function "+c),l[f]+="?")}c=JU.PT.join(l,"(",0)}if(0<=c.indexOf("/")){l=JU.PT.split(c,"/");for(f=l.length-1;0<=--f;){e=l[f];c=b=!1;

for(k=e.length;0<=--k;){h=e.charAt(k);if("."==h){b=!0;break}else if(")"==h){if(c)return NaN;l[f]+="*1.0";break}if(!JU.PT.isDigit(h))break;c=!0}c&&!b&&(l[f]+=".")}c=JU.PT.join(l,"/",0)}return a.evaluateExpressionAsVariable(c).asFloat()},"JV.Viewer,~A,~S")});u("JU");C(null,"JU.TempArray",["JU.P3","$.P3i"],function(){var b=v(function(){this.freeEnum=this.lengthsFreeEnum=this.freeScreens=this.lengthsFreeScreens=this.freePoints=this.lengthsFreePoints=null;r(this,arguments)},JU,"TempArray",null);Q(b,function(){this.lengthsFreePoints=

E(6,0);this.freePoints=Array(6);this.lengthsFreeScreens=E(6,0);this.freeScreens=Array(6);this.lengthsFreeEnum=E(2,0);this.freeEnum=Array(2)});z(b,function(){});c(b,"clear",function(){this.clearTempPoints();this.clearTempScreens()});b.findBestFit=c(b,"findBestFit",function(a,b){for(var c=-1,l=2147483647,f=b.length;0<=--f;){var e=b[f];e>=a&&e<l&&(l=e,c=f)}0<=c&&(b[c]=0);return c},"~N,~A");b.findShorter=c(b,"findShorter",function(a,b){for(var c=b.length;0<=--c;)if(0==b[c])return b[c]=a,c;for(var l=0,

f=b[0],c=b.length;0<--c;)b[c]<f&&(f=b[c],l=c);return f<a?(b[l]=a,l):-1},"~N,~A");c(b,"clearTempPoints",function(){for(var a=0;6>a;a++)this.lengthsFreePoints[a]=0,this.freePoints[a]=null});c(b,"allocTempPoints",function(a){var b;b=JU.TempArray.findBestFit(a,this.lengthsFreePoints);if(0<b)b=this.freePoints[b];else for(b=Array(a);0<=--a;)b[a]=new JU.P3;return b},"~N");c(b,"freeTempPoints",function(a){for(var b=0;b<this.freePoints.length;b++)if(this.freePoints[b]===a){this.lengthsFreePoints[b]=a.length;

return}b=JU.TempArray.findShorter(a.length,this.lengthsFreePoints);0<=b&&(this.freePoints[b]=a)},"~A");c(b,"clearTempScreens",function(){for(var a=0;6>a;a++)this.lengthsFreeScreens[a]=0,this.freeScreens[a]=null});c(b,"allocTempScreens",function(a){var b;b=JU.TempArray.findBestFit(a,this.lengthsFreeScreens);if(0<b)b=this.freeScreens[b];else for(b=Array(a);0<=--a;)b[a]=new JU.P3i;return b},"~N");c(b,"freeTempScreens",function(a){for(var b=0;b<this.freeScreens.length;b++)if(this.freeScreens[b]===a){this.lengthsFreeScreens[b]=

a.length;return}b=JU.TempArray.findShorter(a.length,this.lengthsFreeScreens);0<=b&&(this.freeScreens[b]=a)},"~A");c(b,"allocTempEnum",function(a){var b=JU.TempArray.findBestFit(a,this.lengthsFreeEnum);return 0<b?this.freeEnum[b]:Array(a)},"~N");c(b,"freeTempEnum",function(a){for(var b=0;b<this.freeEnum.length;b++)if(this.freeEnum[b]===a){this.lengthsFreeEnum[b]=a.length;return}b=JU.TempArray.findShorter(a.length,this.lengthsFreeEnum);0<=b&&(this.freeEnum[b]=a)},"~A");b.getSlabWithinRange=c(b,"getSlabWithinRange",

function(a,b){return w(-1,[Integer.$valueOf(1073742114),w(-1,[Float.$valueOf(a),Float.$valueOf(b)]),Boolean.FALSE,null])},"~N,~N");b.getSlabObjectType=c(b,"getSlabObjectType",function(a,b,c,l){return w(-1,[Integer.$valueOf(a),b,Boolean.$valueOf(c),l])},"~N,~O,~B,~O")});u("JU");H(JU,"Txt",null);u("JU");C(["JU.V3"],"JU.Vibration",["JU.P3"],function(){var b=v(function(){this.modDim=-1;this.modScale=NaN;this.showTrace=!1;this.trace=null;this.tracePt=0;r(this,arguments)},JU,"Vibration",JU.V3);c(b,"setCalcPoint",

function(a,b,c){switch(this.modDim){case -2:case -3:break;default:a.scaleAdd2(Math.cos(6.283185307179586*b.x)*c,this,a)}return a},"JU.T3,JU.T3,~N,~N");c(b,"getInfo",function(a){a.put("vibVector",JU.V3.newV(this));a.put("vibType",-2==this.modDim?"spin":-1==this.modDim?"vib":"mod")},"java.util.Map");j(b,"clone",function(){var a=new JU.Vibration;a.setT(this);a.modDim=this.modDim;return a});c(b,"setXYZ",function(a){this.setT(a)},"JU.T3");c(b,"setType",function(a){this.modDim=a;return this},"~N");c(b,

"isNonzero",function(){return 0!=this.x||0!=this.y||0!=this.z});c(b,"getOccupancy100",function(){return-2147483648},"~B");c(b,"startTrace",function(a){this.trace=Array(a);this.tracePt=a},"~N");c(b,"addTracePt",function(a,b){(null==this.trace||0==a||a!=this.trace.length)&&this.startTrace(a);if(null!=b&&2<a){if(0>=--this.tracePt){for(var c=this.trace[this.trace.length-1],l=this.trace.length;1<=--l;)this.trace[l]=this.trace[l-1];this.trace[1]=c;this.tracePt=1}c=this.trace[this.tracePt];null==c&&(c=this.trace[this.tracePt]=

new JU.P3);c.setT(b)}return this.trace},"~N,JU.Point3fi")});u("JV");C(["J.api.EventManager","JU.Rectangle","JV.MouseState"],["JV.MotionPoint","$.ActionManager","$.Gesture"],"JU.AU $.PT J.api.Interface J.i18n.GT JS.SV $.ScriptEval J.thread.HoverWatcherThread JU.BSUtil $.Escape $.Logger $.Point3fi JV.Viewer JV.binding.Binding $.JmolBinding".split(" "),function(){var b=v(function(){this.vwr=null;this.isMultiTouch=this.haveMultiTouchInput=!1;this.predragBinding=this.rasmolBinding=this.dragBinding=this.pfaatBinding=

this.jmolBinding=this.b=null;this.LEFT_DRAGGED=0;this.hoverable=!1;this.dragGesture=this.hoverWatcherThread=null;this.apm=1;this.pickingStyleSelect=this.pickingStyle=this.bondPickingMode=0;this.pickingStyleMeasure=5;this.rootPickingStyle=0;this.mouseDragFactor=this.gestureSwipeFactor=1;this.mouseWheelFactor=1.15;this.dragged=this.pressed=this.clicked=this.moved=this.current=null;this.clickedCount=this.pressedCount=0;this.dragSelectedMode=this.labelMode=this.drawMode=!1;this.measuresEnabled=!0;this.hoverActive=

this.haveSelection=!1;this.mp=null;this.dragAtomIndex=-1;this.rubberbandSelectionMode=this.mkBondPressed=!1;this.rectRubber=null;this.isAltKeyReleased=!0;this.isMultiTouchServer=this.isMultiTouchClient=this.keyProcessing=!1;this.clickAction=this.dragAction=this.pressAction=0;this.measurementQueued=null;this.selectionWorking=this.zoomTrigger=!1;r(this,arguments)},JV,"ActionManager",null,J.api.EventManager);Q(b,function(){this.current=new JV.MouseState("current");this.moved=new JV.MouseState("moved");

this.clicked=new JV.MouseState("clicked");this.pressed=new JV.MouseState("pressed");this.dragged=new JV.MouseState("dragged");this.rectRubber=new JU.Rectangle});c(b,"setViewer",function(a){this.vwr=a;JV.Viewer.isJS||this.createActions();this.setBinding(this.jmolBinding=new JV.binding.JmolBinding);this.LEFT_DRAGGED=JV.binding.Binding.getMouseAction(1,16,1);this.dragGesture=new JV.Gesture(20,a)},"JV.Viewer,~S");c(b,"isHoverable",function(){return this.hoverable});c(b,"checkHover",function(){if(this.zoomTrigger)this.zoomTrigger=

!1,8==this.vwr.currentCursor&&this.vwr.setCursor(0),this.vwr.setInMotion(!1);else if(!this.vwr.getInMotion(!0)&&!this.vwr.tm.spinOn&&!this.vwr.tm.navOn&&!this.vwr.checkObjectHovered(this.current.x,this.current.y)){var a=this.vwr.findNearestAtomIndex(this.current.x,this.current.y);if(!(0>a)){var b=2==this.apm&&this.bnd(JV.binding.Binding.getMouseAction(this.clickedCount,this.moved.modifiers,1),[10]);this.vwr.hoverOn(a,b)}}});c(b,"processMultitouchEvent",function(){},"~N,~N,~N,~N,JU.P3,~N");c(b,"bind",

function(a,b){var c=JV.ActionManager.getActionFromName(b),l=JV.binding.Binding.getMouseActionStr(a);0!=l&&(0<=c?this.b.bindAction(l,c):this.b.bindName(l,b))},"~S,~S");c(b,"clearBindings",function(){this.setBinding(this.jmolBinding=new JV.binding.JmolBinding);this.rasmolBinding=this.dragBinding=this.pfaatBinding=null});c(b,"unbindAction",function(a,b){if(null==a&&null==b)this.clearBindings();else{var c=JV.ActionManager.getActionFromName(b),l=JV.binding.Binding.getMouseActionStr(a);0<=c?this.b.unbindAction(l,

c):0!=l&&this.b.unbindName(l,b);null==b&&this.b.unbindUserAction(a)}},"~S,~S");b.newAction=c(b,"newAction",function(a,b,c){JV.ActionManager.actionInfo[a]=c;JV.ActionManager.actionNames[a]=b},"~N,~S,~S");c(b,"createActions",function(){null==JV.ActionManager.actionInfo[0]&&(JV.ActionManager.newAction(0,"_assignNew",J.i18n.GT.o(J.i18n.GT.$("assign/new atom or bond (requires {0})"),"set picking assignAtom_??/assignBond_?")),JV.ActionManager.newAction(1,"_center",J.i18n.GT.$("center")),JV.ActionManager.newAction(2,

"_clickFrank",J.i18n.GT.$("pop up recent context menu (click on Jmol frank)")),JV.ActionManager.newAction(4,"_deleteAtom",J.i18n.GT.o(J.i18n.GT.$("delete atom (requires {0})"),"set picking DELETE ATOM")),JV.ActionManager.newAction(5,"_deleteBond",J.i18n.GT.o(J.i18n.GT.$("delete bond (requires {0})"),"set picking DELETE BOND")),JV.ActionManager.newAction(6,"_depth",J.i18n.GT.o(J.i18n.GT.$("adjust depth (back plane; requires {0})"),"SLAB ON")),JV.ActionManager.newAction(7,"_dragAtom",J.i18n.GT.o(J.i18n.GT.$("move atom (requires {0})"),

"set picking DRAGATOM")),JV.ActionManager.newAction(8,"_dragDrawObject",J.i18n.GT.o(J.i18n.GT.$("move whole DRAW object (requires {0})"),"set picking DRAW")),JV.ActionManager.newAction(9,"_dragDrawPoint",J.i18n.GT.o(J.i18n.GT.$("move specific DRAW point (requires {0})"),"set picking DRAW")),JV.ActionManager.newAction(10,"_dragLabel",J.i18n.GT.o(J.i18n.GT.$("move label (requires {0})"),"set picking LABEL")),JV.ActionManager.newAction(11,"_dragMinimize",J.i18n.GT.o(J.i18n.GT.$("move atom and minimize molecule (requires {0})"),

"set picking DRAGMINIMIZE")),JV.ActionManager.newAction(12,"_dragMinimizeMolecule",J.i18n.GT.o(J.i18n.GT.$("move and minimize molecule (requires {0})"),"set picking DRAGMINIMIZEMOLECULE")),JV.ActionManager.newAction(13,"_dragSelected",J.i18n.GT.o(J.i18n.GT.$("move selected atoms (requires {0})"),"set DRAGSELECTED")),JV.ActionManager.newAction(14,"_dragZ",J.i18n.GT.o(J.i18n.GT.$("drag atoms in Z direction (requires {0})"),"set DRAGSELECTED")),JV.ActionManager.newAction(15,"_multiTouchSimulation",J.i18n.GT.$("simulate multi-touch using the mouse)")),

JV.ActionManager.newAction(16,"_navTranslate",J.i18n.GT.o(J.i18n.GT.$("translate navigation point (requires {0} and {1})"),w(-1,["set NAVIGATIONMODE","set picking NAVIGATE"]))),JV.ActionManager.newAction(17,"_pickAtom",J.i18n.GT.$("pick an atom")),JV.ActionManager.newAction(3,"_pickConnect",J.i18n.GT.o(J.i18n.GT.$("connect atoms (requires {0})"),"set picking CONNECT")),JV.ActionManager.newAction(18,"_pickIsosurface",J.i18n.GT.o(J.i18n.GT.$("pick an ISOSURFACE point (requires {0}"),"set DRAWPICKING")),

JV.ActionManager.newAction(19,"_pickLabel",J.i18n.GT.o(J.i18n.GT.$("pick a label to toggle it hidden/displayed (requires {0})"),"set picking LABEL")),JV.ActionManager.newAction(20,"_pickMeasure",J.i18n.GT.o(J.i18n.GT.$("pick an atom to include it in a measurement (after starting a measurement or after {0})"),"set picking DISTANCE/ANGLE/TORSION")),JV.ActionManager.newAction(21,"_pickNavigate",J.i18n.GT.o(J.i18n.GT.$("pick a point or atom to navigate to (requires {0})"),"set NAVIGATIONMODE")),JV.ActionManager.newAction(22,

"_pickPoint",J.i18n.GT.o(J.i18n.GT.$("pick a DRAW point (for measurements) (requires {0}"),"set DRAWPICKING")),JV.ActionManager.newAction(23,"_popupMenu",J.i18n.GT.$("pop up the full context menu")),JV.ActionManager.newAction(24,"_reset",J.i18n.GT.$("reset (when clicked off the model)")),JV.ActionManager.newAction(25,"_rotate",J.i18n.GT.$("rotate")),JV.ActionManager.newAction(26,"_rotateBranch",J.i18n.GT.o(J.i18n.GT.$("rotate branch around bond (requires {0})"),"set picking ROTATEBOND")),JV.ActionManager.newAction(27,

"_rotateSelected",J.i18n.GT.o(J.i18n.GT.$("rotate selected atoms (requires {0})"),"set DRAGSELECTED")),JV.ActionManager.newAction(28,"_rotateZ",J.i18n.GT.$("rotate Z")),JV.ActionManager.newAction(29,"_rotateZorZoom",J.i18n.GT.$("rotate Z (horizontal motion of mouse) or zoom (vertical motion of mouse)")),JV.ActionManager.newAction(30,"_select",J.i18n.GT.o(J.i18n.GT.$("select an atom (requires {0})"),"set pickingStyle EXTENDEDSELECT")),JV.ActionManager.newAction(31,"_selectAndDrag",J.i18n.GT.o(J.i18n.GT.$("select and drag atoms (requires {0})"),

"set DRAGSELECTED")),JV.ActionManager.newAction(32,"_selectAndNot",J.i18n.GT.o(J.i18n.GT.$("unselect this group of atoms (requires {0})"),"set pickingStyle DRAG/EXTENDEDSELECT")),JV.ActionManager.newAction(33,"_selectNone",J.i18n.GT.o(J.i18n.GT.$("select NONE (requires {0})"),"set pickingStyle EXTENDEDSELECT")),JV.ActionManager.newAction(34,"_selectOr",J.i18n.GT.o(J.i18n.GT.$("add this group of atoms to the set of selected atoms (requires {0})"),"set pickingStyle DRAG/EXTENDEDSELECT")),JV.ActionManager.newAction(35,

"_selectToggle",J.i18n.GT.o(J.i18n.GT.$("toggle selection (requires {0})"),"set pickingStyle DRAG/EXTENDEDSELECT/RASMOL")),JV.ActionManager.newAction(36,"_selectToggleOr",J.i18n.GT.o(J.i18n.GT.$("if all are selected, unselect all, otherwise add this group of atoms to the set of selected atoms (requires {0})"),"set pickingStyle DRAG")),JV.ActionManager.newAction(37,"_setMeasure",J.i18n.GT.$("pick an atom to initiate or conclude a measurement")),JV.ActionManager.newAction(38,"_slab",J.i18n.GT.o(J.i18n.GT.$("adjust slab (front plane; requires {0})"),

"SLAB ON")),JV.ActionManager.newAction(39,"_slabAndDepth",J.i18n.GT.o(J.i18n.GT.$("move slab/depth window (both planes; requires {0})"),"SLAB ON")),JV.ActionManager.newAction(40,"_slideZoom",J.i18n.GT.$("zoom (along right edge of window)")),JV.ActionManager.newAction(41,"_spinDrawObjectCCW",J.i18n.GT.o(J.i18n.GT.$("click on two points to spin around axis counterclockwise (requires {0})"),"set picking SPIN")),JV.ActionManager.newAction(42,"_spinDrawObjectCW",J.i18n.GT.o(J.i18n.GT.$("click on two points to spin around axis clockwise (requires {0})"),

"set picking SPIN")),JV.ActionManager.newAction(43,"_stopMotion",J.i18n.GT.o(J.i18n.GT.$("stop motion (requires {0})"),"set waitForMoveTo FALSE")),JV.ActionManager.newAction(44,"_swipe",J.i18n.GT.$("spin model (swipe and release button and stop motion simultaneously)")),JV.ActionManager.newAction(45,"_translate",J.i18n.GT.$("translate")),JV.ActionManager.newAction(46,"_wheelZoom",J.i18n.GT.$("zoom")))});b.getActionName=c(b,"getActionName",function(a){return a<JV.ActionManager.actionNames.length?JV.ActionManager.actionNames[a]:

null},"~N");b.getActionFromName=c(b,"getActionFromName",function(a){for(var b=0;b<JV.ActionManager.actionNames.length;b++)if(JV.ActionManager.actionNames[b].equalsIgnoreCase(a))return b;return-1},"~S");c(b,"getBindingInfo",function(a){return this.b.getBindingInfo(JV.ActionManager.actionInfo,JV.ActionManager.actionNames,a)},"~S");c(b,"setBinding",function(a){this.b=a},"JV.binding.Binding");c(b,"bnd",function(a,b){for(var c=b.length;0<=--c;)if(this.b.isBound(a,b[c]))return!0;return!1},"~N,~A");c(b,

"isDrawOrLabelAction",function(a){return this.drawMode&&this.bnd(a,[8,9])||this.labelMode&&this.bnd(a,[10])},"~N");c(b,"getBondPickingMode",function(){return this.bondPickingMode});b.getPickingModeName=c(b,"getPickingModeName",function(a){return 0>a||a>=JV.ActionManager.pickingModeNames.length?"off":JV.ActionManager.pickingModeNames[a]},"~N");b.getPickingMode=c(b,"getPickingMode",function(a){for(var b=JV.ActionManager.pickingModeNames.length;0<=--b;)if(a.equalsIgnoreCase(JV.ActionManager.pickingModeNames[b]))return 38==

b&&(b=6),b;return-1},"~S");b.getPickingStyleName=c(b,"getPickingStyleName",function(a){return 0>a||a>=JV.ActionManager.pickingStyleNames.length?"toggle":JV.ActionManager.pickingStyleNames[a]},"~N");b.getPickingStyleIndex=c(b,"getPickingStyleIndex",function(a){for(var b=JV.ActionManager.pickingStyleNames.length;0<=--b;)if(a.equalsIgnoreCase(JV.ActionManager.pickingStyleNames[b]))return b;return-1},"~S");c(b,"getAtomPickingMode",function(){return this.apm});c(b,"setPickingMode",function(a){var b=!1;

switch(a){case -1:b=!0;this.bondPickingMode=35;a=1;this.vwr.setStringProperty("pickingStyle","toggle");this.vwr.setBooleanProperty("bondPicking",!1);break;case 34:case 33:case 8:this.vwr.getModelkit(!1);case 35:this.vwr.setBooleanProperty("bondPicking",!0);this.bondPickingMode=a;this.resetMeasurement();return}b=(new Boolean(b|this.apm!=a)).valueOf();this.apm=a;b&&this.resetMeasurement()},"~N");c(b,"getPickingState",function(){var a=";set modelkitMode "+this.vwr.getBoolean(603983903)+";set picking "+

JV.ActionManager.getPickingModeName(this.apm);32==this.apm&&(a+="_"+this.vwr.getModelkitPropertySafely("atomtype"));a+=";";0!=this.bondPickingMode&&(a+="set picking "+JV.ActionManager.getPickingModeName(this.bondPickingMode));33==this.bondPickingMode&&(a+="_"+this.vwr.getModelkitPropertySafely("bondtype"));return a+";"});c(b,"getPickingStyle",function(){return this.pickingStyle});c(b,"setPickingStyle",function(a){this.pickingStyle=a;4<=a?(this.pickingStyleMeasure=a,this.resetMeasurement()):(3>a&&

(this.rootPickingStyle=a),this.pickingStyleSelect=a);this.rubberbandSelectionMode=!1;switch(this.pickingStyleSelect){case 2:this.b.name.equals("extendedSelect")||this.setBinding(null==this.pfaatBinding?this.pfaatBinding=JV.binding.Binding.newBinding(this.vwr,"Pfaat"):this.pfaatBinding);break;case 3:this.b.name.equals("drag")||this.setBinding(null==this.dragBinding?this.dragBinding=JV.binding.Binding.newBinding(this.vwr,"Drag"):this.dragBinding);this.rubberbandSelectionMode=!0;break;case 1:this.b.name.equals("selectOrToggle")||

this.setBinding(null==this.rasmolBinding?this.rasmolBinding=JV.binding.Binding.newBinding(this.vwr,"Rasmol"):this.rasmolBinding);break;default:this.b!==this.jmolBinding&&this.setBinding(this.jmolBinding)}this.b.name.equals("drag")||(this.predragBinding=this.b)},"~N");c(b,"setGestureSwipeFactor",function(a){this.gestureSwipeFactor=a},"~N");c(b,"setMouseDragFactor",function(a){this.mouseDragFactor=a},"~N");c(b,"setMouseWheelFactor",function(a){this.mouseWheelFactor=a},"~N");c(b,"setCurrent",function(a,

b,c,l){this.vwr.hoverOff();this.current.set(a,b,c,l)},"~N,~N,~N,~N");c(b,"getCurrentX",function(){return this.current.x});c(b,"getCurrentY",function(){return this.current.y});c(b,"setMouseMode",function(){this.drawMode=this.labelMode=!1;this.dragSelectedMode=this.vwr.getDragSelected();this.measuresEnabled=!this.dragSelectedMode;if(!this.dragSelectedMode)switch(this.apm){default:return;case 32:this.measuresEnabled=!this.vwr.getModelkit(!1).isPickAtomAssignCharge();return;case 4:this.drawMode=!0;this.measuresEnabled=

!1;break;case 2:this.labelMode=!0;this.measuresEnabled=!1;break;case 9:this.measuresEnabled=!1;break;case 19:case 22:case 20:case 21:this.measuresEnabled=!1;return}this.exitMeasurementMode(null)});c(b,"clearMouseInfo",function(){this.pressedCount=this.clickedCount=0;this.dragGesture.setAction(0,0);this.exitMeasurementMode(null)});c(b,"setDragAtomIndex",function(a){this.dragAtomIndex=a;this.setAtomsPicked(JU.BSUtil.newAndSetBit(a),"Label picked for atomIndex = "+a)},"~N");c(b,"isMTClient",function(){return this.isMultiTouchClient});

c(b,"isMTServer",function(){return this.isMultiTouchServer});c(b,"dispose",function(){this.clear()});c(b,"clear",function(){this.startHoverWatcher(!1);null!=this.predragBinding&&(this.b=this.predragBinding);this.vwr.setPickingStyle(null,this.rootPickingStyle);this.isAltKeyReleased=!0});c(b,"startHoverWatcher",function(a){if(!this.vwr.isPreviewOnly)try{a?null==this.hoverWatcherThread&&(this.current.time=-1,this.hoverWatcherThread=new J.thread.HoverWatcherThread(this,this.current,this.moved,this.vwr)):

null!=this.hoverWatcherThread&&(this.current.time=-1,this.hoverWatcherThread.interrupt(),this.hoverWatcherThread=null)}catch(b){if(!F(b,Exception))throw b;}},"~B");c(b,"setModeMouse",function(a){-1==a&&this.startHoverWatcher(!1)},"~N");j(b,"keyPressed",function(a,b){if(this.keyProcessing)return!1;this.keyProcessing=!0;switch(a){case 18:this.dragSelectedMode&&this.isAltKeyReleased&&this.vwr.moveSelectedXY(-2147483648,0,b);this.isAltKeyReleased=!1;this.moved.modifiers|=8;break;case 16:this.moved.keybuf=

0;this.dragged.modifiers|=1;this.moved.modifiers|=1;break;case 17:this.moved.modifiers|=2;break;case 27:this.vwr.hoverOff();this.exitMeasurementMode("escape");break;default:this.vwr.hoverOff()}var c=8464|this.moved.modifiers;!this.labelMode&&!this.b.isUserAction(c)&&this.checkMotionRotateZoom(c,this.current.x,0,0,!1);if(this.vwr.getBoolean(603979889))switch(a){case 38:case 40:case 37:case 39:case 32:case 46:this.vwr.navigate(a,b)}this.keyProcessing=!1;return!0},"~N,~N");j(b,"keyTyped",function(){return!1},

"~N,~N");j(b,"keyReleased",function(a){switch(a){case 18:this.moved.modifiers&=-9;this.dragSelectedMode&&this.vwr.moveSelectedXY(2147483647,0,this.moved.modifiers);this.isAltKeyReleased=!0;break;case 16:this.moved.modifiers&=-2;0<this.moved.keybuf&&this.vwr.isModelKitOpen()&&this.checkKeyBuf(0);break;case 17:this.moved.modifiers&=-3}0==this.moved.modifiers&&this.vwr.setCursor(0);if(65<=a&&this.vwr.isModelKitOpen()&&(this.dragAtomIndex=this.vwr.findNearestAtomIndex(this.current.x,this.current.y),0<=

this.dragAtomIndex)){this.checkKeyBuf(a);return}if(this.vwr.getBoolean(603979889))switch(a){case 38:case 40:case 37:case 39:this.vwr.navigate(0,0)}this.moved.keybuf=0},"~N");c(b,"checkKeyBuf",function(a){var b=0!=(this.moved.modifiers&1);if(0!=a)if(0==this.moved.keybuf){if(this.moved.keybuf=a,b)return}else this.moved.keybuf+=a<<8;0<this.moved.keybuf&&(this.assignNew(this.moved.keybuf),this.moved.keybuf=0)},"~N");j(b,"mouseEnterExit",function(a,b,c,l){this.vwr.tm.stereoDoubleDTI&&(b<<=1);this.setCurrent(a,

b,c,0);l&&this.exitMeasurementMode("mouseExit")},"~N,~N,~N,~B");c(b,"setMouseActions",function(a,b,c){this.pressAction=JV.binding.Binding.getMouseAction(a,b,c?5:4);this.dragAction=JV.binding.Binding.getMouseAction(a,b,1);this.clickAction=JV.binding.Binding.getMouseAction(a,b,2)},"~N,~N,~B");j(b,"mouseAction",function(a,b,c,l,f,e){if(this.vwr.getMouseEnabled())switch(JU.Logger.debuggingHigh&&(0!=a&&this.vwr.getBoolean(603979960))&&this.vwr.showString("mouse action: "+a+" "+e+" "+JV.binding.Binding.getMouseActionName(JV.binding.Binding.getMouseAction(f,

e,a),!1),!1),this.vwr.tm.stereoDoubleDTI&&(c<<=1),a){case 0:this.hoverable||(JU.Logger.info("ActionManager: mouse move detected"),this.hoverable=!0);this.setCurrent(b,c,l,e);this.moved.setCurrent(this.current,0);this.moved.keybuf=0;if(null!=this.mp||this.hoverActive){this.clickAction=JV.binding.Binding.getMouseAction(this.clickedCount,e,0);this.checkClickAction(c,l,b,0);break}if(this.isZoomArea(c)){this.checkMotionRotateZoom(this.LEFT_DRAGGED,0,0,0,!1);break}8==this.vwr.currentCursor&&this.vwr.setCursor(0);

break;case 4:this.setMouseMode();this.pressedCount=this.pressed.check(20,c,l,e,b,700)?this.pressedCount+1:1;1==this.pressedCount&&(this.vwr.checkInMotion(1),this.setCurrent(b,c,l,e));this.pressAction=JV.binding.Binding.getMouseAction(this.pressedCount,e,4);this.vwr.setCursor(12);this.pressed.setCurrent(this.current,1);this.dragged.setCurrent(this.current,1);this.vwr.setFocus();this.dragGesture.setAction(this.dragAction,b);this.checkPressedAction(c,l,b);break;case 1:this.setMouseMode();this.setMouseActions(this.pressedCount,

e,!1);a=c-this.dragged.x;f=l-this.dragged.y;this.setCurrent(b,c,l,e);this.dragged.setCurrent(this.current,-1);this.dragGesture.add(this.dragAction,c,l,b);this.checkDragWheelAction(this.dragAction,c,l,a,f,b,1);break;case 5:this.setMouseActions(this.pressedCount,e,!0);this.setCurrent(b,c,l,e);this.vwr.spinXYBy(0,0,0);e=!this.pressed.check(10,c,l,e,b,9223372036854775E3);this.checkReleaseAction(c,l,b,e);break;case 3:if(this.vwr.isApplet&&!this.vwr.hasFocus())break;this.setCurrent(b,this.current.x,this.current.y,

e);this.checkDragWheelAction(JV.binding.Binding.getMouseAction(0,e,3),this.current.x,this.current.y,0,l,b,3);break;case 2:this.setMouseMode();this.clickedCount=1<f?f:this.clicked.check(10,0,0,e,b,700)?this.clickedCount+1:1;1==this.clickedCount&&this.setCurrent(b,c,l,e);this.setMouseActions(this.clickedCount,e,!1);this.clicked.setCurrent(this.current,this.clickedCount);this.vwr.setFocus();if(9!=this.apm&&this.bnd(JV.binding.Binding.getMouseAction(1,e,4),[31]))break;this.clickAction=JV.binding.Binding.getMouseAction(this.clickedCount,

e,2);this.checkClickAction(c,l,b,this.clickedCount)}},"~N,~N,~N,~N,~N,~N");c(b,"checkPressedAction",function(a,b,c){var l=JV.binding.Binding.getButtonMods(this.pressAction),f=this.bnd(JV.binding.Binding.getMouseAction(1,l,4),[31]);if(0!=l){this.pressAction=this.vwr.notifyMouseClicked(a,b,this.pressAction,4);if(0==this.pressAction)return;l=JV.binding.Binding.getButtonMods(this.pressAction)}this.setMouseActions(this.pressedCount,l,!1);JU.Logger.debuggingHigh&&this.vwr.getBoolean(603979960)&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.pressAction,

!1));if(!this.isDrawOrLabelAction(this.dragAction)||!this.vwr.checkObjectDragged(-2147483648,0,a,b,this.dragAction)){this.checkUserAction(this.pressAction,a,b,0,0,c,4);c=!1;switch(this.apm){case 32:c=this.bnd(this.clickAction,[0]);break;case 28:c=this.bnd(this.dragAction,[7,14]);break;case 26:case 36:case 37:case 27:c=this.bnd(this.dragAction,[7,14,27]);break;case 29:c=this.bnd(this.dragAction,[11,14]);break;case 30:c=this.bnd(this.dragAction,[11,14,27]);break;default:c=34==this.bondPickingMode}if(c){this.dragAtomIndex=

this.vwr.findNearestAtomIndexMovable(a,b,!0);a=34==this.bondPickingMode?this.vwr.getModelkit(!1).getRotateBondIndex():-1;if(0<=this.dragAtomIndex&&(0<=a||32==this.apm||31==this.apm))this.enterMeasurementMode(this.dragAtomIndex),this.mp.addPoint(this.dragAtomIndex,null,!1),0<=a&&this.updateModelkitBranch(a,!0);a=this.vwr.getModelkitPropertySafely("screenxy");this.mkBondPressed=null!=a&&this.pressed.inRange(10,a[0],a[1])}else this.bnd(this.pressAction,[23])?this.doPopup(a,b):this.dragSelectedMode?(this.haveSelection=

!f||0<=this.vwr.findNearestAtomIndexMovable(a,b,!0))&&this.bnd(this.dragAction,[13,14])&&this.vwr.moveSelectedXY(-2147483648,0,l):this.checkMotionRotateZoom(this.dragAction,a,0,0,!0)}},"~N,~N,~N");c(b,"checkDragWheelAction",function(a,b,c,l,f,e,h){var k=JV.binding.Binding.getButtonMods(a);if(0!=k){var j=this.vwr.notifyMouseClicked(b,c,JV.binding.Binding.getMouseAction(this.pressedCount,k,h),h);if(0==j)return;0<j&&(a=j)}if(this.isRubberBandSelect(a))this.calcRectRubberBand(),this.vwr.refresh(3,"rubberBand selection");

else if(!this.checkUserAction(a,b,c,l,f,e,h))if(e=34==this.bondPickingMode?this.vwr.getModelkit(!1).getRotateBondIndex():-1,0<=e&&(0<=this.dragAtomIndex||this.mkBondPressed||this.bnd(a,[26])))0<=this.dragAtomIndex&&this.updateModelkitBranch(e,!1),this.vwr.moveSelected(l,f,-2147483648,b,c,null,null,null,!1,!1,0<=this.dragAtomIndex?0:16);else{e=null;if(0<=this.dragAtomIndex&&2!=this.apm)switch(this.apm){case 26:this.dragSelected(a,l,f,!0);return;case 36:case 37:case 27:case 30:e=this.vwr.ms.getAtoms(37==

this.apm?1094717454:1094713360,JU.BSUtil.newAndSetBit(this.dragAtomIndex)),36==this.apm&&e.and(this.vwr.getAtomBitSet("ligand"));case 28:case 29:1==this.dragGesture.getPointCount()&&this.vwr.undoMoveActionClear(this.dragAtomIndex,2,!0);this.setMotion(13,!0);if(this.bnd(a,[27]))this.vwr.rotateSelected(this.getDegrees(l,!0),this.getDegrees(f,!1),e);else{switch(this.apm){case 36:case 37:case 27:case 30:this.vwr.selectStatus(e,!1,0,!0,!0)}this.vwr.moveAtomWithHydrogens(this.dragAtomIndex,l,f,this.bnd(a,

[14])?-f:-2147483648,null,e);this.vwr.checkCoordinatesChanged(null)}return}if(0<=this.dragAtomIndex&&1==h&&this.bnd(this.clickAction,[0])&&32==this.apm)a=this.vwr.findNearestAtomIndexMovable(b,c,!1),0<=a?(null!=this.mp?this.mp.setCount(1):this.measuresEnabled&&this.enterMeasurementMode(a),this.addToMeasurement(a,null,!0),this.mp.colix=20):null!=this.mp&&(this.mp.setCount(1),this.mp.colix=23),null!=this.mp&&(this.vwr.antialiased&&(b<<=1,c<<=1),this.mp.traceX=b,this.mp.traceY=c,this.vwr.refresh(3,"assignNew"));

else if(!this.drawMode&&!this.labelMode&&this.bnd(a,[45]))this.vwr.translateXYBy(l,f);else if(this.dragSelectedMode&&this.haveSelection&&this.bnd(a,[13,27]))b=this.vwr.bsA().nextSetBit(0),0>b||(1==this.dragGesture.getPointCount()?this.vwr.undoMoveActionClear(b,2,!0):this.vwr.moveSelected(2147483647,0,-2147483648,-2147483648,-2147483648,null,null,null,!1,!1,k),this.dragSelected(a,l,f,!1));else{if(this.isDrawOrLabelAction(a)&&(this.setMotion(13,!0),this.vwr.checkObjectDragged(this.dragged.x,this.dragged.y,

b,c,a)))return;if(this.checkMotionRotateZoom(a,b,l,f,!0))this.vwr.tm.slabEnabled&&this.bnd(a,[39])?this.vwr.slabDepthByPixels(f):this.vwr.zoomBy(f);else if(this.bnd(a,[25]))this.vwr.rotateXYBy(this.getDegrees(l,!0),this.getDegrees(f,!1));else if(this.bnd(a,[29]))0==l&&1<Math.abs(f)?(this.setMotion(8,!0),this.vwr.zoomBy(f+(0<f?-1:1))):0==f&&1<Math.abs(l)&&(this.setMotion(13,!0),this.vwr.rotateZBy(-l+(0<l?1:-1),2147483647,2147483647));else{if(this.vwr.tm.slabEnabled){if(this.bnd(a,[6])){this.vwr.depthByPixels(f);

return}if(this.bnd(a,[38])){this.vwr.slabByPixels(f);return}if(this.bnd(a,[39])){this.vwr.slabDepthByPixels(f);return}}this.bnd(a,[46])?this.zoomByFactor(f,2147483647,2147483647):this.bnd(a,[28])&&(this.setMotion(13,!0),this.vwr.rotateZBy(-l,2147483647,2147483647))}}}},"~N,~N,~N,~N,~N,~N,~N");c(b,"updateModelkitBranch",function(a,b){this.vwr.setModelkitPropertySafely(b?"branchatomclicked":"branchatomdragged",Integer.$valueOf(this.dragAtomIndex));null==this.measurementQueued||0==this.measurementQueued.numSet||

null==this.mp?this.vwr.setPendingMeasurement(this.vwr.getModelkit(!1).setBondMeasure(a,this.measurementQueued=this.mp=this.getMP())):this.measurementQueued.refresh(null)},"~N,~B");c(b,"dragSelected",function(a,b,c,l){this.setMotion(13,!0);this.bnd(a,[27])&&this.vwr.getBoolean(603979785)?this.vwr.rotateSelected(this.getDegrees(b,!0),this.getDegrees(c,!1),null):this.vwr.moveSelected(b,c,l&&this.bnd(a,[14])?-c:-2147483648,-2147483648,-2147483648,null,null,null,!0,!1,this.dragged.modifiers)},"~N,~N,~N,~B");

c(b,"checkReleaseAction",function(a,b,c,l){JU.Logger.debuggingHigh&&this.vwr.getBoolean(603979960)&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.pressAction,!1));this.vwr.checkInMotion(0);this.vwr.setInMotion(!1);this.vwr.setCursor(0);this.dragGesture.add(this.dragAction,a,b,c);0<=this.dragAtomIndex&&!this.vwr.isModelkitPickingRotateBond()&&(29==this.apm||30==this.apm)&&this.minimize(!0);if(32==this.apm&&this.bnd(this.clickAction,[0]))null==this.mp||0>this.dragAtomIndex?this.exitMeasurementMode(null):

34==this.bondPickingMode?(this.vwr.setModelkitPropertySafely("rotatebond",Integer.$valueOf(this.dragAtomIndex)),this.exitMeasurementMode(null)):this.assignNew(-1);else if(this.dragAtomIndex=-1,this.mkBondPressed=!1,this.isRubberBandSelect(this.dragAction)&&this.selectRb(this.clickAction),this.rubberbandSelectionMode=this.b.name.equals("drag"),this.rectRubber.x=2147483647,l&&this.vwr.notifyMouseClicked(a,b,JV.binding.Binding.getMouseAction(this.pressedCount,0,5),5),this.isDrawOrLabelAction(this.dragAction))this.vwr.checkObjectDragged(2147483647,

0,a,b,this.dragAction);else if(this.haveSelection&&(this.dragSelectedMode&&this.bnd(this.dragAction,[13]))&&this.vwr.moveSelectedXY(2147483647,0,this.dragged.modifiers),(!l||!this.checkUserAction(this.pressAction,a,b,0,0,c,5))&&this.vwr.getBoolean(603979780)&&this.bnd(this.dragAction,[44]))a=this.getExitRate(),0<a&&this.vwr.spinXYBy(this.dragGesture.getDX(4,2),this.dragGesture.getDY(4,2),30*a*this.gestureSwipeFactor),this.vwr.g.logGestures&&this.vwr.log("$NOW$ swipe "+this.dragGesture+" "+a)},"~N,~N,~N,~B");

c(b,"checkClickAction",function(a,b,c,l){if(1<l&&(5==this.apm||6==this.apm))this.resetMeasurement(),this.runScript("draw ID sym* delete;spin off;");else{if(0<l){if(this.checkUserAction(this.clickAction,a,b,0,0,c,32768))return;this.clickAction=this.vwr.notifyMouseClicked(a,b,this.clickAction,32768);if(0==this.clickAction)return}JU.Logger.debuggingHigh&&this.vwr.getBoolean(603979960)&&JU.Logger.debug(JV.binding.Binding.getMouseActionName(this.clickAction,!1));if(this.bnd(this.clickAction,[2])){if(this.vwr.frankClicked(a,

b)){this.vwr.popupMenu(-a,b,"j");return}if(this.vwr.frankClickedModelKit(a,b)){this.vwr.popupMenu(10,0,"m");return}}c=null;var f=!1,e=!1,h=null;if(!this.drawMode&&(h=this.vwr.checkObjectClicked(a,b,this.clickAction),null!=h)){if(this.labelMode){this.pickLabel(h.get("atomIndex").intValue());return}f="bond".equals(h.get("type"));e="isosurface".equals(h.get("type"));c=this.getPoint(h);f&&this.vwr.isModelkitPickingRotateBond()&&this.vwr.highlightBond(h.get("index").intValue(),-1,a,b)}f&&(l=1);if(!(null!=

c&&Float.isNaN(c.x))){var k=this.findNearestAtom(a,b,c,0<l);if(this.bnd(this.clickAction,[23]))this.doPopup(a,b);else if(0==l&&32!=this.apm&&!this.vwr.isModelkitPickingRotateBond()){if(null!=this.mp){if(null!=c||0==this.mp.getIndexOf(k))try{this.mp.addPoint(k,c,!1)}catch(j){if(F(j,Exception)){this.exitMeasurementMode(null);return}throw j;}this.mp.haveModified&&this.vwr.setPendingMeasurement(this.mp);this.vwr.refresh(3,"measurementPending")}}else if(this.setMouseMode(),this.bnd(this.clickAction,[43])&&

this.vwr.tm.stopMotion(),this.vwr.getBoolean(603979889)&&23==this.apm&&this.bnd(this.clickAction,[21]))this.vwr.navTranslatePercent(100*a/this.vwr.getScreenWidth()-50,100*b/this.vwr.getScreenHeight()-50);else{if(f){if(this.bnd(this.clickAction,[34==this.bondPickingMode||33==this.bondPickingMode?0:5])){this.bondPicked(h.get("index").intValue());this.vwr.refresh(1,"bondpicked");return}}else{if(e)return;if(32!=this.apm&&null!=this.mp&&this.bnd(this.clickAction,[20])){this.atomOrPointPicked(k,c);4==this.addToMeasurement(k,

c,!1)&&this.toggleMeasurement();return}if(this.bnd(this.clickAction,[37])){null!=this.mp?(this.addToMeasurement(k,c,!0),this.toggleMeasurement()):!this.drawMode&&(!this.labelMode&&!this.dragSelectedMode&&this.measuresEnabled)&&(this.enterMeasurementMode(k),this.addToMeasurement(k,c,!0));this.atomOrPointPicked(k,c);return}}this.isSelectAction(this.clickAction)?e||this.atomOrPointPicked(k,c):this.bnd(this.clickAction,[24])&&0>k&&this.reset()}}}},"~N,~N,~N,~N");c(b,"doPopup",function(a,b){this.vwr.popupMenu(a,

b,this.vwr.isModelKitOpen()?"m":"j")},"~N,~N");c(b,"pickLabel",function(a){var b=this.vwr.ms.at[a].atomPropertyString(this.vwr,1825200146);2==this.pressedCount?(b=this.vwr.apiPlatform.prompt("Set label for atomIndex="+a,b,null,!1),null!=b&&(this.vwr.shm.setAtomLabel(b,a),this.vwr.refresh(1,"label atom"))):this.setAtomsPicked(JU.BSUtil.newAndSetBit(a),"Label picked for atomIndex = "+a+": "+b)},"~N");c(b,"checkUserAction",function(a,b,c,l,f,e,h){if(!this.b.isUserAction(a))return!1;for(var k=!1,j,n=

this.b.getBindings(),p=a+"\t",q,r=n.keySet().iterator();r.hasNext()&&((q=r.next())||1);)if(0==q.indexOf(p)&&JU.AU.isAS(j=n.get(q))){var s=j[1],u=null;if(0<=s.indexOf("_ATOM")){var v=this.findNearestAtom(b,c,null,!0),s=JU.PT.rep(s,"_ATOM","({"+(0<=v?""+v:"")+"})");0<=v&&(s=JU.PT.rep(s,"_POINT",JU.Escape.eP(this.vwr.ms.at[v])))}if(!this.drawMode&&(0<=s.indexOf("_POINT")||0<=s.indexOf("_OBJECT")||0<=s.indexOf("_BOND"))){v=this.vwr.checkObjectClicked(b,c,a);if(null!=v&&null!=(u=v.get("pt")))v.get("type").equals("bond")&&

(s=JU.PT.rep(s,"_BOND","[{"+v.get("index")+"}]")),s=JU.PT.rep(s,"_POINT",JU.Escape.eP(u)),s=JU.PT.rep(s,"_OBJECT",JU.Escape.escapeMap(v));s=JU.PT.rep(s,"_BOND","[{}]");s=JU.PT.rep(s,"_OBJECT","{}")}s=JU.PT.rep(s,"_POINT","{}");s=JU.PT.rep(s,"_ACTION",""+a);s=JU.PT.rep(s,"_X",""+b);s=JU.PT.rep(s,"_Y",""+(this.vwr.getScreenHeight()-c));s=JU.PT.rep(s,"_DELTAX",""+l);s=JU.PT.rep(s,"_DELTAY",""+f);s=JU.PT.rep(s,"_TIME",""+e);s=JU.PT.rep(s,"_MODE",""+h);s.startsWith("+:")&&(k=!0,s=s.substring(2));this.vwr.evalStringQuiet(s)}return!k},

"~N,~N,~N,~N,~N,~N,~N");c(b,"checkMotionRotateZoom",function(a,b,c,l,f){b=this.bnd(a,[40])&&this.isZoomArea(this.pressed.x);var e=this.bnd(a,[25]),h=this.bnd(a,[29]);if(!b&&!e&&!h)return!1;a=(c=h&&(0==c||Math.abs(l)>5*Math.abs(c)))||this.isZoomArea(this.moved.x)||this.bnd(a,[46])?8:e||h?13:this.bnd(a,[1])?12:0;this.setMotion(a,f);return c||b},"~N,~N,~N,~N,~B");c(b,"getExitRate",function(){var a=this.dragGesture.getTimeDifference(2);return this.isMultiTouch?80<a?0:this.dragGesture.getSpeedPixelsPerMillisecond(2,

1):10<a?0:this.dragGesture.getSpeedPixelsPerMillisecond(4,2)});c(b,"isRubberBandSelect",function(a){return this.rubberbandSelectionMode&&this.bnd(a&-8193|32768,[35,34,32])},"~N");c(b,"getRubberBand",function(){return this.rubberbandSelectionMode&&2147483647!=this.rectRubber.x?this.rectRubber:null});c(b,"calcRectRubberBand",function(){var a=this.vwr.antialiased?2:1;this.current.x<this.pressed.x?(this.rectRubber.x=this.current.x*a,this.rectRubber.width=(this.pressed.x-this.current.x)*a):(this.rectRubber.x=

this.pressed.x*a,this.rectRubber.width=(this.current.x-this.pressed.x)*a);this.current.y<this.pressed.y?(this.rectRubber.y=this.current.y*a,this.rectRubber.height=(this.pressed.y-this.current.y)*a):(this.rectRubber.y=this.pressed.y*a,this.rectRubber.height=(this.current.y-this.pressed.y)*a)});c(b,"getDegrees",function(a,b){return 180*(a/Math.min(500,b?this.vwr.getScreenWidth():this.vwr.getScreenHeight()))*this.mouseDragFactor},"~N,~B");c(b,"isZoomArea",function(a){return a>98*this.vwr.getScreenWidth()*

(this.vwr.tm.stereoDoubleFull||this.vwr.tm.stereoDoubleDTI?2:1)/100},"~N");c(b,"getPoint",function(a){var b=new JU.Point3fi;b.setT(a.get("pt"));b.mi=a.get("modelIndex").intValue();return b},"java.util.Map");c(b,"findNearestAtom",function(a,b,c,l){a=this.drawMode||null!=c?-1:this.vwr.findNearestAtomIndexMovable(a,b,!1);return 0<=a&&(l||null==this.mp)&&!this.vwr.slm.isInSelectionSubset(a)?-1:a},"~N,~N,JU.Point3fi,~B");c(b,"isSelectAction",function(a){return this.bnd(a,[17])||!this.drawMode&&!this.labelMode&&

1==this.apm&&this.bnd(a,[1])||this.dragSelectedMode&&this.bnd(this.dragAction,[27,13])||this.bnd(a,[22,35,32,34,36,30])},"~N");c(b,"enterMeasurementMode",function(a){this.vwr.setPicked(a,!0);this.vwr.setCursor(1);this.vwr.setPendingMeasurement(this.mp=this.getMP());this.measurementQueued=this.mp},"~N");c(b,"getMP",function(){return J.api.Interface.getInterface("JM.MeasurementPending",this.vwr,"mouse").set(this.vwr.ms)});c(b,"addToMeasurement",function(a,b,c){if(-1==a&&null==b||null==this.mp)return this.exitMeasurementMode(null),

0;var l=this.mp.count;-2147483648!=this.mp.traceX&&2==l&&this.mp.setCount(l=1);return 4==l&&!c?l:this.mp.addPoint(a,b,!0)},"~N,JU.Point3fi,~B");c(b,"resetMeasurement",function(){this.exitMeasurementMode(null);this.measurementQueued=this.getMP()});c(b,"exitMeasurementMode",function(a){null!=this.mp&&(this.vwr.setPendingMeasurement(this.mp=null),this.vwr.setCursor(0),null!=a&&this.vwr.refresh(3,a))},"~S");c(b,"getSequence",function(){var a=this.measurementQueued.getAtomIndex(1),b=this.measurementQueued.getAtomIndex(2);

if(!(0>a||0>b))try{var c=this.vwr.getSmilesOpt(null,a,b,1048576,null);this.vwr.setStatusMeasuring("measureSequence",-2,c,0)}catch(l){if(F(l,Exception))JU.Logger.error(l.toString());else throw l;}});c(b,"minimize",function(a){var b=this.dragAtomIndex;a&&(this.dragAtomIndex=-1,this.mkBondPressed=!1);this.vwr.dragMinimizeAtom(b)},"~B");c(b,"queueAtom",function(a,b){var c=this.measurementQueued.addPoint(a,b,!0);0<=a&&this.vwr.setStatusAtomPicked(a,"Atom #"+c+":"+this.vwr.getAtomInfo(a),null,!1);return c},

"~N,JU.Point3fi");c(b,"setMotion",function(a,b){switch(this.vwr.currentCursor){case 3:break;default:this.vwr.setCursor(a)}b&&this.vwr.setInMotion(!0)},"~N,~B");c(b,"zoomByFactor",function(a,b,c){0!=a&&(this.setMotion(8,!0),this.vwr.zoomByFactor(Math.pow(this.mouseWheelFactor,a),b,c),this.moved.setCurrent(this.current,0),this.vwr.setInMotion(!0),this.zoomTrigger=!0,this.startHoverWatcher(!0))},"~N,~N,~N");c(b,"runScript",function(a){this.vwr.evalStringGUI(a)},"~S");c(b,"atomOrPointPicked",function(a,

b){if(0>a){this.resetMeasurement();if(this.bnd(this.clickAction,[33])){this.runScript("select none");return}if(5!=this.apm&&6!=this.apm)return}var c=2;switch(this.apm){case 28:case 29:return;case 0:return;case 25:case 24:case 8:var c=8==this.apm,l=25==this.apm;if(!this.bnd(this.clickAction,[c?5:3]))return;if(null==this.measurementQueued||0==this.measurementQueued.count||2<this.measurementQueued.count)this.resetMeasurement(),this.enterMeasurementMode(a);this.addToMeasurement(a,b,!0);if(2!=this.queueAtom(a,

b))return;c=c||this.measurementQueued.isConnected(this.vwr.ms.at,2)?" DELETE":l?"STRUTS":"";this.runScript("connect "+this.measurementQueued.getMeasurementScript(" ",!0)+c);this.resetMeasurement();return;case 21:c++;case 20:c++;case 18:case 19:case 22:if(!this.bnd(this.clickAction,[20]))return;if(null==this.measurementQueued||0==this.measurementQueued.count||this.measurementQueued.count>c)this.resetMeasurement(),this.enterMeasurementMode(a);this.addToMeasurement(a,b,!0);this.queueAtom(a,b);l=this.measurementQueued.count;

1==l&&this.vwr.setPicked(a,!0);if(l<c)return;22==this.apm?this.getSequence():(this.vwr.setStatusMeasuring("measurePicked",c,this.measurementQueued.getStringDetail(),this.measurementQueued.value),(18==this.apm||4==this.pickingStyleMeasure)&&this.runScript("measure "+this.measurementQueued.getMeasurementScript(" ",!0)));this.resetMeasurement();return}c=null!=this.mp&&1!=this.apm?1:this.apm;switch(c){case 3:if(!this.bnd(this.clickAction,[17]))return;null==b?this.zoomTo(a):this.runScript("zoomTo "+JU.Escape.eP(b));

return;case 5:case 6:if(this.bnd(this.clickAction,[17])){this.checkTwoAtomAction(b,a);return}}if(null==b){switch(c){case 1:!this.drawMode&&!this.labelMode&&this.bnd(this.clickAction,[1])?this.zoomTo(a):this.bnd(this.clickAction,[17])&&this.vwr.setStatusAtomPicked(a,null,null,!1);return;case 2:this.bnd(this.clickAction,[19])&&(this.runScript("set labeltoggle {atomindex="+a+"}"),this.pickLabel(a));return;case 31:this.bnd(this.clickAction,[0])&&(this.vwr.invertAtomCoord(null,null,null,a,!0),this.vwr.setStatusAtomPicked(a,

"invert stereo for atomIndex="+a,null,!1));return;case 7:this.bnd(this.clickAction,[4])&&(c=JU.BSUtil.newAndSetBit(a),this.vwr.deleteAtoms(c,!1),this.vwr.setStatusAtomPicked(a,"deleted: "+JU.Escape.eBS(c),null,!1));return}c="atomindex="+a;switch(this.apm){default:return;case 9:this.selectAtoms(c);break;case 10:this.selectAtoms("within(group, "+c+")");break;case 11:this.selectAtoms("within(chain, "+c+")");break;case 13:this.selectAtoms("within(polymer, "+c+")");break;case 14:this.selectAtoms("within(structure, "+

c+")");break;case 12:this.selectAtoms("within(molecule, "+c+")");break;case 16:this.selectAtoms("within(model, "+c+")");break;case 17:this.selectAtoms("visible and within(element, "+c+")");break;case 15:this.selectAtoms("visible and within(site, "+c+")")}this.vwr.clearClickCount();this.vwr.setStatusAtomPicked(a,null,null,!1)}},"~N,JU.Point3fi");c(b,"assignNew",function(a){0>a?this.vwr.getModelkit(!1).handleAssignNew(this.pressed,this.dragged,this.mp,this.dragAtomIndex,a)||this.exitMeasurementMode("bond dropped"):

this.vwr.getModelkit(!1).handleAssignNew(this.current,this.current,null,this.dragAtomIndex,a);this.exitMeasurementMode(null)},"~N");c(b,"bondPicked",function(a){switch(this.bondPickingMode){case 33:this.vwr.undoMoveActionClear(-1,4146,!0);this.vwr.getModelkit(!1).setProperty("assignbond",Integer.$valueOf(a));break;case 8:this.vwr.deleteBonds(JU.BSUtil.newAndSetBit(a))}},"~N");c(b,"checkTwoAtomAction",function(a,b){var c=5==this.apm,l=6==this.apm;if(c||l)if(this.vwr.tm.spinOn||this.vwr.tm.navOn||null!=

this.vwr.getPendingMeasurement())this.resetMeasurement(),this.vwr.tm.spinOn&&this.runScript("spin off");else{2<=this.measurementQueued.count&&this.resetMeasurement();var f=this.measurementQueued.count;if(1==f)if(null==a){if(this.measurementQueued.getAtomIndex(1)==b)return}else if(0==this.measurementQueued.getAtom(1).distance(a))return;if(c||l){if(0<=b||null!=a)f=this.queueAtom(b,a);2>f?c?this.vwr.scriptStatus(1==f?J.i18n.GT.$("pick one more atom in order to spin the model around an axis"):J.i18n.GT.$("pick two atoms in order to spin the model around an axis")):

this.vwr.scriptStatus(1==f?J.i18n.GT.$("pick one more atom in order to display the symmetry relationship"):J.i18n.GT.$("pick two atoms in order to display the symmetry relationship between them")):(l=this.measurementQueued.getMeasurementScript(" ",!1),this.resetMeasurement(),c?this.runScript("spin"+l+" "+this.vwr.getInt(553648157)):this.runScript("draw symop "+l+";print 'all:';show symop "+l))}}},"JU.Point3fi,~N");c(b,"reset",function(){this.runScript("!reset")});c(b,"selectAtoms",function(a){if(!(null!=

this.mp||this.selectionWorking)){this.selectionWorking=!0;var b=this.rubberbandSelectionMode||this.bnd(this.clickAction,[35])?"selected and not ("+a+") or (not selected) and ":this.bnd(this.clickAction,[32])?"selected and not ":this.bnd(this.clickAction,[34])?"selected or ":0==this.clickAction||this.bnd(this.clickAction,[36])?"selected tog ":this.bnd(this.clickAction,[30])?"":null;if(null!=b)try{var c=this.vwr.getAtomBitSetEval(null,b+("("+a+")"));this.setAtomsPicked(c,"selected: "+JU.Escape.eBS(c));

this.vwr.refresh(3,"selections set")}catch(l){if(!F(l,Exception))throw l;}this.selectionWorking=!1}},"~S");c(b,"setAtomsPicked",function(a,b){this.vwr.selectStatus(a,!1,0,!1,!0);this.vwr.setStatusAtomPicked(-1,b,null,!1)},"JU.BS,~S");c(b,"selectRb",function(a){var b=this.vwr.ms.findAtomsInRectangle(this.rectRubber);0<b.length()&&(b=JU.Escape.eBS(b),this.bnd(a,[34])?this.runScript("selectionHalos on;select selected or "+b):this.bnd(a,[32])?this.runScript("selectionHalos on;select selected and not "+

b):this.runScript("selectionHalos on;select selected tog "+b));this.vwr.refresh(3,"mouseReleased")},"~N");c(b,"toggleMeasurement",function(){if(null!=this.mp){var a=this.mp.count;2<=a&&4>=a&&this.runScript("!measure "+this.mp.getMeasurementScript(" ",!0));this.exitMeasurementMode(null)}});c(b,"zoomTo",function(a){this.runScript("zoomTo (atomindex="+a+")");this.vwr.setStatusAtomPicked(a,null,null,!1)},"~N");c(b,"userActionEnabled",function(a){return this.vwr.isFunction(JV.ActionManager.getActionName(a).toLowerCase())},

"~N");c(b,"userAction",function(a,b){if(!this.userActionEnabled(a))return!1;var c=JS.ScriptEval.runUserAction(JV.ActionManager.getActionName(a),b,this.vwr);return!JS.SV.vF.equals(c)},"~N,~A");b.actionInfo=Array(47);b.actionNames=Array(47);JV.ActionManager.pickingModeNames="off identify label center draw spin symmetry deleteatom deletebond atom group chain molecule polymer structure site model element measure distance angle torsion sequence navigate connect struts dragselected dragmolecule dragatom dragminimize dragminimizemolecule invertstereo assignatom assignbond rotatebond identifybond dragligand dragmodel symop".$plit(" ");

JV.ActionManager.pickingStyleNames="toggle selectOrToggle extendedSelect drag measure measureoff".$plit(" ");b=v(function(){this.time=this.y=this.x=this.index=0;r(this,arguments)},JV,"MotionPoint",null);c(b,"set",function(a,b,c,l){this.index=a;this.x=b;this.y=c;this.time=l},"~N,~N,~N,~N");j(b,"toString",function(){return"[x = "+this.x+" y = "+this.y+" time = "+this.time+" ]"});b=v(function(){this.action=0;this.nodes=null;this.time0=this.ptNext=0;this.vwr=null;r(this,arguments)},JV,"Gesture",null);

z(b,function(a,b){this.vwr=b;this.nodes=Array(a);for(var c=0;c<a;c++)this.nodes[c]=new JV.MotionPoint},"~N,JV.Viewer");c(b,"setAction",function(a,b){this.action=a;this.ptNext=0;this.time0=b;for(var c=0;c<this.nodes.length;c++)this.nodes[c].index=-1},"~N,~N");c(b,"add",function(a,b,c,l){this.action=a;this.getNode(this.ptNext).set(this.ptNext,b,c,l-this.time0);this.ptNext++;return this.ptNext},"~N,~N,~N,~N");c(b,"getTimeDifference",function(a){a=this.getPointCount2(a,0);if(2>a)return 0;var b=this.getNode(this.ptNext-

1);a=this.getNode(this.ptNext-a);return b.time-a.time},"~N");c(b,"getSpeedPixelsPerMillisecond",function(a,b){a=this.getPointCount2(a,b);if(2>a)return 0;var c=this.getNode(this.ptNext-1-b),l=this.getNode(this.ptNext-a-b),f=360*((c.x-l.x)/this.vwr.getScreenWidth()),e=360*((c.y-l.y)/this.vwr.getScreenHeight());return Math.sqrt(f*f+e*e)/(c.time-l.time)},"~N,~N");c(b,"getDX",function(a,b){a=this.getPointCount2(a,b);if(2>a)return 0;var c=this.getNode(this.ptNext-1-b),l=this.getNode(this.ptNext-a-b);return c.x-

l.x},"~N,~N");c(b,"getDY",function(a,b){a=this.getPointCount2(a,b);if(2>a)return 0;var c=this.getNode(this.ptNext-1-b),l=this.getNode(this.ptNext-a-b);return c.y-l.y},"~N,~N");c(b,"getPointCount",function(){return this.ptNext});c(b,"getPointCount2",function(a,b){a>this.nodes.length-b&&(a=this.nodes.length-b);for(var c=a+1;0<=--c&&!(0<=this.getNode(this.ptNext-c-b).index););return c},"~N,~N");c(b,"getNode",function(a){return this.nodes[(a+this.nodes.length+this.nodes.length)%this.nodes.length]},"~N");

j(b,"toString",function(){return 0==this.nodes.length?""+this:JV.binding.Binding.getMouseActionName(this.action,!1)+" nPoints = "+this.ptNext+" "+this.nodes[0]})});u("JV");C(["JU.BS"],"JV.AnimationManager",["J.api.Interface","JU.BSUtil"],function(){var b=v(function(){this.vwr=this.animationThread=null;this.animationOn=!1;this.lastFrameDelayMs=this.firstFrameDelayMs=this.animationFps=0;this.bsVisibleModels=null;this.animationReplayMode=1073742070;this.animationFrames=this.bsDisplay=null;this.animationPaused=

this.isMovie=!1;this.morphCount=this.caf=this.cmi=0;this.currentDirection=this.animationDirection=1;this.frameStep=this.lastFrameIndex=this.firstFrameIndex=0;this.backgroundModelIndex=-1;this.firstFrameDelay=this.currentMorphModel=0;this.lastFrameDelay=1;this.intAnimThread=this.lastModelPainted=this.lastFramePainted=0;this.cai=-1;r(this,arguments)},JV,"AnimationManager",null);Q(b,function(){this.bsVisibleModels=new JU.BS});z(b,function(a){this.vwr=a},"JV.Viewer");c(b,"setAnimationOn",function(a){a!=

this.animationOn&&(!a||this.vwr.headless?this.stopThread(!1):(this.vwr.tm.spinOn||this.vwr.refresh(3,"Anim:setAnimationOn"),this.setAnimationRange(-1,-1),this.resumeAnimation()))},"~B");c(b,"stopThread",function(a){var b=!1;null!=this.animationThread&&(this.animationThread.interrupt(),this.animationThread=null,b=!0);this.animationPaused=a;b&&!this.vwr.tm.spinOn&&this.vwr.refresh(3,"Viewer:setAnimationOff");this.animation(!1);this.vwr.setStatusFrameChanged(!1,!1)},"~B");c(b,"setAnimationNext",function(){return this.setAnimationRelative(this.animationDirection)});

c(b,"currentIsLast",function(){return this.isMovie?this.lastFramePainted==this.caf:this.lastModelPainted==this.cmi});c(b,"currentFrameIs",function(a){var b=this.cmi;return 0==this.morphCount?b==a:0.001>Math.abs(this.currentMorphModel-a)},"~N");c(b,"clear",function(){this.setMovie(null);this.initializePointers(0);this.setAnimationOn(!1);this.setModel(0,!0);this.currentDirection=1;this.cai=-1;this.setAnimationDirection(1);this.setAnimationFps(10);this.setAnimationReplayMode(1073742070,0,0);this.initializePointers(0)});

c(b,"getModelSpecial",function(a){switch(a){case -1:if(null!=this.animationFrames)return"1";a=this.firstFrameIndex;break;case 0:if(0<this.morphCount)return"-"+(1+this.currentMorphModel);a=this.cmi;break;case 1:if(null!=this.animationFrames)return""+this.animationFrames.length;a=this.lastFrameIndex}return this.vwr.getModelNumberDotted(a)},"~N");c(b,"setDisplay",function(a){this.bsDisplay=null==a||a.isEmpty()?null:JU.BSUtil.copy(a)},"JU.BS");c(b,"setMorphCount",function(a){this.morphCount=this.isMovie?

0:a},"~N");c(b,"morph",function(a){var b=D(a);0.001>Math.abs(b-a)?a=b:0.999<Math.abs(b-a)&&(a=b+=1);a-=b;b-=1;if(0==a)this.currentMorphModel=b,this.setModel(b,!0);else{var c;this.setModel(b,!0);c=b+1;this.currentMorphModel=b+a;c==b||(0>c||0>b)||this.vwr.ms.morphTrajectories(b,c,a)}},"~N");c(b,"setModel",function(a,b){0>a&&this.stopThread(!1);var c=this.cmi,l=this.vwr.ms,f=null==l?0:l.mc;if(1==f)this.cmi=a=0;else if(0>a||a>=f)a=-1;var l=null,e=!1;if(this.cmi!=a){if(0<f){var f=this.vwr.ms,h=f.isJmolDataFrameForModel(a),

k=f.isJmolDataFrameForModel(this.cmi);k&&f.setJmolDataFrame(null,-1,this.cmi);-1!=this.cmi&&this.vwr.saveModelOrientation();if(k||h)l=f.getJmolFrameType(a)+" "+a+" <-- "+this.cmi+" "+f.getJmolFrameType(this.cmi),e=f.getJmolDataSourceFrame(a)==f.getJmolDataSourceFrame(this.cmi)}this.cmi=a;null!=l&&(0<=a&&this.vwr.restoreModelOrientation(a),e&&(0<=l.indexOf("quaternion")||0>l.indexOf("plot")&&0>l.indexOf("ramachandran")&&0>l.indexOf(" property "))&&this.vwr.restoreModelRotation(c))}this.setViewer(b)},

"~N,~B");c(b,"setBackgroundModelIndex",function(a){var b=this.vwr.ms;if(null==b||0>a||a>=b.mc)a=-1;this.backgroundModelIndex=a;0<=a&&this.vwr.ms.setTrajectory(a);this.vwr.setTainted(!0);this.setFrameRangeVisible()},"~N");c(b,"initializePointers",function(a){this.firstFrameIndex=0;this.lastFrameIndex=(0==a?0:this.getFrameCount())-1;this.frameStep=a;this.vwr.setFrameVariables()},"~N");c(b,"setAnimationDirection",function(a){this.animationDirection=a},"~N");c(b,"setAnimationFps",function(a){1>a&&(a=

1);50<a&&(a=50);this.animationFps=a;this.vwr.setFrameVariables()},"~N");c(b,"setAnimationReplayMode",function(a,b,c){this.firstFrameDelay=0<b?b:0;this.firstFrameDelayMs=D(1E3*this.firstFrameDelay);this.lastFrameDelay=0<c?c:0;this.lastFrameDelayMs=D(1E3*this.lastFrameDelay);this.animationReplayMode=a;this.vwr.setFrameVariables()},"~N,~N,~N");c(b,"setAnimationRange",function(a,b){var c=this.getFrameCount();0>a&&(a=0);0>b&&(b=c);a>=c&&(a=c-1);b>=c&&(b=c-1);this.currentMorphModel=this.firstFrameIndex=

a;this.lastFrameIndex=b;this.frameStep=b<a?-1:1;this.rewindAnimation()},"~N,~N");c(b,"pauseAnimation",function(){this.stopThread(!0)});c(b,"reverseAnimation",function(){this.currentDirection=-this.currentDirection;this.animationOn||this.resumeAnimation()});c(b,"repaintDone",function(){this.lastModelPainted=this.cmi;this.lastFramePainted=this.caf});c(b,"resumeAnimation",function(){0>this.cmi&&this.setAnimationRange(this.firstFrameIndex,this.lastFrameIndex);1>=this.getFrameCount()?this.animation(!1):

(this.animation(!0),this.animationPaused=!1,null==this.animationThread&&(this.intAnimThread++,this.animationThread=J.api.Interface.getOption("thread.AnimationThread",this.vwr,"script"),this.animationThread.setManager(this,this.vwr,E(-1,[this.firstFrameIndex,this.lastFrameIndex,this.intAnimThread])),this.animationThread.start()))});c(b,"setAnimationLast",function(){this.setFrame(0<this.animationDirection?this.lastFrameIndex:this.firstFrameIndex)});c(b,"rewindAnimation",function(){this.setFrame(0<this.animationDirection?

this.firstFrameIndex:this.lastFrameIndex);this.currentDirection=1;this.vwr.setFrameVariables()});c(b,"setAnimationPrevious",function(){return this.setAnimationRelative(-this.animationDirection)});c(b,"getAnimRunTimeSeconds",function(){var a=this.getFrameCount();if(this.firstFrameIndex==this.lastFrameIndex||0>this.lastFrameIndex||0>this.firstFrameIndex||this.lastFrameIndex>=a||this.firstFrameIndex>=a)return 0;for(var b=Math.min(this.firstFrameIndex,this.lastFrameIndex),a=Math.max(this.firstFrameIndex,

this.lastFrameIndex),c=1*(a-b)/this.animationFps+this.firstFrameDelay+this.lastFrameDelay;b<=a;b++)c+=this.vwr.ms.getFrameDelayMs(this.modelIndexForFrame(b))/1E3;return c});c(b,"setMovie",function(a){if(this.isMovie=null!=a&&null==a.get("scripts")){this.animationFrames=a.get("frames");if(null==this.animationFrames||0==this.animationFrames.length)this.isMovie=!1;else if(this.caf=a.get("currentFrame").intValue(),0>this.caf||this.caf>=this.animationFrames.length)this.caf=0;this.setFrame(this.caf)}this.isMovie||

(this.animationFrames=null);this.vwr.setBooleanProperty("_ismovie",this.isMovie);this.bsDisplay=null;this.currentMorphModel=this.morphCount=0;this.vwr.setFrameVariables()},"java.util.Map");c(b,"modelIndexForFrame",function(a){return this.isMovie?this.animationFrames[a]-1:a},"~N");c(b,"getFrameCount",function(){return this.isMovie?this.animationFrames.length:this.vwr.ms.mc});c(b,"setFrame",function(a){try{if(this.isMovie){var b=this.modelIndexForFrame(a);this.caf=a;a=b}else this.caf=a;this.setModel(a,

!0)}catch(c){if(!F(c,Exception))throw c;}},"~N");c(b,"getUnitCellAtomIndex",function(){return this.cai});c(b,"setUnitCellAtomIndex",function(a){this.cai=a},"~N");c(b,"setViewer",function(a){this.vwr.ms.setTrajectory(this.cmi);this.vwr.tm.setFrameOffset(this.cmi);-1==this.cmi&&a&&this.setBackgroundModelIndex(-1);this.vwr.setTainted(!0);a=this.setFrameRangeVisible();this.vwr.setStatusFrameChanged(!1,!1);this.vwr.g.selectAllModels||this.setSelectAllSubset(2>a)},"~B");c(b,"setSelectAllSubset",function(a){null!=

this.vwr.ms&&this.vwr.slm.setSelectionSubset(a?this.vwr.ms.getModelAtomBitSetIncludingDeleted(this.cmi,!0):this.vwr.ms.getModelAtomBitSetIncludingDeletedBs(this.bsVisibleModels))},"~B");c(b,"setFrameRangeVisible",function(){var a=0;this.bsVisibleModels.clearAll();0<=this.backgroundModelIndex&&(this.bsVisibleModels.set(this.backgroundModelIndex),a=1);if(0<=this.cmi)return this.bsVisibleModels.set(this.cmi),++a;if(0==this.frameStep)return a;for(var b=0,a=0,c=this.firstFrameIndex;c!=this.lastFrameIndex;c+=

this.frameStep){var l=this.modelIndexForFrame(c);this.vwr.ms.isJmolDataFrameForModel(l)||(this.bsVisibleModels.set(l),a++,b=c)}l=this.modelIndexForFrame(this.lastFrameIndex);if(this.firstFrameIndex==this.lastFrameIndex||!this.vwr.ms.isJmolDataFrameForModel(l)||0==a)this.bsVisibleModels.set(l),0==a&&(this.firstFrameIndex=this.lastFrameIndex),a=0;1==a&&0>this.cmi&&this.setFrame(b);return a});c(b,"animation",function(a){this.animationOn=a;this.vwr.setBooleanProperty("_animating",a)},"~B");c(b,"setAnimationRelative",

function(a){a=this.getFrameStep(a);var b=(this.isMovie?this.caf:this.cmi)+a,c=0,l=0,f;0<this.morphCount?(c=1/(this.morphCount+1),l=this.currentMorphModel+a*c,f=this.isNotInRange(l)):f=this.isNotInRange(b);if(f)switch(this.animationReplayMode){case 1073742070:return!1;case 528411:l=b=this.animationDirection==this.currentDirection?this.firstFrameIndex:this.lastFrameIndex;break;case 1073742082:this.currentDirection=-this.currentDirection,b-=2*a,l-=2*a*c}if(1>this.morphCount){if(0>b||b>=this.getFrameCount())return!1;

this.setFrame(b);return!0}this.morph(l+1);return!0},"~N");c(b,"isNotInRange",function(a){var b=a-0.001;return b>this.firstFrameIndex&&b>this.lastFrameIndex||(b=a+0.001)<this.firstFrameIndex&&b<this.lastFrameIndex},"~N");c(b,"getFrameStep",function(a){return this.frameStep*a*this.currentDirection},"~N")});u("JV.binding");C(["java.util.Hashtable"],"JV.binding.Binding","java.util.Arrays JU.AU $.Lst $.PT $.SB J.api.Interface JU.Escape $.Logger".split(" "),function(){var b=v(function(){this.bindings=this.name=

null;r(this,arguments)},JV.binding,"Binding",null);Q(b,function(){this.bindings=new java.util.Hashtable});z(b,function(){});b.getMouseAction=c(b,"getMouseAction",function(a,b,c){2<a&&(a=2);switch(a){case 0:break;case 1:a=256;break;default:a=512}switch(c){case 4:c=4096;break;case 1:c=8192;break;case 5:c=16384;break;case 2:c=32768;break;case 3:c=32}return b&63|a|c},"~N,~N,~N");b.getMouseActionStr=c(b,"getMouseActionStr",function(a){if(null==a)return 0;var b=0;a=a.toUpperCase();b=0<=a.indexOf("MIDDLE")?

8:0<=a.indexOf("RIGHT")?4:0<=a.indexOf("WHEEL")?32:16;0<=a.indexOf("DOWN")?b|=4096:0<=a.indexOf("DRAG")?b|=8192:0<=a.indexOf("UP")?b|=16384:32!=b&&(b|=32768);32!=b&&0<=a.indexOf("DOUBLE")?b|=512:0<b&&(b|=256);288!=b&&0<=a.indexOf("ALT")&&(b|=8);0<=a.indexOf("CTRL")&&(b|=2);0<=a.indexOf("SHIFT")&&(b|=1);return b},"~S");b.getButtonMods=c(b,"getButtonMods",function(a){return a&63},"~N");b.getClickCount=c(b,"getClickCount",function(a){return(a&768)>>8},"~N");b.getMouseActionName=c(b,"getMouseActionName",

function(a,b){var c=new JU.SB;if(0==a)return"";var l=JV.binding.Binding.includes(a,8)&&!JV.binding.Binding.includes(a,16)&&!JV.binding.Binding.includes(a,4),f=" ".toCharArray();JV.binding.Binding.includes(a,2)&&(c.append("CTRL+"),f[5]="C");!l&&JV.binding.Binding.includes(a,8)&&(c.append("ALT+"),f[4]="A");JV.binding.Binding.includes(a,1)&&(c.append("SHIFT+"),f[3]="S");JV.binding.Binding.includes(a,16)?(f[2]="L",c.append("LEFT")):JV.binding.Binding.includes(a,4)?(f[2]="R",c.append("RIGHT")):l?

(f[2]="M",c.append("MIDDLE")):JV.binding.Binding.includes(a,32)&&(f[2]="W",c.append("WHEEL"));JV.binding.Binding.includes(a,512)&&(c.append("+double"),f[1]="2");JV.binding.Binding.includes(a,4096)?(c.append("+down"),f[0]="1"):JV.binding.Binding.includes(a,8192)?(c.append("+drag"),f[0]="2"):JV.binding.Binding.includes(a,16384)?(c.append("+up"),f[0]="3"):JV.binding.Binding.includes(a,32768)&&(c.append("+click"),f[0]="4");return b?String.instantialize(f)+":"+c.toString():c.toString()},"~N,~B");c(b,"getBindings",

function(){return this.bindings});c(b,"bindAction",function(a,b){this.addBinding(a+"\t"+b,E(-1,[a,b]))},"~N,~N");c(b,"bindName",function(a,b){this.addBinding(a+"\t",Boolean.TRUE);this.addBinding(a+"\t"+b,w(-1,[JV.binding.Binding.getMouseActionName(a,!1),b]))},"~N,~S");c(b,"unbindAction",function(a,b){0==a?this.unbindJmolAction(b):this.removeBinding(null,a+"\t"+b)},"~N,~N");c(b,"unbindName",function(a,b){null==b?this.unbindMouseAction(a):this.removeBinding(null,a+"\t"+b)},"~N,~S");c(b,"unbindJmolAction",

function(a){var b=this.bindings.keySet().iterator();for(a="\t"+a;b.hasNext();){var c=b.next();c.endsWith(a)&&this.removeBinding(b,c)}},"~N");c(b,"addBinding",function(a,b){JU.Logger.debugging&&JU.Logger.debug("adding binding "+a+"\t==\t"+JU.Escape.e(b));this.bindings.put(a,b)},"~S,~O");c(b,"removeBinding",function(a,b){JU.Logger.debugging&&JU.Logger.debug("removing binding "+b);null==a?this.bindings.remove(b):a.remove()},"java.util.Iterator,~S");c(b,"unbindUserAction",function(a){var b=this.bindings.keySet().iterator();

for(a="\t"+a;b.hasNext();){var c=b.next();c.endsWith(a)&&this.removeBinding(b,c)}},"~S");c(b,"unbindMouseAction",function(a){var b=this.bindings.keySet().iterator();for(a+="\t";b.hasNext();){var c=b.next();c.startsWith(a)&&this.removeBinding(b,c)}},"~N");c(b,"isBound",function(a,b){return this.bindings.containsKey(a+"\t"+b)},"~N,~N");c(b,"isUserAction",function(a){return this.bindings.containsKey(a+"\t")},"~N");c(b,"getBindingInfo",function(a,b,c){var l=new JU.SB;c=null==c||c.equalsIgnoreCase("all")?

null:c.toLowerCase();for(var f=Array(a.length),e=new JU.Lst,h,k=this.bindings.values().iterator();k.hasNext()&&((h=k.next())||1);)if(!y(h,Boolean))if(JU.AU.isAS(h)){var j=h[0],n=h[1];(null==c||0<=c.indexOf("user")||0<=j.indexOf(c)||0<=n.indexOf(c))&&e.addLast(h)}else n=h,j=n[1],null==f[j]&&(f[j]=new JU.Lst),n=JV.binding.Binding.getMouseActionName(n[0],!0),(null==c||0<=(b[j]+";"+a[j]+";"+n).toLowerCase().indexOf(c))&&f[j].addLast(n);for(j=0;j<a.length;j++){var p;null==f[j]||0==(p=f[j].size())||this.addInfo(l,

f[j].toArray(Array(p)),b[j],a[j])}for(j=0;j<e.size();j++)n=e.get(j),this.addInfo(l,w(-1,["USER:::"+n[0]]),"user-defined",n[1]);return l.toString()},"~A,~A,~S");c(b,"addInfo",function(a,b,c,l){java.util.Arrays.sort(b);JU.PT.leftJustify(a," ",c);a.append("\t");c="";for(var f=a.length(),e=0;e<b.length;e++)a.append(c).append(b[e].substring(7)),c=", ";f=a.length()-f;20>f&&a.append(" ".substring(0,20-f));a.append("\t").append(l).appendC("\n")},"JU.SB,~A,~S,~S");b.includes=

c(b,"includes",function(a,b){return(a&b)==b},"~N,~N");b.newBinding=c(b,"newBinding",function(a,b){return J.api.Interface.getInterface("JV.binding."+b+"Binding",a,"script")},"JV.Viewer,~S")});u("JV.binding");C(["JV.binding.JmolBinding"],"JV.binding.DragBinding",null,function(){var b=H(JV.binding,"DragBinding",JV.binding.JmolBinding);z(b,function(){L(this,JV.binding.DragBinding,[]);this.set("drag")});j(b,"setSelectBindings",function(){this.bindAction(33040,30);this.bindAction(33041,35);this.bindAction(33048,

34);this.bindAction(33049,32);this.bindAction(4368,31);this.bindAction(8464,13);this.bindAction(33040,17)})});u("JV.binding");C(["JV.binding.Binding"],"JV.binding.JmolBinding",null,function(){var b=H(JV.binding,"JmolBinding",JV.binding.Binding);z(b,function(){L(this,JV.binding.JmolBinding,[]);this.set("toggle")});c(b,"set",function(a){this.name=a;this.setGeneralBindings();this.setSelectBindings()},"~S");c(b,"setSelectBindings",function(){this.bindAction(33296,30);this.bindAction(33040,36)});c(b,"setGeneralBindings",

function(){this.bindAction(8474,45);this.bindAction(8454,45);this.bindAction(8721,45);this.bindAction(8712,45);this.bindAction(8464,25);this.bindAction(8720,25);this.bindAction(8472,28);this.bindAction(8453,28);this.bindAction(8465,29);this.bindAction(8456,29);this.bindAction(288,46);this.bindAction(8464,40);this.bindAction(8464,16);this.bindAction(4370,23);this.bindAction(4356,23);this.bindAction(33040,2);this.bindAction(8467,38);this.bindAction(8723,6);this.bindAction(8475,39);this.bindAction(290,

46);this.bindAction(289,46);this.bindAction(291,46);this.bindAction(290,38);this.bindAction(289,6);this.bindAction(291,39);this.bindAction(8464,44);this.bindAction(8464,41);this.bindAction(8465,42);this.bindAction(8473,13);this.bindAction(8465,14);this.bindAction(8472,27);this.bindAction(8465,26);this.bindAction(8464,10);this.bindAction(8472,9);this.bindAction(8465,8);this.bindAction(33297,24);this.bindAction(33288,24);this.bindAction(33296,43);this.bindAction(8464,7);this.bindAction(8464,11);this.bindAction(8464,

12);this.bindAction(33040,17);this.bindAction(33040,22);this.bindAction(33040,19);this.bindAction(33040,20);this.bindAction(33296,37);this.bindAction(33040,18);this.bindAction(33043,21);this.bindAction(33040,4);this.bindAction(33040,5);this.bindAction(33040,3);this.bindAction(33040,0);this.bindAction(33043,1)})});u("JV");C(null,"JV.ColorManager","JU.AU J.c.PAL JU.C $.ColorEncoder $.Elements $.Logger JV.JC".split(" "),function(){var b=v(function(){this.colorData=this.altArgbsCpk=this.argbsCpk=this.g3d=

this.vwr=this.ce=null;this.isDefaultColorRasmol=!1;this.colixRubberband=22;this.colixBackgroundContrast=0;r(this,arguments)},JV,"ColorManager",null);z(b,function(a,b){this.vwr=a;this.ce=new JU.ColorEncoder(null,a);this.g3d=b;this.argbsCpk=J.c.PAL.argbsCpk;this.altArgbsCpk=JU.AU.arrayCopyRangeI(JV.JC.altArgbsCpk,0,-1)},"JV.Viewer,JU.GData");c(b,"setDefaultColors",function(a){a?(this.isDefaultColorRasmol=!0,this.argbsCpk=JU.AU.arrayCopyI(JU.ColorEncoder.getRasmolScale(),-1)):(this.isDefaultColorRasmol=

!1,this.argbsCpk=J.c.PAL.argbsCpk);this.altArgbsCpk=JU.AU.arrayCopyRangeI(JV.JC.altArgbsCpk,0,-1);this.ce.createColorScheme(a?"Rasmol=":"Jmol=",!0,!0);for(a=J.c.PAL.argbsCpk.length;0<=--a;)this.g3d.changeColixArgb(a,this.argbsCpk[a]);for(a=JV.JC.altArgbsCpk.length;0<=--a;)this.g3d.changeColixArgb(JU.Elements.elementNumberMax+a,this.altArgbsCpk[a])},"~B");c(b,"setRubberbandArgb",function(a){this.colixRubberband=0==a?0:JU.C.getColix(a)},"~N");c(b,"setColixBackgroundContrast",function(a){this.colixBackgroundContrast=

JU.C.getBgContrast(a)},"~N");c(b,"getColixBondPalette",function(a,b){switch(b){case 19:return this.ce.getColorIndexFromPalette(a.getEnergy(),-2.5,-0.5,7,!1)}return 10},"JM.Bond,~N");c(b,"getColixAtomPalette",function(a,b){var c=0,l;l=this.vwr.ms;switch(b){case 84:return null==this.colorData||a.i>=this.colorData.length||Float.isNaN(this.colorData[a.i])?12:this.ce.getColorIndex(this.colorData[a.i]);case 0:case 1:var c=this.argbsCpk,f=l=a.getAtomicAndIsotopeNumber();f>=JU.Elements.elementNumberMax&&

(l=JU.Elements.altElementIndexFromNumber(f),0<l?(f=l,l+=JU.Elements.elementNumberMax,c=this.altArgbsCpk):f=l=JU.Elements.getElementNumber(f));return this.g3d.getChangeableColix(l,c[f]);case 2:return l=JU.ColorEncoder.quantize4(a.getPartialCharge(),-1,1,JV.JC.PARTIAL_CHARGE_RANGE_SIZE),this.g3d.getChangeableColix(JV.JC.PARTIAL_CHARGE_COLIX_RED+l,JV.JC.argbsRwbScale[l]);case 3:return l=a.getFormalCharge()- -4,this.g3d.getChangeableColix(JV.JC.FORMAL_CHARGE_COLIX_RED+l,JV.JC.argbsFormalCharge[l]);case 68:case 5:return 68==

b?(l=this.vwr.ms.getBfactor100Lo(),c=this.vwr.ms.getBfactor100Hi()):(l=0,c=1E4),this.ce.getColorIndexFromPalette(a.getBfactor100(),l,c,7,!1);case 86:return this.ce.getColorIndexFromPalette(a.group.getGroupParameter(1111490574),-1,1,7,!1);case 70:return c=this.vwr.ms.getSurfaceDistanceMax(),this.ce.getColorIndexFromPalette(a.getSurfaceDistance100(),0,c,7,!1);case 24:return l=a.group.groupID,42<=l&&(l=24+"PGCATU".indexOf(Character.toUpperCase(a.group.group1))-1),this.ce.getColorIndexFromPalette(l,0,

0,17,!1);case 8:return this.ce.getColorIndexFromPalette(a.group.groupID,0,0,5,!1);case 9:return this.ce.getColorIndexFromPalette(a.group.groupID,0,0,4,!1);case 75:return this.ce.getColorIndexFromPalette(a.group.selectedIndex,0,a.group.chain.selectedGroupCount-1,1,!1);case 87:return l=this.vwr.ms.am[a.mi],this.ce.getColorIndexFromPalette(a.group.getBioPolymerIndexInModel(),0,(l.isBioModel?l.getBioPolymerCount():0)-1,1,!1);case 76:return this.ce.getColorIndexFromPalette(a.group.getSelectedMonomerIndex(),

0,a.group.getSelectedMonomerCount()-1,1,!1);case 77:return this.ce.getColorIndexFromPalette(l.getMoleculeIndex(a.i,!0),0,l.getMoleculeCountInModel(a.mi)-1,0,!1);case 14:return c=a.mi,this.ce.getColorIndexFromPalette(l.getAltLocIndexInModel(c,a.altloc),0,l.getAltLocCountInModel(c),0,!1);case 15:return c=a.mi,this.ce.getColorIndexFromPalette(l.getInsertionCodeIndexInModel(c,a.group.getInsertionCode()),0,l.getInsertionCountInModel(c),0,!1);case 16:l=a.getAtomicAndIsotopeNumber();c=this.getJmolOrRasmolArgb(l,

1073741991);break;case 17:l=a.getAtomicAndIsotopeNumber();c=this.getJmolOrRasmolArgb(l,1073742116);break;case 7:c=a.group.getProteinStructureSubType().getColor();break;case 10:l=a.getChainID(),null==JU.ColorEncoder.argbsChainAtom&&(JU.ColorEncoder.argbsChainAtom=this.getArgbs(1153433601),JU.ColorEncoder.argbsChainHetero=this.getArgbs(1612709894)),l=((0>l?0:256<=l?l-256:l)&31)%JU.ColorEncoder.argbsChainAtom.length,c=(a.isHetero()?JU.ColorEncoder.argbsChainHetero:JU.ColorEncoder.argbsChainAtom)[l]}return 0==

c?22:JU.C.getColix(c)},"JM.Atom,~N");c(b,"getArgbs",function(a){return this.vwr.getJBR().getArgbs(a)},"~N");c(b,"getJmolOrRasmolArgb",function(a,b){switch(b){case 1073741991:if(a>=JU.Elements.elementNumberMax)break;return this.ce.getArgbFromPalette(a,0,0,2);case 1073742116:if(a>=JU.Elements.elementNumberMax)break;return this.ce.getArgbFromPalette(a,0,0,3);default:return b}return JV.JC.altArgbsCpk[JU.Elements.altElementIndexFromNumber(a)]},"~N,~N");c(b,"getElementColix",function(a){var b=this.argbsCpk;

if(a>JU.Elements.elementNumberMax){var c=JU.Elements.altElementIndexFromNumber(a);0<c?(a=c,b=this.altArgbsCpk):a=JU.Elements.getElementNumber(a)}return JU.C.getColix(b[a])},"~N");c(b,"setElementArgb",function(a,b){if(!(1073741991==b&&this.argbsCpk===J.c.PAL.argbsCpk)){b=this.getJmolOrRasmolArgb(a,b);this.argbsCpk===J.c.PAL.argbsCpk&&(this.argbsCpk=JU.AU.arrayCopyRangeI(J.c.PAL.argbsCpk,0,-1),this.altArgbsCpk=JU.AU.arrayCopyRangeI(JV.JC.altArgbsCpk,0,-1));var c=a;c<JU.Elements.elementNumberMax?this.argbsCpk[c]=

b:(c=JU.Elements.altElementIndexFromNumber(a),this.altArgbsCpk[c]=b,c+=JU.Elements.elementNumberMax);this.g3d.changeColixArgb(c,b);this.vwr.setModelkitPropertySafely("updatemodelkeys",null)}},"~N,~N");c(b,"getPropertyColorRange",function(){return this.ce.isReversed?K(-1,[this.ce.hi,this.ce.lo]):K(-1,[this.ce.lo,this.ce.hi])});c(b,"setPropertyColorRangeData",function(a,b){this.colorData=a;this.ce.currentPalette=this.ce.createColorScheme(this.vwr.g.propertyColorScheme,!0,!1);this.ce.hi=-3.4028235E38;

this.ce.lo=3.4028235E38;if(null!=a){for(var c=null==b,l,f=c?a.length-1:b.nextSetBit(0);0<=f;f=c?f-1:b.nextSetBit(f+1))if(!Float.isNaN(l=a[f]))this.ce.hi=Math.max(this.ce.hi,l),this.ce.lo=Math.min(this.ce.lo,l);this.setPropertyColorRange(this.ce.lo,this.ce.hi)}},"~A,JU.BS");c(b,"setPropertyColorRange",function(a,b){this.ce.setRange(a,b,a>b);JU.Logger.debugging&&JU.Logger.debug('ColorManager: color "'+this.ce.getCurrentColorSchemeName()+'" range '+a+" "+b)},"~N,~N");c(b,"setPropertyColorScheme",function(a,

b,c){var l=0==a.length;l&&(a="=");var f=this.getPropertyColorRange();this.ce.currentPalette=this.ce.createColorScheme(a,!0,c);l||this.setPropertyColorRange(f[0],f[1]);this.ce.isTranslucent=b},"~S,~B,~B");c(b,"getColorSchemeList",function(a){a=null==a||0==a.length?this.ce.currentPalette:this.ce.createColorScheme(a,!0,!1);return JU.ColorEncoder.getColorSchemeList(this.ce.getColorSchemeArray(a))},"~S");c(b,"getColorEncoder",function(a){if(null==a||0==a.length)return this.ce;var b=new JU.ColorEncoder(this.ce,

this.vwr);b.currentPalette=b.createColorScheme(a,!1,!0);return 2147483647==b.currentPalette?null:b},"~S")});u("JV");C(["javajs.api.BytePoster","java.util.Hashtable"],"JV.FileManager","java.net.URL $.URLEncoder JU.AU $.Base64 $.LimitedLineReader $.Lst $.OC $.PT $.Rdr $.SB J.adapter.smarter.Resolver J.api.Interface J.io.FileReader JU.Escape $.Logger JV.JC $.JmolAsyncException $.Viewer".split(" "),function(){var b=v(function(){this.jzu=this.spartanDoc=this.vwr=null;this.pathForAllFiles="";this.nameAsGiven=

"zapped";this.lastFullPathName=this.fullPathName=null;this.lastNameAsGiven="zapped";this.spardirCache=this.pngjCache=this.cache=this.appletProxy=this.appletDocumentBaseURL=this.lastFileType=this.fileName=null;r(this,arguments)},JV,"FileManager",null,javajs.api.BytePoster);Q(b,function(){this.cache=new java.util.Hashtable});z(b,function(a){this.vwr=a;this.clear()},"JV.Viewer");c(b,"spartanUtil",function(){return null==this.spartanDoc?this.spartanDoc=J.api.Interface.getInterface("J.adapter.readers.spartan.SpartanUtil",

this.vwr,"fm getSpartanUtil()").set(this):this.spartanDoc});c(b,"getJzu",function(){return null==this.jzu?this.jzu=J.api.Interface.getOption("io.JmolUtil",this.vwr,"file"):this.jzu});c(b,"clear",function(){this.setFileInfo(w(-1,[this.vwr.getZapName()]));this.spardirCache=null});c(b,"setLoadState",function(a){this.vwr.getPreserveState()&&a.put("loadState",this.vwr.g.getLoadState(a))},"java.util.Map");c(b,"getPathForAllFiles",function(){return this.pathForAllFiles});c(b,"setPathForAllFiles",function(a){0<

a.length&&(!a.endsWith("/")&&!a.endsWith("|"))&&(a+="/");return this.pathForAllFiles=a},"~S");c(b,"setFileInfo",function(a){null==a?(this.fullPathName=this.lastFullPathName,this.nameAsGiven=this.lastNameAsGiven):(this.fullPathName=a[0],this.fileName=a[Math.min(1,a.length-1)],this.nameAsGiven=a[Math.min(2,a.length-1)],this.nameAsGiven.equals("zapped")||(this.lastNameAsGiven=this.nameAsGiven,this.lastFullPathName=this.fullPathName))},"~A");c(b,"getFileInfo",function(){return w(-1,[this.fullPathName,

this.fileName,this.nameAsGiven])});c(b,"getFullPathName",function(a){var b=null!=this.fullPathName?this.fullPathName:this.nameAsGiven;return!a||!b.equals("zapped")&&!b.equals("string")?b:null!=this.lastFullPathName?this.lastFullPathName:this.lastNameAsGiven},"~B");c(b,"getFileType",function(){return this.lastFileType});c(b,"setFileType",function(a){this.lastFileType=a},"~S");c(b,"getFileName",function(){return null!=this.fileName?this.fileName:this.nameAsGiven});c(b,"getAppletDocumentBase",function(){return null==

this.appletDocumentBaseURL?"":this.appletDocumentBaseURL.toString()});c(b,"setAppletContext",function(a){try{System.out.println('setting document base to "'+a+'"'),this.appletDocumentBaseURL=0==a.length?null:new java.net.URL(Z("java.net.URL"),a,null)}catch(b){if(F(b,"java.net.MalformedURLException"))System.out.println("error setting document base to "+a);else throw b;}},"~S");c(b,"setAppletProxy",function(a){this.appletProxy=null==a||0==a.length?null:a},"~S");c(b,"createAtomSetCollectionFromFile",

function(a,b,c){null==b.get("atomDataOnly")&&this.setLoadState(b);var l=a,f=a.indexOf("::");0>f&&(a=this.vwr.resolveDatabaseFormat(a));!l.equals(a)&&(0>l.indexOf("/")&&JV.Viewer.hasDatabasePrefix(l))&&b.put("dbName",l);a.endsWith("%2D%")&&(l=b.get("filter"),b.put("filter",(null==l?"":l)+"2D"),a=a.substring(0,a.length-4));l=0<=f?a.substring(f+2):a;f=0<=f?a.substring(0,f):null;JU.Logger.info("\nFileManager.getAtomSetCollectionFromFile("+l+")"+(a.equals(l)?"":" //"+a));var e=this.getClassifiedName(l,

!0);if(1==e.length)return e[0];a=e[0];e=e[1];b.put("fullPathName",(null==f?"":f+"::")+JV.FileManager.fixDOSName(a));this.vwr.getBoolean(603979879)&&this.vwr.getBoolean(603979825)&&this.vwr.getChimeMessenger().update(a);b=new J.io.FileReader(this.vwr,e,a,l,f,null,b,c);b.run();return b.getAtomSetCollection()},"~S,java.util.Map,~B");c(b,"createAtomSetCollectionFromFiles",function(a,b,c){this.setLoadState(b);for(var l=Array(a.length),f=Array(a.length),e=Array(a.length),h=0;h<a.length;h++){var k=a[h].indexOf("::"),

j=0<=k?a[h].substring(k+2):a[h],k=0<=k?a[h].substring(0,k):null,n=this.getClassifiedName(j,!0);if(1==n.length)return n[0];l[h]=n[0];a[h]=JV.FileManager.fixDOSName(n[0]);e[h]=k;f[h]=j}b.put("fullPathNames",l);b.put("fileTypes",e);a=this.newFilesReader(l,f,e,null,b,c);a.run();return a.getAtomSetCollection()},"~A,java.util.Map,~B");c(b,"createAtomSetCollectionFromString",function(a,b,c){this.setLoadState(b);var l=0<=a.indexOf("Viewer.AddHydrogens")?this.getFileInfo():null;b=new J.io.FileReader(this.vwr,

"string",null,null,null,JU.Rdr.getBR(a),b,c);b.run();null!=l&&this.setFileInfo(l);!c&&"string"!=typeof b.getAtomSetCollection()&&this.setFileInfo(w(-1,["5\n\nC 0 0 0\nH .63 .63 .63\nH -.63 -.63 .63\nH -.63 .63 -.63\nH .63 -.63 -.63"===a?"Jmol Model Kit":"string"]));return b.getAtomSetCollection()},"~S,java.util.Map,~B");c(b,"createAtomSeCollectionFromStrings",function(a,b,c,l){if(!c.containsKey("isData")){var f='"'+this.vwr.getDataSeparator()+'"',e='"'+(l?"append":"model")+' inline"',h=new JU.SB;

h.append('set dataSeparator "~~~next file~~~";\ndata ').append(e);for(var k=0;k<a.length;k++)0<k&&h.append("~~~next file~~~"),h.append(a[k]);h.append("end ").append(e).append(";set dataSeparator ").append(f);b.appendSB(h)}this.setLoadState(c);JU.Logger.info("FileManager.getAtomSetCollectionFromStrings(string[])");b=Array(a.length);f=Array(a.length);for(k=0;k<a.length;k++)b[k]="string["+k+"]",f[k]=JV.FileManager.newDataReader(this.vwr,a[k]);a=this.newFilesReader(b,b,null,f,c,l);a.run();return a.getAtomSetCollection()},

"~A,JU.SB,java.util.Map,~B");c(b,"createAtomSeCollectionFromArrayData",function(a,b,c){JU.Logger.info("FileManager.getAtomSetCollectionFromArrayData(Vector)");for(var l=a.size(),f=Array(l),e=Array(l),h=0;h<l;h++)f[h]="String["+h+"]",e[h]=JV.FileManager.newDataReader(this.vwr,a.get(h));a=this.newFilesReader(f,f,null,e,b,c);a.run();return a.getAtomSetCollection()},"JU.Lst,java.util.Map,~B");b.newDataReader=c(b,"newDataReader",function(a,b){var c="string"==typeof b?"String":JU.AU.isAS(b)?"Array":y(b,

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function(a){a=this.getBufferedReaderOrErrorMessageFromName(a,Array(2),!0,!0);return y(a,"java.io.BufferedInputStream")?a:null},"~S");c(b,"getBufferedInputStreamOrErrorMessageFromName",function(a,b,c,l,f,e,h){var k=null,j=null;b=(h=h||a.startsWith("cache://"))&&null==f?b=this.getPngjOrDroppedBytes(b,a):null;try{h&&(0<=a.indexOf(".png")&&null==this.pngjCache&&!this.vwr.getBoolean(603979960))&&(this.pngjCache=new java.util.Hashtable);if(null==b){var n=0<=a.indexOf("?POST?_PNGJBIN_"),p=n||0<=a.indexOf("?POST?_PNGJ_");

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function(a,b,c){for(var l=0;l<JV.FileManager.scriptFilePrefixes.length;l++)for(var f=JV.FileManager.scriptFilePrefixes[l],e=-1;0<=(e=a.indexOf(f,e+1));){var h=JU.PT.getQuotedStringAt(a,e);0<=h.indexOf("\\u")&&(h=JU.Escape.unescapeUnicode(h));b.addLast(h);null!=c&&(0<=h.indexOf("\\u")&&(h=JU.Escape.unescapeUnicode(h)),c.addLast(h))}},"~S,JU.Lst,JU.Lst");b.setScriptFileReferences=c(b,"setScriptFileReferences",function(a,b,c,l){null!=b&&(a=JV.FileManager.setScriptFileRefs(a,b,!0));null!=c&&(a=JV.FileManager.setScriptFileRefs(a,

c,!1));a=JU.PT.rep(a,'\u0001"','"');if(null!=l){for(;l.endsWith("/");)l=l.substring(0,l.length-1);for(b=0;b<JV.FileManager.scriptFilePrefixes.length;b++)c=JV.FileManager.scriptFilePrefixes[b],a=JU.PT.rep(a,c+".",c+l)}return a},"~S,~S,~S,~S");b.setScriptFileRefs=c(b,"setScriptFileRefs",function(a,b,c){if(null==b)return a;var l=0==b.length,f=new JU.Lst;JV.FileManager.getFileReferences(a,f,null);for(var e=new JU.Lst,h=new JU.Lst,k=f.size(),j=0;j<k;j++){var n=f.get(j),p=n,q=p.indexOf("::"),r="";0<=q&&

(r=p.substring(q+2),p=p.substring(q+2));c==JU.OC.isLocal(p)&&(q=l?-1:p.indexOf("/"+b+"/"),0<=q?p=p.substring(q+1):(q=p.lastIndexOf("/"),0>q&&!l&&(p="/"+p),(0>q||l)&&q++,p=b+p.substring(q)));p=r+p;JU.Logger.info("FileManager substituting "+n+" --\x3e "+p);e.addLast('"'+n+'"');h.addLast('\u0001"'+p+'"')}return JU.PT.replaceStrings(a,e,h)},"~S,~S,~B");c(b,"cachePut",function(a,b){a=JV.FileManager.fixDOSName(a);JU.Logger.debugging&&JU.Logger.debug("cachePut "+a);null==b||"".equals(b)?this.cache.remove(a):

(this.cache.put(a,b),this.getCachedPngjBytes(a))},"~S,~O");c(b,"cacheGet",function(a,b){a=JV.FileManager.fixDOSName(a);var c=a.indexOf("|");0<=c&&!a.endsWith("##JmolSurfaceInfo##")&&(a=a.substring(0,c));a=this.getFilePath(a,!0,!1);c=null;(c=Jmol.Cache.get(a))||(c=this.cache.get(a));return b&&"string"==typeof c?null:c},"~S,~B");c(b,"cacheClear",function(){JU.Logger.info("cache cleared");this.cache.clear();null!=this.pngjCache&&(this.pngjCache=null,JU.Logger.info("PNGJ cache cleared"))});c(b,"cacheFileByNameAdd",

function(a,b){if(null==a||!b&&a.equalsIgnoreCase(""))return this.cacheClear(),-1;var c;if(b){a=JV.JC.fixProtocol(this.vwr.resolveDatabaseFormat(a));c=this.getFileAsBytes(a,null);if("string"==typeof c)return 0;this.cachePut(a,c)}else{if(a.endsWith("*"))return JU.AU.removeMapKeys(this.cache,a.substring(0,a.length-1));c=this.cache.remove(JV.FileManager.fixDOSName(a))}return null==c?0:c.length},"~S,~B");c(b,"cacheList",function(){for(var a=new java.util.Hashtable,b,c=this.cache.entrySet().iterator();c.hasNext()&&

((b=c.next())||1);)a.put(b.getKey(),Integer.$valueOf(JU.AU.isAB(b.getValue())?b.getValue().length:b.getValue().toString().length));return a});c(b,"getCanonicalName",function(a){var b=this.getClassifiedName(a,!0);return null==b?a:b[2]},"~S");c(b,"recachePngjBytes",function(a,b){null!=this.pngjCache&&this.pngjCache.containsKey(a)&&(this.pngjCache.put(a,b),JU.Logger.info("PNGJ recaching "+a+" ("+b.length+")"))},"~S,~A");c(b,"getPngjOrDroppedBytes",function(a,b){var c=this.getCachedPngjBytes(a);return null==

c?this.cacheGet(b,!0):c},"~S,~S");c(b,"getCachedPngjBytes",function(a){return null==a||null==this.pngjCache||0>a.indexOf(".png")?null:this.getJzu().getCachedPngjBytes(this,a)},"~S");j(b,"postByteArray",function(a,b){if(a.startsWith("cache://"))return this.cachePut(a,b),"OK "+b.length+"cached";var c=this.getBufferedInputStreamOrErrorMessageFromName(a,null,!1,!1,b,!1,!0);if("string"==typeof c)return c;try{c=JU.Rdr.getStreamAsBytes(c,null)}catch(l){if(F(l,"java.io.IOException"))try{c.close()}catch(f){if(!F(f,

"java.io.IOException"))throw f;}else throw l;}return null==c?"":JU.Rdr.fixUTF(c)},"~S,~A");b.isJmolType=c(b,"isJmolType",function(a){return a.equals("PNG")||a.equals("PNGJ")||a.equals("JMOL")||a.equals("ZIP")||a.equals("ZIPALL")},"~S");b.isEmbeddable=c(b,"isEmbeddable",function(a){var b=a.lastIndexOf(".");0<=b&&(a=a.substring(b+1));a=a.toUpperCase();return JV.FileManager.isJmolType(a)||JU.PT.isOneOf(a,";JPG;JPEG;POV;IDTF;")},"~S");c(b,"getEmbeddedFileState",function(a,b,c){if(!JV.FileManager.isEmbeddable(a))return"";

b=this.getZipDirectory(a,!1,b);if(0==b.length)return a=this.vwr.getFileAsString4(a,-1,!1,!0,!1,"file"),0>a.indexOf("**** Jmol Embedded Script ****")?"":JV.FileManager.getEmbeddedScript(a);for(var l=0;l<b.length;l++)if(0<=b[l].indexOf(c))return a=w(-1,[a+"|"+b[l],null]),this.getFileDataAsString(a,-1,!1,!1,!1),a[1];return""},"~S,~B,~S");b.stripTypePrefix=c(b,"stripTypePrefix",function(a){var b=a.indexOf("::");return 0>b||20<=b?a:a.substring(b+2)},"~S");b.getEmbeddedScript=c(b,"getEmbeddedScript",function(a){if(null==

a)return a;var b=a.indexOf("**** Jmol Embedded Script ****");if(0>b)return a;var c=a.lastIndexOf("/*",b),l=a.indexOf(("*"==a.charAt(c+2)?"*":"")+"*/",b);for(0<=c&&l>=b&&(a=a.substring(b+30,l)+"\n");0<=(c=a.indexOf(" #Jmol...\x00"));)a=a.substring(0,c)+a.substring(c+10+4);JU.Logger.debugging&&JU.Logger.debug(a);return a},"~S");c(b,"isZipStream",function(a){return this.vwr.getJzt().isZipStream(a)},"~O");b.SIMULATION_PROTOCOL="http://SIMULATION/";b.scriptFilePrefixes=w(-1,['/*file*/"','FILE0="','FILE1="'])});

u("JV");C(["java.util.Hashtable","JU.P3","J.c.CBK"],"JV.GlobalSettings","JU.DF $.PT $.SB J.c.STR JS.SV JU.Escape $.Logger JV.JC $.StateManager $.Viewer".split(" "),function(){var b=v(function(){this.htUserVariables=this.htPropertyFlagsRemoved=this.htBooleanParameterFlags=this.htNonbooleanParameterValues=this.vwr=null;this.zDepth=0;this.zShadePower=3;this.zSlab=50;this.slabByAtom=this.slabByMolecule=!1;this.appendNew=this.allowEmbeddedScripts=!0;this.appletProxy="";this.applySymmetryToBonds=!1;this.atomTypes=

"";this.autoBond=!0;this.axesOrientationRasmol=!1;this.bondRadiusMilliAngstroms=150;this.bondTolerance=0.45;this.defaultDirectory="";this.defaultStructureDSSP=!0;this.ptDefaultLattice=null;this.defaultLoadFilter=this.defaultLoadScript="";this.defaultDropScript="zap; load SYNC \"%FILE\";if (%ALLOWCARTOONS && _loadScript == '' && defaultLoadScript == '' && _filetype == 'Pdb') {if ({(protein or nucleic)&*/1.1} && {*/1.1}[1].groupindex != {*/1.1}[0].groupindex){select protein or nucleic;cartoons only;}if ({visible && cartoons > 0}){color structure}else{wireframe -0.1};if (!{visible}){spacefill 23%};select *}";

this.forceAutoBond=!1;this.fractionalRelative=!0;this.inlineNewlineChar="|";this.resolverResolver=this.macroDirectory=this.pubChemFormat=this.nihResolverFormat=this.smilesUrlFormat=this.nmrPredictFormat=this.nmrUrlFormat=this.pdbLoadLigandFormat=this.pdbLoadFormat=this.loadFormat=null;this.checkCIR=!1;this.minBondDistance=0.4;this.minPixelSelRadius=6;this.pdbSequential=this.pdbGetHeader=this.pdbAddHydrogens=!1;this.percentVdwAtom=23;this.smallMoleculeMaxAtoms=4E4;this.smartAromatic=!0;this.doublePrecision=

this.legacyJavaFloat=this.legacyHAddition=this.legacyAutoBonding=this.zeroBasedXyzRasmol=!1;this.modulateOccupancy=this.jmolInJSpecView=!0;this.dotSolvent=this.allowMoveAtoms=this.allowRotateSelected=!1;this.defaultTorsionLabel=this.defaultDistanceLabel=this.defaultAngleLabel="%VALUE %UNITS";this.measureAllModels=this.justifyMeasurements=!1;this.minimizationSteps=100;this.minimizationRefresh=!0;this.minimizationSilent=!1;this.minimizationCriterion=0.001;this.minimizationMaxAtoms=200;this.minimizationReportSteps=

10;this.infoFontSize=20;this.antialiasDisplay=!1;this.displayCellParameters=this.antialiasTranslucent=this.imageState=this.antialiasImages=!0;this.dotsSelectedOnly=!1;this.dotSurface=!0;this.dotDensity=3;this.meshScale=this.dotScale=1;this.isosurfaceKey=this.greyscaleRendering=!1;this.isosurfacePropertySmoothing=!0;this.isosurfacePropertySmoothingPower=7;this.platformSpeed=10;this.repaintWaitMs=1E3;this.showHiddenSelectionHalos=!1;this.showMeasurements=this.showKeyStrokes=!0;this.showTiming=!1;this.zoomLarge=

!0;this.zoomHeight=!1;this.backgroundImageFileName=null;this.hbondsBackbone=this.bondModeOr=this.partialDots=!1;this.hbondsAngleMinimum=90;this.hbondNODistanceMaximum=3.25;this.hbondHXDistanceMaximum=2.5;this.hbondsRasmol=!0;this.hbondsSolid=!1;this.modeMultipleBond=2;this.showMultipleBonds=this.showHydrogens=!0;this.ssbondsBackbone=!1;this.multipleBondSpacing=-1;this.multipleBondRadiusFactor=0;this.multipleBondBananas=!1;this.nboCharges=!0;this.cartoonRockets=this.cartoonBaseEdges=!1;this.cartoonBlockHeight=

0.5;this.cipRule6Full=this.chainCaseSensitive=this.cartoonRibose=this.cartoonLadders=this.cartoonFancy=this.cartoonSteps=this.cartoonBlocks=!1;this.hermiteLevel=0;this.rangeSelected=this.highResolutionFlag=!1;this.rasmolHeteroSetting=this.rasmolHydrogenSetting=!0;this.ribbonAspectRatio=16;this.rocketBarrels=this.ribbonBorder=!1;this.sheetSmoothing=1;this.translucent=this.traceAlpha=!0;this.twistedSheets=!1;this.allowAudio=this.autoplayMovie=!0;this.allowGestures=!1;this.allowMultiTouch=this.allowModelkit=

!0;this.hiddenLinesDashed=this.allowKeyStrokes=!1;this.animationFps=10;this.atomPicking=!0;this.autoFps=!1;this.axesMode=603979809;this.axesScale=2;this.axesOffset=0;this.starWidth=0.05;this.bondPicking=!1;this.dataSeparator="~~~";this.debugScript=!1;this.defaultDrawArrowScale=0.5;this.defaultLabelXYZ="%a";this.defaultLabelPDB="%m%r";this.defaultTranslucent=0.5;this.delayMaximumMs=0;this.dipoleScale=1;this.drawFontSize=16;this.drawPicking=this.drawHover=this.dragSelected=this.disablePopupMenu=!1;

this.dsspCalcHydrogen=!0;this.elementKey=!1;this.energyUnits="kJ";this.exportScale=0;this.helpPath="https://chemapps.stolaf.edu/jmol/docs/index.htm";this.fontScaling=!1;this.fontCaching=!0;this.forceField="MMFF";this.helixStep=1;this.hideNameInPopup=!1;this.hoverDelayMs=500;this.labelPointerWidth=2;this.loadAtomDataTolerance=0.01;this.logGestures=this.logCommands=!1;this.measureDistanceUnits="nanometers";this.measurementLabels=!0;this.monitorEnergy=this.messageStyleChime=!1;this.modulationScale=1;

this.multiProcessor=!0;this.particleRadius=20;this.pickingSpinRate=10;this.pickLabel="";this.pointGroupDistanceTolerance=0.2;this.pointGroupLinearTolerance=8;this.preserveState=!0;this.propertyColorScheme="roygb";this.quaternionFrame="p";this.saveProteinStructureState=!0;this.showModVecs=!1;this.showUnitCellDetails=!0;this.solventProbeRadius=1.2;this.scriptDelay=0;this.statusReporting=this.selectAllModels=!0;this.strandCountForStrands=5;this.strandCountForMeshRibbon=7;this.strutSpacing=6;this.strutLengthMaximum=

7;this.strutDefaultRadius=0.3;this.symmetryHermannMauguin=this.strutsMultiple=!1;this.waitForMoveTo=this.useScriptQueue=this.useNumberLocalization=this.useMinimizationThread=!0;this.noDelay=!1;this.vectorScale=1;this.vectorsCentered=this.vectorSymmetry=!1;this.vectorTrail=0;this.vibrationScale=this.vibrationPeriod=1;this.navigationPeriodic=this.navigationMode=this.hideNavigationPoint=this.wireframeRotation=!1;this.navigationSpeed=5;this.showNavigationPointAlways=!1;this.stereoState=null;this.modelKitMode=

!1;this.objMad10=this.objStateOn=this.objColors=null;this.ellipsoidFill=this.ellipsoidArrows=this.ellipsoidArcs=this.ellipsoidDots=this.ellipsoidAxes=!1;this.ellipsoidBall=!0;this.ellipsoidDotCount=200;this.ellipsoidAxisDiameter=0.02;this.testFlag4=this.testFlag3=this.testFlag2=this.testFlag1=!1;this.structureList=null;this.haveSetStructureList=!1;this.bondingVersion=0;r(this,arguments)},JV,"GlobalSettings",null);Q(b,function(){this.htUserVariables=new java.util.Hashtable;this.ptDefaultLattice=new JU.P3;

this.objColors=E(7,0);this.objStateOn=ha(7,!1);this.objMad10=E(7,0);this.structureList=new java.util.Hashtable;this.structureList.put(J.c.STR.TURN,K(-1,[30,90,-15,95]));this.structureList.put(J.c.STR.SHEET,K(-1,[-180,-10,70,180,-180,-45,-180,-130,140,180,90,180]));this.structureList.put(J.c.STR.HELIX,K(-1,[-160,0,-100,45]))});z(b,function(a,b,c){this.vwr=a;this.htNonbooleanParameterValues=new java.util.Hashtable;this.htBooleanParameterFlags=new java.util.Hashtable;this.htPropertyFlagsRemoved=new java.util.Hashtable;

this.loadFormat=this.pdbLoadFormat=JV.JC.databases.get("pdb");this.pdbLoadLigandFormat=JV.JC.databases.get("ligand");this.nmrUrlFormat=JV.JC.databases.get("nmr");this.nmrPredictFormat=JV.JC.databases.get("nmrdb");this.pubChemFormat=JV.JC.databases.get("pubchem");this.resolverResolver=JV.JC.databases.get("resolverresolver");this.macroDirectory="https://chemapps.stolaf.edu/jmol/macros";null==b?this.setB("undoAuto",!a.isApplet):(this.setB("undoAuto",a.getBooleanProperty("undoAuto")),c||(this.setO("_pngjFile",

b.getParameter("_pngjFile",!1)),this.htUserVariables=b.htUserVariables),this.debugScript=b.debugScript,this.disablePopupMenu=b.disablePopupMenu,this.messageStyleChime=b.messageStyleChime,this.measureDistanceUnits=b.measureDistanceUnits,this.defaultDirectory=b.defaultDirectory,this.autoplayMovie=b.autoplayMovie,this.allowAudio=b.allowAudio,this.allowGestures=b.allowGestures,this.allowModelkit=b.allowModelkit,this.allowMultiTouch=b.allowMultiTouch,this.allowKeyStrokes=b.allowKeyStrokes,this.legacyAutoBonding=

b.legacyAutoBonding,this.legacyHAddition=b.legacyHAddition,this.legacyJavaFloat=b.legacyJavaFloat,this.minimizationReportSteps=b.minimizationReportSteps,this.doublePrecision=b.doublePrecision,this.bondingVersion=b.bondingVersion,this.platformSpeed=b.platformSpeed,this.useScriptQueue=b.useScriptQueue,this.showTiming=b.showTiming,this.wireframeRotation=b.wireframeRotation,this.testFlag1=b.testFlag1,this.testFlag2=b.testFlag2,this.testFlag3=b.testFlag3,this.testFlag4=b.testFlag4,this.nihResolverFormat=

b.nihResolverFormat);null==this.nihResolverFormat&&(this.nihResolverFormat=JV.JC.databases.get("nci"));this.setCIR(this.nihResolverFormat,!1);var l;c=0;for(var f=J.c.CBK.values();c<f.length&&((l=f[c])||1);c++)this.resetValue(l.name()+"Callback",b);this.setF("cameraDepth",3);this.setI("undoMax",a.stm.getUndoMax());this.setI("contextDepthMax",100);this.setI("depth",0);this.setF("gestureSwipeFactor",1);this.setB("hideNotSelected",!1);this.setI("historyLevel",0);this.setO("hoverLabel","");this.setB("isKiosk",

a.isKiosk());this.setO("logFile",a.getLogFileName());this.setI("logLevel",JU.Logger.getLogLevel());this.setF("mouseWheelFactor",1.15);this.setF("mouseDragFactor",1);this.setI("navFps",10);this.setI("navigationDepth",0);this.setI("navigationSlab",0);this.setI("navX",0);this.setI("navY",0);this.setI("navZ",0);this.setO("pathForAllFiles","");this.setB("perspectiveDepth",!0);this.setI("perspectiveModel",11);this.setO("picking","identify");this.setO("pickingStyle","toggle");this.setB("refreshing",!0);

this.setI("rotationRadius",0);this.setI("scaleAngstromsPerInch",0);this.setI("scriptReportingLevel",0);this.setB("selectionHalos",!1);this.setB("showaxes",!1);this.setB("showboundbox",!1);this.setB("showfrank",!1);this.setB("showUnitcell",!1);this.setI("slab",100);this.setB("slabEnabled",!1);this.setF("slabrange",0);this.setI("spinX",0);this.setI("spinY",30);this.setI("spinZ",0);this.setI("spinFps",30);this.setF("visualRange",5);this.setI("stereoDegrees",-5);this.setB("syncScript",a.sm.syncingScripts);

this.setB("syncMouse",a.sm.syncingMouse);this.setB("syncStereo",a.sm.stereoSync);this.setB("windowCentered",!0);this.setB("zoomEnabled",!0);this.setI("_version",JV.JC.versionInt);this.setO("_versionDate",JV.Viewer.getJmolVersion());this.setB("axesWindow",!0);this.setB("axesMolecular",!1);this.setB("axesPosition",!1);this.setB("axesUnitcell",!1);this.setI("backgroundModel",0);this.setB("colorRasmol",!1);this.setO("currentLocalPath","");this.setO("defaultLattice","{0 0 0}");this.setO("defaultColorScheme",

"Jmol");this.setO("defaultDirectoryLocal","");this.setO("defaults","Jmol");this.setO("defaultVDW","Jmol");this.setO("exportDrivers","Idtf;Maya;Povray;Vrml;X3d;Stl;Tachyon;Obj");this.setI("propertyAtomNumberColumnCount",0);this.setI("propertyAtomNumberField",0);this.setI("propertyDataColumnCount",0);this.setI("propertyDataField",0);this.setI("undoMax",a.stm.getUndoMax());this.setB("allowEmbeddedScripts",this.allowEmbeddedScripts);this.setB("allowGestures",this.allowGestures);this.setB("allowKeyStrokes",

this.allowKeyStrokes);this.setB("allowModelkit",this.allowModelkit);this.setB("allowMultiTouch",this.allowMultiTouch);this.setB("allowRotateSelected",this.allowRotateSelected);this.setB("allowMoveAtoms",this.allowMoveAtoms);this.setI("animationFps",this.animationFps);this.setB("antialiasImages",this.antialiasImages);this.setB("antialiasDisplay",this.antialiasDisplay);this.setB("antialiasTranslucent",this.antialiasTranslucent);this.setB("appendNew",this.appendNew);this.setO("appletProxy",this.appletProxy);

this.setB("applySymmetryToBonds",this.applySymmetryToBonds);this.setB("atomPicking",this.atomPicking);this.setO("atomTypes",this.atomTypes);this.setB("autoBond",this.autoBond);this.setB("autoFps",this.autoFps);this.setI("axesMode",603979808==this.axesMode?2:603979804==this.axesMode?1:0);this.setF("axesScale",this.axesScale);this.setF("axesOffset",this.axesOffset);this.setB("axesOrientationRasmol",this.axesOrientationRasmol);this.setF("cartoonBlockHeight",this.cartoonBlockHeight);this.setB("cartoonBlocks",

this.cartoonBlocks);this.setB("cartoonSteps",this.cartoonSteps);this.setB("bondModeOr",this.bondModeOr);this.setB("bondPicking",this.bondPicking);this.setI("bondRadiusMilliAngstroms",this.bondRadiusMilliAngstroms);this.setF("bondTolerance",this.bondTolerance);this.setB("cartoonBaseEdges",this.cartoonBaseEdges);this.setB("cartoonFancy",this.cartoonFancy);this.setB("cartoonLadders",this.cartoonLadders);this.setB("cartoonLadders",this.cartoonRibose);this.setB("cartoonRockets",this.cartoonRockets);this.setB("chainCaseSensitive",

this.chainCaseSensitive);this.setB("cipRule6Full",this.cipRule6Full);this.setI("bondingVersion",this.bondingVersion);this.setO("dataSeparator",this.dataSeparator);this.setB("debugScript",this.debugScript);this.setO("defaultAngleLabel",this.defaultAngleLabel);this.setF("defaultDrawArrowScale",this.defaultDrawArrowScale);this.setO("defaultDirectory",this.defaultDirectory);this.setO("defaultDistanceLabel",this.defaultDistanceLabel);this.setO("defaultDropScript",this.defaultDropScript);this.setO("defaultLabelPDB",

this.defaultLabelPDB);this.setO("defaultLabelXYZ",this.defaultLabelXYZ);this.setO("defaultLoadFilter",this.defaultLoadFilter);this.setO("defaultLoadScript",this.defaultLoadScript);this.setB("defaultStructureDSSP",this.defaultStructureDSSP);this.setO("defaultTorsionLabel",this.defaultTorsionLabel);this.setF("defaultTranslucent",this.defaultTranslucent);this.setI("delayMaximumMs",this.delayMaximumMs);this.setF("dipoleScale",this.dipoleScale);this.setB("disablePopupMenu",this.disablePopupMenu);this.setB("displayCellParameters",

this.displayCellParameters);this.setI("dotDensity",this.dotDensity);this.setI("dotScale",this.dotScale);this.setB("dotsSelectedOnly",this.dotsSelectedOnly);this.setB("dotSurface",this.dotSurface);this.setB("dragSelected",this.dragSelected);this.setB("drawHover",this.drawHover);this.setF("drawFontSize",this.drawFontSize);this.setB("drawPicking",this.drawPicking);this.setB("dsspCalculateHydrogenAlways",this.dsspCalcHydrogen);this.setB("elementkey",this.elementKey);this.setB("ellipsoidArcs",this.ellipsoidArcs);

this.setB("ellipsoidArrows",this.ellipsoidArrows);this.setB("ellipsoidAxes",this.ellipsoidAxes);this.setF("ellipsoidAxisDiameter",this.ellipsoidAxisDiameter);this.setB("ellipsoidBall",this.ellipsoidBall);this.setI("ellipsoidDotCount",this.ellipsoidDotCount);this.setB("ellipsoidDots",this.ellipsoidDots);this.setB("ellipsoidFill",this.ellipsoidFill);this.setO("energyUnits",this.energyUnits);this.setF("exportScale",this.exportScale);this.setB("doublePrecision",this.doublePrecision);this.setB("fontScaling",

this.fontScaling);this.setB("fontCaching",this.fontCaching);this.setB("forceAutoBond",this.forceAutoBond);this.setO("forceField",this.forceField);this.setB("fractionalRelative",this.fractionalRelative);this.setF("particleRadius",this.particleRadius);this.setB("greyscaleRendering",this.greyscaleRendering);this.setF("hbondsAngleMinimum",this.hbondsAngleMinimum);this.setF("hbondHXDistanceMaximum",this.hbondHXDistanceMaximum);this.setF("hbondsDistanceMaximum",this.hbondNODistanceMaximum);this.setB("hbondsBackbone",

this.hbondsBackbone);this.setB("hbondsRasmol",this.hbondsRasmol);this.setB("hbondsSolid",this.hbondsSolid);this.setI("helixStep",this.helixStep);this.setO("helpPath",this.helpPath);this.setI("hermiteLevel",this.hermiteLevel);this.setB("hideNameInPopup",this.hideNameInPopup);this.setB("hideNavigationPoint",this.hideNavigationPoint);this.setB("hiddenLinesDashed",this.hiddenLinesDashed);this.setB("highResolution",this.highResolutionFlag);this.setF("hoverDelay",this.hoverDelayMs/1E3);this.setB("imageState",

this.imageState);this.setI("infoFontSize",this.infoFontSize);this.setB("isosurfaceKey",this.isosurfaceKey);this.setB("isosurfacePropertySmoothing",this.isosurfacePropertySmoothing);this.setI("isosurfacePropertySmoothingPower",this.isosurfacePropertySmoothingPower);this.setB("jmolInJSpecView",this.jmolInJSpecView);this.setI("labelPointerWidth",this.labelPointerWidth);this.setB("justifyMeasurements",this.justifyMeasurements);this.setB("legacyAutoBonding",this.legacyAutoBonding);this.setB("legacyHAddition",

this.legacyHAddition);this.setB("legacyJavaFloat",this.legacyJavaFloat);this.setF("loadAtomDataTolerance",this.loadAtomDataTolerance);this.setO("loadFormat",this.loadFormat);this.setO("loadLigandFormat",this.pdbLoadLigandFormat);this.setB("logCommands",this.logCommands);this.setB("logGestures",this.logGestures);this.setB("measureAllModels",this.measureAllModels);this.setB("measurementLabels",this.measurementLabels);this.setO("measurementUnits",this.measureDistanceUnits);this.setI("meshScale",this.meshScale);

this.setB("messageStyleChime",this.messageStyleChime);this.setF("minBondDistance",this.minBondDistance);this.setI("minPixelSelRadius",this.minPixelSelRadius);this.setI("minimizationReportSteps",this.minimizationReportSteps);this.setI("minimizationSteps",this.minimizationSteps);this.setB("minimizationRefresh",this.minimizationRefresh);this.setB("minimizationSilent",this.minimizationSilent);this.setF("minimizationCriterion",this.minimizationCriterion);this.setB("modelKitMode",this.modelKitMode);this.setF("modulationScale",

this.modulationScale);this.setB("monitorEnergy",this.monitorEnergy);this.setF("multipleBondRadiusFactor",this.multipleBondRadiusFactor);this.setB("multipleBondBananas",this.multipleBondBananas);this.setF("multipleBondSpacing",this.multipleBondSpacing);this.setB("multiProcessor",this.multiProcessor&&1<JV.Viewer.nProcessors);this.setB("navigationMode",this.navigationMode);this.setB("navigationPeriodic",this.navigationPeriodic);this.setF("navigationSpeed",this.navigationSpeed);this.setB("nboCharges",

this.nboCharges);this.setB("noDelay",this.noDelay);this.setO("nmrPredictFormat",this.nmrPredictFormat);this.setO("nmrUrlFormat",this.nmrUrlFormat);this.setB("partialDots",this.partialDots);this.setB("pdbAddHydrogens",this.pdbAddHydrogens);this.setB("pdbGetHeader",this.pdbGetHeader);this.setB("pdbSequential",this.pdbSequential);this.setI("percentVdwAtom",this.percentVdwAtom);this.setI("pickingSpinRate",this.pickingSpinRate);this.setO("pickLabel",this.pickLabel);this.setI("platformSpeed",this.platformSpeed);

this.setF("pointGroupLinearTolerance",this.pointGroupLinearTolerance);this.setF("pointGroupDistanceTolerance",this.pointGroupDistanceTolerance);this.setB("preserveState",this.preserveState);this.setO("propertyColorScheme",this.propertyColorScheme);this.setO("quaternionFrame",this.quaternionFrame);this.setB("rangeSelected",this.rangeSelected);this.setI("repaintWaitMs",this.repaintWaitMs);this.setI("ribbonAspectRatio",this.ribbonAspectRatio);this.setB("ribbonBorder",this.ribbonBorder);this.setB("rocketBarrels",

this.rocketBarrels);this.setB("saveProteinStructureState",this.saveProteinStructureState);this.setB("scriptqueue",this.useScriptQueue);this.setB("selectAllModels",this.selectAllModels);this.setB("selectHetero",this.rasmolHeteroSetting);this.setB("selectHydrogen",this.rasmolHydrogenSetting);this.setF("sheetSmoothing",this.sheetSmoothing);this.setB("showHiddenSelectionHalos",this.showHiddenSelectionHalos);this.setB("showHydrogens",this.showHydrogens);this.setB("showKeyStrokes",this.showKeyStrokes);

this.setB("showMeasurements",this.showMeasurements);this.setB("showModulationVectors",this.showModVecs);this.setB("showMultipleBonds",this.showMultipleBonds);this.setB("showNavigationPointAlways",this.showNavigationPointAlways);this.setI("showScript",this.scriptDelay);this.setB("showtiming",this.showTiming);this.setB("slabByMolecule",this.slabByMolecule);this.setB("slabByAtom",this.slabByAtom);this.setB("smartAromatic",this.smartAromatic);this.setI("minimizationMaxAtoms",this.minimizationMaxAtoms);

this.setI("smallMoleculeMaxAtoms",this.smallMoleculeMaxAtoms);this.setO("smilesUrlFormat",this.smilesUrlFormat);this.setO("macroDirectory",this.macroDirectory);this.setO("nihResolverFormat",this.nihResolverFormat);this.setO("pubChemFormat",this.pubChemFormat);this.setB("showUnitCellDetails",this.showUnitCellDetails);this.setB("solventProbe",this.dotSolvent);this.setF("solventProbeRadius",this.solventProbeRadius);this.setB("ssbondsBackbone",this.ssbondsBackbone);this.setF("starWidth",this.starWidth);

this.setB("statusReporting",this.statusReporting);this.setI("strandCount",this.strandCountForStrands);this.setI("strandCountForStrands",this.strandCountForStrands);this.setI("strandCountForMeshRibbon",this.strandCountForMeshRibbon);this.setF("strutDefaultRadius",this.strutDefaultRadius);this.setF("strutLengthMaximum",this.strutLengthMaximum);this.setI("strutSpacing",this.strutSpacing);this.setB("strutsMultiple",this.strutsMultiple);this.setB("symmetryhermannmauguin",this.symmetryHermannMauguin);this.setB("testFlag1",

this.testFlag1);this.setB("testFlag2",this.testFlag2);this.setB("testFlag3",this.testFlag3);this.setB("testFlag4",this.testFlag4);this.setB("traceAlpha",this.traceAlpha);this.setB("translucent",this.translucent);this.setB("twistedSheets",this.twistedSheets);this.setB("useMinimizationThread",this.useMinimizationThread);this.setB("useNumberLocalization",this.useNumberLocalization);this.setB("vectorsCentered",this.vectorsCentered);this.setF("vectorScale",this.vectorScale);this.setB("vectorSymmetry",

this.vectorSymmetry);this.setI("vectorTrail",this.vectorTrail);this.setF("vibrationPeriod",this.vibrationPeriod);this.setF("vibrationScale",this.vibrationScale);this.setB("waitForMoveTo",this.waitForMoveTo);this.setB("wireframeRotation",this.wireframeRotation);this.setI("zDepth",this.zDepth);this.setB("zeroBasedXyzRasmol",this.zeroBasedXyzRasmol);this.setB("zoomHeight",this.zoomHeight);this.setB("zoomLarge",this.zoomLarge);this.setI("zShadePower",this.zShadePower);this.setI("zSlab",this.zSlab)},"JV.Viewer,JV.GlobalSettings,~B");

c(b,"clear",function(){for(var a=this.htUserVariables.keySet().iterator();a.hasNext();){var b=a.next();("@"==b.charAt(0)||b.startsWith("site_"))&&a.remove()}this.vwr.setPicked(-1,!1);this.setI("_atomhovered",-1);this.setO("_pickinfo","");this.setB("selectionhalos",!1);this.setB("hidenotselected",!1);this.setB("measurementlabels",this.measurementLabels=!0);this.setB("drawHover",this.drawHover=!1);this.vwr.stm.saveScene("DELETE",null)});c(b,"setUnits",function(a){var b=this.measureDistanceUnits,c=this.energyUnits;

a.equalsIgnoreCase("angstroms")?this.measureDistanceUnits="angstroms":a.equalsIgnoreCase("nanometers")||a.equalsIgnoreCase("nm")?this.measureDistanceUnits="nanometers":a.equalsIgnoreCase("picometers")||a.equalsIgnoreCase("pm")?this.measureDistanceUnits="picometers":a.equalsIgnoreCase("bohr")||a.equalsIgnoreCase("au")?this.measureDistanceUnits="au":a.equalsIgnoreCase("vanderwaals")||a.equalsIgnoreCase("vdw")?this.measureDistanceUnits="vdw":a.toLowerCase().endsWith("hz")||a.toLowerCase().endsWith("khz")?

this.measureDistanceUnits=a.toLowerCase():a.equalsIgnoreCase("kj")?this.energyUnits="kJ":a.equalsIgnoreCase("kcal")&&(this.energyUnits="kcal");b.equalsIgnoreCase(this.measureDistanceUnits)?c.equalsIgnoreCase(this.energyUnits)||this.setO("energyUnits",this.energyUnits):this.setO("measurementUnits",this.measureDistanceUnits)},"~S");c(b,"isJmolVariable",function(a){return"_"==a.charAt(0)||this.htNonbooleanParameterValues.containsKey(a=a.toLowerCase())||this.htBooleanParameterFlags.containsKey(a)||0<=

JV.GlobalSettings.unreportedProperties.indexOf(";"+a+";")},"~S");c(b,"resetValue",function(a,b){this.setO(a,null==b?"":b.getParameter(a,!0))},"~S,JV.GlobalSettings");c(b,"setB",function(a,b){a=a.toLowerCase();this.htNonbooleanParameterValues.containsKey(a)||this.htBooleanParameterFlags.put(a,b?Boolean.TRUE:Boolean.FALSE)},"~S,~B");c(b,"setI",function(a,b){2147483647!=b&&this.setO(a,Integer.$valueOf(b))},"~S,~N");c(b,"setF",function(a,b){Float.isNaN(b)||this.setO(a,Float.$valueOf(b))},"~S,~N");c(b,

"setO",function(a,b){a=a.toLowerCase();null==b||this.htBooleanParameterFlags.containsKey(a)||this.htNonbooleanParameterValues.put(a,b)},"~S,~O");c(b,"removeParam",function(a){a=a.toLowerCase();this.htBooleanParameterFlags.containsKey(a)?(this.htBooleanParameterFlags.remove(a),this.htPropertyFlagsRemoved.containsKey(a)||this.htPropertyFlagsRemoved.put(a,Boolean.FALSE)):this.htNonbooleanParameterValues.containsKey(a)&&this.htNonbooleanParameterValues.remove(a)},"~S");c(b,"setUserVariable",function(a,

b){null!=b&&(a=a.toLowerCase(),this.htUserVariables.put(a,b.setName(a)));return b},"~S,JS.SV");c(b,"unsetUserVariable",function(a){a.equals("all")||a.equals("variables")?(this.htUserVariables.clear(),JU.Logger.info("all user-defined variables deleted")):this.htUserVariables.containsKey(a)&&(JU.Logger.info("variable "+a+" deleted"),this.htUserVariables.remove(a))},"~S");c(b,"removeUserVariable",function(a){this.htUserVariables.remove(a)},"~S");c(b,"getUserVariable",function(a){if(null==a)return null;

a=a.toLowerCase();return this.htUserVariables.get(a)},"~S");c(b,"getParameterEscaped",function(a,b){a=a.toLowerCase();if(this.htNonbooleanParameterValues.containsKey(a)){var c=this.htNonbooleanParameterValues.get(a);return JV.StateManager.varClip(a,JU.Escape.e(c),b)}return this.htBooleanParameterFlags.containsKey(a)?this.htBooleanParameterFlags.get(a).toString():this.htUserVariables.containsKey(a)?this.htUserVariables.get(a).escape():this.htPropertyFlagsRemoved.containsKey(a)?"false":"<not defined>"},

"~S,~N");c(b,"getParameter",function(a,b){var c=this.getParam(a,!1);return null==c&&b?"":c},"~S,~B");c(b,"getAndSetNewVariable",function(a,b){if(null==a||0==a.length)a="x";var c=this.getParam(a,!0);return null==c&&b&&"_"!=a.charAt(0)?this.setUserVariable(a,JS.SV.newV(4,"")):JS.SV.getVariable(c)},"~S,~B");c(b,"getParam",function(a,b){a=a.toLowerCase();if(a.equals("_memory")){var c=JU.DF.formatDecimal(0,1)+"/"+JU.DF.formatDecimal(0,1);this.htNonbooleanParameterValues.put("_memory",c)}return this.htNonbooleanParameterValues.containsKey(a)?

this.htNonbooleanParameterValues.get(a):this.htBooleanParameterFlags.containsKey(a)?this.htBooleanParameterFlags.get(a):this.htPropertyFlagsRemoved.containsKey(a)?Boolean.FALSE:this.htUserVariables.containsKey(a)?(c=this.htUserVariables.get(a),b?c:JS.SV.oValue(c)):null},"~S,~B");c(b,"getVariableList",function(){return JV.StateManager.getVariableList(this.htUserVariables,0,!0,!1)});c(b,"setStructureList",function(a,b){this.haveSetStructureList=!0;this.structureList.put(b,a)},"~A,J.c.STR");c(b,"getStructureList",

function(){return this.structureList});b.doReportProperty=c(b,"doReportProperty",function(a){return"_"!=a.charAt(0)&&0>JV.GlobalSettings.unreportedProperties.indexOf(";"+a+";")},"~S");c(b,"getAllVariables",function(){var a=new java.util.Hashtable;a.putAll(this.htBooleanParameterFlags);a.putAll(this.htNonbooleanParameterValues);a.putAll(this.htUserVariables);return a});c(b,"getLoadState",function(a){var b=new JU.SB;this.app(b,"set allowEmbeddedScripts false");this.allowEmbeddedScripts&&this.setB("allowEmbeddedScripts",

!0);this.app(b,"set appendNew "+this.appendNew);this.app(b,"set appletProxy "+JU.PT.esc(this.appletProxy));this.app(b,"set applySymmetryToBonds "+this.applySymmetryToBonds);0<this.atomTypes.length&&this.app(b,"set atomTypes "+JU.PT.esc(this.atomTypes));this.app(b,"set autoBond "+this.autoBond);this.axesOrientationRasmol&&this.app(b,"set axesOrientationRasmol true");this.app(b,"set bondRadiusMilliAngstroms "+this.bondRadiusMilliAngstroms);this.app(b,"set bondTolerance "+this.bondTolerance);this.app(b,

"set defaultLattice "+JU.Escape.eP(this.ptDefaultLattice));this.app(b,"set defaultLoadFilter "+JU.PT.esc(this.defaultLoadFilter));this.app(b,'set defaultLoadScript ""');0<this.defaultLoadScript.length&&this.setO("defaultLoadScript",this.defaultLoadScript);this.app(b,"set defaultStructureDssp "+this.defaultStructureDSSP);var c=this.vwr.getDefaultVdwNameOrData(-2147483648,null,null);this.app(b,"set defaultVDW "+c);c.equals("User")&&this.app(b,this.vwr.getDefaultVdwNameOrData(2147483647,null,null));

this.app(b,"set forceAutoBond "+this.forceAutoBond);this.app(b,"#set defaultDirectory "+JU.PT.esc(this.defaultDirectory));this.app(b,"#set loadFormat "+JU.PT.esc(this.loadFormat));this.app(b,"#set loadLigandFormat "+JU.PT.esc(this.pdbLoadLigandFormat));this.app(b,"#set smilesUrlFormat "+JU.PT.esc(this.smilesUrlFormat));this.app(b,"#set nihResolverFormat "+JU.PT.esc(this.nihResolverFormat));this.app(b,"#set pubChemFormat "+JU.PT.esc(this.pubChemFormat));this.app(b,"set bondingVersion "+this.bondingVersion);

this.app(b,"set legacyAutoBonding "+this.legacyAutoBonding);this.app(b,"set legacyAutoBonding "+this.legacyAutoBonding);this.app(b,"set legacyHAddition "+this.legacyHAddition);this.app(b,"set legacyJavaFloat "+this.legacyJavaFloat);this.app(b,"set minBondDistance "+this.minBondDistance);this.app(b,"set minimizationCriterion "+this.minimizationCriterion);this.app(b,"set minimizationSteps "+this.minimizationSteps);this.app(b,"set multipleBondBananas false");this.app(b,"set pdbAddHydrogens "+(null!=

a&&a.get("pdbNoHydrogens")!==Boolean.TRUE?this.pdbAddHydrogens:!1));this.app(b,"set pdbGetHeader "+this.pdbGetHeader);this.app(b,"set pdbSequential "+this.pdbSequential);this.app(b,"set percentVdwAtom "+this.percentVdwAtom);this.app(b,"set smallMoleculeMaxAtoms "+this.smallMoleculeMaxAtoms);this.app(b,"set smartAromatic "+this.smartAromatic);this.zeroBasedXyzRasmol&&this.app(b,"set zeroBasedXyzRasmol true");return b.toString()},"java.util.Map");c(b,"app",function(a,b){0!=b.length&&a.append(" ").append(b).append(";\n")},

"JU.SB,~S");c(b,"setCIR",function(a,b){if(!(null==a||a.equals(this.nihResolverFormat)&&null!=this.smilesUrlFormat)){var c=a.indexOf("/structure");0<c&&(this.nihResolverFormat=a.substring(0,c+10),this.smilesUrlFormat=this.nihResolverFormat+"/%FILE/file?format=sdf&get3d=true",b&&JU.Logger.info("CIR resolver set to "+this.nihResolverFormat+" template="+a))}},"~S,~B");b.unreportedProperties=(";ambientpercent;animationfps;antialiasdisplay;antialiasimages;antialiastranslucent;appendnew;axescolor;axesposition;axesmolecular;axesorientationrasmol;axesunitcell;axeswindow;axis1color;axis2color;axis3color;backgroundcolor;backgroundmodel;bondsymmetryatoms;boundboxcolor;cameradepth;bondingversion;ciprule6full;contextdepthmax;debug;debugscript;defaultlatttice;defaults;defaultdropscript;diffusepercent;;exportdrivers;exportscale;_filecaching;_filecache;fontcaching;fontscaling;forcefield;language;hbondsDistanceMaximum;hbondsangleminimum;jmolinJSV;legacyautobonding;legacyhaddition;legacyjavafloat;loglevel;logfile;loggestures;logcommands;measurestylechime;loadformat;loadligandformat;macrodirectory;mkaddhydrogens;minimizationmaxatoms;smilesurlformat;pubchemformat;nihresolverformat;edsurlformat;edsurlcutoff;multiprocessor;navigationmode;;nodelay;pathforallfiles;perspectivedepth;phongexponent;perspectivemodel;platformspeed;preservestate;refreshing;repaintwaitms;rotationradius;selectallmodels;showaxes;showaxis1;showaxis2;showaxis3;showboundbox;showfrank;showtiming;showunitcell;slabenabled;slab;slabrange;depth;zshade;zshadepower;specular;specularexponent;specularpercent;celshading;celshadingpower;specularpower;stateversion;statusreporting;stereo;stereostate;vibrationperiod;unitcellcolor;visualrange;windowcentered;zerobasedxyzrasmol;zoomenabled;mousedragfactor;mousewheelfactor;scriptqueue;scriptreportinglevel;syncscript;syncmouse;syncstereo;defaultdirectory;currentlocalpath;defaultdirectorylocal;ambient;bonds;colorrasmol;diffuse;fractionalrelative;frank;hetero;hidenotselected;hoverlabel;hydrogen;languagetranslation;measurementunits;navigationdepth;navigationslab;picking;pickingstyle;propertycolorscheme;radius;rgbblue;rgbgreen;rgbred;scaleangstromsperinch;selectionhalos;showscript;showselections;solvent;strandcount;spinx;spiny;spinz;spinfps;navx;navy;navz;navfps;"+

J.c.CBK.getNameList()+";undo;undoauto;undomax;atompicking;drawpicking;bondpicking;pickspinrate;picklabel;modelkitmode;autoplaymovie;allowaudio;allowgestures;allowkeystrokes;allowmultitouch;allowmodelkit;dodrop;hovered;historylevel;imagestate;iskiosk;useminimizationthread;checkcir;resolverresolver;showkeystrokes;saveproteinstructurestate;testflag1;testflag2;testflag3;testflag4;selecthetero;selecthydrogen;pointgrouplineartolerance;pointgroupdistancetolerance;minimizationreportsteps;elementkey;symmetryhermannmauguin;").toLowerCase()});

u("JV");C(["java.util.Hashtable","JU.SB","$.V3","JU.Elements"],"JV.JC",["JU.PT","J.i18n.GT","JU.Logger"],function(){var b=H(JV,"JC",null);b.getNBOTypeFromName=c(b,"getNBOTypeFromName",function(a){a=";AO;;;;PNAO;;NAO;;;PNHO;;NHO;;;PNBO;;NBO;;;PNLMO;NLMO;;MO;;;;NO;;;;;;;;;;PRNBO;RNBO;;;;;;;;".indexOf(";"+a+";");return 0>a?a:B(a/6)+31},"~S");b.getCIPChiralityName=c(b,"getCIPChiralityName",function(a){switch(a){case 13:return"Z";case 5:return"z";case 14:return"E";case 6:return"e";case 17:return"M";case 18:return"P";

case 1:return"R";case 2:return"S";case 9:return"r";case 10:return"s";case 25:return"m";case 26:return"p";case 7:return"?";default:return""}},"~N");b.getCIPRuleName=c(b,"getCIPRuleName",function(a){return JV.JC.ruleNames[a]},"~N");b.getCIPChiralityCode=c(b,"getCIPChiralityCode",function(a){switch(a.charCodeAt(0)){case 90:return 13;case 122:return 5;case 69:return 14;case 101:return 6;case 82:return 1;case 83:return 2;case 114:return 9;case 115:return 10;case 63:return 7;default:return 0}},"~S");b.fixOptimadeCall=

c(b,"fixOptimadeCall",function(a){var b=a.indexOf("response_fields=")+16;if(16>b)b=a.indexOf("?"),a+=(0>b?"?":"&")+"response_fields=chemical_formula_descriptive,dimension_types,lattice_vectors,cartesian_site_positions,species_at_sites,species";else{for(var d=","+a.substring(b,(a+"&").indexOf("&",b))+",",c=d.length,g=0,e=0;0<=g;g=e){e=",chemical_formula_descriptive,dimension_types,lattice_vectors,cartesian_site_positions,species_at_sites,species,".indexOf(",",g+1);if(0>e)break;g=",chemical_formula_descriptive,dimension_types,lattice_vectors,cartesian_site_positions,species_at_sites,species,".substring(g,

e+1);0>d.indexOf(g)&&(d+=g.substring(1))}a=a.substring(0,b)+d.substring(1,d.length-1)+a.substring(b+c-2)}return a},"~S");b.resolveDataBase=c(b,"resolveDataBase",function(a,b,d){if(null==d){if(null==(d=JV.JC.databases.get(a.toLowerCase())))return null;var c=b.indexOf("/");0>c&&(a.equals("pubchem")?b="name/"+b:a.equals("nci")&&(b+="/file?format=sdf&get3d=true"));d.startsWith("'")&&(c=b.indexOf("."),a=0<c?JU.PT.parseInt(b.substring(c+1)):0,0<c&&(b=b.substring(0,c)),d=JU.PT.rep(d,"%n",""+a))}else 0<=

b.indexOf(".")&&0<=d.indexOf("%FILE.")&&(d=d.substring(0,d.indexOf("%FILE")));if(0<=d.indexOf("%c")){c=1;for(a=b.length;c<=a;c++)0<=d.indexOf("%c"+c)&&(d=JU.PT.rep(d,"%c"+c,b.substring(c-1,c).toLowerCase()))}return 0<=d.indexOf("%FILE")?JU.PT.rep(d,"%FILE",b):0<=d.indexOf("%file")?JU.PT.rep(d,"%file",b.toLowerCase()):d+b},"~S,~S,~S");b.fixProtocol=c(b,"fixProtocol",function(a){var b=null!=a&&0<=a.indexOf("http"),b=null==a||!b?a:0==a.indexOf("http://www.rcsb.org/pdb/files/")?JV.JC.resolveDataBase(0<=

a.indexOf("/ligand/")?"ligand":"pdb",a.substring(a.lastIndexOf("/")+1),null):0==a.indexOf("http://www.ebi")||0==a.indexOf("http://rruff")||0==a.indexOf("http://pubchem")||0==a.indexOf("http://cactus")||0==a.indexOf("http://www.materialsproject")?"https://"+a.substring(7):0<a.indexOf("optimade")?JV.JC.fixOptimadeCall(a):a;b!==a&&JU.Logger.info("JC.fixProtocol "+a+" --\x3e "+b);return b},"~S");b.embedScript=c(b,"embedScript",function(a){return"\n/****** Jmol Embedded Script **** \n"+a+"\n**/"},"~S");

b.getShapeVisibilityFlag=c(b,"getShapeVisibilityFlag",function(a){return 16<<Math.min(a,26)},"~N");b.shapeTokenIndex=c(b,"shapeTokenIndex",function(a){switch(a){case 1153433601:case 1073741859:return 0;case 1677721602:case 659488:return 1;case 1613238294:return 2;case 1611141176:return 3;case 659482:return 4;case 1825200146:return 5;case 1745489939:case 537006096:return 6;case 1112152076:return 7;case 1112152070:return 8;case 1114249217:return 9;case 1112152078:return 10;case 1112152066:return 11;

case 1649022989:return 12;case 1112152071:return 13;case 1112152073:return 14;case 1112152074:return 15;case 1112150019:return 16;case 135175:return 17;case 135198:return 18;case 1112150021:return 19;case 1112150020:return 20;case 1275203608:return 21;case 135174:return 23;case 135176:return 22;case 135180:return 24;case 134353926:return 25;case 135182:return 26;case 1073877010:return 27;case 1073877011:return 28;case 135188:return 29;case 135190:return 30;case 537022465:return 31;case 1611272194:return 34;

case 1812599299:return 32;case 1814695966:return 33;case 544771:return 35;case 1611272202:return 36}return-1},"~N");b.getShapeClassName=c(b,"getShapeClassName",function(a,b){return 0>a?JV.JC.shapeClassBases[~a]:"J."+(b?"render":"shape")+(9<=a&&16>a?"bio.":16<=a&&23>a?"special.":24<=a&&30>a?"surface.":23==a?"cgo.":".")+JV.JC.shapeClassBases[a]},"~N,~B");b.getEchoName=c(b,"getEchoName",function(a){return JV.JC.echoNames[a]},"~N");b.setZPosition=c(b,"setZPosition",function(a,b){return a&-49|b},"~N,~N");

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null));this.vwr.getBoolean(1612709894)||this.excludeSelectionSet(this.vwr.ms.getAtoms(1612709894,null));this.selectionChanged(!1);if((a=this.vwr.getBoolean(603979879))||!c)b=this.getSelectionCount(),a?this.vwr.getChimeMessenger().reportSelection(b):c||this.vwr.reportSelection(J.i18n.GT.i(J.i18n.GT.$("{0} atoms selected"),b))},"JU.BS,~N,~B");c(b,"selectAll",function(a){var b=this.vwr.ms.ac;for(this.empty=0==b?1:0;0<=--b;)this.bsSelection.set(b);JU.BSUtil.andNot(this.bsSelection,this.bsDeleted);this.selectionChanged(a)},

"~B");c(b,"clearSelection",function(a){this.setHideNotSelected(!1);this.bsSelection.clearAll();this.empty=1;this.selectionChanged(a)},"~B");c(b,"isAtomSelected",function(a){return((null==this.bsSubset||this.bsSubset.get(a))&&null==this.bsDeleted||!this.bsDeleted.get(a))&&this.bsSelection.get(a)},"~N");c(b,"setSelectedAtom",function(a,b){0>a?this.selectionChanged(!0):null!=this.bsSubset&&!this.bsSubset.get(a)||null!=this.bsDeleted&&this.bsDeleted.get(a)||(this.bsSelection.setBitTo(a,b),this.empty=

b?0:-1)},"~N,~B");c(b,"setSelectionSubset",function(a){this.bsSubset=a},"JU.BS");c(b,"isInSelectionSubset",function(a){return 0>a||null==this.bsSubset||this.bsSubset.get(a)},"~N");c(b,"invertSelection",function(){JU.BSUtil.invertInPlace(this.bsSelection,this.vwr.ms.ac);this.empty=0<this.bsSelection.length()?0:1;this.selectionChanged(!1)});c(b,"excludeSelectionSet",function(a){null==a||1==this.empty||(this.bsSelection.andNot(a),this.empty=-1)},"JU.BS");c(b,"getSelectionCount",function(){if(1==this.empty)return 0;

this.empty=1;var a;null==this.bsSubset?a=this.bsSelection:(this.bsTemp.clearAll(),this.bsTemp.or(this.bsSubset),this.bsTemp.and(this.bsSelection),a=this.bsTemp);a=a.cardinality();0<a&&(this.empty=0);return a});c(b,"addListener",function(a){for(var b=this.listeners.length;0<=--b;)if(this.listeners[b]===a){this.listeners[b]=null;break}for(var c=this.listeners.length,b=c;0<=--b;)if(null==this.listeners[b]){this.listeners[b]=a;return}this.listeners=0==this.listeners.length?Array(1):JU.AU.doubleLength(this.listeners);

this.listeners[c]=a},"J.api.JmolSelectionListener");c(b,"selectionChanged",function(a){this.hideNotSelected&&this.hide(this.vwr.ms,JU.BSUtil.copyInvert(this.bsSelection,this.vwr.ms.ac),0,a);if(!(a||0==this.listeners.length))for(a=this.listeners.length;0<=--a;)null!=this.listeners[a]&&this.listeners[a].selectionChanged(this.bsSelection)},"~B");c(b,"deleteAtoms",function(a){var b=JU.BSUtil.copy(a);null==this.bsDeleted?this.bsDeleted=b:(b.andNot(this.bsDeleted),this.bsDeleted.or(a));this.bsHidden.andNot(this.bsDeleted);

this.bsSelection.andNot(this.bsDeleted);return b.cardinality()},"JU.BS");c(b,"getSelectedAtoms",function(){if(null==this.bsSubset)return this.bsSelection;var a=JU.BSUtil.copy(this.bsSelection);a.and(this.bsSubset);return a});c(b,"getSelectedAtomsNoSubset",function(){return JU.BSUtil.copy(this.bsSelection)});c(b,"excludeAtoms",function(a,b){null!=this.bsDeleted&&a.andNot(this.bsDeleted);!b&&null!=this.bsSubset&&(a=JU.BSUtil.copy(a)).and(this.bsSubset);return a},"JU.BS,~B");c(b,"setMotionFixedAtoms",

function(a){this.bsFixed.clearAll();null!=a&&this.bsFixed.or(a)},"JU.BS");c(b,"getMotionFixedAtoms",function(){return this.bsFixed})});u("JV");C(null,"JV.ShapeManager","JU.BS $.P3 J.api.Interface J.c.PAL $.VDW JM.Atom JU.BSUtil JV.JC".split(" "),function(){var b=v(function(){this.navMinMax=this.bsSlabbedInternal=this.bsRenderableAtoms=this.scaleText=this.vwr=this.shapes=this.ms=null;r(this,arguments)},JV,"ShapeManager",null);Q(b,function(){this.navMinMax=E(4,0)});z(b,function(a){this.vwr=a;this.bsRenderableAtoms=

new JU.BS;this.bsSlabbedInternal=new JU.BS},"JV.Viewer");c(b,"findNearestShapeAtomIndex",function(a,b,c,l){if(null!=this.shapes)for(var f=0;f<this.shapes.length&&null==c[0];++f)null!=this.shapes[f]&&this.shapes[f].findNearestAtomIndex(a,b,c,l)},"~N,~N,~A,JU.BS");c(b,"getShapePropertyIndex",function(a,b,c){if(null==this.shapes||null==this.shapes[a])return null;this.vwr.setShapeErrorState(a,"get "+b);a=this.shapes[a].getProperty(b,c);this.vwr.setShapeErrorState(-1,null);return a},"~N,~S,~N");c(b,"getShapePropertyData",

function(a,b,c){if(null==this.shapes||null==this.shapes[a])return!1;this.vwr.setShapeErrorState(a,"get "+b);a=this.shapes[a].getPropertyData(b,c);this.vwr.setShapeErrorState(-1,null);return a},"~N,~S,~A");c(b,"getShapeIdFromObjectName",function(a){if(null!=this.shapes)for(var b=16;30>b;++b)if(null!=this.shapes[b]&&0<=this.shapes[b].getIndexFromName(a))return b;return null!=this.shapes[6]&&0<=this.shapes[6].getIndexFromName(a)?6:-1},"~S");c(b,"loadDefaultShapes",function(a){this.ms=a;if(null!=this.shapes)for(var b=

0;b<this.shapes.length;++b)null!=this.shapes[b]&&this.shapes[b].setModelSet(a);this.loadShape(0);this.loadShape(1)},"JM.ModelSet");c(b,"loadShape",function(a){if(null==this.shapes)return null;if(null!=this.shapes[a])return this.shapes[a];if(2==a||3==a||4==a)return null;var b=JV.JC.getShapeClassName(a,!1);if(null==(b=J.api.Interface.getInterface(b,this.vwr,"shape")))return null;this.vwr.setShapeErrorState(a,"allocate");b.initializeShape(this.vwr,this.ms,a);this.vwr.setShapeErrorState(-1,null);return this.shapes[a]=

b},"~N");c(b,"notifyAtomPositionsChanged",function(a,b,c){var l=Integer.$valueOf(a);a=this.vwr.getModelUndeletedAtomsBitSet(a);for(var f=0;37>f;f++)null!=this.shapes[f]&&this.setShapePropertyBs(f,"refreshTrajectories",w(-1,[l,b,c]),a)},"~N,JU.BS,JU.M4");c(b,"releaseShape",function(a){null!=this.shapes&&(this.shapes[a]=null)},"~N");c(b,"setScale",function(){null!=this.scaleText&&(this.loadShape(31),this.setShapePropertyBs(31,"%SCALE",this.scaleText,null),this.scaleText=null)});c(b,"resetShapes",function(a){a&&

(a=Array(1),this.getShapePropertyData(31,"%SCALE",a),this.scaleText=a[0]);this.shapes=Array(37)},"~B");c(b,"setShapeProperties",function(a,b){this.vwr.setShapeErrorState(a,"set properties");this.loadShape(a).setProperties(b);this.vwr.setShapeErrorState(-1,null)},"~N,~A");c(b,"setShapeSizeBs",function(a,b,c,l){if(null!=this.shapes){if(null==l&&(1!=a||2147483647!=b))l=this.vwr.bsA();null!=c&&(0!=c.value&&c.vdwType===J.c.VDW.TEMP)&&this.ms.getBfactor100Lo();this.vwr.setShapeErrorState(a,"set size");

(null==c?0!=b:0!=c.value)&&this.loadShape(a);null!=this.shapes[a]&&this.shapes[a].setShapeSizeRD(b,c,l);this.vwr.setShapeErrorState(-1,null)}},"~N,~N,J.atomdata.RadiusData,JU.BS");c(b,"setLabel",function(a,b){if(null==a){if(null==this.shapes[5])return}else this.loadShape(5),this.setShapeSizeBs(5,0,null,b);this.setShapePropertyBs(5,"label",a,b)},"~O,JU.BS");c(b,"setShapePropertyBs",function(a,b,c,l){null==this.shapes||null==this.shapes[a]||(null==l&&(l=this.vwr.bsA()),this.vwr.setShapeErrorState(a,

"set "+b),this.shapes[a].setProperty(b.intern(),c,l),this.vwr.setShapeErrorState(-1,null))},"~N,~S,~O,JU.BS");c(b,"checkFrankclicked",function(a,b){var c=this.shapes[36];return null!=c&&c.wasClicked(a,b)},"~N,~N");c(b,"checkObjectClicked",function(a,b,c,l,f){var e,h=null;if(2==this.vwr.getPickingMode())return null==this.shapes[5]?null:this.shapes[5].checkObjectClicked(a,b,c,l,!1);if(0!=c&&this.vwr.getBondsPickable()&&null!=(h=this.shapes[1].checkObjectClicked(a,b,c,l,!1)))return h;for(var j=0;j<JV.ShapeManager.clickableMax;j++)if(null!=

(e=this.shapes[JV.ShapeManager.hoverable[j]])&&null!=(h=e.checkObjectClicked(a,b,c,l,f)))return h;return null},"~N,~N,~N,JU.BS,~B");c(b,"checkObjectDragged",function(a,b,c,l,f,e,h){for(var j=!1,m=0<h?h+1:37;!j&&h<m;++h)null!=this.shapes[h]&&(j=this.shapes[h].checkObjectDragged(a,b,c,l,f,e));return j},"~N,~N,~N,~N,~N,JU.BS,~N");c(b,"checkObjectHovered",function(a,b,c,l){var f=this.shapes[1];if(l&&null!=f&&f.checkObjectHovered(a,b,c))return!0;for(l=0;l<JV.ShapeManager.hoverable.length;l++)if(f=this.shapes[JV.ShapeManager.hoverable[l]],

null!=f&&f.checkObjectHovered(a,b,c))return!0;return!1},"~N,~N,JU.BS,~B");c(b,"deleteShapeAtoms",function(a,b){if(null!=this.shapes)for(var c=0;37>c;c++)null!=this.shapes[c]&&this.setShapePropertyBs(c,"deleteModelAtoms",a,b)},"~A,JU.BS");c(b,"deleteVdwDependentShapes",function(a){null==a&&(a=this.vwr.bsA());this.setShapeAtomsSafely(24,"deleteVdw",a);this.setShapeAtomsSafely(25,"deleteVdw",a)},"JU.BS");c(b,"setShapeAtomsSafely",function(a,b,c){null!=this.shapes[a]&&this.shapes[a].setProperty(b,null,

c)},"~N,~S,JU.BS");c(b,"notifyAtoms",function(a,b){switch(a){case "atomsDeleted":this.setShapeAtomsSafely(6,a,b[0]);this.vwr.setModelkitPropertySafely("updatemodelkeys",b);break;case "atomsMoved":null!=this.getShape(22)&&this.vwr.setModelkitPropertySafely(a,b[0])}},"~S,~A");c(b,"getAtomShapeValue",function(a,b,c){a=JV.JC.shapeTokenIndex(a);if(0>a||null==this.shapes[a])return 0;c=this.shapes[a].getSize(c);if(0==c){if(0==(b.shapeVisibilityFlags&this.shapes[a].vf))return 0;c=this.shapes[a].getSizeG(b)}return c/

2E3},"~N,JM.Group,~N");c(b,"replaceGroup",function(a,b){if(null!=this.shapes)for(var c=9;16>c;c++)null!=this.shapes[c]&&this.shapes[c].replaceGroup(a,b)},"JM.Group,JM.Group");c(b,"getObjectMap",function(a,b){if(null!=this.shapes)for(var c=Boolean.$valueOf(b),l=16;30>l;++l)this.getShapePropertyData(l,"getNames",w(-1,[a,c]))},"java.util.Map,~B");c(b,"getProperty",function(a){return a.equals("getShapes")?this.shapes:null},"~O");c(b,"getShape",function(a){return null==this.shapes?null:this.shapes[a]},

"~N");c(b,"resetBioshapes",function(a){if(null!=this.shapes)for(var b=0;b<this.shapes.length;++b)null!=this.shapes[b]&&this.shapes[b].isBioShape&&(this.shapes[b].setModelSet(this.ms),this.shapes[b].setShapeSizeRD(0,null,a),this.shapes[b].setProperty("color",J.c.PAL.NONE,a))},"JU.BS");c(b,"setAtomLabel",function(a,b){null!=this.shapes&&this.shapes[5].setProperty("label:"+a,Integer.$valueOf(b),null)},"~S,~N");c(b,"setModelVisibility",function(){var a=this.shapes;if(!(null==a||null==a[0])){for(var b=

this.vwr.getVisibleFramesBitSet(),c=8;33>c;c++)null!=a[c]&&a[c].setModelVisibilityFlags(b);var a=this.vwr.getBoolean(603979922),l=this.vwr.slm.bsDeleted,f=this.ms.at;this.ms.clearVisibleSets();if(0<f.length)for(c=this.ms.ac;0<=--c;){var e=f[c];null!=e&&(e.shapeVisibilityFlags&=-64);if(!(null!=l&&l.get(c))&&b.get(e.mi)){var h=1;if(!this.ms.isAtomHidden(c)&&(a||1!=e.getElementNumber()))h|=8,0!=e.madAtom&&(h|=16),e.setShapeVisibility(h,!0)}}this.setShapeVis()}});c(b,"setShapeVis",function(){for(var a=

0;37>a;++a){var b=this.shapes[a];null!=b&&b.setAtomClickability()}});c(b,"finalizeAtoms",function(a,b){var c=this.vwr,l=c.tm;b&&c.finalizeTransformParameters();if(null!=a){var f=this.ms.getAtomSetCenter(a),e=new JU.P3;l.transformPt3f(f,e);e.add(l.ptOffset);l.unTransformPoint(e,e);e.sub(f);c.setAtomCoordsRelative(e,a);l.ptOffset.set(0,0,0);l.bsSelectedAtoms=null}f=this.bsRenderableAtoms;this.ms.getAtomsInFrame(f);var h=this.ms.vibrations,j=null!=h&&l.vibrationOn,m=null!=this.ms.bsModulated&&null!=

this.ms.occupancies,n=this.ms.at,p,q=!1,r=this.bsSlabbedInternal;r.clearAll();for(var s=f.nextSetBit(0);0<=s;s=f.nextSetBit(s+1)){var e=n[s],u=j&&e.hasVibration()?l.transformPtVib(e,h[s]):l.transformPt(e);1==u.z&&(l.internalSlab&&l.xyzIsSlabbedInternal(e))&&r.set(s);e.sX=u.x;e.sY=u.y;e.sZ=u.z;var v=Math.abs(e.madAtom);v==JM.Atom.MAD_GLOBAL&&(v=D(2E3*c.getFloat(1153433601)));e.sD=ca(c.tm.scaleToScreen(u.z,v));if(m&&null!=h[s]&&-2147483648!=(p=h[s].getOccupancy100(j)))q=!0,e.setShapeVisibility(2,!1),

0<=p&&50>p?e.setShapeVisibility(24,!1):e.setShapeVisibility(8|(0<e.madAtom?16:0),!0),this.ms.occupancies[e.i]=Math.abs(p)}q&&this.setShapeVis();p=c.gdata;if(l.slabEnabled){s=c.getBoolean(603979940);l=c.getBoolean(603979939);h=p.slab;j=p.depth;if(s){m=this.ms.getMolecules();q=this.ms.getMoleculeCountInModel(-1);for(s=0;s<q;s++)if(r=m[s],u=0,e=r.firstAtomIndex,f.get(e)){for(;u<r.ac&&!p.isClippedZ(n[e].sZ-(n[e].sD>>1));u++,e++);if(u!=r.ac){e=r.firstAtomIndex;for(u=0;u<r.ac;u++)f.clear(e),n[e++].sZ=0}}}for(s=

f.nextSetBit(0);0<=s;s=f.nextSetBit(s+1))if(e=n[s],p.isClippedZ(e.sZ-(l?n[s].sD>>1:0)))e.setClickable(0),m=B((l?-1:1)*e.sD/2),(e.sZ+m<h||e.sZ-m>j||!p.isInDisplayRange(e.sX,e.sY))&&f.clear(s)}if(0==this.ms.ac||!c.getShowNavigationPoint())return null;c=2147483647;p=-2147483648;l=2147483647;h=-2147483648;for(s=f.nextSetBit(0);0<=s;s=f.nextSetBit(s+1))e=n[s],e.sX<c&&(c=e.sX),e.sX>p&&(p=e.sX),e.sY<l&&(l=e.sY),e.sY>h&&(h=e.sY);this.navMinMax[0]=c;this.navMinMax[1]=p;this.navMinMax[2]=l;this.navMinMax[3]=

h;return this.navMinMax},"JU.BS,~B");c(b,"setModelSet",function(a){this.ms=a},"JM.ModelSet");c(b,"checkInheritedShapes",function(){null!=this.shapes[24]&&this.setShapePropertyBs(24,"remapInherited",null,null)});c(b,"restrictSelected",function(a,b){var c=this.vwr.slm.getSelectedAtomsNoSubset();if(b){this.vwr.slm.invertSelection();var l=this.vwr.slm.bsSubset;null!=l&&(c=this.vwr.slm.getSelectedAtomsNoSubset(),c.and(l),this.vwr.selectStatus(c,!1,0,!0,!1),JU.BSUtil.invertInPlace(c,this.vwr.ms.ac),c.and(l))}JU.BSUtil.andNot(c,

this.vwr.slm.bsDeleted);l=this.vwr.getBoolean(603979812);a||this.vwr.setBooleanProperty("bondModeOr",!0);this.setShapeSizeBs(1,0,null,null);this.setShapePropertyBs(1,"type",Integer.$valueOf(32768),null);this.setShapeSizeBs(1,0,null,null);this.setShapePropertyBs(1,"type",Integer.$valueOf(1023),null);for(var f=this.vwr.bsA(),e=21;0<=--e;)6!=e&&null!=this.getShape(e)&&this.setShapeSizeBs(e,0,null,f);null!=this.getShape(21)&&this.setShapePropertyBs(21,"off",f,null);this.setLabel(null,f);a||this.vwr.setBooleanProperty("bondModeOr",

l);this.vwr.selectStatus(c,!1,0,!0,!1)},"~B,~B");b.hoverable=E(-1,[31,20,25,24,22,36]);b.clickableMax=JV.ShapeManager.hoverable.length-1});u("JV");C(["java.util.Hashtable"],["JV.Connection","$.Scene","$.StateManager","$.Connections"],"java.util.Arrays JU.BS $.Lst $.SB JM.Orientation JU.BSUtil $.Escape".split(" "),function(){var b=v(function(){this.maxUndo=20;this.saved=this.vwr=null;this.lastUnitcell=this.lastCoordinates=this.lastShape=this.lastState=this.lastSelected=this.lastScene=this.lastConnections=

this.lastContext=this.lastOrientation="";this.redoStateStack=this.undoStateStack=null;r(this,arguments)},JV,"StateManager",null);Q(b,function(){this.saved=new java.util.Hashtable});z(b,function(a){this.vwr=a},"JV.Viewer");b.getVariableList=c(b,"getVariableList",function(a,b,c,l){var f=new JU.SB,e=0,h=Array(a.size()),j;for(a=a.entrySet().iterator();a.hasNext()&&((j=a.next())||1);){var m=j.getKey(),n=j.getValue();if((c||!m.startsWith("site_"))&&(!l||"@"==m.charAt(0)))h[e++]=m+("@"==m.charAt(0)?" "+

n.asString():" = "+JV.StateManager.varClip(m,n.escape(),b))}java.util.Arrays.sort(h,0,e);for(b=0;b<e;b++)null!=h[b]&&f.append(" ").append(h[b]).append(";\n");0==e&&!l&&f.append("# --no global user variables defined--;\n");return f.toString()},"java.util.Map,~N,~B,~B");b.getObjectIdFromName=c(b,"getObjectIdFromName",function(a){if(null==a)return-1;a="background axis1 axis2 axis3 boundbox unitcell frank ".indexOf(a.toLowerCase());return 0>a?a:B(a/11)},"~S");b.getObjectNameFromId=

c(b,"getObjectNameFromId",function(a){return 0>a||7<=a?null:"background axis1 axis2 axis3 boundbox unitcell frank ".substring(11*a,11*a+11).trim()},"~N");c(b,"clear",function(a){this.vwr.setShowAxes(!1);this.vwr.setShowBbcage(!1);this.vwr.setShowUnitCell(!1);a.clear()},"JV.GlobalSettings");c(b,"resetLighting",function(){this.vwr.setIntProperty("ambientPercent",45);this.vwr.setIntProperty("celShadingPower",10);this.vwr.setIntProperty("diffusePercent",84);this.vwr.setIntProperty("phongExponent",

64);this.vwr.setIntProperty("specularExponent",6);this.vwr.setIntProperty("specularPercent",22);this.vwr.setIntProperty("specularPower",40);this.vwr.setIntProperty("zDepth",0);this.vwr.setIntProperty("zShadePower",3);this.vwr.setIntProperty("zSlab",50);this.vwr.setBooleanProperty("specular",!0);this.vwr.setBooleanProperty("celShading",!1);this.vwr.setBooleanProperty("zshade",!1)});c(b,"setCrystallographicDefaults",function(){this.vwr.setAxesMode(603979808);this.vwr.setShowAxes(!0);this.vwr.setShowUnitCell(!0);

this.vwr.setBooleanProperty("perspectiveDepth",!1)});c(b,"setCommonDefaults",function(){this.vwr.setBooleanProperty("perspectiveDepth",!0);this.vwr.setFloatProperty("bondTolerance",0.45);this.vwr.setFloatProperty("minBondDistance",0.4);this.vwr.setIntProperty("bondingVersion",0);this.vwr.setBooleanProperty("translucent",!0)});c(b,"setJmolDefaults",function(){this.setCommonDefaults();this.vwr.setStringProperty("defaultColorScheme","Jmol");this.vwr.setBooleanProperty("axesOrientationRasmol",!1);this.vwr.setBooleanProperty("zeroBasedXyzRasmol",

!1);this.vwr.setIntProperty("percentVdwAtom",23);this.vwr.setIntProperty("bondRadiusMilliAngstroms",150);this.vwr.setVdwStr("auto")});c(b,"setRasMolDefaults",function(){this.setCommonDefaults();this.vwr.setStringProperty("defaultColorScheme","RasMol");this.vwr.setBooleanProperty("axesOrientationRasmol",!0);this.vwr.setBooleanProperty("zeroBasedXyzRasmol",!0);this.vwr.setIntProperty("percentVdwAtom",0);this.vwr.setIntProperty("bondRadiusMilliAngstroms",1);this.vwr.setVdwStr("Rasmol")});c(b,"setPyMOLDefaults",

function(){this.setCommonDefaults();this.vwr.setStringProperty("measurementUnits","ANGSTROMS");this.vwr.setBooleanProperty("zoomHeight",!0)});b.getNoCase=c(b,"getNoCase",function(a,b){for(var c,l=a.entrySet().iterator();l.hasNext()&&((c=l.next())||1);)if(c.getKey().equalsIgnoreCase(b))return c.getValue();return null},"java.util.Map,~S");c(b,"listSavedStates",function(){for(var a="",b,c=this.saved.keySet().iterator();c.hasNext()&&((b=c.next())||1);)a+="\n"+b;return a});c(b,"deleteSavedType",function(a){for(var b=

this.saved.keySet().iterator();b.hasNext();)b.next().startsWith(a)&&b.remove()},"~S");c(b,"deleteSaved",function(a){for(var b=this.saved.keySet().iterator();b.hasNext();){var c=b.next();(c.startsWith(a)||c.endsWith("_"+a)&&c.indexOf("_")==c.lastIndexOf("_"+a))&&b.remove()}},"~S");c(b,"saveSelection",function(a,b){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Selected_"):(a=this.lastSelected="Selected_"+a,this.saved.put(a,JU.BSUtil.copy(b)))},"~S,JU.BS");c(b,"restoreSelection",function(a){a=JV.StateManager.getNoCase(this.saved,

0<a.length?"Selected_"+a:this.lastSelected);if(null==a)return this.vwr.selectStatus(new JU.BS,!1,0,!1,!1),!1;this.vwr.selectStatus(a,!1,0,!1,!1);return!0},"~S");c(b,"saveUnitCell",function(a){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Unitcell_");else{a=this.lastUnitcell="Unitcell_"+a;var b=this.vwr.getCurrentUnitCell();null!=b&&(b="UNITCELL "+JU.Escape.e(b.getUnitCellVectors()),this.saved.put(a,"unitcell reset;"+b))}},"~S");c(b,"getSavedUnitCell",function(a){return JV.StateManager.getNoCase(this.saved,

0<a.length?"Unitcell_"+a:this.lastUnitcell)},"~S");c(b,"restoreUnitCell",function(a){a=this.getSavedUnitCell(a);if(null==a)return this.vwr.ms.setModelCagePts(-1,null,null),!1;this.vwr.runScript(a);return!0},"~S");c(b,"saveState",function(a){a.equalsIgnoreCase("DELETE")?(this.deleteSavedType("State_"),this.clearStateStack()):0==a.length?(this.vwr.setBooleanProperty("undoAuto",!1),this.appendState(this.getStack(603984065)),this.redoStateStack.clear()):(a=this.lastState="State_"+a,this.saved.put(a,this.vwr.getStateInfo()))},

"~S");c(b,"getSavedState",function(a){if(0==a.length)return a=this.getStack(603984065),0<a.size()?a.get(a.size()-1):null;a=JV.StateManager.getNoCase(this.saved,0<a.length?"State_"+a:this.lastState);return null==a?"":a},"~S");c(b,"popStack",function(a){var b=this.getStack(a),b=0<b.size()?b.removeItemAt(b.size()-1):null;null!=b&&this.appendState(this.getStack(603984065==a?4139:603984065));this.checkStack(this.getStack(603984065));return b},"~N");c(b,"appendState",function(a){this.checkStack(a);0<this.maxUndo&&

a.addLast(this.vwr.getStateInfo())},"JU.Lst");c(b,"checkStack",function(a){for(;a.size()>this.maxUndo;)a.removeItemAt(0)},"JU.Lst");c(b,"getStack",function(a){null==this.undoStateStack&&(this.undoStateStack=new JU.Lst,this.redoStateStack=new JU.Lst);return 603984065==a?this.undoStateStack:this.redoStateStack},"~N");c(b,"clearStateStack",function(){null!=this.undoStateStack&&(this.undoStateStack.clear(),this.redoStateStack.clear())});c(b,"saveStructure",function(a){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Shape_"):

(a=this.lastShape="Shape_"+a,this.saved.put(a,this.vwr.getStructureState()))},"~S");c(b,"getSavedStructure",function(a){a=JV.StateManager.getNoCase(this.saved,0<a.length?"Shape_"+a:this.lastShape);return null==a?"":a},"~S");c(b,"saveCoordinates",function(a,b){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Coordinates_"):(a=this.lastCoordinates="Coordinates_"+a,this.saved.put(a,this.vwr.getCoordinateState(b)))},"~S,JU.BS");c(b,"getSavedCoordinates",function(a){a=JV.StateManager.getNoCase(this.saved,

0<a.length?"Coordinates_"+a:this.lastCoordinates);return null==a?"":a},"~S");c(b,"getOrientation",function(){return new JM.Orientation(this.vwr,!1,null)});c(b,"getSavedOrientationText",function(a){var b;if(null!=a)return b=this.getOrientationFor(a),null==b?"":b.getMoveToText(!0);a=new JU.SB;for(var c=this.saved.entrySet().iterator();c.hasNext()&&((b=c.next())||1);)b.getKey().startsWith("Orientation_")&&a.append(b.getValue().getMoveToText(!0));return a.toString()},"~S");c(b,"saveScene",function(a,

b){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Scene_");else{var c=new JV.Scene(b);c.saveName=this.lastScene="Scene_"+a;this.saved.put(c.saveName,c)}},"~S,java.util.Map");c(b,"restoreScene",function(a,b){var c=JV.StateManager.getNoCase(this.saved,0<a.length?"Scene_"+a:this.lastScene);return null!=c&&c.restore(this.vwr,b)},"~S,~N");c(b,"saveOrientation",function(a,b){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Orientation_");else{var c=new JM.Orientation(this.vwr,a.equalsIgnoreCase("default"),

b);c.saveName=this.lastOrientation="Orientation_"+a;this.saved.put(c.saveName,c)}},"~S,~A");c(b,"restoreOrientation",function(a,b,c){a=this.getOrientationFor(a);return null!=a&&a.restore(b,c)},"~S,~N,~B");c(b,"getOrientationFor",function(a){return JV.StateManager.getNoCase(this.saved,0<a.length?"Orientation_"+a:this.lastOrientation)},"~S");c(b,"saveContext",function(a,b){a.equalsIgnoreCase("DELETE")?this.deleteSavedType("Context_"):this.saved.put(this.lastContext="Context_"+a,b)},"~S,~O");c(b,"getContext",

function(a){return this.saved.get(0==a.length?this.lastContext:"Context_"+a)},"~S");c(b,"saveBonds",function(a){if(a.equalsIgnoreCase("DELETE"))this.deleteSavedType("Bonds_");else{var b=new JV.Connections(this.vwr);b.saveName=this.lastConnections="Bonds_"+a;this.saved.put(b.saveName,b)}},"~S");c(b,"restoreBonds",function(a){this.vwr.clearModelDependentObjects();a=JV.StateManager.getNoCase(this.saved,0<a.length?"Bonds_"+a:this.lastConnections);return null!=a&&a.restore()},"~S");b.varClip=c(b,"varClip",

function(a,b,c){0<c&&b.length>c&&(b=b.substring(0,c)+" #...more ("+b.length+" bytes -- use SHOW "+a+" or MESSAGE @"+a+" to view)");return b},"~S,~S,~N");c(b,"getUndoMax",function(){return this.maxUndo});c(b,"setUndoMax",function(a){this.maxUndo=Math.max(a,0);this.checkStack(this.getStack(603984065));this.checkStack(this.getStack(4139))},"~N");c(b,"getUndoRedoState",function(a){return this.popStack(a)},"~N");c(b,"canDo",function(a){return 0<this.maxUndo&&this.vwr.getBoolean(603979898)&&!this.getStack(a).isEmpty()},

"~N");c(b,"getUndoInfo",function(){var a=this.vwr.getBooleanProperty("undoAuto");return this.vwr.getBoolean(603979898)?"undoAuto="+a+(!a?"; user stack sizes: UNDO="+this.getStack(603984065).size()+", REDO="+this.getStack(4139).size():""):"SET preserveState = FALSE -- undo/redo is disabled"});b=v(function(){this.scene=this.saveName=null;r(this,arguments)},JV,"Scene",null);z(b,function(a){this.scene=a},"java.util.Map");c(b,"restore",function(a,b){var c=this.scene.get("generator");null!=c&&c.generateScene(this.scene);

c=this.scene.get("pymolView");return null!=c&&a.tm.moveToPyMOL(a.eval,b,c)},"JV.Viewer,~N");b=v(function(){this.saveName=null;this.bondCount=0;this.vwr=this.connections=null;r(this,arguments)},JV,"Connections",null);z(b,function(a){var b=a.ms;if(null!=b){this.vwr=a;this.bondCount=b.bondCount;this.connections=Array(this.bondCount+1);a=b.bo;for(b=this.bondCount;0<=--b;){var c=a[b];null!=c&&(this.connections[b]=new JV.Connection(c.atom1.i,c.atom2.i,c.mad,c.colix,c.order,c.getEnergy(),c.shapeVisibilityFlags))}}},

"JV.Viewer");c(b,"restore",function(){var a=this.vwr.ms;if(null==a)return!1;a.deleteAllBonds();for(var b=this.bondCount;0<=--b;){var c=this.connections[b],l=a.ac;c.atomIndex1>=l||c.atomIndex2>=l||(l=a.bondAtoms(a.at[c.atomIndex1],a.at[c.atomIndex2],c.order,c.mad,null,c.energy,!1,!0),l.colix=c.colix,l.shapeVisibilityFlags=c.shapeVisibilityFlags)}c=a.bo;for(b=a.bondCount;0<=--b;)null!=c[b]&&(c[b].index=b);this.vwr.setShapeProperty(1,"reportAll",null);return!0});b=v(function(){this.shapeVisibilityFlags=

this.energy=this.order=this.colix=this.mad=this.atomIndex2=this.atomIndex1=0;r(this,arguments)},JV,"Connection",null);z(b,function(a,b,c,l,f,e,h){this.atomIndex1=a;this.atomIndex2=b;this.mad=c;this.colix=l;this.order=f;this.energy=e;this.shapeVisibilityFlags=h},"~N,~N,~N,~N,~N,~N,~N")});u("JV");C(["java.util.Hashtable"],"JV.StatusManager","JU.Lst $.PT J.api.Interface J.c.CBK JS.SV JU.BSUtil $.Logger JV.JC".split(" "),function(){var b=v(function(){this.cbl=this.jsl=this.vwr=null;this.statusList="";

this.allowStatusReporting=!1;this.messageQueue=null;this.statusPtr=0;this.imageMap=this.jmolScriptCallbacks=null;this.echoing=!1;this.minSyncRepeatMs=100;this.stereoSync=this.syncDisabled=this.isSynced=this.drivingSync=this.syncingMouse=this.syncingScripts=!1;this.qualityPNG=this.qualityJPG=-1;this.audios=this.imageType=null;r(this,arguments)},JV,"StatusManager",null);Q(b,function(){this.messageQueue=new java.util.Hashtable;this.jmolScriptCallbacks=new java.util.Hashtable});z(b,function(a){this.vwr=

a},"JV.Viewer");c(b,"recordStatus",function(a){return this.allowStatusReporting&&0<this.statusList.length&&(this.statusList.equals("all")||0<=this.statusList.indexOf(a))},"~S");c(b,"setStatusChanged",function(a,b,c,l){if(this.recordStatus(a)){var f=new JU.Lst;f.addLast(Integer.$valueOf(++this.statusPtr));f.addLast(a);f.addLast(Integer.$valueOf(b));f.addLast(c);b=l?null:this.messageQueue.get(a);null==b?this.messageQueue.put(a,b=new JU.Lst):b.size()==JV.StatusManager.MAXIMUM_QUEUE_LENGTH&&b.removeItemAt(0);

b.addLast(f)}},"~S,~N,~O,~B");c(b,"getStatusChanged",function(a){var b=0<a.length&&"-"==a.charAt(0),c=0<a.length&&"+"==a.charAt(0),l=!1;b?this.statusList=JU.PT.rep(this.statusList,a.substring(1,a.length),""):(a=JU.PT.rep(a,"+",""),this.statusList.equals(a)||c&&0<=this.statusList.indexOf(a)?l=!0:(c||(this.statusList=""),this.statusList+=a,JU.Logger.debugging&&JU.Logger.debug("StatusManager messageQueue = "+this.statusList)));a=new JU.Lst;if(l)for(var f,l=this.messageQueue.entrySet().iterator();l.hasNext()&&

((f=l.next())||1);)a.addLast(f.getValue());this.messageQueue.clear();this.statusPtr=0;return a},"~S");c(b,"setCallbackFunction",function(a,b){var c=J.c.CBK.getCallback(a),l="string"==typeof b?b:null;if(null!=c)if(c=J.c.CBK.getCallback(a).name(),JU.Logger.info("StatusManager "+c+"callback set f="+l),null!=l&&l.startsWith("SYNC:"))if(l.toLowerCase().trim().equals("sync:off"))this.jmolScriptCallbacks.remove("SYNC:"+c),JU.Logger.info("SYNC callback for "+c+" deactivated");else{this.jmolScriptCallbacks.put("SYNC:"+

c,"_");JU.Logger.info("SYNC callback for "+c+" activated");return}else{var f="",e=null==l?0:(f=l.toLowerCase()).startsWith("script:")?7:f.startsWith("jmolscript:")?11:0;if(0==e)null==b&&this.jmolScriptCallbacks.remove(c);else{this.jmolScriptCallbacks.put(c,l.substring(e).trim());return}}null!=this.cbl&&this.cbl.setCallbackFunction(a,b)},"~S,~O");c(b,"notifyEnabled",function(a){return null!=this.cbl&&this.cbl.notifyEnabled(a)},"J.c.CBK");c(b,"getJmolScriptCallback",function(a){return this.jmolScriptCallbacks.get(a.name())},

"J.c.CBK");c(b,"fireJmolScriptCallback",function(a,b,c,l){var f=b.name();if(null!=c[0]){var e=Array(c.length);System.arraycopy(c,0,e,0,c.length);var h="try{\n"+e[0]+"\n}";e[0]=f;this.vwr.evalCallback(h,e,l)}this.jmolScriptCallbacks.containsKey("SYNC:"+b.name())&&(c[0]="SYNC");a&&this.cbl.notifyCallback(b,c)},"~B,J.c.CBK,~A,~B");c(b,"setStatusAppletReady",function(a,b){var c=b?this.getJmolScriptCallback(J.c.CBK.APPLETREADY):null,l=this.notifyEnabled(J.c.CBK.APPLETREADY);(l||null!=c)&&this.fireJmolScriptCallback(l,

J.c.CBK.APPLETREADY,w(-1,[c,a,Boolean.$valueOf(b),null]),!0)},"~S,~B");c(b,"setStatusAtomMoved",function(a){var b=this.getJmolScriptCallback(J.c.CBK.ATOMMOVED);this.setStatusChanged("atomMoved",-1,a,!1);var c=this.notifyEnabled(J.c.CBK.ATOMMOVED);(c||null!=b)&&this.fireJmolScriptCallback(c,J.c.CBK.ATOMMOVED,w(-1,[b,a,Integer.$valueOf(a.cardinality())]),!0)},"JU.BS");c(b,"setStatusSelect",function(a){var b=this.getJmolScriptCallback(J.c.CBK.SELECT);this.setStatusChanged("select",-1,a,!1);var c=this.notifyEnabled(J.c.CBK.SELECT);

(c||null!=b)&&this.fireJmolScriptCallback(c,J.c.CBK.SELECT,w(-1,[b,a,Integer.$valueOf(a.cardinality()),Integer.$valueOf(a.nextSetBit(0)),Integer.$valueOf(a.length())]),!0)},"JU.BS");c(b,"setStatusStructureModified",function(a,b,c,l,f,e){0<=a&&null==e&&(e=JU.BSUtil.newAndSetBit(a));var h=this.getJmolScriptCallback(J.c.CBK.STRUCTUREMODIFIED),j=this.notifyEnabled(J.c.CBK.STRUCTUREMODIFIED);(j||null!=h)&&this.fireJmolScriptCallback(j,J.c.CBK.STRUCTUREMODIFIED,w(-1,[h,Integer.$valueOf(c),Integer.$valueOf(a),

Integer.$valueOf(b),l,Integer.$valueOf(f),e]),!0)},"~N,~N,~N,~S,~N,JU.BS");c(b,"setStatusAtomPicked",function(a,b,c){var l=this.getJmolScriptCallback(J.c.CBK.PICK);JU.Logger.info("setStatusAtomPicked("+a+","+b+")");this.setStatusChanged("atomPicked",a,b,!1);var f=this.notifyEnabled(J.c.CBK.PICK);(f||null!=l)&&this.fireJmolScriptCallback(f,J.c.CBK.PICK,w(-1,[l,b,Integer.$valueOf(a),c]),!0)},"~N,~S,java.util.Map");c(b,"setStatusClicked",function(a,b,c,l,f){var e=this.getJmolScriptCallback(J.c.CBK.CLICK);

f=E(-1,[c,f]);var h=this.notifyEnabled(J.c.CBK.CLICK);(h||null!=e)&&this.fireJmolScriptCallback(h,J.c.CBK.CLICK,w(-1,[e,Integer.$valueOf(a),Integer.$valueOf(b),Integer.$valueOf(c),Integer.$valueOf(l),f]),!0);return f[0]},"~N,~N,~N,~N,~N");c(b,"setStatusResized",function(a,b){var c=this.getJmolScriptCallback(J.c.CBK.RESIZE),l=this.notifyEnabled(J.c.CBK.RESIZE);(l||null!=c)&&this.fireJmolScriptCallback(l,J.c.CBK.RESIZE,w(-1,[c,Integer.$valueOf(a),Integer.$valueOf(b)]),!0)},"~N,~N");c(b,"haveHoverCallback",

function(){return this.jmolScriptCallbacks.containsKey(J.c.CBK.HOVER.name())||this.notifyEnabled(J.c.CBK.HOVER)});c(b,"setStatusAtomHovered",function(a,b){var c=this.getJmolScriptCallback(J.c.CBK.HOVER),l=this.notifyEnabled(J.c.CBK.HOVER);(l||null!=c)&&this.fireJmolScriptCallback(l,J.c.CBK.HOVER,w(-1,[c,b,Integer.$valueOf(a)]),!0)},"~N,~S");c(b,"setStatusObjectHovered",function(a,b,c){var l=this.getJmolScriptCallback(J.c.CBK.HOVER),f=this.notifyEnabled(J.c.CBK.HOVER);(f||null!=l)&&this.fireJmolScriptCallback(f,

J.c.CBK.HOVER,w(-1,[l,b,Integer.$valueOf(-1),a,Float.$valueOf(c.x),Float.$valueOf(c.y),Float.$valueOf(c.z)]),!0)},"~S,~S,JU.T3");c(b,"showImage",function(a,b){var c=JU.PT.split(a,"\u0001");a=2>c.length?"Jmol":3>c.length||c[2].equals("null")?c[1].substring(c[1].lastIndexOf("/")+1):c[2];var c=this.getJmolScriptCallback(J.c.CBK.IMAGE),l=this.notifyEnabled(J.c.CBK.IMAGE);(l||null!=c)&&this.fireJmolScriptCallback(l,J.c.CBK.IMAGE,w(-1,[c,a,b]),!0);if(Boolean.TRUE.equals(b)){if(null!=this.imageMap){for(var c=

new JU.Lst,f,l=this.imageMap.keySet().iterator();l.hasNext()&&((f=l.next())||1);)c.addLast(f);for(f=c.size();0<=--f;)this.imageMap.get(c.get(f)).closeMe()}}else null==this.imageMap&&(this.imageMap=new java.util.Hashtable),f=this.imageMap.get(a),Boolean.FALSE.equals(b)?null!=f&&f.closeMe():(null==f&&null!=b&&(f=this.vwr.apiPlatform.getImageDialog(a,this.imageMap)),null!=f&&(null==b?f.closeMe():f.setImage(b)))},"~S,~O");c(b,"setFileLoadStatus",function(a,b,c,l,f,e,h){null==a&&"resetUndo".equals(b)&&

(b=this.vwr.getProperty("DATA_API","getAppConsole",null),null!=b&&b.zap(),b=this.vwr.getZapName());this.setStatusChanged("fileLoaded",f,a,!1);null!=l&&this.setStatusChanged("fileLoadError",f,l,!1);var j=this.getJmolScriptCallback(J.c.CBK.LOADSTRUCT);if((e=e&&this.notifyEnabled(J.c.CBK.LOADSTRUCT))||null!=j){var m=this.vwr.getP("_smilesString");0!=m.length&&(b=m);this.fireJmolScriptCallback(e,J.c.CBK.LOADSTRUCT,w(-1,[j,a,b,c,l,Integer.$valueOf(f),this.vwr.getP("_modelNumber"),this.vwr.getModelNumberDotted(this.vwr.ms.mc-

1),h]),!0)}},"~S,~S,~S,~S,~N,~B,Boolean");c(b,"setStatusModelKit",function(a){var b=1==a?"ON":"OFF";this.setStatusChanged("modelkit",a,b,!1);a=this.getJmolScriptCallback(J.c.CBK.MODELKIT);var c=this.notifyEnabled(J.c.CBK.MODELKIT);(c||null!=a)&&this.fireJmolScriptCallback(c,J.c.CBK.MODELKIT,w(-1,[a,b]),!0)},"~N");c(b,"setStatusFrameChanged",function(a,b,c,l,f,e,h){if(null!=this.vwr.ms){var j=this.vwr.am.animationOn,m=j?-2-f:f;this.setStatusChanged("frameChanged",m,0<=f?this.vwr.getModelNumberDotted(f):

"",!1);var n=this.getJmolScriptCallback(J.c.CBK.ANIMFRAME),p=this.notifyEnabled(J.c.CBK.ANIMFRAME);(p||null!=n)&&this.fireJmolScriptCallback(p,J.c.CBK.ANIMFRAME,w(-1,[n,E(-1,[m,a,b,c,l,f]),h,Float.$valueOf(e)]),!1);!j&&!this.vwr.isJSNoAWT&&this.vwr.checkMenuUpdate()}},"~N,~N,~N,~N,~N,~N,~S");c(b,"setStatusDragDropped",function(a,b,c,l,f){this.setStatusChanged("dragDrop",0,"",!1);var e=this.getJmolScriptCallback(J.c.CBK.DRAGDROP),h=this.notifyEnabled(J.c.CBK.DRAGDROP);(h||null!=e)&&this.fireJmolScriptCallback(h,

J.c.CBK.DRAGDROP,w(-1,[e,Integer.$valueOf(a),Integer.$valueOf(b),Integer.$valueOf(c),l,f]),!0);return h},"~N,~N,~N,~S,~A");c(b,"setScriptEcho",function(a,b){if(!(null==a||this.echoing)){this.echoing=!0;this.setStatusChanged("scriptEcho",0,a,!1);var c=this.getJmolScriptCallback(J.c.CBK.ECHO),l=this.notifyEnabled(J.c.CBK.ECHO);if(l||null!=c)this.fireJmolScriptCallback(l,J.c.CBK.ECHO,w(-1,[c,a,Integer.$valueOf(b?1:0)]),!0);this.echoing=!1}},"~S,~B");c(b,"setStatusMeasuring",function(a,b,c,l){this.setStatusChanged(a,

b,c,!1);var f=null;a.equals("measureCompleted")?(JU.Logger.info("measurement["+b+"] = "+c),f=this.getJmolScriptCallback(J.c.CBK.MEASURE)):a.equals("measurePicked")&&(this.setStatusChanged("measurePicked",b,c,!1),JU.Logger.info("measurePicked "+b+" "+c));var e=this.notifyEnabled(J.c.CBK.MEASURE);(e||null!=f)&&this.fireJmolScriptCallback(e,J.c.CBK.MEASURE,w(-1,[f,c,Integer.$valueOf(b),a,Float.$valueOf(l)]),!0)},"~S,~N,~S,~N");c(b,"notifyError",function(a,b,c){var l=this.getJmolScriptCallback(J.c.CBK.ERROR),

f=this.notifyEnabled(J.c.CBK.ERROR);(f||null!=l)&&this.fireJmolScriptCallback(f,J.c.CBK.ERROR,w(-1,[l,a,b,this.vwr.getShapeErrorState(),c]),!0)},"~S,~S,~S");c(b,"notifyMinimizationStatus",function(a,b,c,l,f){var e=this.getJmolScriptCallback(J.c.CBK.MINIMIZATION),h=this.notifyEnabled(J.c.CBK.MINIMIZATION);(h||null!=e)&&this.fireJmolScriptCallback(h,J.c.CBK.MINIMIZATION,w(-1,[e,a,b,c,l,f]),!0)},"~S,Integer,Float,Float,~S");c(b,"setScriptStatus",function(a,b,c,l){if(-1>c){var f=-2-c;this.setStatusChanged("scriptStarted",

f,b,!1);a="script "+f+" started"}else if(null==a)return;var f=0==c?this.getJmolScriptCallback(J.c.CBK.SCRIPT):null,e="Script completed"===a;if(this.recordStatus("script")){var h=null!=l;this.setStatusChanged(h?"scriptError":"scriptStatus",0,a,!1);if(h||e)this.setStatusChanged("scriptTerminated",1,"Jmol script terminated"+(h?" unsuccessfully: "+a:" successfully"),!1)}e&&(this.vwr.getBoolean(603979879)&&this.vwr.getBoolean(603979825))&&(a=this.vwr.getChimeMessenger().scriptCompleted(this,b,l));b=w(-1,

[f,a,b,Integer.$valueOf(e?-1:c),l]);((c=this.notifyEnabled(J.c.CBK.SCRIPT))||null!=f)&&this.fireJmolScriptCallback(c,J.c.CBK.SCRIPT,b,!0);this.processScript(b)},"~S,~S,~N,~S");c(b,"processScript",function(a){var b=a[3].intValue();this.vwr.notifyScriptEditor(b,a);0==b&&this.vwr.sendConsoleMessage(null==a[1]?null:a[1].toString())},"~A");c(b,"doSync",function(){return this.isSynced&&this.drivingSync&&!this.syncDisabled});c(b,"setSync",function(a){if(this.syncingMouse){if(null!=a){var b=this.getJmolScriptCallback(J.c.CBK.SYNC);

null!=b&&this.fireJmolScriptCallback(!1,J.c.CBK.SYNC,w(-1,[b,a,"sending mouseSync"]),!0);this.syncSend(a,"*",0)}}else this.syncingScripts||this.syncSend("!"+this.vwr.tm.getMoveToText(this.minSyncRepeatMs/1E3,!1),"*",0)},"~S");c(b,"setSyncDriver",function(a){this.stereoSync&&4!=a&&(this.syncSend("SET_GRAPHICS_OFF","*",0),this.stereoSync=!1);switch(a){case 4:if(!this.syncDisabled)return;this.syncDisabled=!1;break;case 3:this.syncDisabled=!0;break;case 5:this.stereoSync=this.isSynced=this.drivingSync=

!0;break;case 1:this.isSynced=this.drivingSync=!0;break;case 2:this.drivingSync=!1;this.isSynced=!0;break;default:this.isSynced=this.drivingSync=!1}JU.Logger.debugging&&JU.Logger.debug(this.vwr.appletName+" sync mode="+a+"; synced? "+this.isSynced+"; driving? "+this.drivingSync+"; disabled? "+this.syncDisabled)},"~N");c(b,"syncSend",function(a,b,c){return 0!=c||this.notifyEnabled(J.c.CBK.SYNC)?(a=w(-1,[null,a,b,Integer.$valueOf(c)]),null!=this.cbl&&this.cbl.notifyCallback(J.c.CBK.SYNC,a),a[0]):null},

"~S,~O,~N");c(b,"processService",function(a){var b=a.get("service");if(null==b)return null;if(y(b,"JS.SV")){var b=new java.util.Hashtable,c;for(a=a.entrySet().iterator();a.hasNext()&&((c=a.next())||1);)b.put(c.getKey(),JS.SV.oValue(c.getValue()));a=b}this.notifyEnabled(J.c.CBK.SERVICE)&&this.cbl.notifyCallback(J.c.CBK.SERVICE,w(-1,[null,a]));return a},"java.util.Map");c(b,"getSyncMode",function(){return!this.isSynced?0:this.drivingSync?1:2});c(b,"showUrl",function(a){null!=this.jsl&&this.jsl.showUrl(a)},

"~S");c(b,"clearConsole",function(){this.vwr.sendConsoleMessage(null);null!=this.jsl&&this.cbl.notifyCallback(J.c.CBK.MESSAGE,null)});c(b,"functionXY",function(a,b,c){return null==this.jsl?K(Math.abs(b),Math.abs(c),0):this.jsl.functionXY(a,b,c)},"~S,~N,~N");c(b,"functionXYZ",function(a,b,c,l){return null==this.jsl?K(Math.abs(b),Math.abs(c),Math.abs(c),0):this.jsl.functionXYZ(a,b,c,l)},"~S,~N,~N,~N");c(b,"jsEval",function(a){return null==this.jsl?"":this.jsl.eval(a)},"~S");c(b,"createImage",function(a,

b,c,l,f){return null==this.jsl?null:this.jsl.createImage(a,b,null==c?l:c,f)},"~S,~S,~S,~A,~N");c(b,"getRegistryInfo",function(){return null==this.jsl?null:this.jsl.getRegistryInfo()});c(b,"dialogAsk",function(a,b,c){var l=a.equals("Save Image"),f=J.api.Interface.getOption("dialog.Dialog",this.vwr,"status");if(null==f)return null;f.setupUI(!1);l&&f.setImageInfo(this.qualityJPG,this.qualityPNG,this.imageType);a=f.getFileNameFromDialog(this.vwr,a,b);l&&null!=a&&(this.qualityJPG=f.getQuality("JPG"),this.qualityPNG=

f.getQuality("PNG"),l=f.getType(),null!=c&&(c.put("qualityJPG",Integer.$valueOf(this.qualityJPG)),c.put("qualityPNG",Integer.$valueOf(this.qualityPNG)),null!=l&&c.put("dialogImageType",l)),null!=l&&(this.imageType=l));return a},"~S,~S,java.util.Map");c(b,"getJspecViewProperties",function(a){return null==this.jsl?null:this.jsl.getJSpecViewProperty(null==a||0==a.length?"":":"+a)},"~S");c(b,"resizeInnerPanel",function(a,b){return null==this.jsl||a==this.vwr.getScreenWidth()&&b==this.vwr.getScreenHeight()?

E(-1,[a,b]):this.jsl.resizeInnerPanel("preferredWidthHeight "+a+" "+b+";")},"~N,~N");c(b,"resizeInnerPanelString",function(a){null!=this.jsl&&this.jsl.resizeInnerPanel(a)},"~S");c(b,"registerAudio",function(a,b){this.stopAudio(a);null==this.audios&&(this.audios=new java.util.Hashtable);null==b?this.audios.remove(a):this.audios.put(a,b.get("audioPlayer"))},"~S,java.util.Map");c(b,"stopAudio",function(a){null!=this.audios&&(null==a?this.closeAllAudio():(a=this.audios.get(a),null!=a&&a.action("kill")))},

"~S");c(b,"playAudio",function(a){if(this.vwr.getBoolean(603979797))try{var b=null==a?"close":a.get("action"),c=null==a?null:a.get("id");if(null!=b&&0<b.length){if(null==c||0==c.length){if(null==this.audios||this.audios.isEmpty())return;b.equals("close")&&this.closeAllAudio();return}var l=null==this.audios?null:this.audios.get(c);if(null!=l){l.action(b);return}}try{J.api.Interface.getInterface("JU.JmolAudio",this.vwr,"script").playAudio(this.vwr,a)}catch(f){if(F(f,Exception))JU.Logger.info(f.getMessage());

else throw f;}}catch(e){}else null!=a&&(a.put("status","close"),JU.Logger.info("allowAudio is set false"),this.notifyAudioStatus(a))},"java.util.Map");c(b,"closeAllAudio",function(){for(var a,b=this.audios.keySet().iterator();b.hasNext()&&((a=b.next())||1);)System.out.println("AUDIO "+a),this.audios.get(a).action("close");this.audios.clear()});c(b,"notifyAudioStatus",function(a){var b=a.get("status"),c=a.get(b);null!=c&&this.vwr.script(c);var c=this.getJmolScriptCallback(J.c.CBK.AUDIO),l=this.notifyEnabled(J.c.CBK.AUDIO);

(l||null!=c)&&this.fireJmolScriptCallback(l,J.c.CBK.AUDIO,w(-1,[c,a,b]),!0);"ended"===b&&a.get("autoclose")!==Boolean.FALSE&&this.registerAudio(a.get("id"),null)},"java.util.Map");c(b,"syncScript",function(a,b,c){if("GET_GRAPHICS".equalsIgnoreCase(a))this.setSyncDriver(5),this.syncSend(a,b,0),this.vwr.setBooleanProperty("_syncMouse",!1),this.vwr.setBooleanProperty("_syncScript",!1);else{"=".equals(b)&&(b="~",this.setSyncDriver(2));var l="~".equals(b);if(0<c||!l&&!".".equals(b))if(this.syncSend(a,

b,c),!"*".equals(b)||a.startsWith("{"))return;if(a.equalsIgnoreCase("on")||a.equalsIgnoreCase("true"))this.setSyncDriver(1);else if(a.equalsIgnoreCase("off")||a.equalsIgnoreCase("false"))this.setSyncDriver(0);else if(a.equalsIgnoreCase("slave"))this.setSyncDriver(2);else if(b=this.getSyncMode(),0!=b)if(1!=b&&(l=!1),JU.Logger.debugging&&JU.Logger.debug(this.vwr.htmlName+" syncing with script: "+a),l&&this.setSyncDriver(3),0!=a.indexOf("Mouse: ")){b=JV.JC.getServiceCommand(a);switch(b){case 70:case 42:case 49:case 56:case 63:this.syncSend(a,

".",c);return;case 0:case 77:case 28:case 35:if(l)return;case 21:case 7:case 14:if(null==(a=this.vwr.getJSV().processSync(a,b)))return}this.vwr.evalStringQuietSync(a,!0,!1)}else this.mouseScript(a),l&&this.vwr.setSyncDriver(4)}},"~S,~S,~N");c(b,"mouseScript",function(a){var b=JU.PT.getTokens(a),c=b[1];try{switch(c=(c.toLowerCase()+"...............").substring(0,15),"zoombyfactor...zoomby.........rotatezby......rotatexyby.....translatexyby..rotatemolecule.spinxyby.......rotatearcball..".indexOf(c)){case 0:switch(b.length){case 3:this.vwr.zoomByFactor(JU.PT.parseFloat(b[2]),

2147483647,2147483647);return;case 5:this.vwr.zoomByFactor(JU.PT.parseFloat(b[2]),JU.PT.parseInt(b[3]),JU.PT.parseInt(b[4]));return}break;case 15:switch(b.length){case 3:this.vwr.zoomBy(JU.PT.parseInt(b[2]));return}break;case 30:switch(b.length){case 3:this.vwr.rotateZBy(JU.PT.parseInt(b[2]),2147483647,2147483647);return;case 5:this.vwr.rotateZBy(JU.PT.parseInt(b[2]),JU.PT.parseInt(b[3]),JU.PT.parseInt(b[4]))}break;case 45:this.vwr.rotateXYBy(JU.PT.parseFloat(b[2]),JU.PT.parseFloat(b[3]));return;

case 60:this.vwr.translateXYBy(JU.PT.parseInt(b[2]),JU.PT.parseInt(b[3]));return;case 75:this.vwr.rotateSelected(JU.PT.parseFloat(b[2]),JU.PT.parseFloat(b[3]),null);return;case 90:this.vwr.spinXYBy(JU.PT.parseInt(b[2]),JU.PT.parseInt(b[3]),JU.PT.parseFloat(b[4]));return;case 105:this.vwr.rotateXYBy(JU.PT.parseInt(b[2]),JU.PT.parseInt(b[3]));return}}catch(l){if(!F(l,Exception))throw l;}this.vwr.showString("error reading SYNC command: "+a,!1)},"~S");b.MAXIMUM_QUEUE_LENGTH=16});u("JV");C("JU.A4 $.M3 $.M4 $.P3 $.P3i $.V3 J.c.STER JU.Point3fi".split(" "),

"JV.TransformManager","java.util.Hashtable JU.P4 $.Quat $.SB J.api.Interface JU.Escape $.Logger".split(" "),function(){var b=v(function(){this.spinThread=this.vibrationThread=this.movetoThread=this.vwr=null;this.perspectiveModel=11;this.modelRadiusPixels=this.modelRadius=this.modelCenterOffset=this.cameraDistanceFromCenter=this.aperatureAngle=this.referencePlaneOffset=this.cameraScaleFactor=0;this.navigationShiftXY=this.navigationOffset=this.navigationCenter=null;this.navigationDepthPercent=0;this.vectorTemp=

this.matrixTemp=null;this.haveNotifiedNaN=!1;this.spinX=0;this.spinY=30;this.spinZ=0;this.spinFps=30;this.navZ=this.navY=this.navX=0;this.navFps=NaN;this.doTransform4D=this.isSpinSelected=this.isSpinFixed=this.isSpinInternal=!1;this.rotationCenterDefault=this.perspectiveShiftXY=this.perspectiveOffset=this.fixedRotationCenter=this.fixedRotationOffset=null;this.rotationRadiusDefault=0;this.internalRotationCenter=this.internalTranslation=this.internalRotationAxis=this.fixedRotationAxis=null;this.internalRotationAngle=

0;this.rotationAxis=this.pointT2=this.vectorT2=this.vectorT=this.axisangleT=this.matrixTemp4=this.matrixTemp3=this.matrixRotate=null;this.rotationRate=0;this.cameraSetting=this.camera=this.fixedTranslation=null;this.yTranslationFraction=this.xTranslationFraction=0.5;this.previousY=this.previousX=this.prevZoomSetting=0;this.zoomEnabled=!0;this.zmPctSet=this.zmPct=100;this.zoomRatio=0;this.internalSlab=this.zShadeEnabled=this.slabEnabled=!1;this.depthValue=this.slabValue=this.depthPercentSetting=this.slabPercentSetting=

0;this.zSlabPercentSetting=50;this.zDepthPercentSetting=0;this.zSlabPoint=null;this.slabRange=this.zDepthValue=this.zSlabValue=0;this.depthPlane=this.slabPlane=null;this.perspectiveDepth=!0;this.scale3D=!1;this.cameraDepthSetting=this.cameraDepth=3;this.visualRangeAngstroms=0;this.cameraDistance=1E3;this.scale3DAngstromsPerInch=this.scaleDefaultPixelsPerAngstrom=this.scalePixelsPerAngstrom=this.screenPixelCount=this.height=this.width=0;this.zoomHeight=this.useZoomLarge=this.antialias=!1;this.screenHeight=

this.screenWidth=0;this.ptVibTemp=this.iScrPt=this.fScrPt=this.matrixTransformInv=this.matrixTransform=null;this.navigating=!1;this.defaultMode=this.mode=0;this.matrixTest=this.aaTest1=this.ptTest3=this.ptTest2=this.ptTest1=this.untransformedPoint=null;this.vibrationOn=this.spinIsGesture=this.navOn=this.spinOn=!1;this.vibrationScale=this.vibrationPeriodMs=this.vibrationPeriod=0;this.stereoColors=this.stereoMode=this.vibrationT=null;this.stereoDoubleFull=this.stereoDoubleDTI=!1;this.stereoDegrees=

NaN;this.stereoRadians=0;this.stereoFrame=!1;this.matrixStereo=null;this.windowCentered=!1;this.ptOffset=this.bsSelectedAtoms=this.bsFrameOffsets=this.frameOffsets=this.frameOffset=null;this.navMode=1;this.zoomFactor=3.4028235E38;this.navigationSlabOffset=0;this.nav=null;r(this,arguments)},JV,"TransformManager",null);Q(b,function(){this.navigationCenter=new JU.P3;this.navigationOffset=new JU.P3;this.navigationShiftXY=new JU.P3;this.matrixTemp=new JU.M4;this.vectorTemp=new JU.V3;this.fixedRotationOffset=

new JU.P3;this.fixedRotationCenter=new JU.P3;this.perspectiveOffset=new JU.P3;this.perspectiveShiftXY=new JU.P3;this.rotationCenterDefault=new JU.P3;this.fixedRotationAxis=new JU.A4;this.internalRotationAxis=new JU.A4;this.internalRotationCenter=JU.P3.new3(0,0,0);this.matrixRotate=new JU.M3;this.matrixTemp3=new JU.M3;this.matrixTemp4=new JU.M4;this.axisangleT=new JU.A4;this.vectorT=new JU.V3;this.vectorT2=new JU.V3;this.pointT2=new JU.P3;this.rotationAxis=new JU.V3;this.fixedTranslation=new JU.P3;

this.camera=new JU.P3;this.cameraSetting=new JU.P3;this.matrixTransform=new JU.M4;this.matrixTransformInv=new JU.M4;this.fScrPt=new JU.P3;this.iScrPt=new JU.P3i;this.ptVibTemp=new JU.Point3fi;this.untransformedPoint=new JU.P3;this.ptTest1=new JU.P3;this.ptTest2=new JU.P3;this.ptTest3=new JU.P3;this.aaTest1=new JU.A4;this.matrixTest=new JU.M3;this.vibrationT=new JU.P3;this.stereoMode=J.c.STER.NONE;this.matrixStereo=new JU.M3;this.frameOffset=new JU.P3;this.ptOffset=new JU.P3});z(b,function(){});b.getTransformManager=

c(b,"getTransformManager",function(a,b,c,l){l=l?J.api.Interface.getInterface("JV.TransformManager4D",a,"tm"):new JV.TransformManager;l.vwr=a;l.setScreenParameters(b,c,!0,!1,!0,!0);return l},"JV.Viewer,~N,~N,~B");c(b,"setDefaultPerspective",function(){this.setCameraDepthPercent(3,!0);this.setPerspectiveDepth(!0);this.setStereoDegrees(-5);this.visualRangeAngstroms=5;this.setSpinOff();this.setVibrationPeriod(0)});c(b,"homePosition",function(a){a&&this.setSpinOff();this.setNavOn(!1);this.navFps=10;this.navX=

this.navY=this.navZ=0;this.rotationCenterDefault.setT(this.vwr.getBoundBoxCenter());this.setFixedRotationCenter(this.rotationCenterDefault);this.rotationRadiusDefault=this.setRotationRadius(0,!0);this.windowCentered=!0;this.setRotationCenterAndRadiusXYZ(null,!0);this.resetRotation();a=this.vwr.ms.getInfoM("defaultOrientationMatrix");null!=a&&this.setRotation(a);this.setZoomEnabled(!0);this.zoomToPercent(this.vwr.g.modelKitMode?50:100);this.zmPct=this.zmPctSet;this.slabReset();this.resetFitToScreen(!0);

this.vwr.isJmolDataFrame()?this.fixedRotationCenter.set(0,0,0):this.vwr.g.axesOrientationRasmol&&this.matrixRotate.setAsXRotation(3.141592653589793);this.vwr.stm.saveOrientation("default",null);1==this.mode&&this.setNavigationMode(!0)},"~B");c(b,"setRotation",function(a){a.isRotation()?this.matrixRotate.setM3(a):this.resetRotation()},"JU.M3");c(b,"resetRotation",function(){this.matrixRotate.setScale(1)});c(b,"clearThreads",function(){this.clearVibration();this.clearSpin();this.setNavOn(!1);this.stopMotion()});

c(b,"clear",function(){this.fixedRotationCenter.set(0,0,0);this.navigating=!1;this.zSlabPoint=this.depthPlane=this.slabPlane=null;this.resetNavigationPoint(!0)});c(b,"setFixedRotationCenter",function(a){null!=a&&this.fixedRotationCenter.setT(a)},"JU.T3");c(b,"setRotationPointXY",function(a){a=this.transformPt(a);this.fixedTranslation.set(a.x,a.y,0)},"JU.P3");c(b,"spinXYBy",function(a,b,c){if(0==a&&0==b)null!=this.spinThread&&this.spinIsGesture&&this.clearSpin();else{this.clearSpin();var l=JU.P3.newP(this.fixedRotationCenter),

f=new JU.P3;this.transformPt3f(l,f);a=JU.P3.new3(-b,a,0);a.add(f);this.unTransformPoint(a,a);this.vwr.setInMotion(!1);this.rotateAboutPointsInternal(null,a,l,10*c,NaN,!1,!0,null,!0,null,null,null,null,!1)}},"~N,~N,~N");c(b,"rotateXYBy",function(a,b,c){this.rotate3DBall(a,b,c)},"~N,~N,JU.BS");c(b,"rotateZBy",function(a,b,c){2147483647!=b&&2147483647!=c&&this.resetXYCenter(b,c);this.rotateZRadians(a/57.29577951308232)},"~N,~N,~N");c(b,"applyRotation",function(a,b,c,l,f,e,h){null==c?this.matrixRotate.mul2(a,

this.matrixRotate):(this.vwr.moveAtoms(e,a,this.matrixRotate,l,this.internalRotationCenter,b,c,f,h),null!=l&&this.internalRotationCenter.add(l))},"JU.M3,~B,JU.BS,JU.V3,~B,JU.M4,~B");c(b,"rotate3DBall",function(a,b,c){this.matrixTemp3.setAsBallRotation(0.017453292519943295,-b,-a)&&this.applyRotation(this.matrixTemp3,!1,c,null,!1,null,!1)},"~N,~N,JU.BS");c(b,"rotateXRadians",function(a,b){this.applyRotation(this.matrixTemp3.setAsXRotation(a),!1,b,null,!1,null,!1)},"~N,JU.BS");c(b,"rotateYRadians",function(a,

b){this.applyRotation(this.matrixTemp3.setAsYRotation(a),!1,b,null,!1,null,!1)},"~N,JU.BS");c(b,"rotateZRadians",function(a){this.applyRotation(this.matrixTemp3.setAsZRotation(a),!1,null,null,!1,null,!1)},"~N");c(b,"rotateAxisAngle",function(a,b){this.axisangleT.setVA(a,b);this.rotateAxisAngle2(this.axisangleT,null)},"JU.V3,~N");c(b,"rotateAxisAngle2",function(a,b){this.applyRotation(this.matrixTemp3.setAA(a),!1,b,null,!1,null,!1)},"JU.A4,JU.BS");c(b,"rotateAxisAngleAtCenter",function(a,b,c,l,f,e,

h){null!=b&&this.moveRotationCenter(b,!0);e&&this.setSpinOff();this.setNavOn(!1);if(this.vwr.headless){if(e&&3.4028235E38==f)return!1;e=!1}if(Float.isNaN(l)||0==l||0==f)return!1;null!=b&&this.setRotationPointXY(b);this.setFixedRotationCenter(b);this.rotationAxis.setT(c);this.rotationRate=l;if(e)return this.fixedRotationAxis.setVA(c,0.017453292519943295*l),this.isSpinInternal=!1,this.isSpinFixed=!0,this.isSpinSelected=null!=h,this.setSpin(a,!0,f,null,null,h,!1),3.4028235E38!=f;a=0.017453292519943295*

f;this.fixedRotationAxis.setVA(c,f);this.rotateAxisAngleRadiansFixed(a,h);return!0},"J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");c(b,"rotateAxisAngleRadiansFixed",function(a,b){this.axisangleT.setAA(this.fixedRotationAxis);this.axisangleT.angle=a;this.rotateAxisAngle2(this.axisangleT,b)},"~N,JU.BS");c(b,"rotateAboutPointsInternal",function(a,b,c,l,f,e,h,j,m,n,p,q,r,s){h&&this.setSpinOff();this.setNavOn(!1);if(null==q&&(null==n||0.001>n.length())&&(h?Float.isNaN(l)||0==l:0==f))return!1;

var u=null;null==q&&(u=JU.V3.newVsub(c,b),e&&u.scale(-1),this.internalRotationCenter.setT(b),this.rotationAxis.setT(u),this.internalTranslation=null==n?null:JU.V3.newV(n));b=null!=j;if(h)return null==q?(0==f&&(f=NaN),Float.isNaN(f)?this.rotationRate=l:(r=B(Math.abs(f)/Math.abs(l)*this.spinFps+0.5),this.rotationRate=f/r*this.spinFps,null!=n&&this.internalTranslation.scale(1/r)),this.internalRotationAxis.setVA(u,0.017453292519943295*(Float.isNaN(this.rotationRate)?0:this.rotationRate)),this.isSpinInternal=

!0,this.isSpinFixed=!1,this.isSpinSelected=b):f=l,this.setSpin(a,!0,f,p,q,j,m),!Float.isNaN(f);a=0.017453292519943295*f;this.internalRotationAxis.setVA(u,a);this.rotateAxisAngleRadiansInternal(a,j,r,s);return!1},"J.api.JmolScriptEvaluator,JU.T3,JU.T3,~N,~N,~B,~B,JU.BS,~B,JU.V3,JU.Lst,~A,JU.M4,~B");c(b,"rotateAxisAngleRadiansInternal",function(a,b,c,l){this.internalRotationAngle=a;this.vectorT.set(this.internalRotationAxis.x,this.internalRotationAxis.y,this.internalRotationAxis.z);this.matrixRotate.rotate2(this.vectorT,

this.vectorT2);this.axisangleT.setVA(this.vectorT2,a);this.applyRotation(this.matrixTemp3.setAA(this.axisangleT),!0,b,this.internalTranslation,1E6<a,c,l);null==b&&this.getNewFixedRotationCenter()},"~N,JU.BS,JU.M4,~B");c(b,"getNewFixedRotationCenter",function(){this.axisangleT.setAA(this.internalRotationAxis);this.axisangleT.angle=-this.internalRotationAngle;this.matrixTemp4.setToAA(this.axisangleT);this.vectorT.setT(this.internalRotationCenter);this.pointT2.sub2(this.fixedRotationCenter,this.vectorT);

var a=this.matrixTemp4.rotTrans2(this.pointT2,new JU.P3);a.add(this.vectorT);this.setRotationCenterAndRadiusXYZ(a,!1)});c(b,"setTranslationFractions",function(){this.xTranslationFraction=this.fixedTranslation.x/this.width;this.yTranslationFraction=this.fixedTranslation.y/this.height});c(b,"centerAt",function(a,b,c){null==c?this.translateXYBy(a,b):(this.windowCentered&&this.vwr.setBooleanProperty("windowCentered",!1),this.fixedTranslation.x=a,this.fixedTranslation.y=b,this.setFixedRotationCenter(c))},

"~N,~N,JU.P3");c(b,"percentToPixels",function(a,b){switch(a.charCodeAt(0)){case 120:return B(Math.floor(b/100*this.width));case 121:return B(Math.floor(b/100*this.height));case 122:return B(Math.floor(b/100*this.screenPixelCount))}return 0},"~S,~N");c(b,"angstromsToPixels",function(a){return this.scalePixelsPerAngstrom*a},"~N");c(b,"translateXYBy",function(a,b){this.fixedTranslation.x+=a;this.fixedTranslation.y+=b;this.setTranslationFractions()},"~N,~N");c(b,"setCamera",function(a,b){this.cameraSetting.set(a,

b,0==a&&0==b?0:1)},"~N,~N");c(b,"translateToPercent",function(a,b){switch(a.charCodeAt(0)){case 120:this.xTranslationFraction=0.5+b/100;this.fixedTranslation.x=this.width*this.xTranslationFraction;break;case 121:this.yTranslationFraction=0.5+b/100;this.fixedTranslation.y=this.height*this.yTranslationFraction;break;case 122:1==this.mode&&this.setNavigationDepthPercent(b)}},"~S,~N");c(b,"getTranslationXPercent",function(){return 0==this.width?0:100*(this.fixedTranslation.x-this.width/2)/this.width});

c(b,"getTranslationYPercent",function(){return 0==this.height?0:100*(this.fixedTranslation.y-this.height/2)/this.height});c(b,"getTranslationScript",function(){var a="",b=this.getTranslationXPercent();0!=b&&(a+="translate x "+b+";");b=this.getTranslationYPercent();0!=b&&(a+="translate y "+b+";");return a});c(b,"getOrientationText",function(a,b){switch(a){case 4129:return this.getMoveToText(1,!1);case 1073742132:var c=this.getRotationQ();b&&(c=c.inv());return c.toString();case 1073742178:var c=new JU.SB,

l=this.getTranslationXPercent();JV.TransformManager.truncate2(c,b?-l:l);l=this.getTranslationYPercent();JV.TransformManager.truncate2(c,b?-l:l);return c.toString();default:return this.getMoveToText(1,!0)+"\n#OR\n"+this.getRotateZyzText(!0)}},"~N,~B");c(b,"getRotationQ",function(){return JU.Quat.newM(this.matrixRotate)});c(b,"getOrientationInfo",function(){var a=new java.util.Hashtable;a.put("moveTo",this.getMoveToText(1,!1));a.put("center","center "+this.getCenterText());a.put("centerPt",this.fixedRotationCenter);

var b=new JU.A4;b.setM(this.matrixRotate);a.put("axisAngle",b);a.put("quaternion",this.getRotationQ().toPoint4f());a.put("rotationMatrix",this.matrixRotate);a.put("rotateZYZ",this.getRotateZyzText(!1));a.put("rotateXYZ",this.getRotateXyzText());a.put("transXPercent",Float.$valueOf(this.getTranslationXPercent()));a.put("transYPercent",Float.$valueOf(this.getTranslationYPercent()));a.put("zoom",Float.$valueOf(this.zmPct));a.put("modelRadius",Float.$valueOf(this.modelRadius));1==this.mode&&(a.put("navigationCenter",

"navigate center "+JU.Escape.eP(this.navigationCenter)),a.put("navigationOffsetXPercent",Float.$valueOf(this.getNavigationOffsetPercent("X"))),a.put("navigationOffsetYPercent",Float.$valueOf(this.getNavigationOffsetPercent("Y"))),a.put("navigationDepthPercent",Float.$valueOf(this.navigationDepthPercent)));return a});c(b,"getRotation",function(a){a.setM3(this.matrixRotate)},"JU.M3");c(b,"setZoomHeight",function(a,b){this.zoomHeight=a;this.scaleFitToScreen(!1,b,!1,!0)},"~B,~B");c(b,"zoomBy",function(a){20<

a?a=20:-20>a&&(a=-20);var b=a*this.zmPctSet/50;0==b&&(b=0<a?1:0>b?-1:0);this.zoomRatio=(b+this.zmPctSet)/this.zmPctSet;this.zmPctSet+=b},"~N");c(b,"zoomByFactor",function(a,b,c){!(0>=a)&&this.zoomEnabled&&(1!=this.mode?(this.zoomRatio=a,this.zmPctSet*=a,this.resetXYCenter(b,c)):this.getNav()&&this.nav.zoomByFactor(a,b,c))},"~N,~N,~N");c(b,"zoomToPercent",function(a){this.zmPctSet=a;this.zoomRatio=0},"~N");c(b,"translateZBy",function(a){a>=this.screenPixelCount||(a=this.scalePixelsPerAngstrom/(1-1*

a/this.screenPixelCount),a>=this.screenPixelCount||(a=100*(a/this.scaleDefaultPixelsPerAngstrom),this.zoomRatio=a/this.zmPctSet,this.zmPctSet=a))},"~N");c(b,"resetXYCenter",function(a,b){if(!(2147483647==a||2147483647==b)){this.windowCentered&&this.vwr.setBooleanProperty("windowCentered",!1);var c=new JU.P3;this.transformPt3f(this.fixedRotationCenter,c);c.set(a,b,c.z);this.unTransformPoint(c,c);this.fixedTranslation.set(a,b,0);this.setFixedRotationCenter(c)}},"~N,~N");c(b,"zoomByPercent",function(a){var b=

a*this.zmPctSet/100;0==b&&(b=0>a?-1:1);this.zoomRatio=(b+this.zmPctSet)/this.zmPctSet;this.zmPctSet+=b},"~N");c(b,"setScaleAngstromsPerInch",function(a){if(this.scale3D=0<a)this.scale3DAngstromsPerInch=a;this.perspectiveDepth=!this.scale3D},"~N");c(b,"setSlabRange",function(a){this.slabRange=a},"~N");c(b,"setSlabEnabled",function(a){this.vwr.g.setB("slabEnabled",this.slabEnabled=a)},"~B");c(b,"setZShadeEnabled",function(a){this.zShadeEnabled=a;this.vwr.g.setB("zShade",a)},"~B");c(b,"setZoomEnabled",

function(a){this.zoomEnabled=a;this.vwr.g.setB("zoomEnabled",a)},"~B");c(b,"slabReset",function(){this.slabToPercent(100);this.depthToPercent(0);this.slabPlane=this.depthPlane=null;this.setSlabEnabled(!1);this.setZShadeEnabled(!1);this.slabDepthChanged()});c(b,"getSlabPercentSetting",function(){return this.slabPercentSetting});c(b,"slabDepthChanged",function(){this.vwr.g.setI("slab",this.slabPercentSetting);this.vwr.g.setI("depth",this.depthPercentSetting);this.finalizeTransformParameters()});c(b,

"slabByPercentagePoints",function(a){this.slabPlane=null;if(!(0>a?this.slabPercentSetting<=Math.max(0,this.depthPercentSetting):100<=this.slabPercentSetting))this.slabPercentSetting+=a,this.slabDepthChanged(),this.depthPercentSetting>=this.slabPercentSetting&&(this.depthPercentSetting=this.slabPercentSetting-1)},"~N");c(b,"depthByPercentagePoints",function(a){this.depthPlane=null;if(!(0>a?0>=this.depthPercentSetting:this.depthPercentSetting>=Math.min(100,this.slabPercentSetting)))this.depthPercentSetting+=

a,this.slabPercentSetting<=this.depthPercentSetting&&(this.slabPercentSetting=this.depthPercentSetting+1),this.slabDepthChanged()},"~N");c(b,"slabDepthByPercentagePoints",function(a){this.depthPlane=this.slabPlane=null;if(!(0>a?this.slabPercentSetting<=Math.max(0,this.depthPercentSetting):this.depthPercentSetting>=Math.min(100,this.slabPercentSetting)))this.slabPercentSetting+=a,this.depthPercentSetting+=a,this.slabDepthChanged()},"~N");c(b,"slabToPercent",function(a){this.slabPlane=null;this.vwr.setFloatProperty("slabRange",

0);this.slabPercentSetting=a;this.depthPercentSetting>=this.slabPercentSetting&&(this.depthPercentSetting=this.slabPercentSetting-1);this.slabDepthChanged()},"~N");c(b,"depthToPercent",function(a){this.depthPlane=null;this.vwr.g.setI("depth",a);this.depthPercentSetting=a;this.slabPercentSetting<=this.depthPercentSetting&&(this.slabPercentSetting=this.depthPercentSetting+1);this.slabDepthChanged()},"~N");c(b,"zSlabToPercent",function(a){this.zSlabPercentSetting=a;this.zDepthPercentSetting>this.zSlabPercentSetting&&

(this.zDepthPercentSetting=a)},"~N");c(b,"zDepthToPercent",function(a){this.zDepthPercentSetting=a;this.zDepthPercentSetting>this.zSlabPercentSetting&&(this.zSlabPercentSetting=a)},"~N");c(b,"slabInternal",function(a,b){b?(this.depthPlane=a,this.depthPercentSetting=0):(this.slabPlane=a,this.slabPercentSetting=100);this.slabDepthChanged()},"JU.P4,~B");c(b,"setSlabDepthInternal",function(a){a?this.depthPlane=null:this.slabPlane=null;this.finalizeTransformParameters();this.slabInternal(this.getSlabDepthPlane(a),

a)},"~B");c(b,"getSlabDepthPlane",function(a){if(a){if(null!=this.depthPlane)return this.depthPlane}else if(null!=this.slabPlane)return this.slabPlane;var b=this.matrixTransform;return JU.P4.new4(-b.m20,-b.m21,-b.m22,-b.m23+(a?this.depthValue:this.slabValue))},"~B");c(b,"getCameraFactors",function(){this.aperatureAngle=360*Math.atan2(this.screenPixelCount/2,this.referencePlaneOffset)/3.141592653589793;this.cameraDistanceFromCenter=this.referencePlaneOffset/this.scalePixelsPerAngstrom;var a=JU.P3.new3(B(this.screenWidth/

2),B(this.screenHeight/2),this.referencePlaneOffset);this.unTransformPoint(a,a);var b=JU.P3.new3(B(this.screenWidth/2),B(this.screenHeight/2),0);this.unTransformPoint(b,b);b.sub(this.fixedRotationCenter);var c=JU.P3.new3(B(this.screenWidth/2),B(this.screenHeight/2),this.cameraDistanceFromCenter*this.scalePixelsPerAngstrom);this.unTransformPoint(c,c);c.sub(this.fixedRotationCenter);b.add(c);return w(-1,[a,b,this.fixedRotationCenter,JU.P3.new3(this.cameraDistanceFromCenter,this.aperatureAngle,this.scalePixelsPerAngstrom)])});

c(b,"setPerspectiveDepth",function(a){this.perspectiveDepth!=a&&(this.perspectiveDepth=a,this.vwr.g.setB("perspectiveDepth",a),this.resetFitToScreen(!1))},"~B");c(b,"getPerspectiveDepth",function(){return this.perspectiveDepth});c(b,"setCameraDepthPercent",function(a,b){this.resetNavigationPoint(b);var c=0>a?-a/100:a;0!=c&&(this.cameraDepthSetting=c,this.vwr.g.setF("cameraDepth",this.cameraDepthSetting),this.cameraDepth=NaN)},"~N,~B");c(b,"getCameraDepth",function(){return this.cameraDepthSetting});

c(b,"setScreenParameters0",function(a,b,c,l,f,e){2147483647!=a&&(this.screenWidth=a,this.screenHeight=b,this.useZoomLarge=c,this.width=(this.antialias=l)?2*a:a,this.height=l?2*b:b,this.scaleFitToScreen(!1,c,f,e))},"~N,~N,~B,~B,~B,~B");c(b,"setAntialias",function(a){var b=this.antialias!=a;this.width=(this.antialias=a)?2*this.screenWidth:this.screenWidth;this.height=this.antialias?2*this.screenHeight:this.screenHeight;b&&this.scaleFitToScreen(!1,this.useZoomLarge,!1,!1)},"~B");c(b,"defaultScaleToScreen",

function(a){return this.screenPixelCount/2/a},"~N");c(b,"resetFitToScreen",function(a){this.scaleFitToScreen(a,this.vwr.g.zoomLarge,!0,!0)},"~B");c(b,"scaleFitToScreen",function(a,b,c,l){0==this.width||0==this.height?this.screenPixelCount=1:(this.fixedTranslation.set(this.width*(a?0.5:this.xTranslationFraction),this.height*(a?0.5:this.yTranslationFraction),0),this.setTranslationFractions(),a&&this.camera.set(0,0,0),l&&this.resetNavigationPoint(c),this.zoomHeight&&(b=this.height>this.width),this.screenPixelCount=

b==this.height>this.width?this.height:this.width);2<this.screenPixelCount&&(this.screenPixelCount-=2);this.scaleDefaultPixelsPerAngstrom=this.defaultScaleToScreen(this.modelRadius)},"~B,~B,~B,~B");c(b,"scaleToScreen",function(a,b){if(0==b||2>a)return 0;var c=this.scaleToPerspective(a,b*this.scalePixelsPerAngstrom/1E3);return 0<c?c:1},"~N,~N");c(b,"unscaleToScreen",function(a,b){var c=b/this.scalePixelsPerAngstrom;return this.perspectiveDepth?c/this.getPerspectiveFactor(a):c},"~N,~N");c(b,"scaleToPerspective",

function(a,b){return this.perspectiveDepth?b*this.getPerspectiveFactor(a):b},"~N,~N");c(b,"setNavigationMode",function(a){this.mode=a?1:this.defaultMode;this.resetNavigationPoint(!0)},"~B");c(b,"isNavigating",function(){return this.navigating||this.navOn});c(b,"finalizeTransformParameters",function(){this.haveNotifiedNaN=!1;this.fixedRotationOffset.setT(this.fixedTranslation);this.camera.setT(this.cameraSetting);this.internalSlab=this.slabEnabled&&(null!=this.slabPlane||null!=this.depthPlane);var a=

this.getZoomSetting();this.zmPct!=a&&(this.zmPct=a,this.vwr.g.fontCaching||this.vwr.gdata.clearFontCache());this.calcCameraFactors();this.calcTransformMatrix();1==this.mode?this.calcNavigationPoint():this.calcSlabAndDepthValues()});c(b,"getZoomSetting",function(){5>this.zmPctSet&&(this.zmPctSet=5);2E5<this.zmPctSet&&(this.zmPctSet=2E5);return this.zoomEnabled||1==this.mode?this.zmPctSet:100});c(b,"calcSlabAndDepthValues",function(){this.slabValue=1>this.slabRange?this.zValueFromPercent(this.slabPercentSetting):

B(Math.floor(this.modelCenterOffset*this.slabRange/(2*this.modelRadius)*(this.zmPctSet/100)));this.depthValue=this.zValueFromPercent(this.depthPercentSetting);this.zSlabPercentSetting==this.zDepthPercentSetting?(this.zSlabValue=this.slabValue,this.zDepthValue=this.depthValue):(this.zSlabValue=this.zValueFromPercent(this.zSlabPercentSetting),this.zDepthValue=this.zValueFromPercent(this.zDepthPercentSetting));if(null!=this.zSlabPoint)try{this.transformPt3f(this.zSlabPoint,this.pointT2),this.zSlabValue=

D(this.pointT2.z)}catch(a){if(!F(a,Exception))throw a;}this.vwr.g.setO("_slabPlane",JU.Escape.eP4(this.getSlabDepthPlane(!1)));this.vwr.g.setO("_depthPlane",JU.Escape.eP4(this.getSlabDepthPlane(!0)));this.slabEnabled||(this.slabValue=0,this.depthValue=2147483647)});c(b,"zValueFromPercent",function(a){return B(Math.floor((1-a/50)*this.modelRadiusPixels+this.modelCenterOffset))},"~N");c(b,"calcTransformMatrix",function(){this.matrixTransform.setIdentity();this.vectorTemp.sub2(this.frameOffset,this.fixedRotationCenter);

this.matrixTransform.setTranslation(this.vectorTemp);this.matrixTemp.setToM3(this.stereoFrame?this.matrixStereo:this.matrixRotate);this.matrixTransform.mul2(this.matrixTemp,this.matrixTransform);this.matrixTemp.setIdentity();this.matrixTemp.m00=this.matrixTemp.m11=this.matrixTemp.m22=this.scalePixelsPerAngstrom;this.matrixTemp.m11=this.matrixTemp.m22=-this.scalePixelsPerAngstrom;this.matrixTransform.mul2(this.matrixTemp,this.matrixTransform);this.matrixTransform.m23+=this.modelCenterOffset;try{this.matrixTransformInv.setM4(this.matrixTransform).invert()}catch(a){if(F(a,

Exception))System.out.println("ERROR INVERTING matrixTransform!");else throw a;}});c(b,"rotatePoint",function(a,b){this.matrixRotate.rotate2(a,b);b.y=-b.y},"JU.T3,JU.T3");c(b,"getScreenTemp",function(a){this.matrixTransform.rotTrans2(a,this.fScrPt)},"JU.T3");c(b,"transformPtScr",function(a,b){b.setT(this.transformPt(a))},"JU.T3,JU.P3i");c(b,"transformPtScrT3",function(a,b){this.transformPt(a);b.setT(this.fScrPt)},"JU.T3,JU.T3");c(b,"transformPt3f",function(a,b){this.applyPerspective(a,a);b.setT(this.fScrPt)},

"JU.T3,JU.P3");c(b,"transformPtNoClip",function(a,b){this.applyPerspective(a,null);b.setT(this.fScrPt)},"JU.T3,JU.T3");c(b,"transformPt",function(a){return this.applyPerspective(a,this.internalSlab?a:null)},"JU.T3");c(b,"transformPtVib",function(a,b){this.ptVibTemp.setT(a);return this.applyPerspective(this.getVibrationPoint(b,this.ptVibTemp,NaN),a)},"JU.P3,JU.Vibration");c(b,"getVibrationPoint",function(a,b,c){return a.setCalcPoint(b,this.vibrationT,Float.isNaN(c)?this.vibrationScale:c,this.vwr.g.modulationScale)},

"JU.Vibration,JU.T3,~N");c(b,"transformPt2Df",function(a,b){-3.4028235E38==a.z||3.4028235E38==a.z?(this.transformPt2D(a),b.set(this.iScrPt.x,this.iScrPt.y,this.iScrPt.z)):this.transformPt3f(a,b)},"JU.T3,JU.P3");c(b,"transformPtScrT32D",function(a,b){-3.4028235E38==a.z||3.4028235E38==a.z?(this.transformPt2D(a),b.set(this.iScrPt.x,this.iScrPt.y,this.iScrPt.z)):this.transformPtScrT3(a,b)},"JU.T3,JU.P3");c(b,"transformPt2D",function(a){-3.4028235E38==a.z?(this.iScrPt.x=B(Math.floor(a.x/100*this.screenWidth)),

this.iScrPt.y=B(Math.floor((1-a.y/100)*this.screenHeight))):(this.iScrPt.x=D(a.x),this.iScrPt.y=this.screenHeight-D(a.y));this.antialias&&(this.iScrPt.x<<=1,this.iScrPt.y<<=1);this.matrixTransform.rotTrans2(this.fixedRotationCenter,this.fScrPt);this.iScrPt.z=D(this.fScrPt.z);return this.iScrPt},"JU.T3");c(b,"applyPerspective",function(a,b){this.getScreenTemp(a);var c=this.fScrPt.z;Float.isNaN(c)?(!this.haveNotifiedNaN&&JU.Logger.debugging&&JU.Logger.debug("NaN seen in TransformPoint"),this.haveNotifiedNaN=

!0,c=this.fScrPt.z=1):0>=c&&(c=this.fScrPt.z=1);switch(this.mode){case 1:this.fScrPt.x-=this.navigationShiftXY.x;this.fScrPt.y-=this.navigationShiftXY.y;break;case 2:this.fScrPt.x+=this.perspectiveShiftXY.x,this.fScrPt.y+=this.perspectiveShiftXY.y}this.perspectiveDepth&&(c=this.getPerspectiveFactor(c),this.fScrPt.x*=c,this.fScrPt.y*=c);switch(this.mode){case 1:this.fScrPt.x+=this.navigationOffset.x;this.fScrPt.y+=this.navigationOffset.y;break;case 2:this.fScrPt.x-=this.perspectiveShiftXY.x,this.fScrPt.y-=

this.perspectiveShiftXY.y;case 0:this.fScrPt.x+=this.fixedRotationOffset.x,this.fScrPt.y+=this.fixedRotationOffset.y}Float.isNaN(this.fScrPt.x)&&!this.haveNotifiedNaN&&(JU.Logger.debugging&&JU.Logger.debug("NaN found in transformPoint "),this.haveNotifiedNaN=!0);this.iScrPt.set(D(this.fScrPt.x),D(this.fScrPt.y),D(this.fScrPt.z));null!=b&&this.xyzIsSlabbedInternal(b)&&(this.fScrPt.z=this.iScrPt.z=1);return this.iScrPt},"JU.T3,JU.T3");c(b,"xyzIsSlabbedInternal",function(a){return null!=this.slabPlane&&

0<a.x*this.slabPlane.x+a.y*this.slabPlane.y+a.z*this.slabPlane.z+this.slabPlane.w||null!=this.depthPlane&&0>a.x*this.depthPlane.x+a.y*this.depthPlane.y+a.z*this.depthPlane.z+this.depthPlane.w},"JU.T3");c(b,"move",function(a,b,c,l,f,e,h){this.movetoThread=J.api.Interface.getOption("thread.MoveToThread",this.vwr,"tm");this.movetoThread.setManager(this,this.vwr,w(-1,[b,l,K(-1,[c,f,e,h])]));0<e&&this.movetoThread.setEval(a);this.movetoThread.run()},"J.api.JmolScriptEvaluator,JU.V3,~N,JU.V3,~N,~N,~N");

c(b,"isInPosition",function(a,b){if(Float.isNaN(b))return!0;this.aaTest1.setVA(a,b/57.29577951308232);this.ptTest1.set(4.321,1.23456,3.14159);this.getRotation(this.matrixTest);this.matrixTest.rotate2(this.ptTest1,this.ptTest2);this.matrixTest.setAA(this.aaTest1).rotate2(this.ptTest1,this.ptTest3);return 0.1>this.ptTest3.distance(this.ptTest2)},"JU.V3,~N");c(b,"moveToPyMOL",function(a,b,c){var l=JU.M3.newA9(c);l.invert();var f=c[9],e=-c[10],h=-c[11],j=JU.P3.new3(c[12],c[13],c[14]),m=c[15],n=c[16],

p=c[17];this.setPerspectiveDepth(!(0<=p));var p=Math.abs(p)/2,q=Math.tan(3.141592653589793*p/180),p=h*q,q=0.5/q-0.5,r=50/p;0<m&&(m=50+D((h-m)*r),h=50+D((h-n)*r),this.setSlabEnabled(!0),this.slabToPercent(m),this.depthToPercent(h),21==c.length&&(n=0!=c[18],r=0!=c[19],c=c[20],this.setZShadeEnabled(n),n&&(r?this.vwr.setIntProperty("zSlab",D(Math.min(100,m+c*(h-m)))):this.vwr.setIntProperty("zSlab",D((m+h)/2)),this.vwr.setIntProperty("zDepth",h))));this.moveTo(a,b,j,null,0,l,100,NaN,NaN,p,null,NaN,NaN,

NaN,q,f,e);return!0},"J.api.JmolScriptEvaluator,~N,~A");c(b,"moveTo",function(a,b,c,l,f,e,h,j,m,n,p,q,r,s,u,v,y){if(null==e)if(e=new JU.M3,l=JU.V3.newV(l),Float.isNaN(f))e.m00=NaN;else if(0.01>f&&-0.01<f)e.setScale(1);else{if(0==l.x&&0==l.y&&0==l.z)return;var z=new JU.A4;z.setVA(l,f/57.29577951308232);e.setAA(z)}v==this.cameraSetting.x&&(v=NaN);y==this.cameraSetting.y&&(y=NaN);u==this.cameraDepth&&(u=NaN);Float.isNaN(v)||(j=50*v/n/this.width*this.screenPixelCount);Float.isNaN(y)||(m=50*y/n/this.height*

this.screenPixelCount);f=null==c?this.scaleDefaultPixelsPerAngstrom:this.defaultScaleToScreen(n);if(0>=b)this.setAll(c,e,p,h,j,m,n,f,s,q,r,u,v,y),this.vwr.moveUpdate(b),this.vwr.finalizeTransformParameters();else try{null==this.movetoThread&&(this.movetoThread=J.api.Interface.getOption("thread.MoveToThread",this.vwr,"tm"));var B=this.movetoThread.setManager(this,this.vwr,w(-1,[c,e,p,K(-1,[b,h,j,m,n,f,s,q,r,u,v,y])]));0>=B||this.vwr.g.waitForMoveTo?(0<B&&this.movetoThread.setEval(a),this.movetoThread.run(),

this.vwr.isSingleThreaded||(this.movetoThread=null)):this.movetoThread.start()}catch(C){if(!F(C,Exception))throw C;}},"J.api.JmolScriptEvaluator,~N,JU.P3,JU.T3,~N,JU.M3,~N,~N,~N,~N,JU.P3,~N,~N,~N,~N,~N,~N");c(b,"setAll",function(a,b,c,l,f,e,h,j,m,n,p,q,r,s){Float.isNaN(b.m00)||this.setRotation(b);null!=a&&this.moveRotationCenter(a,!this.windowCentered);null!=c&&1==this.mode&&this.navigationCenter.setT(c);Float.isNaN(q)||this.setCameraDepthPercent(q,!1);!Float.isNaN(r)&&!Float.isNaN(s)&&this.setCamera(r,

s);Float.isNaN(l)||this.zoomToPercent(l);Float.isNaN(h)||(this.modelRadius=h);Float.isNaN(j)||(this.scaleDefaultPixelsPerAngstrom=j);!Float.isNaN(f)&&!Float.isNaN(e)&&(this.translateToPercent("x",f),this.translateToPercent("y",e));1==this.mode&&(!Float.isNaN(n)&&!Float.isNaN(p)&&this.navTranslatePercentOrTo(0,n,p),Float.isNaN(m)||this.setNavigationDepthPercent(m))},"JU.P3,JU.M3,JU.P3,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N,~N");c(b,"stopMotion",function(){this.movetoThread=null});c(b,"getRotationText",function(){this.axisangleT.setM(this.matrixRotate);

var c=new JU.SB;c.append("moveto ");b&&c.append("/* time, axisAngle */ ");c.appendF(a);c.append(" ").append(this.getRotationText());b&&c.append(" /* zoom, translation */ ");JV.TransformManager.truncate2(c,this.zmPctSet);JV.TransformManager.truncate2(c,this.getTranslationXPercent());JV.TransformManager.truncate2(c,this.getTranslationYPercent());c.append(" ");b&&c.append(" /* center, rotationRadius */ ");c.append(this.getCenterText());c.append(" ").appendF(this.modelRadius);c.append(this.getNavigationText(b));

b&&c.append(" /* cameraDepth, cameraX, cameraY */ ");JV.TransformManager.truncate2(c,this.cameraDepth);JV.TransformManager.truncate2(c,this.cameraSetting.x);JV.TransformManager.truncate2(c,this.cameraSetting.y);c.append(";");return c.toString()},"~N,~B");c(b,"getCenterText",function(){return JU.Escape.eP(this.fixedRotationCenter)});c(b,"getRotateXyzText",function(){var a=new JU.SB,b=this.matrixRotate.m20,c=-(57.29577951308232*Math.asin(b)),l;0.999<b||-0.999>b?(b=-(57.29577951308232*Math.atan2(this.matrixRotate.m12,

this.matrixRotate.m11)),l=0):(b=57.29577951308232*Math.atan2(this.matrixRotate.m21,this.matrixRotate.m22),l=57.29577951308232*Math.atan2(this.matrixRotate.m10,this.matrixRotate.m00));a.append("reset");a.append(";center ").append(this.getCenterText());0!=b&&(a.append("; rotate x"),JV.TransformManager.truncate2(a,b));0!=c&&(a.append("; rotate y"),JV.TransformManager.truncate2(a,c));0!=l&&(a.append("; rotate z"),JV.TransformManager.truncate2(a,l));a.append(";");this.addZoomTranslationNavigationText(a);

return a.toString()});c(b,"addZoomTranslationNavigationText",function(a){100!=this.zmPct&&(a.append(" zoom"),JV.TransformManager.truncate2(a,this.zmPct),a.append(";"));var b=this.getTranslationXPercent();0!=b&&(a.append(" translate x"),JV.TransformManager.truncate2(a,b),a.append(";"));b=this.getTranslationYPercent();0!=b&&(a.append(" translate y"),JV.TransformManager.truncate2(a,b),a.append(";"));if(this.modelRadius!=this.rotationRadiusDefault||10==this.modelRadius)a.append(" set rotationRadius"),

JV.TransformManager.truncate2(a,this.modelRadius),a.append(";");1==this.mode&&(a.append("navigate 0 center ").append(JU.Escape.eP(this.navigationCenter)),a.append(";navigate 0 translate"),JV.TransformManager.truncate2(a,this.getNavigationOffsetPercent("X")),JV.TransformManager.truncate2(a,this.getNavigationOffsetPercent("Y")),a.append(";navigate 0 depth "),JV.TransformManager.truncate2(a,this.navigationDepthPercent),a.append(";"))},"JU.SB");c(b,"getRotateZyzText",function(a){var b=new JU.SB,c=this.vwr.ms.getInfoM("defaultOrientationMatrix");

null==c?c=this.matrixRotate:(c=JU.M3.newM3(c),c.invert(),c.mul2(this.matrixRotate,c));var l=c.m22,f=57.29577951308232*Math.acos(l);0.999<l||-0.999>l?(l=57.29577951308232*Math.atan2(c.m10,c.m11),c=0):(l=57.29577951308232*Math.atan2(c.m21,-c.m20),c=57.29577951308232*Math.atan2(c.m12,c.m02));0!=l&&(0!=f&&0!=c&&a)&&b.append("#Follows Z-Y-Z convention for Euler angles\n");b.append("reset");b.append(";center ").append(this.getCenterText());0!=l&&(b.append("; rotate z"),JV.TransformManager.truncate2(b,l));

0!=f&&(b.append("; rotate y"),JV.TransformManager.truncate2(b,f));0!=c&&(b.append("; rotate z"),JV.TransformManager.truncate2(b,c));b.append(";");this.addZoomTranslationNavigationText(b);return b.toString()},"~B");b.truncate0=c(b,"truncate0",function(a,b){a.appendC(" ");a.appendI(Math.round(b))},"JU.SB,~N");b.truncate2=c(b,"truncate2",function(a,b){a.appendC(" ");a.appendF(Math.round(100*b)/100)},"JU.SB,~N");c(b,"setSpinXYZ",function(a,b,c){Float.isNaN(a)||(this.spinX=a);Float.isNaN(b)||(this.spinY=

b);Float.isNaN(c)||(this.spinZ=c);(this.isSpinInternal||this.isSpinFixed)&&this.clearSpin()},"~N,~N,~N");c(b,"setSpinFps",function(a){0>=a?a=1:50<a&&(a=50);this.spinFps=a},"~N");c(b,"setNavXYZ",function(a,b,c){Float.isNaN(a)||(this.navX=a);Float.isNaN(b)||(this.navY=b);Float.isNaN(c)||(this.navZ=c)},"~N,~N,~N");c(b,"clearSpin",function(){this.setSpinOff();this.setNavOn(!1);this.isSpinFixed=this.isSpinInternal=!1});c(b,"setSpinOn",function(){this.setSpin(null,!0,3.4028235E38,null,null,null,!1)});c(b,

"setSpinOff",function(){this.setSpin(null,!1,3.4028235E38,null,null,null,!1)});c(b,"setSpin",function(a,b,c,l,f,e,h){this.navOn&&b&&this.setNavOn(!1);this.spinOn!=b&&(this.spinOn=b,this.vwr.g.setB("_spinning",b),b?null==this.spinThread&&(this.spinThread=J.api.Interface.getOption("thread.SpinThread",this.vwr,"tm"),this.spinThread.setManager(this,this.vwr,w(-1,[Float.$valueOf(c),l,f,e,h?Boolean.TRUE:null])),this.spinIsGesture=h,Float.isNaN(c)||3.4028235E38==c||!this.vwr.g.waitForMoveTo?this.spinThread.start():

(this.spinThread.setEval(a),this.spinThread.run())):null!=this.spinThread&&(this.spinThread.reset(),this.spinThread=null))},"J.api.JmolScriptEvaluator,~B,~N,JU.Lst,~A,JU.BS,~B");c(b,"setNavOn",function(a){if(!Float.isNaN(this.navFps)){var b=this.navOn;a&&this.spinOn&&this.setSpin(null,!1,0,null,null,null,!1);this.navOn=a;this.vwr.g.setB("_navigating",a);a||this.navInterrupt();a?(0==this.navX&&(0==this.navY&&0==this.navZ)&&(this.navZ=1),0==this.navFps&&(this.navFps=10),null==this.spinThread&&(this.spinThread=

J.api.Interface.getOption("thread.SpinThread",this.vwr,"tm"),this.spinThread.setManager(this,this.vwr,null),this.spinThread.start())):b&&null!=this.spinThread&&(this.spinThread.interrupt(),this.spinThread=null)}},"~B");c(b,"setVibrationScale",function(a){this.vibrationScale=a},"~N");c(b,"setVibrationPeriod",function(a){if(Float.isNaN(a))a=this.vibrationPeriod;else if(0==a)this.vibrationPeriodMs=this.vibrationPeriod=0;else{this.vibrationPeriod=Math.abs(a);this.vibrationPeriodMs=D(1E3*this.vibrationPeriod);

if(0<a)return;a=-a}this.setVibrationOn(0<a&&0<=this.vwr.ms.getLastVibrationVector(this.vwr.am.cmi,0))},"~N");c(b,"setVibrationT",function(a){this.vibrationT.x=this.vibrationT.y=this.vibrationT.z=a;0==this.vibrationScale&&(this.vibrationScale=this.vwr.g.vibrationScale)},"~N");c(b,"isVibrationOn",function(){return this.vibrationOn});c(b,"setVibrationOn",function(a){a?1>this.vwr.ms.mc?(this.vibrationOn=!1,this.vibrationT.x=0):(null==this.vibrationThread&&(this.vibrationThread=J.api.Interface.getOption("thread.VibrationThread",

this.vwr,"tm"),this.vibrationThread.setManager(this,this.vwr,null),this.vibrationThread.start()),this.vibrationOn=!0):(null!=this.vibrationThread&&(this.vibrationThread.interrupt(),this.vibrationThread=null),this.vibrationOn=!1,this.vibrationT.x=0)},"~B");c(b,"clearVibration",function(){this.setVibrationOn(!1);this.vibrationScale=0});c(b,"setStereoMode2",function(a){this.stereoMode=J.c.STER.CUSTOM;this.stereoColors=a},"~A");c(b,"setStereoMode",function(a){this.stereoColors=null;this.stereoMode=a;

this.stereoDoubleDTI=a===J.c.STER.DTI;this.stereoDoubleFull=a===J.c.STER.DOUBLE},"J.c.STER");c(b,"setStereoDegrees",function(a){this.stereoDegrees=a;this.stereoRadians=0.017453292519943295*a},"~N");c(b,"getStereoRotationMatrix",function(a){this.stereoFrame=a;if(!a)return this.matrixRotate;this.matrixTemp3.setAsYRotation(-this.stereoRadians);this.matrixStereo.mul2(this.matrixTemp3,this.matrixRotate);return this.matrixStereo},"~B");c(b,"isWindowCentered",function(){return this.windowCentered});c(b,

"setWindowCentered",function(a){this.windowCentered=a;this.resetNavigationPoint(!0)},"~B");c(b,"setRotationRadius",function(a,b){a=this.modelRadius=0>=a?this.vwr.ms.calcRotationRadius(this.vwr.am.cmi,this.fixedRotationCenter,!0):a;b&&this.vwr.setRotationRadius(a,!1);return a},"~N,~B");c(b,"setRotationCenterAndRadiusXYZ",function(a,b){this.resetNavigationPoint(!1);null==a?(this.setFixedRotationCenter(this.rotationCenterDefault),this.modelRadius=this.rotationRadiusDefault):(this.setFixedRotationCenter(a),

b&&this.windowCentered&&(this.modelRadius=this.vwr.ms.calcRotationRadius(this.vwr.am.cmi,this.fixedRotationCenter,!0)))},"JU.T3,~B");c(b,"setNewRotationCenter",function(a,b){null==a&&(a=this.rotationCenterDefault);this.windowCentered?(this.translateToPercent("x",0),this.translateToPercent("y",0),this.setRotationCenterAndRadiusXYZ(a,!0),b&&this.resetFitToScreen(!0)):this.moveRotationCenter(a,!0)},"JU.P3,~B");c(b,"moveRotationCenter",function(a,b){this.setRotationCenterAndRadiusXYZ(a,!1);b&&this.setRotationPointXY(this.fixedRotationCenter)},

"JU.P3,~B");c(b,"setCenter",function(){this.setRotationCenterAndRadiusXYZ(this.fixedRotationCenter,!0)});c(b,"setCenterAt",function(a,b){var c=JU.P3.newP(b);switch(a){case 1073741826:break;case 96:c.add(this.vwr.ms.getAverageAtomPoint());break;case 1812599299:c.add(this.vwr.getBoundBoxCenter());break;default:c.setT(this.rotationCenterDefault)}this.setRotationCenterAndRadiusXYZ(c,!0);this.resetFitToScreen(!0)},"~N,JU.P3");c(b,"setFrameOffset",function(a){null==this.frameOffsets||0>a||a>=this.frameOffsets.length?

this.frameOffset.set(0,0,0):this.frameOffset.setT(this.frameOffsets[a])},"~N");c(b,"setSelectedTranslation",function(a,b,c,l){if(this.perspectiveDepth)switch(this.bsSelectedAtoms=a,b.charCodeAt(0)){case 88:case 120:this.ptOffset.x+=c;break;case 89:case 121:this.ptOffset.y+=c;break;case 90:case 122:this.ptOffset.z+=c}else{c=new JU.V3;switch(b.charCodeAt(0)){case 88:case 120:c.set(l,0,0);break;case 89:case 121:c.set(0,l,0);break;case 90:case 122:c.set(0,0,l)}this.vwr.moveAtoms(null,null,this.matrixRotate,

c,this.internalRotationCenter,!1,a,!0,!1)}},"JU.BS,~S,~N,~N");c(b,"setNavFps",function(a){this.navFps=a},"~N");c(b,"calcCameraFactors",function(){Float.isNaN(this.cameraDepth)&&(this.cameraDepth=this.cameraDepthSetting,this.zoomFactor=3.4028235E38);this.cameraDistance=this.cameraDepth*this.screenPixelCount;this.referencePlaneOffset=this.cameraDistance+this.screenPixelCount/2;this.scalePixelsPerAngstrom=this.scale3D&&!this.perspectiveDepth&&1!=this.mode?72/this.scale3DAngstromsPerInch*(this.antialias?

2:1):this.screenPixelCount/this.visualRangeAngstroms;1!=this.mode&&(this.mode=0==this.camera.z?0:2);this.perspectiveShiftXY.set(0==this.camera.z?0:100*(this.camera.x*this.scalePixelsPerAngstrom/this.screenWidth),0==this.camera.z?0:100*(this.camera.y*this.scalePixelsPerAngstrom/this.screenHeight),0);this.modelRadiusPixels=this.modelRadius*this.scalePixelsPerAngstrom;var a=2*this.modelRadius/this.visualRangeAngstroms*this.referencePlaneOffset;if(1==this.mode)this.calcNavCameraFactors(a);else{this.zoomFactor=

3.4028235E38;this.modelCenterOffset=this.referencePlaneOffset;if(!this.scale3D||this.perspectiveDepth)this.scalePixelsPerAngstrom*=this.modelCenterOffset/a*this.zmPct/100;this.modelRadiusPixels=this.modelRadius*this.scalePixelsPerAngstrom}});c(b,"calcNavCameraFactors",function(a){3.4028235E38==this.zoomFactor?(1E4<this.zmPct&&(this.zmPct=1E4),this.modelCenterOffset=100*a/this.zmPct):this.prevZoomSetting!=this.zmPctSet&&(this.modelCenterOffset=0==this.zoomRatio?100*a/this.zmPctSet:this.modelCenterOffset+

(1-this.zoomRatio)*this.referencePlaneOffset,this.navMode=-1);this.prevZoomSetting=this.zmPctSet;this.zoomFactor=this.modelCenterOffset/this.referencePlaneOffset;this.zmPct=0==this.zoomFactor?1E4:100*(a/this.modelCenterOffset)},"~N");c(b,"getPerspectiveFactor",function(a){return 0>=a?this.referencePlaneOffset:this.referencePlaneOffset/a},"~N");c(b,"unTransformPoint",function(a,b){this.untransformedPoint.setT(a);switch(this.mode){case 1:this.untransformedPoint.x-=this.navigationOffset.x;this.untransformedPoint.y-=

this.navigationOffset.y;break;case 2:this.fScrPt.x+=this.perspectiveShiftXY.x,this.fScrPt.y+=this.perspectiveShiftXY.y;case 0:this.untransformedPoint.x-=this.fixedRotationOffset.x,this.untransformedPoint.y-=this.fixedRotationOffset.y}if(this.perspectiveDepth){var c=this.getPerspectiveFactor(this.untransformedPoint.z);this.untransformedPoint.x/=c;this.untransformedPoint.y/=c}switch(this.mode){case 1:this.untransformedPoint.x+=this.navigationShiftXY.x;this.untransformedPoint.y+=this.navigationShiftXY.y;

break;case 2:this.untransformedPoint.x-=this.perspectiveShiftXY.x,this.untransformedPoint.y-=this.perspectiveShiftXY.y}this.matrixTransformInv.rotTrans2(this.untransformedPoint,b)},"JU.T3,JU.T3");c(b,"resetNavigationPoint",function(a){5>this.zmPct&&1!=this.mode?(this.perspectiveDepth=!0,this.mode=1):(1==this.mode?(this.navMode=1,this.slabPercentSetting=0,this.perspectiveDepth=!0):a&&(this.slabPercentSetting=100),this.vwr.setFloatProperty("slabRange",0),a&&this.setSlabEnabled(1==this.mode),this.zoomFactor=

3.4028235E38,this.zmPctSet=this.zmPct)},"~B");c(b,"setNavigatePt",function(a){this.navigationCenter.setT(a);this.navMode=3;this.navigating=!0;this.finalizeTransformParameters();this.navigating=!1},"JU.P3");c(b,"setNavigationSlabOffsetPercent",function(a){this.vwr.g.setF("navigationSlab",a);this.calcCameraFactors();this.navigationSlabOffset=a/50*this.modelRadiusPixels},"~N");c(b,"getNavigationOffset",function(){this.transformPt3f(this.navigationCenter,this.navigationOffset);return this.navigationOffset});

c(b,"getNavPtHeight",function(){return this.height/2});c(b,"getNavigationOffsetPercent",function(a){this.getNavigationOffset();return 0==this.width||0==this.height?0:"X"==a?100*(this.navigationOffset.x-this.width/2)/this.width:100*(this.navigationOffset.y-this.getNavPtHeight())/this.height},"~S");c(b,"getNavigationText",function(a){a=a?" /* navigation center, translation, depth */ ":" ";if(1!=this.mode)return a+"{0 0 0} 0 0 0";this.getNavigationOffset();return a+JU.Escape.eP(this.navigationCenter)+

" "+this.getNavigationOffsetPercent("X")+" "+this.getNavigationOffsetPercent("Y")+" "+this.navigationDepthPercent},"~B");c(b,"setScreenParameters",function(a,b,c,l,f,e){var h=1==this.mode?JU.P3.newP(this.navigationCenter):null,j=JU.P3.newP(this.navigationOffset);j.x/=this.width;j.y/=this.height;this.setScreenParameters0(a,b,c,l,f,e);null!=h&&(this.navigationCenter.setT(h),this.navTranslatePercentOrTo(-1,j.x*this.width,j.y*this.height),this.setNavigatePt(h))},"~N,~N,~B,~B,~B,~B");c(b,"navInterrupt",

function(){null!=this.nav&&this.nav.interrupt()});c(b,"getNav",function(){if(null!=this.nav)return!0;this.nav=J.api.Interface.getOption("navigate.Navigator",this.vwr,"tm");if(null==this.nav)return!1;this.nav.set(this,this.vwr);return!0});c(b,"navigateList",function(a,b){this.getNav()&&this.nav.navigateList(a,b)},"J.api.JmolScriptEvaluator,JU.Lst");c(b,"navigateAxis",function(a,b){this.getNav()&&this.nav.navigateAxis(a,b)},"JU.V3,~N");c(b,"setNavigationOffsetRelative",function(){this.getNav()&&this.nav.setNavigationOffsetRelative()});

c(b,"navigateKey",function(a,b){this.getNav()&&this.nav.navigateKey(a,b)},"~N,~N");c(b,"setNavigationDepthPercent",function(a){this.getNav()&&this.nav.setNavigationDepthPercent(a)},"~N");c(b,"navTranslatePercentOrTo",function(a,b,c){this.getNav()&&this.nav.navTranslatePercentOrTo(a,b,c)},"~N,~N,~N");c(b,"calcNavigationPoint",function(){this.getNav()&&this.nav.calcNavigationPoint()});c(b,"getNavigationState",function(){return 1==this.mode&&this.getNav()?this.nav.getNavigationState():""})});u("JV");

C("java.lang.Enum J.api.JmolViewer $.PlatformViewer J.atomdata.AtomDataServer java.util.Hashtable JU.P3".split(" "),"JV.Viewer","java.util.Arrays JU.AU $.BS $.CU $.DF $.Lst $.P3i $.PT $.Quat $.Rdr $.SB J.adapter.smarter.SmarterJmolAdapter J.api.Interface J.atomdata.RadiusData J.c.FIL $.STER $.VDW J.i18n.GT JM.Measurement $.ModelSet JS.SV $.T J.thread.TimeoutThread JU.BSUtil $.C $.CommandHistory $.Elements $.Escape $.GData $.JmolMolecule $.Logger $.Parser $.TempArray JV.ActionManager $.AnimationManager $.ColorManager $.FileManager $.GlobalSettings $.JC $.ModelManager $.SelectionManager $.ShapeManager $.StateManager $.StatusManager $.TransformManager JV.binding.Binding".split(" "),

function(){var b=v(function(){this.queueOnHold=this.isSingleThreaded=this.isWebGL=this.isJSNoAWT=this.haveDisplay=this.autoExit=this.testAsync=!1;this.fullName="";this.fm=this.ms=this.definedAtomSets=this.compiler=null;this.mustRender=this.listCommands=this.isSyntaxCheck=this.isSyntaxAndFileCheck=this.isJNLP=this.isApplet=!1;this.appletName=this.htmlName="";this.tryPt=0;this.insertedCommand="";this.tm=this.sm=this.g=this.rm=this.slm=this.shm=this.dm=this.cm=this.am=this.acm=this.html5Applet=this.gdata=

null;this.logFilePath=this.syncId="";this.useCommandThread=this.noGraphicsAllowed=this.multiTouch=this.isSilent=this.isSignedAppletLocal=this.isSignedApplet=this.isPrintOnly=this.allowScripting=!1;this.tempArray=this.eval=this.scm=this.stm=this.mm=this.commandHistory=this.internalAccessPath=this.access=this.access0=this.modelAdapter=this.display=this.vwrOptions=this.commandOptions=null;this.async=this.allowArrayDotNotation=!1;this.executor=null;this.screenHeight=this.screenWidth=0;this.errorMessageUntranslated=

this.errorMessage=this.chainList=this.chainMap=this.rd=this.defaultVdw=null;this.privateKey=0;this.dataOnly=!1;this.maximumSize=2147483647;this.gRight=null;this.isStereoSlave=!1;this.imageFontScaling=1;this.antialiased=!1;this.prevFrame=-2147483648;this.prevMorphModel=0;this.haveJDX=!1;this.jzt=this.outputManager=this.jsv=null;this.headless=this.isPreviewOnly=!1;this.movableBitSet=null;this.hasSelected=!1;this.lastData=this.jsc=this.smilesMatcher=this.minimizer=this.dssrParser=this.annotationParser=

this.ligandModelSet=this.ligandModels=this.mouse=null;this.motionEventNumber=0;this.inMotion=!1;this.refreshing=!0;this.axesAreTainted=!1;this.jsParams=this.captureParams=null;this.cirChecked=!1;this.hoverAtomIndex=-1;this.hoverText=null;this.hoverLabel="%U";this.hoverEnabled=!0;this.currentCursor=0;this.ptTemp=null;this.selectionHalosEnabled=!1;this.noFrankEcho=this.frankOn=!0;this.scriptEditorVisible=!1;this.pm=this.headlessImageParams=this.modelkit=this.jmolpopup=this.scriptEditor=this.appConsole=

null;this.isTainted=!0;this.showSelected=this.movingSelected=!1;this.ptNew=this.ptScreenNew=this.ptScreen=null;this.atomHighlighted=-1;this.creatingImage=!1;this.userVdwMars=this.userVdws=this.bsUserVdws=null;this.currentShapeID=-1;this.localFunctions=this.currentShapeState=null;this.$isKiosk=!1;this.displayLoadErrors=!0;this.$isParallel=!1;this.stateScriptVersionInt=2147483647;this.timeouts=this.jsExporter3D=null;this.chainCaseSpecified=!1;this.macros=this.nboParser=this.triangulator=this.jsonParser=

this.jcm=this.jbr=this.logFileName=this.nmrCalculation=null;this.consoleFontScale=1;r(this,arguments)},JV,"Viewer",J.api.JmolViewer,[J.atomdata.AtomDataServer,J.api.PlatformViewer]);Q(b,function(){this.ptScreen=new JU.P3;this.ptScreenNew=new JU.P3;this.ptNew=new JU.P3});z(b,function(a){L(this,JV.Viewer,[]);this.commandHistory=new JU.CommandHistory;this.rd=new J.atomdata.RadiusData(null,0,null,null);this.defaultVdw=J.c.VDW.JMOL;this.localFunctions=new java.util.Hashtable;this.privateKey=Math.random();

this.chainMap=new java.util.Hashtable;this.chainList=new JU.Lst;this.setOptions(a)},"java.util.Map");c(b,"finalize",function(){JU.Logger.debugging&&JU.Logger.debug("vwr finalize "+this);$(this,JV.Viewer,"finalize",[])});c(b,"setInsertedCommand",function(a){this.insertedCommand=a},"~S");b.getJmolVersion=j(b,"getJmolVersion",function(){return null==JV.Viewer.version_date?JV.Viewer.version_date=JV.JC.version+" "+JV.JC.date:JV.Viewer.version_date});b.allocateViewer=c(b,"allocateViewer",function(a,b,

c,f,e,h,j,m){var n=new java.util.Hashtable;n.put("display",a);n.put("adapter",b);n.put("statusListener",j);n.put("platform",m);n.put("options",h);n.put("fullName",c);n.put("documentBase",f);n.put("codeBase",e);return new JV.Viewer(n)},"~O,J.api.JmolAdapter,~S,java.net.URL,java.net.URL,~S,J.api.JmolStatusListener,J.api.GenericPlatform");c(b,"haveAccess",function(a){return this.access===a},"JV.Viewer.ACCESS");j(b,"getModelAdapter",function(){return null==this.modelAdapter?this.modelAdapter=new J.adapter.smarter.SmarterJmolAdapter:

this.modelAdapter});j(b,"getSmartsMatch",function(a,b){null==b&&(b=this.bsA());return this.getSmilesMatcher().getSubstructureSet(a,this.ms.at,this.ms.ac,b,2)},"~S,JU.BS");c(b,"isSubstructure",function(a,b){try{var c=this.getSmilesMatcher().find(a,b,10);return null!=c&&0<c.length}catch(f){if(F(f,Exception))return!1;throw f;}},"~S,~S");c(b,"hasStructure",function(a,b,c){try{return 1==this.getSmilesMatcher().hasStructure(a,w(-1,[b]),(c?2:1)|8)[0]}catch(f){if(F(f,Exception))return!1;throw f;}},"~S,~S,~B");

c(b,"getSmartsMatchForNodes",function(a,b){return this.getSmilesMatcher().getSubstructureSet(a,b,b.length,null,2)},"~S,~A");c(b,"getSmartsMap",function(a,b,c){null==b&&(b=this.bsA());0==c&&(c=2);return this.getSmilesMatcher().getCorrelationMaps(a,this.ms.at,this.ms.ac,b,c)},"~S,JU.BS,~N");c(b,"setOptions",function(a){this.vwrOptions=a;JU.Logger.debugging&&JU.Logger.debug("Viewer constructor "+this);this.modelAdapter=a.get("adapter");var b=a.get("statusListener");this.fullName=a.get("fullName");null==

this.fullName&&(this.fullName="");var c=a.get("codePath");null==c&&(c="../java/");JV.Viewer.appletCodeBase=c.toString();JV.Viewer.appletIdiomaBase=JV.Viewer.appletCodeBase.substring(0,JV.Viewer.appletCodeBase.lastIndexOf("/",JV.Viewer.appletCodeBase.length-2)+1)+"idioma";c=a.get("documentBase");JV.Viewer.appletDocumentBase=null==c?"":c.toString();c=a.get("options");this.commandOptions=null==c?"":c.toString();(a.containsKey("debug")||0<=this.commandOptions.indexOf("-debug"))&&JU.Logger.setLogLevel(5);

this.isApplet&&a.containsKey("maximumSize")&&this.setMaximumSize(a.get("maximumSize").intValue());(this.isJNLP=this.checkOption2("isJNLP","-jnlp"))&&JU.Logger.info("setting JNLP mode TRUE");this.isApplet=(this.isSignedApplet=this.isJNLP||this.checkOption2("signedApplet","-signed"))||this.checkOption2("applet","-applet");this.allowScripting=!this.checkOption2("noscripting","-noscripting");var f=this.fullName.indexOf("__");this.htmlName=0>f?this.fullName:this.fullName.substring(0,f);this.appletName=

JU.PT.split(this.htmlName+"_","_")[0];this.syncId=0>f?"":this.fullName.substring(f+2,this.fullName.length-2);this.access=this.access0=this.checkOption2("access:READSPT","-r")?JV.Viewer.ACCESS.READSPT:this.checkOption2("access:NONE","-R")?JV.Viewer.ACCESS.NONE:JV.Viewer.ACCESS.ALL;(this.isPreviewOnly=a.containsKey("previewOnly"))&&a.remove("previewOnly");this.isPrintOnly=this.checkOption2("printOnly","-p");this.dataOnly=this.checkOption2("isDataOnly","\x00");this.autoExit=this.checkOption2("exit",

"-x");c=a.get("platform");f="unknown";null==c&&(c=this.commandOptions.contains("platform=")?this.commandOptions.substring(this.commandOptions.indexOf("platform=")+9):"J.awt.Platform");if("string"==typeof c){f=c;this.isWebGL=0<=f.indexOf(".awtjs.");JV.Viewer.isJS=this.isJSNoAWT=this.isWebGL||0<=f.indexOf(".awtjs2d.");this.async=!this.dataOnly&&!this.autoExit&&(this.testAsync||JV.Viewer.isJS&&a.containsKey("async"));var e=c=null,h="?";self.Jmol&&(e=Jmol,c=Jmol._applets[this.htmlName.split("_object")[0]],

h=Jmol._version);null!=h&&(this.html5Applet=c,JV.Viewer.jmolObject=e,JV.Viewer.strJavaVersion=h,JV.Viewer.strJavaVendor="Java2Script "+(this.isWebGL?"(WebGL)":"(HTML5)"));c=J.api.Interface.getInterface(f,this,"setOptions")}this.apiPlatform=c;this.display=a.get("display");this.isSingleThreaded=this.apiPlatform.isSingleThreaded();this.noGraphicsAllowed=this.checkOption2("noDisplay","-n");this.headless=this.apiPlatform.isHeadless();this.haveDisplay=this.isWebGL||null!=this.display&&!this.noGraphicsAllowed&&

!this.headless&&!this.dataOnly;this.noGraphicsAllowed=(new Boolean(this.noGraphicsAllowed&null==this.display)).valueOf();this.headless=(new Boolean(this.headless|this.noGraphicsAllowed)).valueOf();this.haveDisplay?(this.mustRender=!0,this.multiTouch=this.checkOption2("multiTouch","-multitouch"),this.isWebGL||(this.display=document.getElementById(this.display))):this.display=null;this.apiPlatform.setViewer(this,this.display);c=a.get("graphicsAdapter");null==c&&!this.isWebGL&&(c=J.api.Interface.getOption("g3d.Graphics3D",

this,"setOptions"));this.gdata=null==c&&(this.isWebGL||!JV.Viewer.isJS)?new JU.GData:c;this.gdata.initialize(this,this.apiPlatform);this.stm=new JV.StateManager(this);this.cm=new JV.ColorManager(this,this.gdata);this.sm=new JV.StatusManager(this);f=a.containsKey("4DMouse");this.tm=JV.TransformManager.getTransformManager(this,2147483647,0,f);this.slm=new JV.SelectionManager(this);this.haveDisplay&&(this.acm=this.multiTouch?J.api.Interface.getOption("multitouch.ActionManagerMT",null,null):new JV.ActionManager,

this.acm.setViewer(this,this.commandOptions+"-multitouch-"+a.get("multiTouch")),this.mouse=this.apiPlatform.getMouseManager(this.privateKey,this.display),this.multiTouch&&!this.checkOption2("-simulated","-simulated")&&this.apiPlatform.setTransparentCursor(this.display));this.mm=new JV.ModelManager(this);this.shm=new JV.ShapeManager(this);this.tempArray=new JU.TempArray;this.am=new JV.AnimationManager(this);c=a.get("repaintManager");null==c&&(c=J.api.Interface.getOption("render.RepaintManager",this,

"setOptions"));if(JV.Viewer.isJS||null!=c&&!c.equals(""))(this.rm=c).set(this,this.shm);this.ms=new JM.ModelSet(this,null);this.initialize(!0,!1);this.fm=new JV.FileManager(this);this.definedAtomSets=new java.util.Hashtable;this.setJmolStatusListener(b);this.isApplet?(JU.Logger.info("vwrOptions: \n"+JU.Escape.escapeMap(this.vwrOptions)),b=this.vwrOptions.get("documentLocation"),!JV.Viewer.isJS&&(null!=b&&b.startsWith("file:/"))&&(b=b.substring(0,b.substring(0,(b+"?").indexOf("?")).lastIndexOf("/")),

JU.Logger.info("setting current directory to "+b),this.cd(b)),b=JV.Viewer.appletDocumentBase,f=b.indexOf("#"),0<=f&&(b=b.substring(0,f)),f=b.lastIndexOf("?"),0<=f&&(b=b.substring(0,f)),f=b.lastIndexOf("/"),0<=f&&(b=b.substring(0,f)),JV.Viewer.jsDocumentBase=b,this.fm.setAppletContext(JV.Viewer.appletDocumentBase),b=a.get("appletProxy"),null!=b&&this.setStringProperty("appletProxy",b),this.isSignedApplet?(this.logFilePath=JU.PT.rep(JV.Viewer.appletCodeBase,"file://",""),this.logFilePath=JU.PT.rep(this.logFilePath,

"file:/",""),0<=this.logFilePath.indexOf("//")?this.logFilePath=null:this.isSignedAppletLocal=!0):JV.Viewer.isJS||(this.logFilePath=null),new J.i18n.GT(this,a.get("language")),JV.Viewer.isJS&&this.acm.createActions()):(this.gdata.setBackgroundTransparent(this.checkOption2("backgroundTransparent","-b")),(this.isSilent=this.checkOption2("silent","-i"))&&JU.Logger.setLogLevel(3),this.headless&&!this.isSilent&&JU.Logger.info("Operating headless display="+this.display+" nographicsallowed="+this.noGraphicsAllowed),

this.isSyntaxCheck=(this.isSyntaxAndFileCheck=this.checkOption2("checkLoad","-C"))||this.checkOption2("check","-c"),this.listCommands=this.checkOption2("listCommands","-l"),this.cd("."),this.headless&&(this.headlessImageParams=a.get("headlessImage"),c=a.get("headlistMaxTimeMs"),null==c&&(c=Integer.$valueOf(6E4)),this.setTimeout(""+Math.random(),c.intValue(),"exitJmol")));this.useCommandThread=!this.headless&&this.checkOption2("useCommandThread","-threaded");this.setStartupBooleans();this.setIntProperty("_nProcessors",

JV.Viewer.nProcessors);this.isSilent||JU.Logger.info("(C) 2015 Jmol Development\nJmol Version: "+JV.Viewer.getJmolVersion()+"\njava.vendor: "+JV.Viewer.strJavaVendor+"\njava.version: "+JV.Viewer.strJavaVersion+"\nos.name: "+JV.Viewer.strOSName+"\nAccess: "+this.access+"\nmemory: "+this.getP("_memory")+"\nprocessors available: "+JV.Viewer.nProcessors+"\nuseCommandThread: "+this.useCommandThread+(!this.isApplet?"":"\nappletId:"+this.htmlName+(this.isSignedApplet?" (signed)":"")));this.zap(!1,!0,!1);

this.g.setO("language",J.i18n.GT.getLanguage());this.g.setO("_hoverLabel",this.hoverLabel);this.stm.setJmolDefaults();JU.Elements.covalentVersion=1;this.allowArrayDotNotation=!0;this.allowScripting&&this.getScriptManager()},"java.util.Map");c(b,"setMaximumSize",function(a){this.maximumSize=Math.max(a,100)},"~N");c(b,"setStereo",function(a,b){this.isStereoSlave=a;this.gRight=b},"~B,~O");c(b,"getMenu",function(a){this.getPopupMenu();return a.equals("\x00")?(this.popupMenu(this.screenWidth-120,0,"j"),

"OK"):null==this.jmolpopup?"":this.jmolpopup.jpiGetMenuAsString("Jmol version "+JV.Viewer.getJmolVersion()+"|_GET_MENU|"+a)},"~S");j(b,"resizeInnerPanel",function(a,b){if(!this.autoExit&&this.haveDisplay)return this.sm.resizeInnerPanel(a,b);this.setScreenDimension(a,b);return E(-1,[this.screenWidth,this.screenHeight])},"~N,~N");j(b,"setScreenDimension",function(a,b){b=Math.min(b,this.maximumSize);a=Math.min(a,this.maximumSize);this.tm.stereoDoubleFull&&(a=B((a+1)/2));this.screenWidth==a&&this.screenHeight==

b||this.resizeImage(a,b,!1,!1,!0)},"~N,~N");c(b,"resizeImage",function(a,b,c,f,e){if(c||!this.creatingImage){var h=this.antialiased;this.antialiased=e?this.g.antialiasDisplay&&this.checkMotionRendering(603979786):c&&!f?this.g.antialiasImages:!1;!f&&(!c&&(0<a||h!=this.antialiased))&&this.setShapeProperty(5,"clearBoxes",null);this.imageFontScaling=(this.antialiased?2:1)*(e||this.tm.scale3D||0>=a?1:1*(this.g.zoomLarge==b>a?b:a)/this.getScreenDim());0<a?(this.screenWidth=a,this.screenHeight=b,c||(this.g.setI("_width",

a),this.g.setI("_height",b))):(a=0==this.screenWidth?this.screenWidth=500:this.screenWidth,b=0==this.screenHeight?this.screenHeight=500:this.screenHeight);this.tm.setScreenParameters(a,b,c||e?this.g.zoomLarge:!1,this.antialiased,!1,!1);this.gdata.setWindowParameters(a,b,this.antialiased);this.setModelkitPropertySafely("frameresized",null);0<a&&!c&&this.setStatusResized(a,b)}},"~N,~N,~B,~B,~B");j(b,"getScreenWidth",function(){return this.screenWidth});j(b,"getScreenHeight",function(){return this.screenHeight});

c(b,"getScreenDim",function(){return this.g.zoomLarge==this.screenHeight>this.screenWidth?this.screenHeight:this.screenWidth});c(b,"setWidthHeightVar",function(){this.g.setI("_width",this.screenWidth);this.g.setI("_height",this.screenHeight)});c(b,"getBoundBoxCenterX",function(){return B(this.screenWidth/2)});c(b,"getBoundBoxCenterY",function(){return B(this.screenHeight/2)});c(b,"updateWindow",function(a,b){if(!this.refreshing||this.creatingImage)return this.refreshing?!1:!JV.Viewer.isJS;(this.isTainted||

this.tm.slabEnabled)&&this.setModelVisibility();this.isTainted=!1;null!=this.rm&&0!=a&&this.setScreenDimension(a,b);return!0},"~N,~N");c(b,"getImage",function(a,b){var c=null;try{this.beginRendering(a,b),this.render(),this.gdata.endRendering(),c=this.gdata.getScreenImage(b)}catch(f){if(F(f,Error))this.gdata.getScreenImage(b),this.handleError(f,!1),this.setErrorMessage("Error during rendering: "+f,null);else if(F(f,Exception))System.out.println("render error"+f);else throw f;}return c},"~B,~B");c(b,

"beginRendering",function(a,b){this.gdata.beginRendering(this.tm.getStereoRotationMatrix(a),this.g.translucent,b,!this.checkMotionRendering(1111490588))},"~B,~B");c(b,"render",function(){if(!(null==this.mm.modelSet||!this.mustRender||!this.refreshing&&!this.creatingImage||null==this.rm)){var a=this.antialiased&&this.g.antialiasTranslucent,b=this.shm.finalizeAtoms(this.tm.bsSelectedAtoms,!0);this.isWebGL?(this.rm.renderExport(this.gdata,this.ms,this.jsParams),this.notifyViewerRepaintDone()):(this.rm.render(this.gdata,

this.ms,!0,b),this.gdata.setPass2(a)&&(this.tm.setAntialias(a),this.rm.render(this.gdata,this.ms,!1,null),this.tm.setAntialias(this.antialiased)))}});c(b,"drawImage",function(a,b,c,f,e){null!=a&&null!=b&&this.apiPlatform.drawImage(a,b,c,f,this.screenWidth,this.screenHeight,e);this.gdata.releaseScreenImage()},"~O,~O,~N,~N,~B");c(b,"getScreenImage",function(){return this.getScreenImageBuffer(null,!0)});j(b,"getScreenImageBuffer",function(a,b){if(this.isWebGL)return b?this.apiPlatform.allocateRgbImage(0,

0,null,0,!1,!0):null;var c=this.tm.stereoDoubleFull||this.tm.stereoDoubleDTI,f=this.tm.stereoMode.isBiColor(),e=null==a&&c;f?(this.beginRendering(!0,b),this.render(),this.gdata.endRendering(),this.gdata.snapshotAnaglyphChannelBytes(),this.beginRendering(!1,b),this.render(),this.gdata.endRendering(),this.gdata.applyAnaglygh(this.tm.stereoMode,this.tm.stereoColors),f=this.gdata.getScreenImage(b)):f=this.getImage(c,b);var h=null;e&&(h=this.apiPlatform.newBufferedImage(f,this.tm.stereoDoubleDTI?this.screenWidth:

this.screenWidth<<1,this.screenHeight),a=this.apiPlatform.getGraphics(h));null!=a&&(c&&(this.tm.stereoMode===J.c.STER.DTI?(this.drawImage(a,f,this.screenWidth>>1,0,!0),f=this.getImage(!1,!1),this.drawImage(a,f,0,0,!0),a=null):(this.drawImage(a,f,this.screenWidth,0,!1),f=this.getImage(!1,!1))),null!=a&&this.drawImage(a,f,0,0,!1));return e?h:f},"~O,~B");c(b,"evalStringWaitStatusQueued",function(a,b,c,f,e){return null==this.getScriptManager()?null:this.scm.evalStringWaitStatusQueued(a,b,c,f,e)},"~S,~S,~S,~B,~B");

c(b,"popupMenu",function(a,b,c){if(this.haveDisplay&&this.refreshing&&!this.isPreviewOnly&&!this.g.disablePopupMenu)switch(c.charCodeAt(0)){case 106:try{this.getPopupMenu(),this.jmolpopup.jpiShow(a,b)}catch(f){JU.Logger.info(f.toString()),this.g.disablePopupMenu=!0}break;case 97:case 98:case 109:if(null==this.getModelkit(!0))break;this.modelkit.showMenu(a,b)}},"~N,~N,~S");c(b,"getModelkit",function(a){null==this.modelkit?(this.modelkit=J.api.Interface.getInterface("J.modelkit.ModelKit",this,"script")).setMenu(this.apiPlatform.getMenuPopup(null,

"m")):a&&this.modelkit.updateMenu();return this.modelkit},"~B");c(b,"getPopupMenu",function(){if(this.g.disablePopupMenu)return null;if(null==this.jmolpopup&&(this.jmolpopup=this.allowScripting?this.apiPlatform.getMenuPopup(this.menuStructure,"j"):null,null==this.jmolpopup))return this.async||(this.g.disablePopupMenu=!0),null;this.isJSNoAWT&&this.checkMenuUpdate();return this.jmolpopup.jpiGetMenuAsObject()});j(b,"setMenu",function(a,b){b&&JU.Logger.info("Setting menu "+(0==a.length?"to Jmol defaults":

"from file "+a));0==a.length?a=null:b&&(a=this.getFileAsString3(a,!1,null));this.getProperty("DATA_API","setMenu",a);this.sm.setCallbackFunction("menu",a)},"~S,~B");c(b,"setStatusFrameChanged",function(a){a&&(this.prevFrame=-2147483648);this.tm.setVibrationPeriod(NaN);var b=this.am.firstFrameIndex,c=this.am.lastFrameIndex,f=this.am.isMovie;a=this.am.cmi;b==c&&!f&&(a=b);var e=this.getModelFileNumber(a),h=this.am.cmi,j=e,m=e%1E6,n=f?b:this.getModelFileNumber(b),p=f?c:this.getModelFileNumber(c),q;f?

q=""+(h+1):0==j?(q=this.getModelNumberDotted(b),b!=c&&(q+=" - "+this.getModelNumberDotted(c)),B(n/1E6)==B(p/1E6)&&(j=n)):q=this.getModelNumberDotted(a);0!=j&&(j=1E6>j?1:B(j/1E6));f||(this.g.setI("_currentFileNumber",j),this.g.setI("_currentModelNumberInFile",m));b=this.am.currentMorphModel;this.g.setI("_currentFrame",h);this.g.setI("_morphCount",this.am.morphCount);this.g.setF("_currentMorphFrame",b);this.g.setI("_frameID",e);this.g.setI("_modelIndex",a);this.g.setO("_modelNumber",q);this.g.setO("_modelName",

0>a?"":this.getModelName(a));e=0>a?"":this.ms.getModelTitle(a);this.g.setO("_modelTitle",null==e?"":e);this.g.setO("_modelFile",0>a?"":this.ms.getModelFileName(a));this.g.setO("_modelType",0>a?"":this.ms.getModelFileType(a));h==this.prevFrame&&b==this.prevMorphModel||(this.prevFrame=h,this.prevMorphModel=b,e=this.getModelName(h),f?e=""+(""===e?h+1:this.am.caf+1)+": "+e:(f=""+this.getModelNumberDotted(h),f.equals(e)||(e=f+": "+e)),this.sm.setStatusFrameChanged(j,m,0>this.am.animationDirection?-n:n,

0>this.am.currentDirection?-p:p,h,b,e),this.doHaveJDX()&&this.getJSV().setModel(a),JV.Viewer.isJS&&this.updateJSView(a,-1))},"~B,~B");c(b,"doHaveJDX",function(){return this.haveJDX||(this.haveJDX=this.getBooleanProperty("_jspecview"))});c(b,"getJSV",function(){null==this.jsv&&(this.jsv=J.api.Interface.getOption("jsv.JSpecView",this,"script"),this.jsv.setViewer(this));return this.jsv});c(b,"getJDXBaseModelIndex",function(a){return!this.doHaveJDX()?a:this.getJSV().getBaseModelIndex(a)},"~N");c(b,"getJspecViewProperties",

function(a){a=this.sm.getJspecViewProperties(""+a);null!=a&&(this.haveJDX=!0);return a},"~O");c(b,"scriptEcho",function(a){JU.Logger.isActiveLevel(4)&&(JV.Viewer.isJS&&System.out.println(a),this.sm.setScriptEcho(a,this.isScriptQueued()),this.listCommands&&(null!=a&&0==a.indexOf("$["))&&JU.Logger.info(a))},"~S");c(b,"isScriptQueued",function(){return null!=this.scm&&this.scm.isScriptQueued()});c(b,"notifyError",function(a,b,c){this.g.setO("_errormessage",c);this.sm.notifyError(a,b,c)},"~S,~S,~S");

c(b,"jsEval",function(a){return""+this.sm.jsEval(a)},"~S");c(b,"jsEvalSV",function(a){return JS.SV.getVariable(JV.Viewer.isJS?this.sm.jsEval(a):this.jsEval(a))},"~S");c(b,"setFileLoadStatus",function(a,b,c,f,e,h){this.setErrorMessage(e,null);this.g.setI("_loadPoint",a.getCode());var j=a!==J.c.FIL.CREATING_MODELSET;j&&this.setStatusFrameChanged(!1,!1);this.sm.setFileLoadStatus(b,c,f,e,a.getCode(),j,h);j&&(this.doHaveJDX()&&this.getJSV().setModel(this.am.cmi),JV.Viewer.isJS&&this.updateJSView(this.am.cmi,

-2))},"J.c.FIL,~S,~S,~S,~S,Boolean");c(b,"getZapName",function(){return this.g.modelKitMode?"Jmol Model Kit":"zapped"});c(b,"setStatusMeasuring",function(a,b,c,f){this.sm.setStatusMeasuring(a,b,c,f)},"~S,~N,~S,~N");c(b,"notifyMinimizationStatus",function(){var a=this.getP("_minimizationStep"),b=this.getP("_minimizationForceField"),c=this.getP("_minimizationStatus"),f="starting".equals(c),e="done".equals(c)||"failed".equals(c),h=null!=this.minimizer&&(e||f)?this.minimizer.bsAtoms:null,j=null==h?-1:

h.nextSetBit(0),m=0<=j?this.getModelIndexForAtom(j):-1;f&&0<=j&&this.sm.setStatusStructureModified(j,m,3,"minimize:"+c,h.cardinality(),h);this.sm.notifyMinimizationStatus(c,"string"==typeof a?Integer.$valueOf(0):a,this.getP("_minimizationEnergy"),a.toString().equals("0")?Float.$valueOf(0):this.getP("_minimizationEnergyDiff"),b);e&&0<=j&&this.sm.setStatusStructureModified(j,m,-3,"minimize:"+c,h.cardinality(),h)});c(b,"setStatusAtomPicked",function(a,b,c,f){f&&this.setSelectionSet(JU.BSUtil.newAndSetBit(a));

null==b&&(b=this.g.pickLabel,b=0==b.length?this.getAtomInfoXYZ(a,this.g.messageStyleChime?4:2)+(null==this.getOperativeSymmetry()?"":" ("+this.getAtomInfoXYZ(a,3)+")"):this.ms.getAtomInfo(a,b,this.ptTemp));this.setPicked(a,!1);0>a&&(f=this.getPendingMeasurement(),null!=f&&(b=b.substring(0,b.length-1)+',"'+f.getString()+'"]'));this.g.setO("_pickinfo",b);this.sm.setStatusAtomPicked(a,b,c);0>a||(1==this.sm.getSyncMode()&&this.doHaveJDX()&&this.getJSV().atomPicked(a),JV.Viewer.isJS&&this.updateJSView(this.ms.at[a].mi,

a))},"~N,~S,java.util.Map,~B");j(b,"getProperty",function(a,b,c){if(!"DATA_API".equals(a))return this.getPropertyManager().getProperty(a,b,c);switch("scriptCheck.........consoleText.........scriptEditor........scriptEditorState...getAppConsole.......getScriptEditor.....setMenu.............spaceGroupInfo......disablePopupMenu....defaultDirectory....getPopupMenu........shapeManager........getPreference.......".indexOf(b)){case 0:return this.scriptCheckRet(c,!0);case 20:return null==this.appConsole?

"":this.appConsole.getText();case 40:return this.showEditor(c),null;case 60:return this.scriptEditorVisible=c.booleanValue(),null;case 80:return this.$isKiosk?this.appConsole=null:y(c,"J.api.JmolAppConsoleInterface")?this.appConsole=c:null!=c&&!c.booleanValue()?this.appConsole=null:null==this.appConsole&&(null!=c&&c.booleanValue())&&(JV.Viewer.isJS&&(this.appConsole=J.api.Interface.getOption("consolejs.AppletConsole",this,"script")),null!=this.appConsole&&this.appConsole.start(this)),this.scriptEditor=

JV.Viewer.isJS||null==this.appConsole?null:this.appConsole.getScriptEditor(),this.appConsole;case 100:return null==this.appConsole&&(null!=c&&c.booleanValue())&&(this.getProperty("DATA_API","getAppConsole",Boolean.TRUE),this.scriptEditor=null==this.appConsole?null:this.appConsole.getScriptEditor()),this.scriptEditor;case 120:return null!=this.jmolpopup&&this.jmolpopup.jpiDispose(),this.jmolpopup=null,this.menuStructure=c;case 140:return this.getSymTemp().getSpaceGroupInfo(this.ms,null,-1,!1,null);

case 160:return this.g.disablePopupMenu=!0,null;case 180:return this.g.defaultDirectory;case 200:return"string"==typeof c?this.getMenu(c):this.getPopupMenu();case 220:return this.shm.getProperty(c);case 240:return this.sm.syncSend("getPreference",c,1)}JU.Logger.error("ERROR in getProperty DATA_API: "+b);return null},"~S,~S,~O");c(b,"notifyMouseClicked",function(a,b,c,f){var e=JV.binding.Binding.getButtonMods(c),h=JV.binding.Binding.getClickCount(c);this.g.setI("_mouseX",a);this.g.setI("_mouseY",this.screenHeight-

b);this.g.setI("_mouseAction",c);this.g.setI("_mouseModifiers",e);this.g.setI("_clickCount",h);return this.sm.setStatusClicked(a,this.screenHeight-b,c,h,f)},"~N,~N,~N,~N");c(b,"getOutputManager",function(){return null!=this.outputManager?this.outputManager:(this.outputManager=J.api.Interface.getInterface("JV.OutputManager"+(JV.Viewer.isJS?"JS":"Awt"),this,"file")).setViewer(this,this.privateKey)});c(b,"getJzt",function(){return null==this.jzt?this.jzt=J.api.Interface.getInterface("JU.ZipTools",this,

"zip"):this.jzt});c(b,"readFileAsMap",function(a,b,c){this.getJzt().readFileAsMap(a,b,c)},"java.io.BufferedInputStream,java.util.Map,~S");c(b,"getZipDirectoryAsString",function(a){a=this.fm.getBufferedInputStreamOrErrorMessageFromName(a,a,!1,!1,null,!1,!0);return this.getJzt().getZipDirectoryAsStringAndClose(a)},"~S");j(b,"getImageAsBytes",function(a,b,c,f,e){return this.getOutputManager().getImageAsBytes(a,b,c,f,e)},"~S,~N,~N,~N,~A");j(b,"releaseScreenImage",function(){this.gdata.releaseScreenImage()});

c(b,"setDisplay",function(a){this.display=a;this.apiPlatform.setViewer(this,a)},"~O");c(b,"newMeasurementData",function(a,b){return J.api.Interface.getInterface("JM.MeasurementData",this,"script").init(a,this,b)},"~S,JU.Lst");c(b,"getDataManager",function(){return null==this.dm?this.dm=J.api.Interface.getInterface("JV.DataManager",this,"script").set(this):this.dm});c(b,"getScriptManager",function(){if(this.allowScripting&&null==this.scm){this.scm=J.api.Interface.getInterface("JS.ScriptManager",this,

"setOptions");if(JV.Viewer.isJS&&null==this.scm)throw new NullPointerException;if(null==this.scm)return this.allowScripting=!1,null;this.eval=this.scm.setViewer(this);this.useCommandThread&&this.scm.startCommandWatcher(!0)}return this.scm});c(b,"checkOption2",function(a,b){return this.vwrOptions.containsKey(a)&&!this.vwrOptions.get(a).toString().equals("false")||0<=this.commandOptions.indexOf(b)},"~S,~S");c(b,"setStartupBooleans",function(){this.setBooleanProperty("_applet",this.isApplet);this.setBooleanProperty("_jspecview",

!1);this.setBooleanProperty("_signedApplet",this.isSignedApplet);this.setBooleanProperty("_headless",this.headless);this.setStringProperty("_restrict",'"'+this.access+'"');this.setBooleanProperty("_useCommandThread",this.useCommandThread);this.setBooleanPropertyTok("doubleprecision",603979831,!1)});c(b,"getExportDriverList",function(){return this.haveAccess(JV.Viewer.ACCESS.ALL)?this.g.getParameter("exportDrivers",!0):""});j(b,"dispose",function(){this.gRight=null;null!=this.mouse&&(this.acm.dispose(),

this.mouse.dispose(),this.mouse=null);this.clearScriptQueue();this.clearThreads();this.haltScriptExecution();null!=this.scm&&this.scm.clear(!0);this.gdata.destroy();null!=this.jmolpopup&&this.jmolpopup.jpiDispose();null!=this.modelkit&&this.modelkit.dispose();try{null!=this.appConsole&&(this.appConsole.dispose(),this.appConsole=null),null!=this.scriptEditor&&(this.scriptEditor.dispose(),this.scriptEditor=null)}catch(a){if(!F(a,Exception))throw a;}});c(b,"reset",function(a){this.ms.setBoundBox(null,

null,!0,0);this.axesAreTainted=!0;this.tm.homePosition(a);this.ms.setCrystallographicDefaults()?this.stm.setCrystallographicDefaults():this.setAxesMode(603979809);this.prevFrame=-2147483648;this.tm.spinOn||this.setSync()},"~B");j(b,"homePosition",function(){this.evalString("reset spin")});c(b,"initialize",function(a,b){this.g=new JV.GlobalSettings(this,this.g,a);this.setStartupBooleans();this.setWidthHeightVar();this.haveDisplay&&(this.g.setB("_is2D",JV.Viewer.isJS&&!this.isWebGL),this.g.setB("_multiTouchClient",

this.acm.isMTClient()),this.g.setB("_multiTouchServer",this.acm.isMTServer()));this.cm.setDefaultColors(!1);this.setObjectColor("background","black");this.setObjectColor("axis1","red");this.setObjectColor("axis2","green");this.setObjectColor("axis3","blue");this.am.setAnimationOn(!1);this.am.setAnimationFps(this.g.animationFps);this.sm.playAudio(null);this.sm.allowStatusReporting=this.g.statusReporting;this.setBooleanPropertyTok("antialiasDisplay",603979786,b?!0:this.g.antialiasDisplay);this.stm.resetLighting();

this.tm.setDefaultPerspective()},"~B,~B");c(b,"saveModelOrientation",function(){this.ms.saveModelOrientation(this.am.cmi,this.stm.getOrientation())});c(b,"restoreModelOrientation",function(a){a=this.ms.getModelOrientation(a);null!=a&&a.restore(-1,!0)},"~N");c(b,"restoreModelRotation",function(a){a=this.ms.getModelOrientation(a);null!=a&&a.restore(-1,!1)},"~N");c(b,"getGLmolView",function(){var a=this.tm,b=a.fixedRotationCenter,c=a.getRotationQ();return{center:b,quaternion:c,xtrans:a.xTranslationFraction,

ytrans:a.yTranslationFraction,scale:a.scalePixelsPerAngstrom,zoom:a.zmPctSet,cameraDistance:a.cameraDistance,pixelCount:a.screenPixelCount,perspective:a.perspectiveDepth,width:a.width,height:a.height}});c(b,"setRotationRadius",function(a,b){b&&(a=this.tm.setRotationRadius(a,!1));this.ms.setRotationRadius(this.am.cmi,a)&&this.g.setF("rotationRadius",a)},"~N,~B");c(b,"setCenterBitSet",function(a,b){this.isJmolDataFrame()||this.tm.setNewRotationCenter(0<JU.BSUtil.cardinalityOf(a)?this.ms.getAtomSetCenter(a):

null,b)},"JU.BS,~B");c(b,"setNewRotationCenter",function(a){this.isJmolDataFrame()||this.tm.setNewRotationCenter(a,!0)},"JU.P3");c(b,"navigate",function(a,b){this.isJmolDataFrame()||(this.tm.navigateKey(a,b),!this.tm.vibrationOn&&0!=a&&this.refresh(1,"Viewer:navigate()"))},"~N,~N");c(b,"move",function(a,b,c,f,e,h,j){this.tm.move(a,b,c,f,e,h,j);this.moveUpdate(h)},"J.api.JmolScriptEvaluator,JU.V3,~N,JU.V3,~N,~N,~N");c(b,"moveTo",function(a,b,c,f,e,h,j,m,n,p,q,r,s,u,v,w,y){this.haveDisplay||(b=0);this.setTainted(!0);

this.tm.moveTo(a,b,c,f,e,h,j,m,n,p,q,r,s,u,v,w,y)},"J.api.JmolScriptEvaluator,~N,JU.P3,JU.V3,~N,JU.M3,~N,~N,~N,~N,JU.P3,~N,~N,~N,~N,~N,~N");c(b,"moveUpdate",function(a){0<a?this.requestRepaintAndWait("moveUpdate"):0==a&&this.setSync()},"~N");c(b,"navigatePt",function(a){this.tm.setNavigatePt(a);this.setSync()},"JU.P3");c(b,"navigateAxis",function(a,b){this.tm.navigateAxis(a,b);this.setSync()},"JU.V3,~N");c(b,"navTranslatePercent",function(a,b){this.isJmolDataFrame()||(this.tm.navTranslatePercentOrTo(0,

a,b),this.setSync())},"~N,~N");c(b,"zoomBy",function(a){this.tm.zoomBy(a);this.refresh(2,this.sm.syncingMouse?"Mouse: zoomBy "+a:"")},"~N");c(b,"zoomByFactor",function(a,b,c){this.tm.zoomByFactor(a,b,c);this.refresh(2,!this.sm.syncingMouse?"":"Mouse: zoomByFactor "+a+(2147483647==b?"":" "+b+" "+c))},"~N,~N,~N");c(b,"rotateXYBy",function(a,b){this.tm.rotateXYBy(a,b,null);this.refresh(2,this.sm.syncingMouse?"Mouse: rotateXYBy "+a+" "+b:"")},"~N,~N");c(b,"spinXYBy",function(a,b,c){this.tm.spinXYBy(a,

b,c);0==a&&0==b||this.refresh(2,this.sm.syncingMouse?"Mouse: spinXYBy "+a+" "+b+" "+c:"")},"~N,~N,~N");c(b,"rotateZBy",function(a,b,c){this.tm.rotateZBy(a,b,c);this.refresh(2,this.sm.syncingMouse?"Mouse: rotateZBy "+a+(2147483647==b?"":" "+b+" "+c):"")},"~N,~N,~N");c(b,"rotateSelected",function(a,b,c){this.isJmolDataFrame()||(this.tm.rotateXYBy(a,b,this.setMovableBitSet(c,!0)),this.refreshMeasures(!0),this.refresh(2,this.sm.syncingMouse?"Mouse: rotateMolecule "+a+" "+b:""))},"~N,~N,JU.BS");c(b,"setMovableBitSet",

function(a,b){null==a&&(a=this.bsA());a=JU.BSUtil.copy(a);JU.BSUtil.andNot(a,this.getMotionFixedAtoms(null,null));b&&!this.g.allowMoveAtoms&&(a=this.ms.getMoleculeBitSet(a));return this.movableBitSet=a},"JU.BS,~B");c(b,"translateXYBy",function(a,b){this.tm.translateXYBy(a,b);this.refresh(2,this.sm.syncingMouse?"Mouse: translateXYBy "+a+" "+b:"")},"~N,~N");j(b,"rotateFront",function(){this.tm.resetRotation();this.refresh(1,"Viewer:rotateFront()")});c(b,"translate",function(a,b,c,f){var e="\x00"==c?

b:"%"==c?this.tm.percentToPixels(a,b):this.tm.angstromsToPixels(b*("n"==c?10:1));if(null!=f){if(0==b)return;this.tm.setSelectedTranslation(f,a,e,b)}else switch(a.charCodeAt(0)){case 88:case 120:"\x00"==c?this.tm.translateToPercent("x",b):this.tm.translateXYBy(D(e),0);break;case 89:case 121:"\x00"==c?this.tm.translateToPercent("y",b):this.tm.translateXYBy(0,D(e));break;case 90:case 122:"\x00"==c?this.tm.translateToPercent("z",b):this.tm.translateZBy(D(e))}this.refresh(1,"Viewer:translate()")},"~S,~N,~S,JU.BS");

c(b,"slabByPixels",function(a){this.tm.slabByPercentagePoints(a);this.refresh(3,"slabByPixels")},"~N");c(b,"depthByPixels",function(a){this.tm.depthByPercentagePoints(a);this.refresh(3,"depthByPixels")},"~N");c(b,"slabDepthByPixels",function(a){this.tm.slabDepthByPercentagePoints(a);this.refresh(3,"slabDepthByPixels")},"~N");c(b,"finalizeTransformParameters",function(){this.tm.finalizeTransformParameters();this.gdata.setSlabAndZShade(this.tm.slabValue,this.tm.depthValue,this.tm.zShadeEnabled?this.tm.zSlabValue:

2147483647,this.tm.zDepthValue,this.g.zShadePower)});c(b,"getScalePixelsPerAngstrom",function(a){return this.tm.scalePixelsPerAngstrom*(a||!this.antialiased?1:0.5)},"~B");c(b,"setSpin",function(a,b){if(JU.PT.isOneOf(a,";x;y;z;fps;X;Y;Z;FPS;")){var c="x;y;z;fps;X;Y;Z;FPS".indexOf(a);switch(c){case 0:this.tm.setSpinXYZ(b,NaN,NaN);break;case 2:this.tm.setSpinXYZ(NaN,b,NaN);break;case 4:this.tm.setSpinXYZ(NaN,NaN,b);break;default:this.tm.setSpinFps(b);break;case 10:this.tm.setNavXYZ(b,NaN,NaN);break;

case 12:this.tm.setNavXYZ(NaN,b,NaN);break;case 14:this.tm.setNavXYZ(NaN,NaN,b);break;case 16:this.tm.setNavFps(b)}this.g.setI((10>c?"spin":"nav")+a,b)}},"~S,~N");c(b,"getSpinState",function(){return this.getStateCreator().getSpinState(!1)});c(b,"getOrientation",function(a,b,c,f){switch(a){case 1312817669:case 1814695966:case 1073741864:case 1111492629:case 1111492630:case 1111492631:case 134221850:null==c&&(c=this.bsA());if(c.isEmpty())return 1312817669==a?"0":1814695966==a||1073741864==a?null:new JU.Quat;

c=this.ms.getBoundBoxOrientation(a,c,f);return"best"===b&&1312817669!=a?c.div(this.tm.getRotationQ()):c;case 1073742034:return this.stm.getSavedOrientationText(b);default:return this.tm.getOrientationText(a,"best"===b)}},"~N,~S,JU.BS,~A");c(b,"getCurrentColorRange",function(){return this.cm.getPropertyColorRange()});c(b,"setDefaultColors",function(a){this.cm.setDefaultColors(a);this.g.setB("colorRasmol",a);this.g.setO("defaultColorScheme",a?"rasmol":"jmol")},"~B");c(b,"setElementArgb",function(a,

b){this.g.setO("=color "+JU.Elements.elementNameFromNumber(a),JU.Escape.escapeColor(b));this.cm.setElementArgb(a,b)},"~N,~N");j(b,"setVectorScale",function(a){this.g.setF("vectorScale",a);this.g.vectorScale=a},"~N");j(b,"setVibrationScale",function(a){this.tm.setVibrationScale(a);this.g.vibrationScale=a;this.g.setF("vibrationScale",a)},"~N");j(b,"setVibrationPeriod",function(a){Double.isNaN(a)&&(a=this.g.vibrationPeriod);this.tm.setVibrationPeriod(a);a=Math.abs(a);this.g.vibrationPeriod=a;this.g.setF("vibrationPeriod",

a)},"~N");c(b,"setObjectColor",function(a,b){null==b||0==b.length||this.setObjectArgb(a,JU.CU.getArgbFromString(b))},"~S,~S");c(b,"setObjectVisibility",function(a,b){var c=JV.StateManager.getObjectIdFromName(a);0<=c&&this.setShapeProperty(c,"display",b?Boolean.TRUE:Boolean.FALSE)},"~S,~B");c(b,"setObjectArgb",function(a,b){var c=JV.StateManager.getObjectIdFromName(a);if(0>c)a.equalsIgnoreCase("axes")&&(this.setObjectArgb("axis1",b),this.setObjectArgb("axis2",b),this.setObjectArgb("axis3",b));else{this.g.objColors[c]=

b;switch(c){case 0:this.gdata.setBackgroundArgb(b),this.cm.setColixBackgroundContrast(b)}this.g.setO(a+"Color",JU.Escape.escapeColor(b))}},"~S,~N");c(b,"setBackgroundImage",function(a,b){this.g.backgroundImageFileName=a;this.gdata.setBackgroundImage(b)},"~S,~O");c(b,"getObjectColix",function(a){a=this.g.objColors[a];return 0==a?this.cm.colixBackgroundContrast:JU.C.getColix(a)},"~N");j(b,"setColorBackground",function(a){this.setObjectColor("background",a)},"~S");j(b,"getBackgroundArgb",function(){return this.g.objColors[0]});

c(b,"setObjectMad10",function(a,b,c){var f=JV.StateManager.getObjectIdFromName(b.equalsIgnoreCase("axes")?"axis":b);if(!(0>f)){if(-2==c||-4==c){var e=c+3;c=this.getObjectMad10(f);0==c&&(c=e)}this.g.setB("show"+b,0!=c);this.g.objStateOn[f]=0!=c;0!=c&&(this.g.objMad10[f]=c,this.setShapeSize(a,c,null))}},"~N,~S,~N");c(b,"getObjectMad10",function(a){return this.g.objStateOn[a]?this.g.objMad10[a]:0},"~N");c(b,"setPropertyColorScheme",function(a,b,c){this.g.propertyColorScheme=a;a.startsWith("translucent ")&&

(b=!0,a=a.substring(12).trim());this.cm.setPropertyColorScheme(a,b,c)},"~S,~B,~B");c(b,"getLightingState",function(){return this.getStateCreator().getLightingState(!0)});c(b,"getColorPointForPropertyValue",function(a){return JU.CU.colorPtFromInt(this.gdata.getColorArgbOrGray(this.cm.ce.getColorIndex(a)),null)},"~N");c(b,"select",function(a,b,c,f){b&&(a=this.getUndeletedGroupAtomBits(a));this.slm.select(a,c,f);this.shm.setShapeSizeBs(1,2147483647,null,null);this.hasSelected=!0},"JU.BS,~B,~N,~B");j(b,

"setSelectionSet",function(a){this.selectStatus(a,!1,0,!0,!0)},"JU.BS");c(b,"selectBonds",function(a){this.shm.setShapeSizeBs(1,2147483647,null,a)},"JU.BS");c(b,"displayAtoms",function(a,b,c,f,e){c&&(a=this.getUndeletedGroupAtomBits(a));b?this.slm.display(this.ms,a,f,e):this.slm.hide(this.ms,a,f,e)},"JU.BS,~B,~B,~N,~B");c(b,"getUndeletedGroupAtomBits",function(a){a=this.ms.getAtoms(1086324742,a);JU.BSUtil.andNot(a,this.slm.bsDeleted);return a},"JU.BS");c(b,"reportSelection",function(a){this.selectionHalosEnabled&&

this.setTainted(!0);(this.isScriptQueued()||this.g.debugScript)&&this.scriptStatus(a)},"~S");c(b,"clearAtomSets",function(){this.slm.setSelectionSubset(null);this.definedAtomSets.clear();this.haveDisplay&&this.acm.exitMeasurementMode("clearAtomSets")});c(b,"getDefinedAtomSet",function(a){a=this.definedAtomSets.get(a.toLowerCase());return y(a,"JU.BS")?a:new JU.BS},"~S");j(b,"selectAll",function(){this.slm.selectAll(!1)});j(b,"clearSelection",function(){this.slm.clearSelection(!0);this.g.setB("hideNotSelected",

!1)});c(b,"bsA",function(){return this.slm.getSelectedAtoms()});j(b,"addSelectionListener",function(a){this.slm.addListener(a)},"J.api.JmolSelectionListener");j(b,"removeSelectionListener",function(a){this.slm.addListener(a)},"J.api.JmolSelectionListener");c(b,"getAtomBitSetEval",function(a,b){return this.allowScripting?this.getScriptManager().getAtomBitSetEval(a,b):new JU.BS},"J.api.JmolScriptEvaluator,~O");c(b,"processTwoPointGesture",function(a){this.mouse.processTwoPointGesture(a)},"~A");c(b,

"processMouseEvent",function(a,b,c,f,e){return this.mouse.processEvent(a,b,c,f,e)},"~N,~N,~N,~N,~N");c(b,"processKeyEvent",function(a){this.mouse.processKeyEvent(a)},"~O");c(b,"getRubberBandSelection",function(){return this.haveDisplay?this.acm.getRubberBand():null});c(b,"isBound",function(a,b){return this.haveDisplay&&this.acm.bnd(a,[b])},"~N,~N");c(b,"getCursorX",function(){return this.haveDisplay?this.acm.getCurrentX():0});c(b,"getCursorY",function(){return this.haveDisplay?this.acm.getCurrentY():

0});c(b,"getDefaultDirectory",function(){return this.g.defaultDirectory});c(b,"getLocalUrl",function(a){return this.apiPlatform.getLocalUrl(a)},"~S");c(b,"getFileAsString",function(a){return this.getAsciiFileOrNull(a)},"~S");j(b,"getBufferedInputStream",function(a){return this.fm.getBufferedInputStream(a)},"~S");c(b,"setLoadParameters",function(a,b){null==a&&(a=new java.util.Hashtable);a.put("vwr",this);0<this.g.atomTypes.length&&a.put("atomTypes",this.g.atomTypes);a.containsKey("lattice")||a.put("lattice",

this.g.ptDefaultLattice);this.g.applySymmetryToBonds&&a.put("applySymmetryToBonds",Boolean.TRUE);this.g.pdbGetHeader&&a.put("getHeader",Boolean.TRUE);this.g.pdbSequential&&a.put("isSequential",Boolean.TRUE);(this.g.legacyJavaFloat||this.g.doublePrecision)&&a.put("highPrecision",Boolean.TRUE);this.g.doublePrecision||a.put("lowPrecision",Boolean.TRUE);a.put("stateScriptVersionInt",Integer.$valueOf(this.stateScriptVersionInt));if(!a.containsKey("filter")){var c=this.g.defaultLoadFilter;0<c.length&&a.put("filter",

c)}c=b&&!this.g.appendNew&&0<this.ms.ac;a.put("baseAtomIndex",Integer.$valueOf(b?this.ms.ac:0));a.put("baseBondIndex",Integer.$valueOf(b?this.ms.bondCount:0));a.put("baseModelIndex",Integer.$valueOf(0==this.ms.ac?0:this.ms.mc+(c?-1:0)));c&&a.put("merging",Boolean.TRUE);return a},"java.util.Map,~B");j(b,"openFileAsyncSpecial",function(a,b){this.getScriptManager().openFileAsync(a,b,null)},"~S,~N");j(b,"openFileAsyncSpecialType",function(a,b,c){this.getScriptManager().openFileAsync(a,b,c)},"~S,~N,~S");

j(b,"openFile",function(a){this.zap(!0,!0,!1);return this.loadModelFromFileRepaint(null,a,null,null)},"~S");j(b,"openFiles",function(a){this.zap(!0,!0,!1);return this.loadModelFromFileRepaint(null,null,a,null)},"~A");c(b,"openReader",function(a,b,c){this.zap(!0,!0,!1);return this.loadModelFromFileRepaint(a,b,null,c)},"~S,~S,~O");j(b,"openDOM",function(a){this.zap(!0,!0,!1);return this.loadModelFromFileRepaint("?","?",null,a)},"~O");c(b,"loadModelFromFileRepaint",function(a,b,c,f){a=this.loadModelFromFile(a,

b,c,f,!1,null,null,null,0," ");this.refresh(1,"loadModelFromFileRepaint");return a},"~S,~S,~A,~O");c(b,"loadModelFromFile",function(a,b,c,f,e,h,j,m,n,p){null==h&&(h=this.setLoadParameters(null,e));0!=n&&h.put("dataType",JS.T.nameOf(n));" "!==p&&h.put("concatenate",Boolean.TRUE);var q=this.fm.getFileInfo();if(null!=c){if(null==j){j=(new JU.SB).append("load files");for(a=0;a<c.length;a++)j.append(0==a||null==p?" ":p).append("/*file*/$FILENAME"+(a+1)+"$");0<m.length()&&j.append(" /*options*/ ").append(m.toString())}a=

System.currentTimeMillis();m=this.fm.createAtomSetCollectionFromFiles(c,this.setLoadParameters(h,e),e);a=System.currentTimeMillis()-a;JU.Logger.info("openFiles("+c.length+") "+a+" ms");c=h.get("fullPathNames");p=h.get("fileTypes");j=j.toString();for(a=0;a<c.length;a++)b=c[a],null!=p&&null!=p[a]&&(b=p[a]+"::"+b),j=JU.PT.rep(j,"$FILENAME"+(a+1)+"$",JU.PT.esc(JV.FileManager.fixDOSName(b)));j=(new JU.SB).append(j)}else if(null==f)null==j&&(j=(new JU.SB).append("load /*file*/$FILENAME$")),m=this.openFileFull(b,

e,h,j);else if(y(f,"java.io.Reader")||y(f,"java.io.BufferedInputStream")||JU.AU.isAB(f))m=this.fm.createAtomSetCollectionFromReader(a,b,f,this.setLoadParameters(h,e));else return"ERROR - invalid reader";if(0!=n)return this.fm.setFileInfo(q),this.loadAtomDataAndReturnError(m,n);if(h.containsKey("isData"))return m;null!=j&&"string"!=typeof m&&(b=h.get("fullPathName"),null==b&&(b=""),h.containsKey("loadScript")&&(j=h.get("loadScript")),h.put("loadScript",j=(new JU.SB).append(JU.PT.rep(j.toString(),"$FILENAME$",

JU.PT.esc(JV.FileManager.fixDOSName(b))))));return this.createModelSetAndReturnError(m,e,j,h)},"~S,~S,~A,~O,~B,java.util.Map,JU.SB,JU.SB,~N,~S");c(b,"setLigandModel",function(a,b){null==this.ligandModels&&(this.ligandModels=new java.util.Hashtable);this.ligandModels.put(a,b)},"~S,~S");c(b,"getLigandModel",function(a,b,c,f){if(null==a){if(null!=this.ligandModelSet)for(a=this.ligandModels.entrySet().iterator();a.hasNext();){var e=a.next();y(e.getValue(),Boolean)&&a.remove()}return null}a=a.$replace("\\",

"/");var h=b.equals("ligand_");a=0<=a.indexOf("/cif")?a:h?a.toUpperCase():a.substring(a.lastIndexOf("/")+1);null==this.ligandModelSet&&(this.ligandModelSet=new java.util.Hashtable);this.ligandModelSet.put(a,Boolean.TRUE);null==this.ligandModels&&(this.ligandModels=new java.util.Hashtable);var j=a.indexOf("|");0<=j&&(a=a.substring(a.indexOf("|")+1));var m=null==f?this.ligandModels.get(a):null,e=null;if(y(m,Boolean))return null;if(null==m&&(null==f||0<=j))m=this.ligandModels.get(a+c);var j=!1,n=null==

m;if(n){if(h){e=this.setLoadFormat(!1,"#"+a,"#",!1);if(0==e.length)return null;this.scriptEcho("fetching "+e);m=this.getFileAsString3(e,!1,null)}else this.scriptEcho("fetching "+b),m=this.getFileAsString3(b,!1,null),f=null==f?-1:m.indexOf(f),0<=f&&(m=m.substring(0,f));(j=0==m.indexOf("java."))||this.ligandModels.put(a+c,m)}if(!h)return n||this.scriptEcho(b+" loaded from cache"),m;!j&&"string"==typeof m&&(b=m,0!=b.length&&(c=new java.util.Hashtable,c.put("modelOnly",Boolean.TRUE),m=this.getModelAdapter().getAtomSetCollectionReader("ligand",

null,JU.Rdr.getBR(b),c),j="string"==typeof m,j||(m=this.getModelAdapter().getAtomSetCollection(m),j="string"==typeof m,null!=e&&!j&&this.scriptEcho(this.getModelAdapter().getAtomSetCollectionAuxiliaryInfo(m).get("modelLoadNote")))));return j?(this.scriptEcho(m.toString()),this.ligandModels.put(a,Boolean.FALSE),null):m},"~S,~S,~S,~S");c(b,"openFileFull",function(a,b,c,f){if(null==a||a.equals("String[]"))return null;var e,h="openFile("+a+")";JU.Logger.startTimer(h);c=this.setLoadParameters(c,b);var j=

a.startsWith("@"),m=c.containsKey("fileData");0==a.indexOf("$")&&c.put("smilesString",a.substring(1));var n=a.equals("string")||a.equals("Jmol Model Kit");e=null;if(m){if(e=c.get("fileData"),c.containsKey("isData"))return h=this.loadInlineScript(e,"\x00",b,c),this.lastData=this.g.preserveState?this.getDataManager().createFileData(e):null,h}else if(n){e=this.ms.getInlineData(-1);if(null==e)if(this.g.modelKitMode)e="5\n\nC 0 0 0\nH .63 .63 .63\nH -.63 -.63 .63\nH -.63 .63 -.63\nH .63 -.63 -.63";else return"cannot find string data";

null!=f&&c.put("loadScript",f=(new JU.SB).append(JU.PT.rep(f.toString(),"/*file*/$FILENAME$",'/*data*/data "model inline"\n'+e+'end "model inline"')))}null!=e?(b||this.zap(!0,!1,!1),!j&&(!m||n)&&this.getStateCreator().getInlineData(f,e,b,c.get("appendToModelIndex"),this.g.defaultLoadFilter),e=this.fm.createAtomSetCollectionFromString(e,c,b)):e=this.fm.createAtomSetCollectionFromFile(a,c,b);JU.Logger.checkTimer(h,!1);return e},"~S,~B,java.util.Map,JU.SB");j(b,"openStringInline",function(a){a=this.openStringInlineParamsAppend(a,

null,!1);this.refresh(1,"openStringInline");return a},"~S");c(b,"loadInline",function(a){return this.loadInlineScriptRepaint(a,this.g.inlineNewlineChar,!1)},"~S");c(b,"loadInline",function(a,b){return this.loadInlineScriptRepaint(a,b,!1)},"~S,~S");j(b,"loadInlineAppend",function(a,b){return this.loadInlineScriptRepaint(a,"\x00",b)},"~S,~B");c(b,"loadInlineScriptRepaint",function(a,b,c){a=this.loadInlineScript(a,b,c,null);this.refresh(1,"loadInlineScript");return a},"~S,~S,~B");c(b,"loadInline",function(a){return this.loadInline(a,

!1)},"~A");c(b,"loadInline",function(a,b){if(null==a||0==a.length)return null;var c=this.openStringsInlineParamsAppend(a,new java.util.Hashtable,b);this.refresh(1,"loadInline String[]");return c},"~A,~B");c(b,"loadInline",function(a,b){if(null==a||0==a.size())return null;b||this.zap(!0,!1,!1);for(var c=new JU.Lst,f=0;f<a.size();f++)c.addLast(a.get(f));c=this.fm.createAtomSeCollectionFromArrayData(c,this.setLoadParameters(null,b),b);c=this.createModelSetAndReturnError(c,b,null,new java.util.Hashtable);

this.refresh(1,"loadInline");return c},"java.util.List,~B");c(b,"loadInlineScript",function(a,b,c,f){if(null==a||0==a.length)return null;a=JV.Viewer.fixInlineString(a,b);0!=b.charCodeAt(0)&&JU.Logger.info("loading model inline, "+a.length+" bytes, with newLine character "+b.charCodeAt(0)+" isAppend="+c);JU.Logger.debugging&&JU.Logger.debug(a);b=this.getDataSeparator();var e;if(null!=b&&""!==b&&0<=(e=a.indexOf(b))&&0>a.indexOf("# Jmol state")){for(var h=2;0<=(e=a.indexOf(b,e+1));)h++;var j=Array(h),

m=0,n=0;for(e=0;e<h;e++)m=a.indexOf(b,n),0>m&&(m=a.length),j[e]=a.substring(n,m),n=m+b.length;return this.openStringsInlineParamsAppend(j,f,c)}return this.openStringInlineParamsAppend(a,f,c)},"~S,~S,~B,java.util.Map");b.fixInlineString=c(b,"fixInlineString",function(a,b){var c;0<=a.indexOf("\\/n")&&(a=JU.PT.rep(a,"\n",""),a=JU.PT.rep(a,"\\/n","\n"),b=String.fromCharCode(0));if(0!=b.charCodeAt(0)&&"\n"!=b){var f=0<=a.indexOf("\n"),e=a.length;for(c=0;c<e&&" "==a.charAt(c);++c);c<e&&a.charAt(c)==b&&

(a=a.substring(c+1));a=f?JU.PT.rep(a,""+b,""):a.$replace(b,"\n")}return a},"~S,~S");c(b,"openStringInlineParamsAppend",function(a,b,c){b=this.setLoadParameters(b,c);var f=this.getModelAdapter().getFileTypeName(b.get("filter"));if(null==f&&null==(f=this.getModelAdapter().getFileTypeName(JU.Rdr.getBR(a))))return"unknown file type";if(f.equals("spt"))return"cannot open script inline";var f=b.get("loadScript"),e=b.containsKey("isData");null==f&&(f=new JU.SB);c||this.zap(!0,!1,!1);e||this.getStateCreator().getInlineData(f,

a,c,b.get("appendToModelIndex"),this.g.defaultLoadFilter);a=this.fm.createAtomSetCollectionFromString(a,b,c);return this.createModelSetAndReturnError(a,c,f,b)},"~S,java.util.Map,~B");c(b,"openStringsInlineParamsAppend",function(a,b,c){var f=new JU.SB;c||this.zap(!0,!1,!1);a=this.fm.createAtomSeCollectionFromStrings(a,f,this.setLoadParameters(b,c),c);return this.createModelSetAndReturnError(a,c,f,b)},"~A,java.util.Map,~B");c(b,"getInlineChar",function(){return this.g.inlineNewlineChar});c(b,"getDataSeparator",

function(){return this.g.getParameter("dataseparator",!0)});c(b,"createModelSetAndReturnError",function(a,b,c,f){JU.Logger.startTimer("creating model");var e=this.fm.getFullPathName(!1),h=this.fm.getFileName();null==c&&(this.setBooleanPropertyTok("preserveState",603979898,!1),c=(new JU.SB).append('load "???"'));if("string"==typeof a)return this.setFileLoadStatus(J.c.FIL.NOT_LOADED,e,null,null,a,null),this.displayLoadErrors&&(!b&&!a.equals("#CANCELED#")&&!a.startsWith(JV.JC.READER_NOT_FOUND))&&this.zapMsg(a),

a;b?this.clearAtomSets():this.g.modelKitMode&&!h.equals("Jmol Model Kit")&&this.setModelKitMode(!1);this.setFileLoadStatus(J.c.FIL.CREATING_MODELSET,e,h,null,null,null);this.pushHoldRepaintWhy("createModelSet");this.setErrorMessage(null,null);try{var j=new JU.BS;this.mm.createModelSet(e,h,c,a,j,b);if(!j.isEmpty()){var m=this.ms.getInfoM("jmolscript");if(this.ms.getMSInfoB("doMinimize"))try{var n=f.get("eval"),p=this.getAtomBitSet("_C & connected(3) & !connected(double)");p.and(j);0<=p.nextSetBit(0)&&

j.or(this.addHydrogens(p,41));this.minimize(n,2147483647,0,j,null,null,0,185)}catch(q){if(!F(q,Exception))throw q;}else this.addHydrogens(j,9);null!=m&&this.ms.msInfo.put("jmolscript",m)}this.initializeModel(b)}catch(r){if(F(r,Error))this.handleError(r,!0),a=this.getShapeErrorState(),a="ERROR creating model: "+r+(0==a.length?"":"|"+a),this.zapMsg(a),this.setErrorMessage(a,null);else throw r;}this.popHoldRepaint("createModelSet \u0001## REPAINT_IGNORE ##");a=this.getErrorMessage();this.setFileLoadStatus(J.c.FIL.CREATED,

e,h,this.ms.modelSetName,a,f.get("async"));b&&(this.selectAll(),this.setTainted(!0),this.axesAreTainted=!0);JU.Logger.checkTimer("creating model",!1);System.gc();return a},"~O,~B,JU.SB,java.util.Map");c(b,"loadAtomDataAndReturnError",function(a,b){if("string"==typeof a)return a;this.setErrorMessage(null,null);try{var c=this.mm.createAtomDataSet(a,b);switch(b){case 1145047049:null!=c&&this.runScriptCautiously(c);break;case 4166:this.setStatusFrameChanged(!0,!1);break;case 1648363544:this.shm.deleteVdwDependentShapes(null)}}catch(f){if(F(f,

Error))this.handleError(f,!0),c=this.getShapeErrorState(),c="ERROR adding atom data: "+f+(0==c.length?"":"|"+c),this.zapMsg(c),this.setErrorMessage(c,null),this.setParallel(!1);else throw f;}return this.getErrorMessage()},"~O,~N");c(b,"getCurrentFileAsString",function(a){var b=this.fm.getFullPathName(!1);return b.equals("string")||b.equals("Jmol Model Kit")?this.ms.getInlineData(this.am.cmi):b.equals("String[]")?b:"JSNode"===b?"<DOM NODE>":this.getFileAsString4(b,-1,!0,!1,!1,a)},"~S");c(b,"getFullPathNameOrError",

function(a){var b=Array(2);this.fm.getFullPathNameOrError(a,!1,b);return b},"~S");c(b,"getFileAsString3",function(a,b,c){return this.getFileAsString4(a,-1,!1,!1,b,c)},"~S,~B,~S");c(b,"getFileAsString4",function(a,b,c,f,e,h){if(null==a)return this.getCurrentFileAsString(h);a=w(-1,[a,null]);this.fm.getFileDataAsString(a,b,c,f,e);return a[1]},"~S,~N,~B,~B,~B,~S");c(b,"getAsciiFileOrNull",function(a){a=w(-1,[a,null]);return this.fm.getFileDataAsString(a,-1,!1,!1,!1)?a[1]:null},"~S");c(b,"autoCalculate",

function(a,b){switch(a){case 1111490575:this.ms.getSurfaceDistanceMax();break;case 1111490574:this.ms.calculateStraightnessAll();break;case 1111490587:this.ms.calculateDssrProperty(b)}},"~N,~S");c(b,"calculateStraightness",function(){this.ms.haveStraightness=!1;this.ms.calculateStraightnessAll()});c(b,"calculateSurface",function(a,b){null==a&&(a=this.bsA());if(3.4028235E38==b||-1==b)this.ms.addStateScript("calculate surfaceDistance "+(3.4028235E38==b?"FROM":"WITHIN"),null,a,null,"",!1,!0);return this.ms.calculateSurface(a,

b)},"JU.BS,~N");c(b,"getStructureList",function(){return this.g.getStructureList()});c(b,"setStructureList",function(a,b){this.g.setStructureList(a,b);this.ms.setStructureList(this.getStructureList())},"~A,J.c.STR");c(b,"calculateStructures",function(a,b,c,f){null==a&&(a=this.bsA());return this.ms.calculateStructures(a,b,!this.am.animationOn,this.g.dsspCalcHydrogen,c,f)},"JU.BS,~B,~B,~N");c(b,"getAnnotationParser",function(a){return a?null==this.dssrParser?this.dssrParser=J.api.Interface.getOption("dssx.DSSR1",

this,"script"):this.dssrParser:null==this.annotationParser?this.annotationParser=J.api.Interface.getOption("dssx.AnnotationParser",this,"script"):this.annotationParser},"~B");j(b,"getSelectedAtomIterator",function(a,b,c,f){return this.ms.getSelectedAtomIterator(a,b,c,!1,f)},"JU.BS,~B,~B,~B");j(b,"setIteratorForAtom",function(a,b,c){this.ms.setIteratorForAtom(a,-1,b,c,null)},"J.api.AtomIndexIterator,~N,~N");j(b,"setIteratorForPoint",function(a,b,c,f){this.ms.setIteratorForPoint(a,b,c,f)},"J.api.AtomIndexIterator,~N,JU.T3,~N");

j(b,"fillAtomData",function(a,b){a.programInfo="Jmol Version "+JV.Viewer.getJmolVersion();a.fileName=this.fm.getFileName();this.ms.fillAtomData(a,b)},"J.atomdata.AtomData,~N");c(b,"addStateScript",function(a,b,c){return this.ms.addStateScript(a,null,null,null,null,b,c)},"~S,~B,~B");c(b,"getMinimizer",function(a){return null==this.minimizer&&a?(this.minimizer=J.api.Interface.getInterface("JM.Minimizer",this,"script")).setProperty("vwr",this):this.minimizer},"~B");c(b,"getSmilesMatcher",function(){return null==

this.smilesMatcher?this.smilesMatcher=J.api.Interface.getInterface("JS.SmilesMatcher",this,"script"):this.smilesMatcher});c(b,"clearModelDependentObjects",function(){this.setFrameOffsets(null,!1);this.stopMinimization();this.smilesMatcher=this.minimizer=null;null!=this.modelkit&&this.modelkit.clearAtomConstraints()});c(b,"zap",function(a,b,c){this.clearThreads();null==this.mm.modelSet?this.mm.zap():(this.ligandModelSet=null,this.clearModelDependentObjects(),this.fm.clear(),this.clearRepaintManager(-1),

this.am.clear(),this.tm.clear(),this.slm.clear(),this.hasSelected=!0,this.clearAllMeasurements(),this.clearMinimization(),this.gdata.clear(),this.mm.zap(),null!=this.scm&&this.scm.clear(!1),null!=this.nmrCalculation&&this.getNMRCalculation().setChemicalShiftReference(null,0),this.haveDisplay&&(this.mouse.clear(),this.clearTimeouts(),this.acm.clear()),this.stm.clear(this.g),this.tempArray.clear(),this.chainMap.clear(),this.chainList.clear(),this.chainCaseSpecified=!1,this.definedAtomSets.clear(),this.lastData=

null,null!=this.dm&&this.dm.clear(),!this.g.doublePrecision&&this.g.legacyJavaFloat&&this.setBooleanPropertyTok("legacyjavafloat",603979874,!1),b&&(c&&this.g.removeParam("_pngjFile"),c&&this.g.modelKitMode?this.loadDefaultModelKitModel(null):this.setPickingMode(null,1),this.undoMoveAction(4165,-2)),System.gc());this.initializeModel(!1);a&&this.setFileLoadStatus(J.c.FIL.ZAPPED,null,b?"resetUndo":this.getZapName(),null,null,null);JU.Logger.debugging&&JU.Logger.checkMemory()},"~B,~B,~B");c(b,"loadDefaultModelKitModel",

function(a){this.getModelkit(!1).isHidden()||null!=this.getOperativeSymmetry()||(this.openStringInlineParamsAppend(this.getModelkit(!1).getDefaultModel(),a,!0),this.setRotationRadius(5,!0),this.setStringProperty("picking","assignAtom_C"),this.setStringProperty("picking","assignBond_p"))},"java.util.Map");c(b,"zapMsg",function(a){this.zap(!0,!0,!1);this.echoMessage(a)},"~S");c(b,"echoMessage",function(a){this.shm.loadShape(31);this.setShapeProperty(31,"font",this.getFont3D("SansSerif","Plain",20));

this.setShapeProperty(31,"target","error");this.setShapeProperty(31,"text",a)},"~S");c(b,"initializeModel",function(a){this.clearThreads();a?this.am.initializePointers(1):(this.reset(!0),this.selectAll(),this.setModelkitPropertySafely("initializemodel",null),this.movingSelected=!1,this.slm.noneSelected=Boolean.FALSE,this.setHoverEnabled(!0),this.setSelectionHalosEnabled(!1),this.tm.setCenter(),this.am.initializePointers(1),this.setBooleanPropertyTok("multipleBondBananas",603979886,!1),this.ms.getMSInfoB("isPyMOL")||

(this.clearAtomSets(),this.setCurrentModelIndex(0)),this.setBackgroundModelIndex(-1),this.setFrankOn(this.getShowFrank()),this.shm.setScale(),this.startHoverWatcher(!0),this.setTainted(!0),this.finalizeTransformParameters())},"~B");c(b,"startHoverWatcher",function(a){a&&this.inMotion||(!this.haveDisplay||a&&(!this.hoverEnabled&&!this.sm.haveHoverCallback()||this.am.animationOn))||this.acm.startHoverWatcher(a)},"~B");j(b,"getModelSetPathName",function(){return this.mm.modelSetPathName});j(b,"getModelSetFileName",

function(){return null==this.mm.fileName?this.getZapName():this.mm.fileName});c(b,"getUnitCellInfoText",function(){var a=this.getCurrentUnitCell();return null==a?"not applicable":a.getUnitCellInfo(!0)});c(b,"getUnitCellInfo",function(a){var b=this.getCurrentUnitCell();return null==b?NaN:b.getUnitCellInfoType(a)},"~N");c(b,"getV0abc",function(a,b){var c=0>a?this.getCurrentUnitCell():this.getUnitCell(a);null==c&&(c=this.getSymTemp());return null==c?null:c.getV0abc(b,null)},"~N,~O");c(b,"getCurrentUnitCell",

function(){var a=this.am.getUnitCellAtomIndex();return 0<=a?this.ms.getUnitCellForAtom(a):this.getUnitCell(this.am.cmi)});c(b,"getUnitCell",function(a){if(0<=a)return this.ms.getUnitCell(a);a=this.getVisibleFramesBitSet();for(var b=null,c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1)){var f=this.ms.getUnitCell(c);if(null!=f)if(null==b)b=f;else if(!b.unitCellEquals(f))return null}return b},"~N");c(b,"getPolymerPointsAndVectors",function(a,b){this.ms.getPolymerPointsAndVectors(a,b,this.g.traceAlpha,this.g.sheetSmoothing)},

"JU.BS,JU.Lst");c(b,"getHybridizationAndAxes",function(a,b,c,f){return this.ms.getHybridizationAndAxes(a,0,b,c,f,!0,!0,!1,null)},"~N,JU.V3,JU.V3,~S");c(b,"getAllAtoms",function(){return this.getModelUndeletedAtomsBitSet(-1)});c(b,"getFrameAtoms",function(){return this.getModelUndeletedAtomsBitSetBs(this.getVisibleFramesBitSet())});j(b,"getVisibleFramesBitSet",function(){var a=JU.BSUtil.copy(this.am.bsVisibleModels);null!=this.ms.trajectory&&this.ms.trajectory.selectDisplayed(a);return a});c(b,"getModelUndeletedAtomsBitSet",

function(a){return this.slm.excludeAtoms(this.ms.getModelAtomBitSetIncludingDeleted(a,!0),!1)},"~N");c(b,"getModelUndeletedAtomsBitSetBs",function(a){return this.slm.excludeAtoms(this.ms.getModelAtomBitSetIncludingDeletedBs(a),!1)},"JU.BS");j(b,"getBoundBoxCenter",function(){return this.ms.getBoundBoxCenter(this.am.cmi)});c(b,"calcBoundBoxDimensions",function(a,b){this.ms.calcBoundBoxDimensions(a,b);this.axesAreTainted=!0},"JU.BS,~N");j(b,"getBoundBoxCornerVector",function(){return this.ms.getBoundBoxCornerVector()});

j(b,"getModelSetProperties",function(){return this.ms.modelSetProperties});j(b,"getModelProperties",function(a){return this.ms.am[a].properties},"~N");c(b,"getModelForAtomIndex",function(a){return this.ms.am[this.ms.at[a].mi]},"~N");c(b,"getModelIndexForAtom",function(a){return this.ms.at[a].mi},"~N");j(b,"getModelSetAuxiliaryInfo",function(){return this.ms.getModelSetAuxiliaryInfo(null)});j(b,"getModelNumber",function(a){return 0>a?a:this.ms.getModelNumber(a)},"~N");c(b,"getModelFileNumber",function(a){return 0>

a?0:this.ms.modelFileNumbers[a]},"~N");j(b,"getModelNumberDotted",function(a){return 0>a?"0":this.ms.getModelNumberDotted(a)},"~N");j(b,"getModelName",function(a){return this.ms.getModelName(a)},"~N");c(b,"modelHasVibrationVectors",function(a){return 0<=this.ms.getLastVibrationVector(a,4166)},"~N");c(b,"getBondsForSelectedAtoms",function(a){return this.ms.getBondsForSelectedAtoms(a,this.g.bondModeOr||1==JU.BSUtil.cardinalityOf(a))},"JU.BS");c(b,"frankClicked",function(a,b){return!this.g.disablePopupMenu&&

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c(b,"toUnitCell",function(a,b){var c=this.getCurrentUnitCell();null!=c&&c.toUnitCell(a,b)},"JU.P3,JU.P3");c(b,"setCurrentCage",function(a){a=w(-1,[a,null]);this.shm.getShapePropertyData(24,"unitCell",a);this.ms.setModelCage(this.am.cmi,a[1])},"~S");c(b,"addUnitCellOffset",function(a){var b=this.getCurrentUnitCell();null!=b&&a.add(b.getCartesianOffset())},"JU.P3");c(b,"setAtomData",function(a,b,c,f){this.ms.setAtomData(a,b,c,f);2==a&&this.checkCoordinatesChanged(null);this.refreshMeasures(!0)},"~N,~S,~S,~B");

j(b,"setCenterSelected",function(){this.setCenterBitSet(this.bsA(),!0)});c(b,"setApplySymmetryToBonds",function(a){this.g.applySymmetryToBonds=a},"~B");j(b,"setBondTolerance",function(a){this.g.setF("bondTolerance",a);this.g.bondTolerance=a},"~N");j(b,"setMinBondDistance",function(a){this.g.setF("minBondDistance",a);this.g.minBondDistance=a},"~N");c(b,"getAtomsNearPt",function(a,b,c){null==c&&(c=new JU.BS);this.ms.getAtomsWithin(a,b,c,-1);return c},"~N,JU.P3,JU.BS");c(b,"getBranchBitSet",function(a,

b,c){return 0>a||a>=this.ms.ac?new JU.BS:JU.JmolMolecule.getBranchBitSet(this.ms.at,a,this.getModelUndeletedAtomsBitSet(this.ms.at[a].mi),null,b,c,!0)},"~N,~N,~B");j(b,"getElementsPresentBitSet",function(a){return this.ms.getElementsPresentBitSet(a)},"~N");c(b,"getFileHeader",function(){return this.ms.getFileHeader(this.am.cmi)});c(b,"getFileData",function(){return this.ms.getFileData(this.am.cmi)});c(b,"getCifData",function(a){return this.readCifData(this.ms.getModelFileName(a),this.ms.getModelFileType(a).toUpperCase())},

"~N");c(b,"readCifData",function(a,b){var c=null==a?this.ms.getModelFileName(this.am.cmi):a;if(null==b&&null!=c&&0<=c.toUpperCase().indexOf("BCIF")){c=this.fm.getBufferedInputStream(c);try{return J.api.Interface.getInterface("JU.MessagePackReader",this,"script").getMapForStream(c)}catch(f){if(F(f,Exception))return f.printStackTrace(),new java.util.Hashtable;throw f;}}c=null==a||0==a.length?this.getCurrentFileAsString("script"):this.getFileAsString3(a,!1,null);if(null==c||2>c.length)return null;c=

JU.Rdr.getBR(c);null==b&&(b=this.getModelAdapter().getFileTypeName(c));return null==b?null:this.readCifData(null,c,b)},"~S,~S");c(b,"readCifData",function(a,b,c){null==b&&(b=this.getFileAsString(a));a=y(b,"java.io.BufferedReader")?b:JU.Rdr.getBR(b);return JU.Rdr.readCifData(J.api.Interface.getInterface("Cif2".equals(c)?"J.adapter.readers.cif.Cif2DataParser":"JU.CifDataParser",this,"script"),a)},"~S,~O,~S");c(b,"getStateCreator",function(){null==this.jsc&&(this.jsc=J.api.Interface.getInterface("JV.StateCreator",

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a)},"JU.BS");c(b,"setCurrentColorRange",function(a){var b=this.getDataObj(a,null,1);a=null==b?null:this.getDataObj(a,null,-1)[2];null!=a&&this.g.rangeSelected&&a.and(this.bsA());this.cm.setPropertyColorRangeData(b,a)},"~S");c(b,"setData",function(a,b,c,f,e,h,j){this.getDataManager().setData(a,this.lastData=b,c,this.ms.ac,f,e,h,j)},"~S,~A,~N,~N,~N,~N,~N");c(b,"getDataObj",function(a,b,c){return null==a&&-2==c?this.lastData:this.getDataManager().getData(a,b,c)},"~S,JU.BS,~N");c(b,"autoHbond",function(a,

b,c){null==a&&(a=b=this.bsA());return this.ms.autoHbond(a,b,c)},"JU.BS,JU.BS,~B");c(b,"getDefaultMeasurementLabel",function(a){switch(a){case 2:return this.g.defaultDistanceLabel;case 3:return this.g.defaultAngleLabel;default:return this.g.defaultTorsionLabel}},"~N");j(b,"getMeasurementCount",function(){var a=this.getShapePropertyAsInt(6,"count");return 0>=a?0:a});j(b,"getMeasurementStringValue",function(a){return""+this.shm.getShapePropertyIndex(6,"stringValue",a)},"~N");c(b,"getMeasurementInfoAsString",

function(){return this.getShapeProperty(6,"infostring")});j(b,"getMeasurementCountPlusIndices",function(a){return this.shm.getShapePropertyIndex(6,"countPlusIndices",a)},"~N");c(b,"setPendingMeasurement",function(a){this.shm.loadShape(6);this.setShapeProperty(6,"pending",a)},"JM.MeasurementPending");c(b,"getPendingMeasurement",function(){return this.getShapeProperty(6,"pending")});c(b,"clearAllMeasurements",function(){this.setShapeProperty(6,"clear",null)});j(b,"clearMeasurements",function(){this.evalString("measures delete")});

c(b,"setAnimation",function(a){switch(a){case 1073742098:this.am.reverseAnimation();case 1073742096:case 4143:this.am.animationOn||this.am.resumeAnimation();break;case 20487:this.am.animationOn&&!this.am.animationPaused&&this.am.pauseAnimation();break;case 1073742037:this.am.setAnimationNext();break;case 1073742108:this.am.setAnimationPrevious();break;case 1073741942:case 1073742125:this.am.rewindAnimation();break;case 1073741993:this.am.setAnimationLast()}},"~N");j(b,"setAnimationFps",function(a){this.am.setAnimationFps(a)},

"~N");c(b,"setAnimationMode",function(a){a.equalsIgnoreCase("once")?this.am.setAnimationReplayMode(1073742070,0,0):a.equalsIgnoreCase("loop")?this.am.setAnimationReplayMode(528411,1,1):a.startsWith("pal")&&this.am.setAnimationReplayMode(1073742082,1,1)},"~S");c(b,"setAnimationOn",function(a){a!=this.am.animationOn&&this.am.setAnimationOn(a)},"~B");c(b,"setAnimationRange",function(a,b){this.am.setAnimationRange(a,b)},"~N,~N");c(b,"defineAtomSets",function(a){this.definedAtomSets.putAll(a)},"java.util.Map");

c(b,"setAnimDisplay",function(a){this.am.setDisplay(a);this.am.animationOn||this.am.morph(this.am.currentMorphModel+1)},"JU.BS");c(b,"setCurrentModelIndex",function(a){-2147483648==a?(this.prevFrame=-2147483648,this.setCurrentModelIndexClear(this.am.cmi,!0)):this.am.setModel(a,!0)},"~N");c(b,"getTrajectoryState",function(){return null==this.ms.trajectory?"":this.ms.trajectory.getState()});c(b,"setFrameOffsets",function(a,b){this.tm.bsFrameOffsets=null;b?this.clearModelDependentObjects():this.tm.bsFrameOffsets=

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this.am.animationFps);this.g.setO("_firstFrame",this.am.getModelSpecial(-1));this.g.setO("_lastFrame",this.am.getModelSpecial(1));this.g.setF("_animTimeSec",this.am.getAnimRunTimeSeconds());this.g.setB("_animMovie",this.am.isMovie)});c(b,"getInMotion",function(a){return this.inMotion||a&&this.am.animationOn},"~B");j(b,"getMotionEventNumber",function(){return this.motionEventNumber});j(b,"setInMotion",function(a){(new Boolean(this.inMotion^a)).valueOf()&&(this.inMotion=a,this.resizeImage(0,0,!1,!1,

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null!=this.captureParams&&Boolean.FALSE!==this.captureParams.get("captureEnabled")&&(this.captureParams.remove("imagePixels"),a=this.captureParams.get("endTime").longValue(),0<a&&System.currentTimeMillis()+50>a&&this.captureParams.put("captureMode","end"),this.processWriteOrCapture(this.captureParams));this.notifyViewerRepaintDone()},"~O,~B,~N,~N");c(b,"updateJS",function(){this.isWebGL?(null==this.jsParams&&(this.jsParams=new java.util.Hashtable,this.jsParams.put("type","JS")),this.updateWindow(0,

0)&&this.render(),this.notifyViewerRepaintDone()):this.isStereoSlave||this.renderScreenImageStereo(this.apiPlatform.getGraphics(null),!0,0,0)});c(b,"updateJSView",function(a,b){if(null!=this.html5Applet){var c=this.html5Applet,f=!0;(f=null!=c&&null!=c._viewSet)&&this.html5Applet._atomPickedCallback(a,b)}},"~N,~N");j(b,"evalFile",function(a){return this.evalFileArgs(a,null)},"~S");j(b,"evalFileArgs",function(a,b){return this.allowScripting&&null!=this.getScriptManager()?this.scm.evalFileArgs(a,b):

null},"~S,~S");c(b,"getInsertedCommand",function(){var a=this.insertedCommand;this.insertedCommand="";JU.Logger.debugging&&""!==a&&JU.Logger.debug("inserting: "+a);return a});j(b,"script",function(a){return this.evalStringQuietSync(a,!1,!0)},"~S");j(b,"evalString",function(a){return this.evalStringQuietSync(a,!1,!0)},"~S");j(b,"evalStringQuiet",function(a){return this.evalStringQuietSync(a,!0,!0)},"~S");c(b,"evalStringQuietSync",function(a,b,c){return null==this.getScriptManager()?null:this.scm.evalStringQuietSync(a,

b,c)},"~S,~B,~B");c(b,"clearScriptQueue",function(){null!=this.scm&&this.scm.clearQueue()});c(b,"setScriptQueue",function(a){(this.g.useScriptQueue=a)||this.clearScriptQueue()},"~B");j(b,"checkHalt",function(a,b){return null!=this.scm&&this.scm.checkHalt(a,b)},"~S,~B");j(b,"scriptWait",function(a){return this.evalWait("JSON",a,"+scriptStarted,+scriptStatus,+scriptEcho,+scriptTerminated")},"~S");j(b,"scriptWaitStatus",function(a,b){return this.evalWait("object",a,b)},"~S,~S");c(b,"evalWait",function(a,

b,c){if(null==this.getScriptManager())return null;this.scm.waitForQueue();var f=J.i18n.GT.setDoTranslate(!1);a=this.evalStringWaitStatusQueued(a,b,c,!1,!1);J.i18n.GT.setDoTranslate(f);return a},"~S,~S,~S");c(b,"exitJmol",function(){if(!this.isApplet||this.isJNLP){if(null!=this.headlessImageParams)try{this.headless&&this.outputToFile(this.headlessImageParams)}catch(a){if(!F(a,Exception))throw a;}JU.Logger.debugging&&JU.Logger.debug("exitJmol -- exiting");System.out.flush();System.exit(0)}});c(b,"scriptCheckRet",

function(a,b){return null==this.getScriptManager()?null:this.scm.scriptCheckRet(a,b)},"~S,~B");j(b,"scriptCheck",function(a){return this.scriptCheckRet(a,!1)},"~S");j(b,"isScriptExecuting",function(){return null!=this.eval&&this.eval.isExecuting()});j(b,"haltScriptExecution",function(){null!=this.eval&&(this.eval.haltExecution(),this.eval.stopScriptThreads());this.setStringPropertyTok("pathForAllFiles",545259572,"");this.clearTimeouts()});c(b,"pauseScriptExecution",function(){null!=this.eval&&this.eval.pauseExecution(!0)});

c(b,"resolveDatabaseFormat",function(a){return JV.Viewer.hasDatabasePrefix(a)||0<=a.indexOf("cactus.nci.nih.gov/chemical/structure")?this.setLoadFormat(!1,a,a.charAt(0),!1):a},"~S");b.hasDatabasePrefix=c(b,"hasDatabasePrefix",function(a){return 0!=a.length&&JV.Viewer.isDatabaseCode(a.charAt(0))},"~S");b.isDatabaseCode=c(b,"isDatabaseCode",function(a){return"*"==a||"$"==a||"="==a||":"==a},"~S");c(b,"setLoadFormat",function(a,b,c,f){var e=null,h=b.substring(1);switch(c.charCodeAt(0)){case 99:return b;

case 104:return this.g.checkCIR&&this.checkCIR(!1),this.g.nihResolverFormat+b.substring(b.indexOf("/structure")+10);case 61:if(b.startsWith("==")){if(h=h.substring(1),h.equals("?")&&null==(h=this.getDBID("chemical component from RCSB")))return null}else{if(h.equals("?")&&null==(h=this.getDBID("PDB ID from RCSB")))return null;if(0<h.indexOf("/"))try{var j=h.indexOf("/"),m=h.substring(0,j),h=h.substring(j+1);m.equalsIgnoreCase("aflowlib")&&(c=1,j=h.indexOf("."),0<=j&&(c=JU.PT.parseInt(h.substring(j+

1)),h=h.substring(0,j)),0>h.indexOf("_")&&(h=this.getSymTemp().getSpaceGroupJSON(this,"AFLOW",h,c)));h=JV.JC.resolveDataBase(m,h,null);null!=h&&h.startsWith("'")&&(h=this.evaluateExpression(h).toString());return null==h||0==h.length?b:h}catch(n){if(F(n,Exception))return b;throw n;}if(!a&&h.endsWith(".bcif"))return h=h.substring(0,h.indexOf(".bcif")),JV.JC.resolveDataBase("bcif",h.toLowerCase(),null);if(h.endsWith(".mmtf"))return h=h.substring(0,h.indexOf(".mmtf")),JV.JC.resolveDataBase("mmtf",h.toUpperCase(),

null);e=this.g.loadFormat}case 35:return null==e&&(e=this.g.pdbLoadLigandFormat),JV.JC.resolveDataBase(null,h,e);case 42:if(h.equals("?")&&null==(h=this.getDBID("PDB ID from EBI")))return null;j=b.lastIndexOf("/");if(b.startsWith("*dom/"))return h=b.substring(j+1),e=4<j?b.substring(5):"mappings",JU.PT.rep(JV.JC.resolveDataBase("map",h,null),"%TYPE",e);if(b.startsWith("*val/"))return h=b.substring(j+1),e=4<j?b.substring(5):"validation/outliers/all",JU.PT.rep(JV.JC.resolveDataBase("map",h,null),"%TYPE",

e);if(b.startsWith("*rna3d/"))return h=b.substring(j+1),e=6<j?b.substring(6):"loops",JU.PT.rep(JV.JC.resolveDataBase("rna3d",h,null),"%TYPE",e);if(b.startsWith("*dssr--"))return h=b.substring(j+1),h=JV.JC.resolveDataBase("dssr",h,null),h+"%20"+JU.PT.rep(b.substring(5,j)," ","%20");if(b.startsWith("*dssr/"))return h=b.substring(j+1),JV.JC.resolveDataBase("dssr",h,null);if(b.startsWith("*dssr1/"))return h=b.substring(j+1),JV.JC.resolveDataBase("dssr1",h,null);c="pdbe";5==h.length&&"*"==h.charAt(4)&&

(c="pdbe2",h=h.substring(0,4));return JV.JC.resolveDataBase(c,h,null);case 58:e=this.g.pubChemFormat;if(h.equals("?")&&null==(h=this.getDBID("structure from PubChem")))return null;if(""===h)try{h="smiles:"+this.getOpenSmiles(this.bsA())}catch(p){if(!F(p,Exception))throw p;}c=h.toLowerCase();j=-2147483648;try{j=Integer.parseInt(h)}catch(q){if(!F(q,Exception))throw q;}-2147483648!=j?h="cid/"+j:c.startsWith("smiles:")?(e+="?POST?smiles="+h.substring(7),h="smiles"):h.startsWith("cid:")||h.startsWith("inchikey:")||

h.startsWith("cas:")?h=h.$replace(":","/"):(c.startsWith("name:")&&(h=h.substring(5)),h="name/"+JU.PT.escapeUrl(h));return JU.PT.formatStringS(e,"FILE",h);case 36:this.checkCIR(!1);if(h.equals("?")&&null==(h=this.getDBID("structure from NCI/CADD")))return null;if(b.equals("$"))try{h=this.getOpenSmiles(this.bsA())}catch(r){if(!F(r,Exception))throw r;}else if(b.startsWith("$$")){h=h.substring(1);if(0==h.length)try{h=this.getOpenSmiles(this.bsA())}catch(s){if(!F(s,Exception))throw s;}e=JU.PT.rep(this.g.smilesUrlFormat,

"get3d","get2d");return JU.PT.formatStringS(e,"FILE",JU.PT.escapeUrl(h))}case 77:case 78:case 50:case 73:case 75:case 83:case 84:case 47:h=JU.PT.escapeUrl(h);switch(c.charCodeAt(0)){case 77:case 78:e=this.g.nihResolverFormat+"/%FILE/names";break;case 50:e=this.g.nihResolverFormat+"/%FILE/image";break;case 73:case 84:e=this.g.nihResolverFormat+"/%FILE/stdinchi";break;case 75:e=this.g.nihResolverFormat+"/%FILE/inchikey";break;case 83:e=this.g.nihResolverFormat+"/%FILE/stdinchikey";break;case 47:e=this.g.nihResolverFormat+

"/%FILE/";break;default:e=this.g.smilesUrlFormat}return(f?"MOL3D::":"")+JU.PT.formatStringS(e,"FILE",h);case 63:case 45:case 95:(e=h.startsWith("*")||h.startsWith("="))&&(h=h.substring(1));b=null;j=h.indexOf(".");0<=j&&(b=h.substring(j+1),h=h.substring(0,j));(m=h.startsWith("density"))&&(h="em"+h.substring(7));if(h.equals("emdb")||h.equals("em"))h+="/";h.startsWith("em/")&&(h="emdb"+h.substring(2));if(h.startsWith("emdb/")){h=h.substring(5);0==h.length?h="=":h.startsWith("*")&&(h="="+h.substring(1));

a="#-sigma=10";if(h.startsWith("=")){h=h.equals("=")?this.getPdbID():h.substring(1);if(null==h||"?"==c)break;j=JV.JC.resolveDataBase("emdbquery",h,null);f=this.fm.cacheGet(j,!1);if(null==f){this.showString("retrieving "+j,!1);f=this.getFileAsString(j);if(null==f){this.showString("EM retrieve failed for "+h,!1);if(!m)return null;f="FAILED"}else this.showString(f,!1);this.fm.cachePut(j,f)}j=f.indexOf("EMD-");if(0<=j)h=f.substring(j+4),j=h.indexOf("\n"),0<j&&(h=h.substring(0,j)),j=h.indexOf(","),0<j&&

(a="#-cutoff="+h.substring(j+1),h=h.substring(0,j));else{if(!m)return null;a=null}}if(null!=a)return JV.JC.resolveDataBase("emdbmap"+("-"==c?"server":""),h,null)+a}h=JV.JC.resolveDataBase((e?"pdbemapdiff":"pdbemap")+("-"==c?"server":""),h,null);"cif".equals(b)&&(h=h.$replace("bcif","cif"))}return h},"~B,~S,~S,~B");c(b,"getDBID",function(a){return this.prompt("load a "+a,"",null,!1)},"~S");c(b,"checkCIR",function(a){if(!(this.cirChecked&&!a||null==this.g.resolverResolver)){try{this.g.removeParam("_cirStatus");

var b=this.getModelSetAuxiliaryInfo();b.remove("cirInfo");var c=this.getFileAsString(this.g.resolverResolver);System.out.println(c);var f=this.parseJSONMap(c);b.put("cirInfo",f);this.ms.msInfo=b;c=f.get("status");this.g.setO("_cirStatus",c);this.g.setCIR(f.get("rfc6570Template"),!this.isSilent);this.isSilent||JU.Logger.info("Viewer.checkCIR _.cirInfo.status = "+c)}catch(e){System.out.println("Viewer.checkCIR failed at "+this.g.resolverResolver+": "+e)}this.cirChecked=!0}},"~B");c(b,"getStandardLabelFormat",

function(a){switch(a){default:case 0:return"%[identify]";case 1:return this.g.defaultLabelXYZ;case 2:return this.g.defaultLabelPDB}},"~N");c(b,"getAdditionalHydrogens",function(a,b,c){null==a&&(a=this.bsA());var f=E(1,0);a=this.ms.calculateHydrogens(a,f,b,c);f=Array(f[0]);for(c=b=0;b<a.length;b++)if(null!=a[b])for(var e=0;e<a[b].length;e++)f[c++]=a[b][e];return f},"JU.BS,JU.Lst,~N");j(b,"setMarBond",function(a){this.g.bondRadiusMilliAngstroms=a;this.g.setI("bondRadiusMilliAngstroms",a);this.setShapeSize(1,

2*a,JU.BSUtil.setAll(this.ms.ac))},"~N");c(b,"setHoverLabel",function(a){this.shm.loadShape(35);this.setShapeProperty(35,"label",a);this.setHoverEnabled(null!=a);this.g.setO("_hoverLabel",this.hoverLabel=a);!this.hoverEnabled&&!this.sm.haveHoverCallback()&&this.startHoverWatcher(!1)},"~S");c(b,"setHoverEnabled",function(a){this.hoverEnabled=a;this.g.setB("_hoverEnabled",a)},"~B");c(b,"hoverOn",function(a,b){this.g.removeParam("_objecthovered");this.g.setI("_atomhovered",a);this.g.setO("_hoverLabel",

this.hoverLabel);this.g.setUserVariable("hovered",JS.SV.getVariable(JU.BSUtil.newAndSetBit(a)));this.sm.haveHoverCallback()&&this.sm.setStatusAtomHovered(a,this.getAtomInfoXYZ(a,2));if(this.hoverEnabled&&!(null!=this.eval&&this.isScriptExecuting()||a==this.hoverAtomIndex||0==this.g.hoverDelayMs||!this.slm.isInSelectionSubset(a))){var c=b?J.i18n.GT.$("Drag to move label"):this.isModelKitOpen()||this.isModelkitPickingActive()?this.getModelkit(!1).setProperty("hoverlabel",Integer.$valueOf(a)):null;this.shm.loadShape(35);

null!=c&&(!b||this.ms.at[a].isVisible(512))&&this.setShapeProperty(35,"specialLabel",c);this.setShapeProperty(35,"text",this.hoverText=null);this.setShapeProperty(35,"target",Integer.$valueOf(this.hoverAtomIndex=a));this.refresh(3,"hover on atom")}},"~N,~B");c(b,"isModelkitPickingActive",function(){if(32==this.acm.getAtomPickingMode())return!0;switch(this.acm.getBondPickingMode()){case 34:case 33:case 8:case 35:return this.g.bondPicking}return!1});c(b,"isModelkitPickingRotateBond",function(){return 34==

this.acm.getBondPickingMode()});c(b,"hoverOnPt",function(a,b,c,f,e){null!=this.eval&&this.isScriptExecuting()||(this.g.setO("_hoverLabel",c),null!=f&&null!=e&&(this.g.setO("_objecthovered",f),this.g.setI("_atomhovered",-1),this.g.setUserVariable("hovered",JS.SV.getVariable(e)),this.sm.haveHoverCallback()&&this.sm.setStatusObjectHovered(f,c,e)),this.hoverEnabled&&(this.shm.loadShape(35),this.gdata.antialiasEnabled&&(a<<=1,b<<=1),this.setShapeProperty(35,"xy",JU.P3i.new3(a,b,0)),this.setShapeProperty(35,

"target",null),this.setShapeProperty(35,"specialLabel",null),this.setShapeProperty(35,"text",c),this.hoverAtomIndex=-1,this.hoverText=c,this.refresh(3,"hover on point")))},"~N,~N,~S,~S,JU.T3");c(b,"hoverOff",function(){try{if((this.isModelKitOpen()||null!=this.modelkit&&this.modelkit.wasRotating())&&!this.isModelkitPickingRotateBond()&&this.highlight(null),this.hoverEnabled){var a=null!=this.hoverText||0<=this.hoverAtomIndex;0<=this.hoverAtomIndex&&(this.setShapeProperty(35,"target",null),this.hoverAtomIndex=

-1);null!=this.hoverText&&(this.setShapeProperty(35,"text",null),this.hoverText=null);this.setShapeProperty(35,"specialLabel",null);a&&this.refresh(3,"hover off")}}catch(b){if(!F(b,Exception))throw b;}});j(b,"setDebugScript",function(a){this.g.debugScript=a;this.g.setB("debugScript",a);null!=this.eval&&this.eval.setDebugging()},"~B");c(b,"clearClickCount",function(){this.setTainted(!0)});c(b,"setCursor",function(a){if(!this.$isKiosk&&!(this.currentCursor==a||this.multiTouch||!this.haveDisplay))this.apiPlatform.setCursor(this.currentCursor=

a,this.display)},"~N");c(b,"setPickingMode",function(a,b){if(this.haveDisplay){var c=this.acm.getAtomPickingMode();this.showSelected=!1;var f=null;if(null!=a){var e=a.indexOf("_");0<=e&&(f=a.substring(e+1),a=a.substring(0,e));b=JV.ActionManager.getPickingMode(a)}0>b&&(b=1);this.acm.setPickingMode(b);e=JV.ActionManager.getPickingModeName(this.acm.getAtomPickingMode());this.g.setO("picking",e);if(null!=this.modelkit)switch(this.modelkit.setProperty("atompickingmode",e),this.acm.setPickingMode(b),b){case 1:b!=

c&&this.setModelKitMode(!1);break;case 8:case 35:this.modelkit.setProperty("bondpickingmode",a.toLowerCase())}if(!(null==f||0==f.length))switch(f=Character.toUpperCase(f.charAt(0))+(1==f.length?"":f.substring(1,2)),b){case 32:this.getModelkit(!1).setProperty("atomtype",f);break;case 33:this.setBooleanPropertyTok("bondPicking",603979814,!0);this.getModelkit(!1).setProperty("bondtype",f);break;default:JU.Logger.error("Bad picking mode: "+a+"_"+f)}}},"~S,~N");c(b,"getPickingMode",function(){return this.haveDisplay?

this.acm.getAtomPickingMode():0});c(b,"setPickingStyle",function(a,b){this.haveDisplay&&(null!=a&&(b=JV.ActionManager.getPickingStyleIndex(a)),0>b&&(b=0),this.acm.setPickingStyle(b),this.g.setO("pickingStyle",JV.ActionManager.getPickingStyleName(this.acm.getPickingStyle())))},"~S,~N");c(b,"getDrawHover",function(){return this.haveDisplay&&this.g.drawHover});c(b,"getAtomInfo",function(a){null==this.ptTemp&&(this.ptTemp=new JU.P3);return 0<=a?this.ms.getAtomInfo(a,null,this.ptTemp):this.shm.getShapePropertyIndex(6,

"pointInfo",-a)},"~N");c(b,"getAtomInfoXYZ",function(a,b){var c=this.ms.at[a];if(4==b)return this.getChimeMessenger().getInfoXYZ(c);null==this.ptTemp&&(this.ptTemp=new JU.P3);return c.getIdentityXYZ(this.ptTemp,b)},"~N,~N");c(b,"setSync",function(){this.sm.doSync()&&this.sm.setSync(null)});j(b,"setJmolCallbackListener",function(a){this.sm.cbl=a},"J.api.JmolCallbackListener");j(b,"setJmolStatusListener",function(a){this.sm.cbl=this.sm.jsl=a},"J.api.JmolStatusListener");c(b,"getStatusChanged",function(a){return null==

a?null:this.sm.getStatusChanged(a)},"~S");c(b,"menuEnabled",function(){return!this.g.disablePopupMenu&&null!=this.getPopupMenu()});c(b,"setStatusDragDropped",function(a,b,c,f,e){0==a&&(this.g.setO("_fileDropped",f),this.g.setUserVariable("doDrop",JS.SV.vT),this.g.setUserVariable("dropFileType",JS.SV.newS("")),this.g.setUserVariable("dropFileName",JS.SV.newS(f)));a=this.sm.setStatusDragDropped(a,b,c,f,e);b=this.getP("dropFileType").toString();0<b.length&&null!=e&&(e[0]=b);return!a||this.getP("doDrop").toString().equals("true")},

"~N,~N,~N,~S,~A");c(b,"setStatusResized",function(a,b){this.sm.setStatusResized(a,b)},"~N,~N");c(b,"scriptStatus",function(a){this.setScriptStatus(a,"",0,null)},"~S");c(b,"scriptStatusMsg",function(a,b){this.setScriptStatus(a,b,0,null)},"~S,~S");c(b,"setScriptStatus",function(a,b,c,f){this.sm.setScriptStatus(a,b,c,f)},"~S,~S,~N,~S");j(b,"showUrl",function(a){if(null!=a){if(0>a.indexOf(":")){var b=this.fm.getAppletDocumentBase();""===b&&(b=this.fm.getFullPathName(!1));0<=b.indexOf("/")?b=b.substring(0,

b.lastIndexOf("/")+1):0<=b.indexOf("\\")&&(b=b.substring(0,b.lastIndexOf("\\")+1));a=b+a}JU.Logger.info("showUrl:"+a);this.sm.showUrl(a)}},"~S");c(b,"setMeshCreator",function(a){this.shm.loadShape(24);this.setShapeProperty(24,"meshCreator",a)},"~O");c(b,"showConsole",function(a){if(this.haveDisplay)try{null==this.appConsole&&a&&this.getConsole(),this.appConsole.setVisible(!0)}catch(b){}},"~B");c(b,"getConsole",function(){this.getProperty("DATA_API","getAppConsole",Boolean.TRUE);return this.appConsole});

j(b,"getParameter",function(a){return this.getP(a)},"~S");c(b,"getP",function(a){return this.g.getParameter(a,!0)},"~S");c(b,"getPOrNull",function(a){return this.g.getParameter(a,!1)},"~S");c(b,"unsetProperty",function(a){a=a.toLowerCase();(a.equals("all")||a.equals("variables"))&&this.fm.setPathForAllFiles("");this.g.unsetUserVariable(a)},"~S");j(b,"notifyStatusReady",function(a){System.out.println("Jmol applet "+this.fullName+(a?" ready":" destroyed"));a||this.dispose();this.sm.setStatusAppletReady(this.fullName,

a)},"~B");j(b,"getBooleanProperty",function(a){a=a.toLowerCase();if(this.g.htBooleanParameterFlags.containsKey(a))return this.g.htBooleanParameterFlags.get(a).booleanValue();if(a.endsWith("p!")){if(null==this.acm)return!1;var b=this.acm.getPickingState().toLowerCase();a=a.substring(0,a.length-2)+";";return 0<=b.indexOf(a)}if(a.equalsIgnoreCase("executionPaused"))return null!=this.eval&&this.eval.isPaused();if(a.equalsIgnoreCase("executionStepping"))return null!=this.eval&&this.eval.isStepping();if(a.equalsIgnoreCase("haveBFactors"))return null!=

this.ms.getBFactors();if(a.equalsIgnoreCase("colorRasmol"))return this.cm.isDefaultColorRasmol;if(a.equalsIgnoreCase("frank"))return this.getShowFrank();if(a.equalsIgnoreCase("spinOn"))return this.tm.spinOn;if(a.equalsIgnoreCase("isNavigating"))return this.tm.isNavigating();if(a.equalsIgnoreCase("showSelections"))return this.selectionHalosEnabled;if(this.g.htUserVariables.containsKey(a)){b=this.g.getUserVariable(a);if(1073742335==b.tok)return!0;if(1073742334==b.tok)return!1}JU.Logger.error("vwr.getBooleanProperty("+

a+") - unrecognized");return!1},"~S");j(b,"getInt",function(a){switch(a){case 553648132:return this.am.animationFps;case 553648139:return this.g.dotDensity;case 553648140:return this.g.dotScale;case 553648142:return this.g.helixStep;case 553648145:return this.g.infoFontSize;case 553648147:return this.g.labelPointerWidth;case 553648149:return this.g.meshScale;case 553648150:return this.g.minimizationReportSteps;case 553648153:return this.g.minPixelSelRadius;case 553648154:return this.g.percentVdwAtom;

case 553648157:return this.g.pickingSpinRate;case 553648166:return this.g.ribbonAspectRatio;case 536870922:return this.g.scriptDelay;case 553648152:return this.g.minimizationMaxAtoms;case 553648170:return this.g.smallMoleculeMaxAtoms;case 553648183:return this.g.strutSpacing;case 553648184:return this.stm.getUndoMax();case 553648185:return this.g.vectorTrail}JU.Logger.error("viewer.getInt("+JS.T.nameOf(a)+") - not listed");return 0},"~N");c(b,"getDelayMaximumMs",function(){return this.haveDisplay?

this.g.delayMaximumMs:1});c(b,"getHermiteLevel",function(){return this.tm.spinOn&&0<this.g.hermiteLevel?0:this.g.hermiteLevel});c(b,"getHoverDelay",function(){return this.isModelKitOpen()||this.isModelkitPickingActive()||this.getDrawHover()?20:this.g.hoverDelayMs});j(b,"getBoolean",function(a){switch(a){case 603979970:return this.g.useMinimizationThread;case 603979891:return this.g.nboCharges;case 603979856:return this.g.hiddenLinesDashed;case 1073742086:return this.ms.getMSInfoB(JV.JC.getBoolName(4));

case 603979802:return this.g.autoplayMovie;case 603979797:return!this.headless&&this.g.allowAudio;case 603979780:return this.g.allowGestures;case 603979784:return this.g.allowMultiTouch;case 603979785:return this.g.allowRotateSelected;case 603979792:return this.g.appendNew;case 603979794:return this.g.applySymmetryToBonds;case 603979796:return this.g.atomPicking;case 603979798:return this.g.autoBond;case 603979800:return this.g.autoFps;case 603979806:return this.g.axesOrientationRasmol;case 603979811:return this.g.cartoonSteps;

case 603979810:return this.g.cartoonBlocks;case 603979821:return this.g.checkCIR;case 603979812:return this.g.bondModeOr;case 603979815:return this.g.cartoonBaseEdges;case 603979816:return this.g.cartoonFancy;case 603979817:return this.g.cartoonLadders;case 603979818:return this.g.cartoonRibose;case 603979819:return this.g.cartoonRockets;case 603979822:return this.g.chainCaseSensitive||this.chainCaseSpecified;case 603979823:return this.g.cipRule6Full;case 603979825:return this.g.debugScript;case 603979826:return this.g.defaultStructureDSSP;

case 603979827:return this.g.disablePopupMenu;case 603979828:return this.g.displayCellParameters;case 603979830:return this.g.dotSurface;case 603979829:return this.g.dotsSelectedOnly;case 603979831:return this.g.doublePrecision;case 603979834:return this.g.drawPicking;case 603979838:return this.g.elementKey;case 603979846:return this.g.fontCaching;case 603979847:return this.g.fontScaling;case 603979848:return this.g.forceAutoBond;case 603979849:return!1;case 603979850:return this.g.greyscaleRendering;

case 603979852:return this.g.hbondsBackbone;case 603979853:return this.g.hbondsRasmol;case 603979854:return this.g.hbondsSolid;case 1612709894:return this.g.rasmolHeteroSetting;case 603979858:return this.g.hideNameInPopup;case 603979864:return this.g.highResolutionFlag;case 1612709900:return this.g.rasmolHydrogenSetting;case 603979867:return this.g.isosurfaceKey;case 603979869:return this.g.jmolInJSpecView;case 603979870:return this.g.justifyMeasurements;case 603979872:return this.g.legacyAutoBonding;

case 603979873:return this.g.legacyHAddition;case 603979874:return this.g.legacyJavaFloat;case 603979876:return this.g.logGestures;case 603979877:return this.g.measureAllModels;case 603979878:return this.g.measurementLabels;case 603979879:return this.g.messageStyleChime;case 603983903:return this.g.modelKitMode;case 603979886:return this.g.multipleBondBananas;case 603979889:return this.g.navigationMode;case 603979890:return this.g.navigationPeriodic;case 603979893:return this.g.partialDots;case 603979894:return this.g.pdbAddHydrogens;

case 603979896:return this.g.pdbSequential;case 603979898:return this.g.preserveState;case 603979900:return this.refreshing;case 603979901:return this.g.ribbonBorder;case 603979902:return this.g.rocketBarrels;case 603979892:return this.g.noDelay;case 603979906:return this.g.selectAllModels;case 603979920:return this.g.showHiddenSelectionHalos;case 603979922:return this.g.showHydrogens;case 603979926:return this.g.showMeasurements;case 603979927:return this.g.showModVecs;case 603979928:return this.g.showMultipleBonds;

case 603979934:return this.g.showTiming;case 603979937:return this.g.showUnitCellDetails;case 603979939:return this.g.slabByAtom;case 603979940:return this.g.slabByMolecule;case 603979944:return this.g.smartAromatic;case 603979948:return this.g.dotSolvent;case 603979952:return this.g.ssbondsBackbone;case 603979955:return this.g.strutsMultiple;case 603979956:return this.g.symmetryHermannMauguin;case 603979960:return this.g.testFlag1;case 603979962:return this.g.testFlag2;case 603979964:return this.g.testFlag3;

case 603979965:return this.g.testFlag4;case 603979966:return this.g.traceAlpha;case 1111490588:return this.g.translucent;case 603979968:return this.g.twistedSheets;case 603979972:return this.g.vectorsCentered;case 603979973:return this.g.vectorSymmetry;case 603979975:return this.g.waitForMoveTo;case 603979978:return this.g.zeroBasedXyzRasmol}JU.Logger.error("viewer.getBoolean("+JS.T.nameOf(a)+") - not listed");return!1},"~N");c(b,"allowEmbeddedScripts",function(){return this.g.allowEmbeddedScripts&&

!this.isPreviewOnly});c(b,"getDragSelected",function(){return this.g.dragSelected&&!this.g.modelKitMode});c(b,"getBondsPickable",function(){return this.g.bondPicking||this.isModelkitPickingActive()||this.isModelKitOpen()&&this.getModelkitPropertySafely("ismolecular")===Boolean.TRUE});c(b,"isModelKitOpen",function(){return this.g.modelKitMode&&null!=this.modelkit&&!this.modelkit.isHidden()});c(b,"useMinimizationThread",function(){return this.g.useMinimizationThread&&!this.autoExit});j(b,"getFloat",

function(a){switch(a){case 1153433601:return this.g.particleRadius;case 570425345:return this.g.axesOffset;case 570425346:return this.g.axesScale;case 570425348:return this.g.bondTolerance;case 570425353:return this.g.defaultTranslucent;case 570425352:return this.g.defaultDrawArrowScale;case 570425354:return this.g.dipoleScale;case 570425355:return this.g.drawFontSize;case 570425357:return this.g.exportScale;case 570425359:return this.g.hbondsAngleMinimum;case 570425361:return this.g.hbondHXDistanceMaximum;

case 570425360:return this.g.hbondNODistanceMaximum;case 570425363:return this.g.loadAtomDataTolerance;case 570425364:return this.g.minBondDistance;case 1275072532:return this.g.modulationScale;case 570425370:return this.g.multipleBondSpacing;case 570425369:return this.g.multipleBondRadiusFactor;case 570425374:return this.g.navigationSpeed;case 570425382:return this.g.pointGroupDistanceTolerance;case 570425384:return this.g.pointGroupLinearTolerance;case 570425388:return this.tm.modelRadius;case 570425392:return this.g.sheetSmoothing;

case 570425394:return this.g.solventProbeRadius;case 570425403:return this.g.starWidth;case 570425406:return this.g.strutDefaultRadius;case 570425408:return this.g.strutLengthMaximum;case 1648361473:return this.g.vectorScale;case 570425412:return this.g.vibrationPeriod;case 570425347:return this.g.cartoonBlockHeight}JU.Logger.error("viewer.getFloat("+JS.T.nameOf(a)+") - not listed");return 0},"~N");j(b,"setStringProperty",function(a,b){if(!(null==b||null==a||0==a.length))if("_"==a.charAt(0))this.g.setO(a,

b);else{var c=JS.T.getTokFromName(a);switch(JS.T.getParamType(c)){case 603979776:this.setBooleanPropertyTok(a,c,JS.SV.newV(4,b).asBoolean());break;case 553648128:this.setIntPropertyTok(a,c,JS.SV.newV(4,b).asInt());break;case 570425344:this.setFloatPropertyTok(a,c,JU.PT.parseFloat(b));break;default:this.setStringPropertyTok(a,c,b)}}},"~S,~S");c(b,"setStringPropertyTok",function(a,b,c){switch(b){case 545259567:this.g.macroDirectory=c=null==c||0==c.length?"https://chemapps.stolaf.edu/jmol/macros":c;

this.macros=null;break;case 545259570:this.g.nihResolverFormat=c;break;case 545259521:this.setAnimationMode(c);return;case 545259569:this.g.nmrPredictFormat=c;break;case 545259548:this.g.defaultDropScript=c;break;case 545259572:c=this.fm.setPathForAllFiles(c);break;case 545259558:this.setUnits(c,!1);return;case 545259560:this.g.forceField.equals(c)||(this.g.forceField=c="UFF".equalsIgnoreCase(c)?"UFF":"UFF2D".equalsIgnoreCase(c)?"UFF2D":"MMFF2D".equalsIgnoreCase(c)?"MMFF2D":"MMFF",this.minimizer=

null);break;case 545259571:this.g.nmrUrlFormat=c;break;case 545259568:this.setUnits(c,!0);return;case 545259565:this.g.pdbLoadLigandFormat=c;break;case 545259543:this.g.defaultLabelPDB=c;break;case 545259544:this.g.defaultLabelXYZ=c;break;case 545259549:this.g.defaultLoadFilter=c;break;case 545259566:c=this.getOutputManager().setLogFile(c);if(null==c)return;break;case 545259559:break;case 545259524:this.g.atomTypes=c;break;case 545259538:break;case 545259576:this.g.pickLabel=c;break;case 545259580:this.g.quaternionFrame=

2==c.length&&c.startsWith("R")?c.substring(0,2):""+(c.toLowerCase()+"p").charAt(0);JU.PT.isOneOf(this.g.quaternionFrame,"RC;RP;a;b;c;n;p;q;x;")||(this.g.quaternionFrame="p");this.ms.haveStraightness=!1;break;case 545259555:this.setVdwStr(c);return;case 545259563:new J.i18n.GT(this,c);b=J.i18n.GT.getLanguage();this.modelkit=null;null!=this.jmolpopup&&(this.jmolpopup.jpiDispose(),this.jmolpopup=null,this.getPopupMenu());this.sm.setCallbackFunction("language",b);c=J.i18n.GT.getLanguage();break;case 545259564:this.g.loadFormat=

c;break;case 545259534:this.setObjectColor("background",c);return;case 545259528:this.setObjectColor("axis1",c);return;case 545259530:this.setObjectColor("axis2",c);return;case 545259532:this.setObjectColor("axis3",c);return;case 545259536:this.setObjectColor("boundbox",c);return;case 545259586:this.setObjectColor("unitcell",c);return;case 545259578:this.setPropertyColorScheme(c,!1,!1);break;case 545259562:this.shm.loadShape(35);this.setShapeProperty(35,"atomLabel",c);break;case 545259547:this.g.defaultDistanceLabel=

c;break;case 545259542:this.g.defaultAngleLabel=c;break;case 545259554:this.g.defaultTorsionLabel=c;break;case 545259550:this.g.defaultLoadScript=c;break;case 545259522:this.fm.setAppletProxy(c);break;case 545259546:null==c&&(c="");c=c.$replace("\\","/");this.g.defaultDirectory=c;break;case 545259561:this.g.helpPath=c;break;case 545259552:!c.equalsIgnoreCase("RasMol")&&!c.equalsIgnoreCase("PyMOL")&&(c="Jmol");this.setDefaultsType(c);break;case 545259545:this.setDefaultColors(c.equalsIgnoreCase("rasmol"));

return;case 545259573:this.setPickingMode(c,0);return;case 545259574:this.setPickingStyle(c,0);return;case 545259540:break;default:if(a.toLowerCase().endsWith("callback")){this.sm.setCallbackFunction(a,0==c.length||c.equalsIgnoreCase("none")?null:c);break}if(!this.g.htNonbooleanParameterValues.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.newV(4,c));return}}this.g.setO(a,c)},"~S,~N,~S");j(b,"setFloatProperty",function(a,b){if(!(null==a||0==a.length))if("_"==a.charAt(0))this.g.setF(a,

b);else{var c=JS.T.getTokFromName(a);switch(JS.T.getParamType(c)){case 545259520:this.setStringPropertyTok(a,c,""+b);break;case 603979776:this.setBooleanPropertyTok(a,c,0!=b);break;case 553648128:this.setIntPropertyTok(a,c,D(b));break;case 570425344:if(Float.isNaN(b))break;default:this.setFloatPropertyTok(a,c,b)}}},"~S,~N");c(b,"setFloatPropertyTok",function(a,b,c){switch(b){case 570425347:this.g.cartoonBlockHeight=c;break;case 570425366:this.ms.setModulation(null,!1,null,!1);this.g.modulationScale=

c=Math.max(0.1,c);this.ms.setModulation(null,!0,null,!1);break;case 570425381:this.g.particleRadius=Math.abs(c);break;case 570425355:this.g.drawFontSize=c;this.shm.setShapePropertyBs(22,"font",null,null);break;case 570425357:this.g.exportScale=c;break;case 570425403:this.g.starWidth=c;break;case 570425369:this.g.multipleBondRadiusFactor=c;break;case 570425370:this.g.multipleBondSpacing=c;break;case 570425393:this.tm.setSlabRange(c);break;case 570425365:this.g.minimizationCriterion=c;break;case 570425358:this.haveDisplay&&

this.acm.setGestureSwipeFactor(c);break;case 570425367:this.haveDisplay&&this.acm.setMouseDragFactor(c);break;case 570425368:this.haveDisplay&&this.acm.setMouseWheelFactor(c);break;case 570425408:this.g.strutLengthMaximum=c;break;case 570425406:this.g.strutDefaultRadius=c;break;case 570425376:this.setSpin("X",D(c));break;case 570425378:this.setSpin("Y",D(c));break;case 570425380:this.setSpin("Z",D(c));break;case 570425371:if(Float.isNaN(c))return;this.setSpin("FPS",D(c));break;case 570425363:this.g.loadAtomDataTolerance=

c;break;case 570425359:this.g.hbondsAngleMinimum=c;break;case 570425361:this.g.hbondHXDistanceMaximum=c;break;case 570425360:this.g.hbondNODistanceMaximum=c;break;case 570425382:this.g.pointGroupDistanceTolerance=c;break;case 570425384:this.g.pointGroupLinearTolerance=c;break;case 570425356:this.g.ellipsoidAxisDiameter=c;break;case 570425398:this.setSpin("x",D(c));break;case 570425400:this.setSpin("y",D(c));break;case 570425402:this.setSpin("z",D(c));break;case 570425396:this.setSpin("fps",D(c));

break;case 570425352:this.g.defaultDrawArrowScale=c;break;case 570425353:this.g.defaultTranslucent=c;break;case 570425345:this.setAxesScale(b,c);break;case 570425346:this.setAxesScale(b,c);break;case 570425416:this.tm.visualRangeAngstroms=c;this.refresh(1,"set visualRange");break;case 570425372:this.setNavigationDepthPercent(c);break;case 570425374:this.g.navigationSpeed=c;break;case 570425373:this.tm.setNavigationSlabOffsetPercent(c);break;case 570425350:this.tm.setCameraDepthPercent(c,!1);this.refresh(1,

"set cameraDepth");return;case 570425388:this.setRotationRadius(c,!0);return;case 570425362:this.g.hoverDelayMs=D(1E3*c);break;case 570425392:this.g.sheetSmoothing=c;break;case 570425354:c=JV.Viewer.checkFloatRange(c,-10,10);this.g.dipoleScale=c;break;case 570425404:this.tm.setStereoDegrees(c);break;case 1648361473:this.setVectorScale(c);return;case 570425412:this.setVibrationPeriod(c);return;case 570425414:this.setVibrationScale(c);return;case 570425348:this.setBondTolerance(c);return;case 570425364:this.setMinBondDistance(c);

return;case 570425390:this.tm.setScaleAngstromsPerInch(c);break;case 570425394:c=JV.Viewer.checkFloatRange(c,0,10);this.g.solventProbeRadius=c;break;default:if(!this.g.htNonbooleanParameterValues.containsKey(a.toLowerCase())){this.g.setUserVariable(a,JS.SV.newF(c));return}}this.g.setF(a,c)},"~S,~N,~N");j(b,"setIntProperty",function(a,b){if(!(-2147483648==b||null==a||0==a.length))if("_"==a.charAt(0))this.g.setI(a,b);else{var c=JS.T.getTokFromName(a);switch(JS.T.getParamType(c)){case 545259520:this.setStringPropertyTok(a,

c,""+b);break;case 603979776:this.setBooleanPropertyTok(a,c,0!=b);break;case 570425344:this.setFloatPropertyTok(a,c,b);break;default:this.setIntPropertyTok(a,c,b)}}},"~S,~N");c(b,"setIntPropertyTok",function(a,b,c){switch(b){case 553648150:this.g.minimizationReportSteps=Math.min(Math.max(c,1),20);break;case 553648184:this.stm.setUndoMax(c);break;case 553648147:this.g.labelPointerWidth=c;break;case 553648152:this.g.minimizationMaxAtoms=c;break;case 553648145:this.g.infoFontSize=Math.max(0,c);break;

case 553648167:case 553648144:case 553648168:c=this.eval.setStatic(b,c);break;case 553648185:this.g.vectorTrail=c;break;case 553648136:c=0==c?0:1;this.g.bondingVersion=JU.Elements.bondingVersion=c;break;case 553648135:this.gdata.setCelPower(c);break;case 553648129:this.gdata.setAmbientOcclusion(c);break;case 553648158:this.g.platformSpeed=Math.min(Math.max(c,0),10);break;case 553648149:this.g.meshScale=c;break;case 553648153:this.g.minPixelSelRadius=c;break;case 553648146:this.g.isosurfacePropertySmoothingPower=

c;break;case 553648165:this.g.repaintWaitMs=c;break;case 553648170:this.g.smallMoleculeMaxAtoms=c;break;case 553648151:this.g.minimizationSteps=c;break;case 553648183:this.g.strutSpacing=c;break;case 553648156:c=JV.Viewer.checkIntRange(c,0,1E3);this.gdata.setPhongExponent(c);break;case 553648142:this.g.helixStep=c;this.ms.haveStraightness=!1;break;case 553648140:this.g.dotScale=c;break;case 553648139:this.g.dotDensity=c;break;case 553648137:this.g.delayMaximumMs=c;break;case 553648148:JU.Logger.setLogLevel(c);

JU.Logger.info("logging level set to "+c);this.g.setI("logLevel",c);null!=this.eval&&this.eval.setDebugging();return;case 553648133:this.setAxesMode(2==c?603979808:1==c?603979804:603979809);return;case 553648178:this.setStrandCount(0,c);return;case 553648182:this.setStrandCount(12,c);return;case 553648180:this.setStrandCount(13,c);return;case 553648155:return;case 536870922:this.g.scriptDelay=c;break;case 553648176:c=0>c?JV.Viewer.checkIntRange(c,-10,-1):JV.Viewer.checkIntRange(c,0,100);this.gdata.setSpecularPower(c);

break;case 553648172:c=JV.Viewer.checkIntRange(-c,-10,-1);this.gdata.setSpecularPower(c);break;case 553648134:this.setMarBond(c);return;case 536870924:this.setBooleanPropertyTok(a,b,1==c);return;case 553648174:c=JV.Viewer.checkIntRange(c,0,100);this.gdata.setSpecularPercent(c);break;case 553648138:c=JV.Viewer.checkIntRange(c,0,100);this.gdata.setDiffusePercent(c);break;case 553648130:c=JV.Viewer.checkIntRange(c,0,100);this.gdata.setAmbientPercent(c);break;case 553648186:this.tm.zDepthToPercent(c);

break;case 553648188:this.tm.zSlabToPercent(c);break;case 554176526:this.tm.depthToPercent(c);break;case 554176565:this.tm.slabToPercent(c);break;case 553648190:this.g.zShadePower=c=Math.max(c,0);break;case 553648166:this.g.ribbonAspectRatio=c;break;case 553648157:this.g.pickingSpinRate=1>c?1:c;break;case 553648132:this.setAnimationFps(c);return;case 553648154:this.setPercentVdwAtom(c);break;case 553648143:this.g.hermiteLevel=c;break;case 553648141:case 553648161:case 553648160:case 553648162:case 553648164:break;

default:if(!this.g.htNonbooleanParameterValues.containsKey(a)){this.g.setUserVariable(a,JS.SV.newI(c));return}}this.g.setI(a,c)},"~S,~N,~N");b.checkIntRange=c(b,"checkIntRange",function(a,b,c){return a<b?b:a>c?c:a},"~N,~N,~N");b.checkFloatRange=c(b,"checkFloatRange",function(a,b,c){return a<b?b:a>c?c:a},"~N,~N,~N");j(b,"setBooleanProperty",function(a,b){if(!(null==a||0==a.length))if("_"==a.charAt(0))this.g.setB(a,b);else{var c=JS.T.getTokFromName(a);switch(JS.T.getParamType(c)){case 545259520:this.setStringPropertyTok(a,

c,"");break;case 553648128:this.setIntPropertyTok(a,c,b?1:0);break;case 570425344:this.setFloatPropertyTok(a,c,b?1:0);break;default:this.setBooleanPropertyTok(a,c,b)}}},"~S,~B");c(b,"setBooleanPropertyTok",function(a,b,c){var f=!0;switch(b){case 603979838:this.g.elementKey=c;this.getModelkit(!1).setProperty("setelementkey",Boolean.$valueOf(c));break;case 603979956:this.g.symmetryHermannMauguin=c;break;case 603979831:c=(new Boolean(c&JV.Viewer.isJS)).valueOf();this.g.doublePrecision=c;JV.Viewer.isHighPrecision=

this.g.doublePrecision;this.setBooleanPropertyTok("legacyJavaFloat",603979874,c);break;case 603979821:(this.g.checkCIR=c)&&this.checkCIR(!0);break;case 603979823:this.g.cipRule6Full=c;break;case 603979802:this.g.autoplayMovie=c;break;case 603979797:c=!1;this.g.allowAudio=c;break;case 603979892:this.g.noDelay=c;break;case 603979891:this.g.nboCharges=c;break;case 603979856:this.g.hiddenLinesDashed=c;break;case 603979886:this.g.multipleBondBananas=c;break;case 603979884:this.g.modulateOccupancy=c;break;

case 603979874:if(c||!this.g.doublePrecision)this.g.legacyJavaFloat=c;c=this.g.legacyJavaFloat;break;case 603979927:this.g.showModVecs=c;break;case 603979937:this.g.showUnitCellDetails=c;break;case 603979849:f=!1;break;case 603979972:this.g.vectorsCentered=c;break;case 603979810:this.g.cartoonBlocks=c;break;case 603979811:this.g.cartoonSteps=c;break;case 603979818:this.g.cartoonRibose=c;break;case 603979840:this.g.ellipsoidArrows=c;break;case 1111490588:this.g.translucent=c;break;case 603979817:this.g.cartoonLadders=

c;break;case 603979968:b=this.g.twistedSheets;this.g.twistedSheets=c;b!=c&&this.checkCoordinatesChanged(null);break;case 603979820:this.gdata.setCel(c);break;case 603979816:this.g.cartoonFancy=c;break;case 603979934:this.g.showTiming=c;break;case 603979973:this.g.vectorSymmetry=c;break;case 603979867:this.g.isosurfaceKey=c;break;case 603979893:this.g.partialDots=c;break;case 603979872:this.g.legacyAutoBonding=c;break;case 603979826:this.g.defaultStructureDSSP=c;break;case 603979835:this.g.dsspCalcHydrogen=

c;break;case 603979782:(this.g.allowModelkit=c)||this.setModelKitMode(!1);break;case 603983903:this.setModelKitMode(c);break;case 603979887:this.g.multiProcessor=c&&1<JV.Viewer.nProcessors;break;case 603979885:this.g.monitorEnergy=c;break;case 603979853:this.g.hbondsRasmol=c;break;case 603979880:this.g.minimizationRefresh=c;break;case 603979881:this.g.minimizationSilent=c;break;case 603979866:c&&(this.$isKiosk=!0,this.g.disablePopupMenu=!0,null!=this.display&&this.apiPlatform.setTransparentCursor(this.display));

break;case 603979975:this.g.waitForMoveTo=c;break;case 603979875:this.g.logCommands=!0;break;case 603979876:this.g.logGestures=!0;break;case 603979784:this.g.allowMultiTouch=c;break;case 603979898:this.g.preserveState=c;this.ms.setPreserveState(c);this.undoMoveAction(4165,-2);break;case 603979955:this.g.strutsMultiple=c;break;case 603979845:break;case 603979939:this.g.slabByAtom=c;break;case 603979940:this.g.slabByMolecule=c;break;case 603979903:this.g.saveProteinStructureState=c;break;case 603979780:this.g.allowGestures=

c;break;case 603979865:this.g.imageState=c;break;case 603979970:this.g.useMinimizationThread=c;break;case 603979781:this.g.allowKeyStrokes=c;break;case 603979832:this.g.dragSelected=c;this.showSelected=!1;break;case 603979924:this.g.showKeyStrokes=c;break;case 603979846:this.g.fontCaching=c;break;case 603979796:this.g.atomPicking=c;break;case 603979814:this.highlight(null);this.g.bondPicking=c;break;case 603979906:(this.g.selectAllModels=c)?this.slm.setSelectionSubset(null):this.am.setSelectAllSubset(!1);

break;case 603979879:this.g.messageStyleChime=c;break;case 603979896:this.g.pdbSequential=c;break;case 603979894:this.g.pdbAddHydrogens=c;break;case 603979895:this.g.pdbGetHeader=c;break;case 603979841:this.g.ellipsoidAxes=c;break;case 603979839:this.g.ellipsoidArcs=c;break;case 603979842:this.g.ellipsoidBall=c;break;case 603979843:this.g.ellipsoidDots=c;break;case 603979844:this.g.ellipsoidFill=c;break;case 603979847:this.g.fontScaling=c;break;case 603979957:this.setSyncTarget(0,c);break;case 603979958:this.setSyncTarget(1,

c);break;case 603979977:this.g.wireframeRotation=c;break;case 603979868:this.g.isosurfacePropertySmoothing=c;break;case 603979834:this.g.drawPicking=c;break;case 603979786:case 603979790:case 603979788:this.setAntialias(b,c);break;case 603979944:this.g.smartAromatic=c;break;case 603979794:this.setApplySymmetryToBonds(c);break;case 603979792:this.g.appendNew=c;break;case 603979800:this.g.autoFps=c;break;case 603979971:JU.DF.setUseNumberLocalization(this.g.useNumberLocalization=c);break;case 603979918:case 1611272202:a=

"showFrank";this.setFrankOn(c);break;case 1612709912:a="solventProbe";this.g.dotSolvent=c;break;case 603979948:this.g.dotSolvent=c;break;case 603979785:this.g.allowRotateSelected=c;break;case 603979783:this.g.allowMoveAtoms=c;this.showSelected=!1;break;case 536870922:this.setIntPropertyTok("showScript",b,c?1:0);return;case 603979778:this.g.allowEmbeddedScripts=c;break;case 603979890:this.g.navigationPeriodic=c;break;case 603979984:this.tm.setZShadeEnabled(c);return;case 603979833:this.haveDisplay&&

(this.g.drawHover=c);break;case 603979889:this.setNavigationMode(c);break;case 603979888:return;case 603979860:this.g.hideNavigationPoint=c;break;case 603979930:this.g.showNavigationPointAlways=c;break;case 603979900:this.setRefreshing(c);break;case 603979869:this.g.jmolInJSpecView=c;break;case 603979870:this.g.justifyMeasurements=c;break;case 603979952:this.g.ssbondsBackbone=c;break;case 603979852:this.g.hbondsBackbone=c;break;case 603979854:this.g.hbondsSolid=c;break;case 536870924:this.gdata.setSpecular(c);

break;case 603979942:this.tm.setSlabEnabled(c);return;case 603979980:this.tm.setZoomEnabled(c);return;case 603979864:this.g.highResolutionFlag=c;break;case 603979966:this.g.traceAlpha=c;break;case 603979983:this.g.zoomLarge=c;this.tm.setZoomHeight(this.g.zoomHeight,c);break;case 603979982:this.g.zoomHeight=c;this.tm.setZoomHeight(c,this.g.zoomLarge);break;case 603979871:J.i18n.GT.setDoTranslate(c);break;case 603979862:this.slm.setHideNotSelected(c);break;case 603979904:this.setScriptQueue(c);break;

case 603979830:this.g.dotSurface=c;break;case 603979829:this.g.dotsSelectedOnly=c;break;case 1611141172:this.setSelectionHalosEnabled(c);break;case 603979910:this.g.rasmolHydrogenSetting=c;break;case 603979908:this.g.rasmolHeteroSetting=c;break;case 603979928:this.g.showMultipleBonds=c;break;case 603979920:this.g.showHiddenSelectionHalos=c;break;case 603979976:this.tm.setWindowCentered(c);break;case 603979828:this.g.displayCellParameters=c;break;case 603979960:this.g.testFlag1=c;break;case 603979962:this.g.testFlag2=

c;break;case 603979964:this.g.testFlag3=c;break;case 603979965:this.jmolTest();this.g.testFlag4=c;break;case 603979901:this.g.ribbonBorder=c;break;case 603979815:this.g.cartoonBaseEdges=c;break;case 603979819:this.g.cartoonRockets=c;break;case 603979902:this.g.rocketBarrels=c;break;case 603979850:this.gdata.setGreyscaleMode(this.g.greyscaleRendering=c);break;case 603979878:this.g.measurementLabels=c;break;case 603979809:case 603979804:case 603979808:this.setAxesMode(b);return;case 603979806:this.setAxesOrientationRasmol(c);

return;case 603979824:this.setStringPropertyTok("defaultcolorscheme",545259545,c?"rasmol":"jmol");return;case 603979825:this.setDebugScript(c);return;case 603979897:this.setPerspectiveDepth(c);return;case 603979798:this.setAutoBond(c);return;case 603979914:this.setShowAxes(c);return;case 603979916:this.setShowBbcage(c);return;case 603979922:this.setShowHydrogens(c);return;case 603979926:this.setShowMeasurements(c);return;case 603979936:this.setShowUnitCell(c);return;case 603979812:f=!1;this.g.bondModeOr=

c;break;case 603979978:f=!1;this.g.zeroBasedXyzRasmol=c;this.reset(!0);break;case 603979899:f=!1;this.g.rangeSelected=c;break;case 603979877:f=!1;this.g.measureAllModels=c;break;case 603979954:f=!1;this.sm.allowStatusReporting=c;break;case 603979822:f=!1;this.g.chainCaseSensitive=c;break;case 603979858:f=!1;this.g.hideNameInPopup=c;break;case 603979827:f=!1;this.g.disablePopupMenu=c;break;case 603979848:f=!1;this.g.forceAutoBond=c;break;default:if(!this.g.htBooleanParameterFlags.containsKey(a.toLowerCase())){this.g.setUserVariable(a,

JS.SV.getBoolean(c));return}}this.g.setB(a,c);f&&this.setTainted(!0)},"~S,~N,~B");c(b,"setModelKitMode",function(a){if(null!=this.acm&&this.allowScripting){if(a||this.g.modelKitMode)this.setPickingMode(null,a?33:1),this.setPickingMode(null,a?32:1);var b=this.g.modelKitMode!=a;this.g.modelKitMode=a;this.g.setB("modelkitmode",a);this.highlight(null);b&&this.setModelkitPropertySafely("constraint",null);a?(this.setNavigationMode(!1),this.selectAll(),this.setStringProperty("picking","assignAtom_C"),this.setStringProperty("picking",

"assignBond_p"),this.isApplet||this.popupMenu(10,0,"m"),b&&this.sm.setStatusModelKit(1),this.g.modelKitMode=!0,null==this.getOperativeSymmetry()&&(0==this.ms.ac?this.zap(!1,!0,!0):0<=this.am.cmi&&this.getModelUndeletedAtomsBitSet(this.am.cmi).isEmpty()&&(a=new java.util.Hashtable,a.put("appendToModelIndex",Integer.$valueOf(this.am.cmi)),this.loadDefaultModelKitModel(a)))):(this.acm.setPickingMode(-1),b?this.sm.setStatusModelKit(0):a||this.getModelkit(!1).setProperty("hidemenu",null))}},"~B");c(b,

"setSmilesString",function(a){null==a?this.g.removeParam("_smilesString"):this.g.setO("_smilesString",a)},"~S");c(b,"removeUserVariable",function(a){this.g.removeUserVariable(a);a.endsWith("callback")&&this.sm.setCallbackFunction(a,null)},"~S");c(b,"jmolTest",function(){});c(b,"showParameter",function(a,b,c){c=""+this.g.getParameterEscaped(a,c);(b||0>c.indexOf("<not defined>"))&&this.showString(a+" = "+c,!1)},"~S,~B,~N");c(b,"showString",function(a,b){!JV.Viewer.isJS&&(this.isScriptQueued()&&(!this.isSilent||

b)&&!"\x00".equals(a))&&JU.Logger.warn(a);this.scriptEcho(a)},"~S,~B");c(b,"getAllSettings",function(a){return this.getStateCreator().getAllSettings(a)},"~S");c(b,"getBindingInfo",function(a){return this.haveDisplay?this.acm.getBindingInfo(a):""},"~S");c(b,"getIsosurfacePropertySmoothing",function(a){return a?this.g.isosurfacePropertySmoothingPower:this.g.isosurfacePropertySmoothing?1:0},"~B");c(b,"setNavigationDepthPercent",function(a){this.tm.setNavigationDepthPercent(a);this.refresh(1,"set navigationDepth")},

"~N");c(b,"getShowNavigationPoint",function(){return!this.g.navigationMode?!1:this.tm.isNavigating()&&!this.g.hideNavigationPoint||this.g.showNavigationPointAlways||this.getInMotion(!0)});j(b,"setPerspectiveDepth",function(a){this.tm.setPerspectiveDepth(a)},"~B");j(b,"setAxesOrientationRasmol",function(a){this.g.setB("axesOrientationRasmol",a);this.g.axesOrientationRasmol=a;this.reset(!0)},"~B");c(b,"setAxesScale",function(a,b){b=JV.Viewer.checkFloatRange(b,-100,100);570425345==a?this.g.axesOffset=

b:this.g.axesScale=b;this.axesAreTainted=!0},"~N,~N");c(b,"setAxesMode",function(a){this.g.axesMode=a;this.axesAreTainted=!0;switch(a){case 603979808:this.g.removeParam("axesmolecular");this.g.removeParam("axeswindow");this.g.setB("axesUnitcell",!0);a=2;break;case 603979804:this.g.removeParam("axesunitcell");this.g.removeParam("axeswindow");this.g.setB("axesMolecular",!0);a=1;break;case 603979809:this.g.removeParam("axesunitcell"),this.g.removeParam("axesmolecular"),this.g.setB("axesWindow",!0),a=

0}this.g.setI("axesMode",a)},"~N");c(b,"getSelectionHalosEnabled",function(){return this.selectionHalosEnabled});c(b,"setSelectionHalosEnabled",function(a){this.selectionHalosEnabled!=a&&(this.g.setB("selectionHalos",a),this.shm.loadShape(8),this.selectionHalosEnabled=a)},"~B");c(b,"getShowSelectedOnce",function(){var a=this.showSelected;this.showSelected=!1;return a});c(b,"setStrandCount",function(a,b){b=JV.Viewer.checkIntRange(b,0,20);switch(a){case 12:this.g.strandCountForStrands=b;break;case 13:this.g.strandCountForMeshRibbon=

b;break;default:this.g.strandCountForStrands=b,this.g.strandCountForMeshRibbon=b}this.g.setI("strandCount",b);this.g.setI("strandCountForStrands",this.g.strandCountForStrands);this.g.setI("strandCountForMeshRibbon",this.g.strandCountForMeshRibbon)},"~N,~N");c(b,"getStrandCount",function(a){return 12==a?this.g.strandCountForStrands:this.g.strandCountForMeshRibbon},"~N");c(b,"setNavigationMode",function(a){this.g.navigationMode=a;this.tm.setNavigationMode(a)},"~B");j(b,"setAutoBond",function(a){this.g.setB("autobond",

a);this.g.autoBond=a},"~B");c(b,"makeConnections",function(a,b,c,f,e,h,j,m,n,p){this.clearModelDependentObjects();this.clearMinimization();return this.ms.makeConnections(a,b,c,f,e,h,j,m,n,p)},"~N,~N,~N,~N,JU.BS,JU.BS,JU.BS,~B,~B,~N");j(b,"rebond",function(){this.rebondState(!1)});c(b,"rebondState",function(a){this.clearModelDependentObjects();this.ms.deleteAllBonds();a=a&&this.g.legacyAutoBonding;this.ms.autoBondBs4(null,null,null,null,this.getMadBond(),a,null);this.addStateScript(a?"set legacyAutoBonding TRUE;connect;set legacyAutoBonding FALSE;":

"connect;",!1,!0)},"~B");j(b,"setPercentVdwAtom",function(a){this.g.setI("percentVdwAtom",a);this.g.percentVdwAtom=a;this.rd.value=a/100;this.rd.factorType=J.atomdata.RadiusData.EnumType.FACTOR;this.rd.vdwType=J.c.VDW.AUTO;this.shm.setShapeSizeBs(0,0,this.rd,null)},"~N");j(b,"getMadBond",function(){return 2*this.g.bondRadiusMilliAngstroms});j(b,"setShowHydrogens",function(a){this.g.setB("showHydrogens",a);this.g.showHydrogens=a},"~B");c(b,"setShowBbcage",function(a){this.setObjectMad10(32,"boundbox",

a?-4:0);this.g.setB("showBoundBox",a)},"~B");c(b,"getShowBbcage",function(){return 0!=this.getObjectMad10(4)});c(b,"setShowUnitCell",function(a){this.setObjectMad10(33,"unitcell",a?-2:0);this.g.setB("showUnitCell",a)},"~B");c(b,"getShowUnitCell",function(){return 0!=this.getObjectMad10(5)});c(b,"setShowAxes",function(a){this.setObjectMad10(34,"axes",a?-2:0);this.g.setB("showAxes",a)},"~B");c(b,"getShowAxes",function(){return 0!=this.getObjectMad10(1)});j(b,"setFrankOn",function(a){this.isPreviewOnly&&

(a=!1);this.frankOn=a;this.setObjectMad10(36,"frank",a?1:0)},"~B");c(b,"getShowFrank",function(){return this.isPreviewOnly||this.isApplet&&this.creatingImage?!1:this.isSignedApplet&&!this.isSignedAppletLocal&&!JV.Viewer.isJS||this.frankOn});j(b,"setShowMeasurements",function(a){this.g.setB("showMeasurements",a);this.g.showMeasurements=a},"~B");c(b,"setUnits",function(a,b){var c="default".equals(a);(!b||!c)&&this.g.setUnits(a);b&&this.setShapeProperty(6,"reformatDistances",a)},"~S,~B");j(b,"setRasmolDefaults",

function(){this.setDefaultsType("RasMol")});j(b,"setJmolDefaults",function(){this.setDefaultsType("Jmol")});c(b,"setDefaultsType",function(a){a.equalsIgnoreCase("RasMol")?this.stm.setRasMolDefaults():a.equalsIgnoreCase("PyMOL")?this.stm.setPyMOLDefaults():(this.stm.setJmolDefaults(),this.setIntProperty("bondingVersion",0),this.shm.setShapeSizeBs(0,0,this.rd,this.getAllAtoms()))},"~S");c(b,"setAntialias",function(a,b){var c=!1;switch(a){case 603979786:c=this.g.antialiasDisplay!=b;this.g.antialiasDisplay=

b;break;case 603979790:c=this.g.antialiasTranslucent!=b;this.g.antialiasTranslucent=b;break;case 603979788:this.g.antialiasImages=b;return}c&&(this.resizeImage(0,0,!1,!1,!0),this.refresh(3,"Viewer:setAntialias()"))},"~N,~B");c(b,"allocTempPoints",function(a){return this.tempArray.allocTempPoints(a)},"~N");c(b,"freeTempPoints",function(a){this.tempArray.freeTempPoints(a)},"~A");c(b,"allocTempScreens",function(a){return this.tempArray.allocTempScreens(a)},"~N");c(b,"freeTempScreens",function(a){this.tempArray.freeTempScreens(a)},

"~A");c(b,"allocTempEnum",function(a){return this.tempArray.allocTempEnum(a)},"~N");c(b,"freeTempEnum",function(a){this.tempArray.freeTempEnum(a)},"~A");c(b,"getFont3D",function(a,b,c){return this.gdata.getFont3DFSS(a,b,c)},"~S,~S,~N");c(b,"getAtomGroupQuaternions",function(a,b){return this.ms.getAtomGroupQuaternions(a,b,this.getQuaternionFrame())},"JU.BS,~N");c(b,"setStereoMode",function(a,b,c){this.setFloatProperty("stereoDegrees",c);this.setBooleanPropertyTok("greyscaleRendering",603979850,b.isBiColor());

null!=a?this.tm.setStereoMode2(a):this.tm.setStereoMode(b)},"~A,J.c.STER,~N");c(b,"getChimeInfo",function(a){return this.getPropertyManager().getChimeInfo(a,this.bsA())},"~N");c(b,"getModelFileInfo",function(){return this.getPropertyManager().getModelFileInfo(this.getVisibleFramesBitSet())});c(b,"getModelFileInfoAll",function(){return this.getPropertyManager().getModelFileInfo(null)});c(b,"showEditor",function(a){var b=this.getProperty("DATA_API","getScriptEditor",Boolean.TRUE);null!=b&&b.show(a)},

"~A");c(b,"getPropertyManager",function(){null==this.pm&&(this.pm=J.api.Interface.getInterface("JV.PropertyManager",this,"prop")).setViewer(this);return this.pm});c(b,"setTainted",function(a){this.isTainted=this.axesAreTainted=a&&(this.refreshing||this.creatingImage)},"~B");c(b,"checkObjectClicked",function(a,b,c){return this.shm.checkObjectClicked(a,b,c,this.getVisibleFramesBitSet(),this.g.drawPicking)},"~N,~N,~N");c(b,"checkObjectHovered",function(a,b){return 0<=a&&null!=this.shm&&this.shm.checkObjectHovered(a,

b,this.getVisibleFramesBitSet(),this.getBondsPickable())},"~N,~N");c(b,"checkObjectDragged",function(a,b,c,f,e){var h=0;switch(this.getPickingMode()){case 2:h=5;break;case 4:h=22}return this.shm.checkObjectDragged(a,b,c,f,e,this.getVisibleFramesBitSet(),h)?(this.refresh(1,"checkObjectDragged"),22==h&&this.scriptEcho(this.getShapeProperty(22,"command")),!0):!1},"~N,~N,~N,~N,~N");c(b,"rotateAxisAngleAtCenter",function(a,b,c,f,e,h,j){(a=this.tm.rotateAxisAngleAtCenter(a,b,c,f,e,h,j))&&this.setSync();

return a},"J.api.JmolScriptEvaluator,JU.P3,JU.V3,~N,~N,~B,JU.BS");c(b,"rotateAboutPointsInternal",function(a,b,c,f,e,h,j,m,n,p,q,r){null==a&&(a=this.eval);if(this.headless){if(h&&3.4028235E38==e)return!1;h=!1}(a=this.tm.rotateAboutPointsInternal(a,b,c,f,e,!1,h,j,!1,m,n,p,q,r))&&this.setSync();return a},"J.api.JmolScriptEvaluator,JU.P3,JU.P3,~N,~N,~B,JU.BS,JU.V3,JU.Lst,~A,JU.M4,~B");c(b,"startSpinningAxis",function(a,b,c){this.tm.spinOn||this.tm.navOn?(this.tm.setSpinOff(),this.tm.setNavOn(!1)):this.tm.rotateAboutPointsInternal(null,

a,b,this.g.pickingSpinRate,3.4028235E38,c,!0,null,!1,null,null,null,null,!1)},"JU.T3,JU.T3,~B");c(b,"getModelDipole",function(){return this.ms.getModelDipole(this.am.cmi)});c(b,"calculateMolecularDipole",function(a){try{return this.ms.calculateMolecularDipole(this.am.cmi,a)}catch(b){if(F(b,"JV.JmolAsyncException"))return null!=this.eval&&this.eval.loadFileResourceAsync(b.getFileName()),null;throw b;}},"JU.BS");c(b,"setDefaultLattice",function(a){Float.isNaN(a.x+a.y+a.z)||this.g.ptDefaultLattice.setT(a);

this.g.setO("defaultLattice",JU.Escape.eP(a))},"JU.P3");c(b,"getDefaultLattice",function(){return this.g.ptDefaultLattice});c(b,"getModelExtract",function(a,b,c,f){return this.getPropertyManager().getModelExtract(this.getAtomBitSet(a),b,c,f,!1)},"~O,~B,~B,~S");j(b,"getData",function(a,b){return this.getModelFileData(a,b,!0)},"~S,~S");c(b,"getModelFileData",function(a,b,c){return this.getPropertyManager().getAtomData(a,b,c)},"~S,~S,~B");c(b,"getModelCml",function(a,b,c,f){return this.getPropertyManager().getModelCml(a,

b,c,f,!1)},"JU.BS,~N,~B,~B");c(b,"getPdbAtomData",function(a,b,c,f){return this.getPropertyManager().getPdbAtomData(null==a?this.bsA():a,b,c,f,!1)},"JU.BS,JU.OC,~B,~B");c(b,"isJmolDataFrame",function(){return this.ms.isJmolDataFrameForModel(this.am.cmi)});c(b,"setFrameTitle",function(a,b){this.ms.setFrameTitle(JU.BSUtil.newAndSetBit(a),b)},"~N,~S");c(b,"setFrameTitleObj",function(a){this.shm.loadShape(31);this.ms.setFrameTitle(this.getVisibleFramesBitSet(),a)},"~O");c(b,"getFrameTitle",function(){return this.ms.getFrameTitle(this.am.cmi)});

c(b,"setAtomProperty",function(a,b,c,f,e,h,j){1648363544==b&&this.shm.deleteVdwDependentShapes(a);this.clearMinimization();this.ms.setAtomProperty(a,b,c,f,e,h,j);switch(b){case 1086326789:this.setModelkitPropertySafely("updateatomkeys",a);case 1111492609:case 1111492610:case 1111492611:case 1111492612:case 1111492613:case 1111492614:case 1111490577:case 1111490578:case 1111490579:this.refreshMeasures(!0)}},"JU.BS,~N,~N,~N,~S,~A,~A");c(b,"checkCoordinatesChanged",function(a){this.ms.recalculatePositionDependentQuantities(a,

null);this.refreshMeasures(!0)},"JU.BS");c(b,"setAtomCoords",function(a,b,c){if(!a.isEmpty()){var f=this.ms.at[a.nextSetBit(0)],e=a.cardinality();this.sm.setStatusStructureModified(f.i,f.mi,3,"setAtomCoords",e,a);this.ms.setAtomCoords(a,b,c);this.setStatusAtomMoved(!0,a);this.sm.setStatusStructureModified(f.i,f.mi,-3,"OK",e,a)}},"JU.BS,~N,~O");c(b,"setAtomCoordsRelative",function(a,b){null==b&&(b=this.bsA());if(!b.isEmpty()){var c=0!=a.lengthSquared(),f=this.ms.at[b.nextSetBit(0)],e=b.cardinality();

c&&this.sm.setStatusStructureModified(f.i,f.mi,3,"setAtomCoords",e,b);this.ms.setAtomCoordsRelative(a,b);this.checkMinimization();c&&(this.setStatusAtomMoved(!1,b),this.sm.setStatusStructureModified(f.i,f.mi,-3,"OK",e,b))}},"JU.T3,JU.BS");c(b,"invertAtomCoord",function(a,b,c,f,e){if(0<=f){c=JU.JmolMolecule.getBranchesForInversion(this.ms.at,f,this.ms.getMoleculeBitSetForAtom(f));var h=c.cardinality();switch(h){case 0:case 1:return;case 3:case 4:for(var j=E(h,0),m=E(h,0),n=0,p=c.nextSetBit(0);0<=p;p=

c.nextSetBit(p+1),n++)j[n]=this.getBranchBitSet(p,f,!0).cardinality(),m[n]=p;for(n=0;n<h-2;n++){for(var q=-2147483648,r=0,p=0;p<h;p++)j[p]>=q&&c.get(m[p])&&(r=m[p],q=j[p]);c.clear(r)}}e&&!c.isEmpty()&&this.undoMoveActionClear(f,2,!0)}h=c.cardinality();0!=h&&(j=this.ms.at[c.nextSetBit(0)],this.sm.setStatusStructureModified(j.i,j.mi,3,"invertAtomCoords",h,c),this.ms.invertSelected(a,b,f,c),this.setStatusAtomMoved(!0,c),this.sm.setStatusStructureModified(j.i,j.mi,-3,"OK",h,c),e&&this.setStatusAtomPicked(f,

"inverted: "+JU.Escape.eBS(c),null,!1))},"JU.P3,JU.P4,JU.BS,~N,~B");c(b,"invertSelected",function(a,b,c,f){null==f&&(f=this.bsA());f.isEmpty()||(this.ms.invertSelected(a,b,c,f),this.setStatusAtomMoved(!0,f))},"JU.P3,JU.P4,~N,JU.BS");c(b,"moveAtoms",function(a,b,c,f,e,h,j,m,n){if(!j.isEmpty()){var p=this.getMotionFixedAtoms(null,null);if(!j.intersects(p)){n=n?this.getOperativeSymmetry():null;var q=null;null!=n&&(q=this.ms.saveAtomPositions());this.ms.moveAtoms(a,b,c,f,j,e,h,m);null!=n&&this.getModelkit(!1).checkMovedAtoms(p,

j,q);this.setStatusAtomMoved(!0,j)}}},"JU.M4,JU.M3,JU.M3,JU.V3,JU.P3,~B,JU.BS,~B,~B");c(b,"moveSelectedXY",function(a,b,c){this.moveSelected(a,b,-2147483648,-2147483648,-2147483648,null,null,null,!1,!1,c)},"~N,~N,~N");c(b,"moveSelected",function(a,b,c,f,e,h,j,m,n,p,q){if(0==c&&null==m||this.isJmolDataFrame())return 0;if(null==m){-2147483648==f&&null!=this.modelkit&&this.setModelkitPropertySafely("rotatebondindex",Integer.$valueOf(-2147483648));if(-2147483648==a)return this.showSelected=!0,this.movableBitSet=

this.setMovableBitSet(null,!p),this.shm.loadShape(8),this.refresh(6,"moveSelected"),0;if(2147483647==a){if(!this.showSelected)return 0;this.showSelected=!1;this.movableBitSet=null;this.refresh(6,"moveSelected");return 0}}if(this.movingSelected)return 0;this.movingSelected=!0;this.stopMinimization();null==m&&-2147483648!=f&&null!=this.modelkit&&null!=this.modelkit.getProperty("rotatebondindex")?this.modelkit.actionRotateBond(a,b,f,e,0!=(q&16)):(null==h&&(h=this.bsA()),f=h.nextSetBit(0),h=this.setMovableBitSet(h,

!p),h.isEmpty()?(h.set(f),this.sm.setStatusStructureModified(f,this.getModelIndexForAtom(f),-3,"FAILED",1,h)):n?(j=null==j?this.ms.getAtomSetCenter(h):j,null==m&&(this.tm.finalizeTransformParameters(),m=this.g.antialiasDisplay?2:1,this.tm.transformPt3f(j,this.ptScreen),-2147483648!=c?this.ptScreenNew.set(this.ptScreen.x,this.ptScreen.y,this.ptScreen.z+c):this.ptScreenNew.set(this.ptScreen.x+a*m,this.ptScreen.y+b*m,this.ptScreen.z),this.tm.unTransformPoint(this.ptScreenNew,this.ptNew),m=this.ptNew,

null!=this.getOperativeSymmetry()&&(m.sub(j),m.add(this.ms.at[f]),this.getModelkit(!1).cmdAssignMoveAtoms(h,f,m,null,!0,!p))),Float.isNaN(m.x)||(m.sub(j),this.setAtomCoordsRelative(m,h))):this.tm.rotateXYBy(a,b,h));this.refresh(2,"");this.movingSelected=!1;return null==h?0:h.cardinality()},"~N,~N,~N,~N,~N,JU.BS,JU.P3,JU.P3,~B,~B,~N");c(b,"highlightBond",function(a,b,c,f){if(this.hoverEnabled){b=null;if(0<=a){var e=this.ms.bo[a];b=JU.BSUtil.newAndSetBit(e.atom2.i);b.set(e.atom1.i)}this.highlight(b);

this.getModelkit(!1);this.setModelkitPropertySafely("screenxy",E(-1,[c,f]));this.setModelkitPropertySafely("bondindex",Integer.$valueOf(a));a=this.setModelkitPropertySafely("hoverlabel",Integer.$valueOf(-2-a));null!=a&&this.hoverOnPt(c,f,a,null,null);this.refresh(3,"highlightBond")}},"~N,~N,~N,~N");c(b,"highlight",function(a){this.atomHighlighted=null!=a&&1==a.cardinality()?a.nextSetBit(0):-1;null==a?this.setCursor(0):(this.shm.loadShape(8),this.setCursor(12));this.setModelkitPropertySafely("highlight",

a);this.setShapeProperty(8,"highlight",a)},"JU.BS");c(b,"refreshMeasures",function(a){this.setShapeProperty(6,"refresh",null);this.setStatusMeasuring("refreshed",-3,"",0);a&&this.stopMinimization()},"~B");c(b,"functionXY",function(a,b,c){var f=null;if(0==a.indexOf("file:"))f=this.getFileAsString3(a.substring(5),!1,null);else if(0!=a.indexOf("data2d_"))return this.sm.functionXY(a,b,c);b=Math.abs(b);c=Math.abs(c);if(null==f){a=this.getDataObj(a,null,2);if(null!=a)return a;f=""}a=K(b,c,0);var e=K(b*

c,0);JU.Parser.parseStringInfestedFloatArray(f,null,e);for(var h=f=0;f<b;f++)for(var j=0;j<c;j++)a[f][j]=e[h++];return a},"~S,~N,~N");c(b,"functionXYZ",function(a,b,c,f){var e=null;if(0==a.indexOf("file:"))e=this.getFileAsString3(a.substring(5),!1,null);else if(0!=a.indexOf("data3d_"))return this.sm.functionXYZ(a,b,c,f);b=Math.abs(b);c=Math.abs(c);f=Math.abs(f);if(null==e){a=this.getDataObj(a,null,2);if(null!=a)return a;e=""}a=K(b,c,f,0);var h=K(b*c*f,0);JU.Parser.parseStringInfestedFloatArray(e,

null,h);for(var j=e=0;e<b;e++)for(var m=0;m<c;m++)for(var n=0;n<f;n++)a[e][m][n]=h[j++];return a},"~S,~N,~N,~N");j(b,"extractMolData",function(a){if(null==a){a=this.am.cmi;if(0>a||0==this.ms.ac)return null;a=this.getModelNumberDotted(a)}return this.getModelExtract(a,!0,!1,"V2000")},"~S");c(b,"getNMRPredict",function(a){a=a.toUpperCase();if(a.equals("H")||a.equals("1H")||a.equals(""))a="H1";else if(a.equals("C")||a.equals("13C"))a="C13";if(!a.equals("NONE")){if(!a.equals("C13")&&!a.equals("H1"))return"Type must be H1 or C13";

var b=this.getModelExtract("selected",!0,!1,"V2000"),c=b.indexOf("\n");if(0>c)return null;b="Jmol "+JV.Viewer.version_date+b.substring(c);if(this.isApplet)return this.showUrl(this.g.nmrUrlFormat+b),"opening "+this.g.nmrUrlFormat}this.syncScript("true","*",0);this.syncScript(a+"Simulate:",".",0);return"sending request to JSpecView"},"~S");c(b,"getHelp",function(a){0>this.g.helpPath.indexOf("?")?(0<a.length&&0!=a.indexOf("?")&&(a="?search="+JU.PT.rep(a," ","%20")),a+=(0==a.length?"?ver=":"&ver=")+JV.JC.majorVersion):

a="&"+a;this.showUrl(this.g.helpPath+a)},"~S");c(b,"getChemicalInfo",function(a,b,c){b=b.toLowerCase();var f="/";switch(";inchi;inchikey;stdinchi;stdinchikey;name;image;drawing;names;".indexOf(";"+b+";")){case 0:f="I";break;case 6:f="K";break;case 15:f="T";break;case 24:f="S";break;case 36:f="M";break;case 41:case 47:f="2";break;case 55:f="N"}var e=this.setLoadFormat(!1,"_"+a,f,!1);if("2"==f)return this.fm.loadImage(e,"\u0001"+a,!1),e;"/"==f&&(e=JU.PT.isOneOf(b,";alc;cdxml;cerius;charmm;cif;cml;ctx;gjf;gromacs;hyperchem;jme;maestro;mol;mol2;sybyl2;mrv;pdb;sdf;sdf3000;sln;smiles;xyz")?

e+("file?format="+b):e+JU.PT.rep(b," ","%20"));e=this.getFileAsString4(e,-1,!1,!1,!1,"file");"M"==f&&0<e.indexOf("\n")?e=e.substring(0,e.indexOf("\n")):b.equals("jme")&&(e=this.getPropertyManager().fixJMEFormalCharges(c,e));return e},"~S,~S,JU.BS");c(b,"addCommand",function(a){if(!this.autoExit&&this.haveDisplay&&this.getPreserveState()){if(a.startsWith("pause ")||a.equals("pause"))a="resume";this.commandHistory.addCommand(JU.PT.replaceAllCharacters(a,"\r\n\t"," "))}},"~S");c(b,"pushState",function(){!this.autoExit&&

(this.haveDisplay&&this.getPreserveState())&&this.commandHistory.pushState(this.getStateInfo())});c(b,"popState",function(){if(!this.autoExit&&this.haveDisplay&&this.getPreserveState()){var a=this.commandHistory.popState();null!=a&&this.evalStringQuiet(a)}});c(b,"removeCommand",function(){return this.commandHistory.removeCommand()});j(b,"getSetHistory",function(a){return this.commandHistory.getSetHistory(a)},"~N");c(b,"historyFind",function(a,b){return this.commandHistory.find(a,b)},"~S,~N");c(b,

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j(b,"clipImageOrPasteText",function(a){return!this.haveAccess(JV.Viewer.ACCESS.ALL)?"no":this.getOutputManager().clipImageOrPasteText(a)},"~S");j(b,"getClipboardText",function(){if(!this.haveAccess(JV.Viewer.ACCESS.ALL))return"no";try{return this.getOutputManager().getClipboardText()}catch(a){if(F(a,Error))return J.i18n.GT.$("clipboard is not accessible -- use signed applet");throw a;}});c(b,"processWriteOrCapture",function(a){return this.getOutputManager().processWriteOrCapture(a)},"java.util.Map");

c(b,"createZip",function(a,b,c){var f=this.getStateInfo(),e=c.get("data");null!=a&&c.put("fileName",a);c.put("type",b);c.put("text",f);y(e,Array)?c.put("scripts",e):y(e,"JU.Lst")&&c.put("imageData",e);return this.getOutputManager().outputToFile(c)},"~S,~S,java.util.Map");j(b,"outputToFile",function(a){return this.getOutputManager().outputToFile(a)},"java.util.Map");c(b,"setSyncTarget",function(a,b){switch(a){case 0:this.sm.syncingMouse=b;break;case 1:this.sm.syncingScripts=b;break;case 2:this.sm.syncSend(b?

"GET_GRAPHICS":"SET_GRAPHICS_OFF","*",0);Float.isNaN(this.tm.stereoDegrees)&&this.setFloatProperty("stereoDegrees",-5);b&&(this.setBooleanProperty("_syncMouse",!1),this.setBooleanProperty("_syncScript",!1));return}!this.sm.syncingScripts&&!this.sm.syncingMouse&&this.setSync()},"~N,~B");j(b,"syncScript",function(a,b,c){this.sm.syncScript(a,b,c)},"~S,~S,~N");j(b,"getModelIndexFromId",function(a){return this.ms.getModelIndexFromId(a)},"~S");c(b,"setSyncDriver",function(a){this.sm.setSyncDriver(a)},"~N");

c(b,"setProteinType",function(a,b){this.ms.setProteinType(null==b?this.bsA():b,a)},"J.c.STR,JU.BS");c(b,"getVanderwaalsMar",function(a){return this.defaultVdw===J.c.VDW.USER?this.userVdwMars[a]:JU.Elements.getVanderwaalsMar(a,this.defaultVdw)},"~N");c(b,"getVanderwaalsMarType",function(a,b){if(null==b)b=this.defaultVdw;else switch(b){case J.c.VDW.AUTO:case J.c.VDW.AUTO_BABEL:case J.c.VDW.AUTO_JMOL:case J.c.VDW.AUTO_RASMOL:this.defaultVdw!==J.c.VDW.AUTO&&(b=this.defaultVdw)}b===J.c.VDW.USER&&null==

this.bsUserVdws&&(b=J.c.VDW.JMOL);return b===J.c.VDW.USER?this.userVdwMars[a&127]:JU.Elements.getVanderwaalsMar(a,b)},"~N,J.c.VDW");c(b,"setVdwStr",function(a){a=J.c.VDW.getVdwType(a);null==a&&(a=J.c.VDW.AUTO);switch(a){case J.c.VDW.JMOL:case J.c.VDW.BABEL:case J.c.VDW.RASMOL:case J.c.VDW.AUTO:case J.c.VDW.USER:break;default:a=J.c.VDW.JMOL}a!==this.defaultVdw&&(a===J.c.VDW.USER&&null==this.bsUserVdws)&&this.setUserVdw(this.defaultVdw);this.defaultVdw=a;this.g.setO("defaultVDW",a.getVdwLabel())},"~S");

c(b,"setUserVdw",function(a){this.userVdwMars=E(JU.Elements.elementNumberMax,0);this.userVdws=K(JU.Elements.elementNumberMax,0);this.bsUserVdws=new JU.BS;a===J.c.VDW.USER&&(a=J.c.VDW.JMOL);for(var b=1;b<JU.Elements.elementNumberMax;b++)this.userVdwMars[b]=JU.Elements.getVanderwaalsMar(b,a),this.userVdws[b]=this.userVdwMars[b]/1E3},"J.c.VDW");c(b,"getDefaultVdwNameOrData",function(a,b,c){switch(a){case -2147483648:return this.defaultVdw.getVdwLabel();case 2147483647:if(null==(c=this.bsUserVdws))return"";

b=J.c.VDW.USER}if(null==b||b===J.c.VDW.AUTO)b=this.defaultVdw;b===J.c.VDW.USER&&null==this.bsUserVdws&&this.setUserVdw(this.defaultVdw);return this.getDataManager().getDefaultVdwNameOrData(b,c)},"~N,J.c.VDW,JU.BS");c(b,"deleteAtoms",function(a,b){var c=null==a?-1:a.nextSetBit(0);if(0>c)return 0;this.clearModelDependentObjects();var f=this.ms.at[c];if(null==f)return 0;var e=f.mi;if(b)return this.deleteModels(e,a);this.sm.setStatusStructureModified(c,f.mi,4,"deleting atoms "+a,a.cardinality(),a);this.ms.deleteAtoms(a);

f=this.slm.deleteAtoms(a);this.setTainted(!0);this.sm.setStatusStructureModified(c,e,-4,"OK",f,a);return f},"JU.BS,~B");c(b,"deleteModels",function(a,b){var c=null==b?JU.BSUtil.newAndSetBit(a):this.ms.getModelBS(b,!1);this.clearModelDependentObjects();b=this.getModelUndeletedAtomsBitSetBs(c);var f=b.cardinality(),e=this.am.cmi;this.setCurrentModelIndexClear(0,!1);this.am.setAnimationOn(!1);var h=JU.BSUtil.copy(this.slm.bsDeleted),c=this.ms.deleteModels(c);if(null==c)return this.setCurrentModelIndexClear(e,

!1),0;this.sm.setStatusStructureModified(-1,a,5,"deleting model "+this.getModelNumberDotted(a),f,b);this.slm.processDeletedModelAtoms(c);null!=this.eval&&this.eval.deleteAtomsInVariables(c);this.setAnimationRange(0,0);this.clearRepaintManager(-1);this.am.clear();this.am.initializePointers(1);this.setCurrentModelIndexClear(1<this.ms.mc?-1:0,1<this.ms.mc);this.hoverAtomIndex=-1;this.setFileLoadStatus(J.c.FIL.DELETED,null,null,null,null,null);this.refreshMeasures(!0);null!=h&&c.andNot(h);f=JU.BSUtil.cardinalityOf(c);

this.sm.setStatusStructureModified(-1,a,-5,"OK",f,c);return f},"~N,JU.BS");c(b,"deleteBonds",function(a){for(var b=this.ms.bondCount,c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1))(c>=b||null==this.ms.bo[c])&&a.clear(c);b=a.nextSetBit(0);0>b||(b=this.ms.bo[b].atom1.mi,this.sm.setStatusStructureModified(-1,b,2,"delete bonds "+JU.Escape.eBond(a),a.cardinality(),a),this.ms.deleteBonds(a,!1),this.sm.setStatusStructureModified(-1,b,-2,"OK",a.cardinality(),a))},"JU.BS");c(b,"deleteModelAtoms",function(a,b,

c,f){var e=f.cardinality();0!=e&&(this.sm.setStatusStructureModified(-1,a,7,"delete atoms "+JU.Escape.eBS(f),e,f),JU.BSUtil.deleteBits(this.tm.bsFrameOffsets,f),this.getDataManager().deleteModelAtoms(b,c,f),this.sm.setStatusStructureModified(-1,a,-7,"OK",e,f))},"~N,~N,~N,JU.BS");c(b,"getQuaternionFrame",function(){return this.g.quaternionFrame.charAt(2==this.g.quaternionFrame.length?1:0)});c(b,"loadImageData",function(a,b,c,f){null==a&&null!=b&&this.scriptEcho(b);null==c?this.setBackgroundImage(null==

a?null:b,a):c.startsWith("\u0001")?this.sm.showImage(c,a):c.startsWith("\x00")?null!=a&&this.setWindowDimensions(K(-1,[this.apiPlatform.getImageWidth(a),this.apiPlatform.getImageHeight(a)])):(this.shm.loadShape(31),this.setShapeProperty(31,"text",b),null!=a&&this.setShapeProperty(31,"image",a));JV.Viewer.isJS&&null!=f&&(f.mustResumeEval=!0,this.eval.resumeEval(f));return!1},"~O,~S,~S,~O");c(b,"cd",function(a){null==a?a=".":0==a.length&&(this.setStringProperty("defaultDirectory",""),a=".");a=this.fm.getDefaultDirectory(a+

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b){this.haveDisplay&&this.acm.unbindAction(a,b)},"~S,~S");c(b,"calculateStruts",function(a,b){return this.ms.calculateStruts(null==a?this.bsA():a,null==b?this.bsA():b)},"JU.BS,JU.BS");c(b,"getPreserveState",function(){return this.g.preserveState&&null!=this.scm});c(b,"isKiosk",function(){return this.$isKiosk});c(b,"hasFocus",function(){return this.haveDisplay&&(this.$isKiosk||this.apiPlatform.hasFocus(this.display))});c(b,"setFocus",function(){this.haveDisplay&&!this.apiPlatform.hasFocus(this.display)&&

this.apiPlatform.requestFocusInWindow(this.display)});c(b,"stopMinimization",function(){null!=this.minimizer&&this.minimizer.setProperty("stop",null)});c(b,"clearMinimization",function(){null!=this.minimizer&&this.minimizer.setProperty("clear",null)});c(b,"getMinimizationInfo",function(){return null==this.minimizer?"":this.minimizer.getProperty("log",0)});c(b,"checkMinimization",function(){this.refreshMeasures(!0);if(this.g.monitorEnergy){try{this.minimize(null,0,0,this.getFrameAtoms(),null,null,

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(f=this.getThisModelAtoms(),v&&f.and(this.bsA()));if(!f.isEmpty())if(n=q||!v?JU.BSUtil.copy(this.ms.am[this.ms.at[f.nextSetBit(0)].mi].bsAsymmetricUnit):null,q&&null==n)this.scriptStatusMsg("MODELKIT MINIMIZE is only applicable to crystal structures.","minimization: not a crystal structure");else try{if(q)this.getModelkit(!1).cmdMinimize(a,n,b,c,j,m);else{var y=null==n?this.g.forceField:"UFF";this.getModelForAtomIndex(f.nextSetBit(0)).auxiliaryInfo.put("dimension","3D");s&&(h=f);var z=JU.BSUtil.copy(w?

e:this.slm.getMotionFixedAtoms()),B=!z.isEmpty();B&&f.andNot(z);var C=null!=n&&q?this.getThisModelAtoms():v||!B?new JU.BS:this.ms.getAtomsWithinRadius(0>=j?5:j,f,!0,null,null);C.andNot(f);B?z.and(C):z=C;z.and(h);m|=(B?4:0)|(this.getBooleanProperty("minimizationSilent")?1:0);if(!s||!this.getBoolean(603979962)){if(s)try{r||JU.Logger.info("Minimizing "+f.cardinality()+" atoms"),this.getMinimizer(!0).minimize(b,c,f,z,null,m,"UFF")}catch(D){if(F(D,Exception))JU.Logger.error("Minimization error: "+D.toString()),

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"MMFF":y),s){this.g.forceField="MMFF";this.setHydrogens(f);var I=this.getMinimizer(!1).getForceFieldUsed();null!=I&&this.showString("Minimized by Jmol using "+I,!1)}}}}catch(K){if(F(K,"JV.JmolAsyncException"))null!=a&&a.loadFileResourceAsync(K.getFileName());else if(F(K,Exception))a=K,JU.Logger.error("Minimization error: "+a.toString()),a.printStackTrace();else throw K;}},"J.api.JmolScriptEvaluator,~N,~N,JU.BS,JU.BS,JU.BS,~N,~N");c(b,"setHydrogens",function(a){for(var b=E(1,0),b=this.ms.calculateHydrogens(a,

b,null,2056),c=a.nextSetBit(0);0<=c;c=a.nextSetBit(c+1)){var f=b[c];if(!(null==f||0==f.length))for(var e=this.ms.at[c],h=e.bonds,j=0,m=0,n=e.getBondCount();j<n;j++){var p=h[j].getOtherAtom(e);if(1==p.getAtomicAndIsotopeNumber()){var q=f[m++];null!=q&&this.ms.setAtomCoord(p.i,q.x,q.y,q.z)}}}this.ms.resetMolecules()},"JU.BS");c(b,"setMotionFixedAtoms",function(a){this.slm.setMotionFixedAtoms(a)},"JU.BS");c(b,"setMotionFixed",function(a){this.slm.setMotionFixedAtoms(a)},"JU.BS");c(b,"getMotionFixedAtoms",

function(a,b){if(0>this.am.cmi)return new JU.BS;null==b&&(b=new JU.BS);b.or(this.slm.getMotionFixedAtoms());b.and(this.getThisModelAtoms());null==a&&(a=this.getOperativeSymmetry());null!=a&&null!=this.getModelkit(!1)&&this.modelkit.addLockedAtoms(a,b);return b},"J.api.SymmetryInterface,JU.BS");c(b,"getAtomicPropertyState",function(a,b,c,f,e){this.getStateCreator().getAtomicPropertyStateBuffer(a,b,c,f,e)},"JU.SB,~N,JU.BS,~S,~A");c(b,"getCenterAndPoints",function(a,b){return this.ms.getCenterAndPoints(a,

b)},"JU.Lst,~B");c(b,"writeFileData",function(a,b,c,f){return this.getOutputManager().writeFileData(a,b,c,f)},"~S,~S,~N,~A");c(b,"getPdbData",function(a,b,c,f,e,h){return this.getPropertyManager().getPdbData(a,b,null==c?this.bsA():c,f,e,h)},"~N,~S,JU.BS,~A,JU.OC,~B");c(b,"getGroupsWithin",function(a,b){return this.ms.getGroupsWithin(a,b)},"~N,JU.BS");c(b,"setShapeSize",function(a,b,c){null==c&&(c=this.bsA());this.shm.setShapeSizeBs(a,b,null,c)},"~N,~N,JU.BS");c(b,"setShapeProperty",function(a,b,c){0<=

a&&this.shm.setShapePropertyBs(a,b,c,null)},"~N,~S,~O");c(b,"getShapeProperty",function(a,b){return this.shm.getShapePropertyIndex(a,b,-2147483648)},"~N,~S");c(b,"getShapePropertyAsInt",function(a,b){var c=this.getShapeProperty(a,b);return null==c||!y(c,Integer)?-2147483648:c.intValue()},"~N,~S");c(b,"setModelVisibility",function(){null!=this.shm&&this.shm.setModelVisibility()});c(b,"resetShapes",function(a){this.shm.resetShapes(!a);a&&(this.shm.loadDefaultShapes(this.ms),this.clearRepaintManager(-1))},

"~B");c(b,"setParallel",function(a){return this.$isParallel=this.g.multiProcessor&&a},"~B");c(b,"isParallel",function(){return this.g.multiProcessor&&this.$isParallel});c(b,"undoMoveAction",function(a,b){return this.g.preserveState?this.getStateCreator().undoMoveAction(a,b):0},"~N,~N");c(b,"undoMoveActionClear",function(a,b,c){this.g.preserveState&&null==this.getOperativeSymmetry()&&this.getStateCreator().undoMoveActionClear(a,b,c)},"~N,~N,~B");c(b,"moveAtomWithHydrogens",function(a,b,c,f,e,h){this.stopMinimization();

-1,-1,16|(null==a&&JU.Logger.debugging?131072:0),null)},"JU.BS");j(b,"getOpenSmiles",function(a){return this.getSmilesOpt(a,-1,-1,5|(null==a&&JU.Logger.debugging?131072:0),"/open///")},"JU.BS");c(b,"getBioSmiles",function(a){return this.getSmilesOpt(a,-1,-1,24117248|(JU.Logger.debugging?131072:0),null)},"JU.BS");c(b,"getSmilesOpt",function(a,b,c,f,e){var h=17825792==(f&17825792)?JV.Viewer.getJmolVersion()+" "+this.getModelName(this.am.cmi):e,j=this.ms.at;null==a&&(0>b||0>c?a=this.bsA():(1048576==

(f&1048576)&&(b>c&&(a=b,b=c,c=a),b=j[b].group.firstAtomIndex,c=j[c].group.lastAtomIndex),a=new JU.BS,a.setBits(b,c+1)));f|=this.isModel2D(a)?134217728:0;b=this.getSmilesMatcher();return JV.JC.isSmilesCanonical(e)?(f=b.getSmiles(j,this.ms.ac,a,"/noAromatic/",f),this.getChemicalInfo(f,"smiles",null).trim()):b.getSmiles(j,this.ms.ac,a,h,f)},"JU.BS,~N,~N,~N,~S");c(b,"isModel2D",function(a){a=this.getModelForAtomIndex(a.nextSetBit(0));return null!=a&&"2D".equals(a.auxiliaryInfo.get("dimension"))},"JU.BS");

c(b,"alert",function(a){this.prompt(a,null,null,!0)},"~S");c(b,"prompt",function(a,b,c,f){return this.$isKiosk?"null":this.apiPlatform.prompt(a,b,c,f)},"~S,~S,~A,~B");c(b,"dialogAsk",function(a,b){return prompt(a,b)},"~S,~S,java.util.Map");c(b,"initializeExporter",function(a){var b=a.get("type").equals("JS");if(b){if(null!=this.jsExporter3D)return this.jsExporter3D.initializeOutput(this,this.privateKey,a),this.jsExporter3D}else{var c=a.get("fileName"),f=a.get("fullPath"),c=this.getOutputChannel(c,

f);if(null==c)return null;a.put("outputChannel",c)}c=J.api.Interface.getOption("export.Export3D",this,"export");if(null==c)return null;a=c.initializeExporter(this,this.privateKey,this.gdata,a);b&&null!=a&&(this.jsExporter3D=c);return null==a?null:c},"java.util.Map");c(b,"getMouseEnabled",function(){return this.refreshing&&!this.creatingImage});j(b,"calcAtomsMinMax",function(a,b){this.ms.calcAtomsMinMax(a,b)},"JU.BS,JU.BoxInfo");c(b,"getObjectMap",function(a,b){switch(b.charCodeAt(0)){case 123:null!=

this.getScriptManager()&&(null!=this.definedAtomSets&&a.putAll(this.definedAtomSets),JS.T.getTokensType(a,2097152));break;case 36:case 48:this.shm.getObjectMap(a,"$"==b)}},"java.util.Map,~S");c(b,"setPicked",function(a,b){var c=null,f=null;0<=a&&(b&&this.setPicked(-1,!1),this.g.setI("_atompicked",a),c=this.g.getParam("picked",!0),f=this.g.getParam("pickedList",!0));if(null==c||10!=c.tok)c=JS.SV.newV(10,new JU.BS),f=JS.SV.getVariableList(new JU.Lst),this.g.setUserVariable("picked",c),this.g.setUserVariable("pickedList",

f);0>a||(JS.SV.getBitSet(c,!1).set(a),c=f.pushPop(null,null),10==c.tok&&f.pushPop(null,c),(10!=c.tok||!c.value.get(a))&&f.pushPop(null,JS.SV.newV(10,JU.BSUtil.newAndSetBit(a))))},"~N,~B");j(b,"runScript",function(a){return""+this.evaluateExpression(w(-1,[w(-1,[JS.T.tokenScript,JS.T.tokenLeftParen,JS.SV.newS(a),JS.T.tokenRightParen])]))},"~S");j(b,"runScriptCautiously",function(a){var b=new JU.SB;try{if(null==this.getScriptManager())return null;this.eval.runScriptBuffer(a,b,!1)}catch(c){if(F(c,Exception))return this.eval.getErrorMessage();

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c(b,"getEvalContextAndHoldQueue",function(a){if(null==a||!JV.Viewer.isJS&&!this.testAsync)return null;a.pushContextDown("getEvalContextAndHoldQueue");a=a.getThisContext();a.setMustResume();this.queueOnHold=a.isJSThread=!0;return a},"J.api.JmolScriptEvaluator");c(b,"getDefaultPropertyParam",function(a){return this.getPropertyManager().getDefaultPropertyParam(a)},"~N");c(b,"getPropertyNumber",function(a){return this.getPropertyManager().getPropertyNumber(a)},"~S");c(b,"checkPropertyParameter",function(a){return this.getPropertyManager().checkPropertyParameter(a)},

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0:this.eval.evalFunctionFloat(a,b,c)},"~O,~O,~A");c(b,"evalParallel",function(a,b){this.displayLoadErrors=!1;var c=null!=this.getScriptManager()&&this.eval.evalParallel(a,null==b?this.shm:b);this.displayLoadErrors=!0;return c},"JS.ScriptContext,JV.ShapeManager");j(b,"evaluateExpression",function(a){return null==this.getScriptManager()?null:this.eval.evaluateExpression(a,!1,!1)},"~O");j(b,"evaluateExpressionAsVariable",function(a){return null==this.getScriptManager()?null:this.eval.evaluateExpression(a,

!0,!1)},"~O");c(b,"getAtomBitSet",function(a){if(y(a,"JU.BS"))return this.slm.excludeAtoms(a,!1);this.getScriptManager();return this.getAtomBitSetEval(this.eval,a)},"~O");c(b,"getScriptContext",function(a){return null==this.getScriptManager()?null:this.eval.getScriptContext(a)},"~S");c(b,"getAtomDefs",function(a){var b=new JU.Lst,c;for(a=a.entrySet().iterator();a.hasNext()&&((c=a.next())||1);)y(c.getValue(),"JU.BS")&&b.addLast("{"+c.getKey()+"} <"+c.getValue().cardinality()+" atoms>\n");c=b.size();

a=Array(c);b.toArray(a);java.util.Arrays.sort(a);for(var b=new JU.SB,f=0;f<c;f++)b.append(a[f]);return b.append("\n").toString()},"java.util.Map");c(b,"setCGO",function(a){this.shm.loadShape(23);this.shm.setShapePropertyBs(23,"setCGO",a,null)},"JU.Lst");c(b,"setModelSet",function(a){this.ms=this.mm.modelSet=a},"JM.ModelSet");c(b,"setObjectProp",function(a,b){this.getScriptManager();null==a&&(a="*");return null==this.eval?null:this.eval.setObjectPropSafe(a,b)},"~S,~N");c(b,"setDihedrals",function(a,

b,c){null==b&&(b=this.ms.getBsBranches(a));this.ms.setDihedrals(a,b,c)},"~A,~A,~N");c(b,"getChainID",function(a,b){var c=this.chainMap.get(a);if(null!=c)return c.intValue();var f=a.charAt(0).charCodeAt(0);if(1<a.length)f=300+this.chainList.size();else if((b||this.chainCaseSpecified)&&97<=f&&122>=f)f+=159;if(256<=f){c=this.chainMap.get(a);if(null!=c)return c.intValue();this.chainCaseSpecified=(new Boolean(this.chainCaseSpecified|b)).valueOf();this.chainList.addLast(a)}c=Integer.$valueOf(f);this.chainMap.put(c,

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2*this.g.hoverDelayMs,"!setInMotion");break;case 2:this.setInMotion(!0),this.refresh(3,"timeoutThread set in motion")}},"~N");c(b,"checkMotionRendering",function(a){if(!this.getInMotion(!0)&&!this.tm.spinOn&&!this.tm.vibrationOn&&!this.am.animationOn)return!0;if(this.g.wireframeRotation)return!1;var b=0;switch(a){case 1677721602:case 1153433601:b=2;break;case 1112150020:b=3;break;case 1112150021:b=4;break;case 1112152066:b=5;break;case 1073742018:b=6;break;case 1111490588:b=7;break;case 603979786:b=

8}return this.g.platformSpeed>=b},"~N");c(b,"openExportChannel",function(a,b,c){return this.getOutputManager().openOutputChannel(a,b,c,!1)},"~N,~S,~B");j(b,"log",function(a){null!=a&&this.getOutputManager().logToFile(a)},"~S");c(b,"getLogFileName",function(){return null==this.logFileName?"":this.logFileName});c(b,"getCommands",function(a,b,c){return this.getStateCreator().getCommands(a,b,c)},"java.util.Map,java.util.Map,~S");c(b,"allowCapture",function(){return!this.isApplet||this.isSignedApplet});

c(b,"compileExpr",function(a){var b=null==this.getScriptManager()?null:this.eval.evaluateExpression(a,!1,!0);return y(b,Array)?b:w(-1,[JS.T.o(4,a)])},"~S");c(b,"checkSelect",function(a,b){return null!=this.getScriptManager()&&this.eval.checkSelect(a,b)},"java.util.Map,~A");c(b,"getAnnotationInfo",function(a,b,c){return this.getAnnotationParser(1111490587==c).getAnnotationInfo(this,a,b,c,this.am.cmi)},"JS.SV,~S,~N");c(b,"getAtomValidation",function(a,b){return this.getAnnotationParser(!1).getAtomValidation(this,

a,b)},"~S,JM.Atom");c(b,"dragMinimizeAtom",function(a){this.stopMinimization();var b=0,c=this.getOperativeSymmetry();null!=c&&(b=256);c=0!=b?null:this.getMotionFixedAtoms(c,null).isEmpty()?this.ms.getAtoms(this.ms.isAtomPDB(a)?1086324742:1094713360,JU.BSUtil.newAndSetBit(a)):JU.BSUtil.setAll(this.ms.ac);try{this.minimize(this.eval,2147483647,0,c,null,null,0,b)}catch(f){if(F(f,Exception)){if(this.async){var e=(V("JV.Viewer$1")?0:JV.Viewer.$Viewer$1$(),U(JV.Viewer$1,this,la("me",this,"iAtom",a)));setTimeout(function(){e.run()},

100)}}else throw f;}},"~N");c(b,"getJBR",function(){return null==this.jbr?this.jbr=J.api.Interface.getInterface("JM.BioResolver",this,"file").setViewer(this):this.jbr});c(b,"checkMenuUpdate",function(){null!=this.jmolpopup&&this.jmolpopup.jpiUpdateComputedMenus()});c(b,"getChimeMessenger",function(){return null==this.jcm?this.jcm=J.api.Interface.getInterface("JV.ChimeMessenger",this,"script").set(this):this.jcm});c(b,"getModelSetAuxiliaryInfoForAtoms",function(a){return this.ms.getModelSetAuxiliaryInfo(this.ms.getModelBS(this.getAtomBitSet(a),

!1))},"~O");c(b,"getJSJSONParser",function(){return null==this.jsonParser?this.jsonParser=J.api.Interface.getInterface("JU.JSJSONParser",this,"script"):this.jsonParser});c(b,"parseJSON",function(a){return null==a?null:(a=a.trim()).startsWith("{")?this.parseJSONMap(a):this.parseJSONArray(a)},"~S");c(b,"parseJSONMap",function(a){return this.getJSJSONParser().parseMap(a,!0)},"~S");c(b,"parseJSONArray",function(a){return this.getJSJSONParser().parse(a,!0)},"~S");c(b,"getSymTemp",function(){return J.api.Interface.getSymmetry(this,

"ms").setViewer(this)});c(b,"getSymStatic",function(){return null==JV.Viewer.symStatic?(JV.Viewer.symStatic=J.api.Interface.getSymmetry(this,"ms")).setViewer(this):JV.Viewer.symStatic});c(b,"setWindowDimensions",function(a){this.resizeInnerPanel(D(a[0]),D(a[1]))},"~A");c(b,"getTriangulator",function(){return null==this.triangulator?this.triangulator=J.api.Interface.getUtil("Triangulator",this,"script"):this.triangulator});c(b,"getCurrentModelAuxInfo",function(){return 0<=this.am.cmi?this.ms.getModelAuxiliaryInfo(this.am.cmi):

null});c(b,"startNBO",function(a){var b=new java.util.Hashtable;b.put("service","nbo");b.put("action","showPanel");b.put("options",a);this.sm.processService(b)},"~S");c(b,"startPlugin",function(a){"nbo".equalsIgnoreCase(a)&&this.startNBO("all")},"~S");c(b,"connectNBO",function(a){0>this.am.cmi||this.getNBOParser().connectNBO(this.am.cmi,a)},"~S");c(b,"getNBOParser",function(){return null==this.nboParser?this.nboParser=J.api.Interface.getInterface("J.adapter.readers.quantum.NBOParser",this,"script").set(this):

this.nboParser});c(b,"getNBOAtomLabel",function(a){return this.getNBOParser().getNBOAtomLabel(a)},"JM.Atom");c(b,"calculateChirality",function(a){null==a&&(a=this.bsA());return this.ms.calculateChiralityForAtoms(a,!0)},"JU.BS");c(b,"getSubstructureSetArray",function(a,b,c){return this.getSmilesMatcher().getSubstructureSetArray(a,this.ms.at,this.ms.ac,b,null,c)},"~S,JU.BS,~N");c(b,"getSubstructureSetArrayForNodes",function(a,b,c){return this.getSmilesMatcher().getSubstructureSetArray(a,b,b.length,

null,null,c)},"~S,~A,~N");c(b,"getSmilesAtoms",function(a){return this.getSmilesMatcher().getAtoms(a)},"~S");c(b,"calculateChiralityForSmiles",function(a){try{return J.api.Interface.getSymmetry(this,"ms").calculateCIPChiralityForSmiles(this,a)}catch(b){if(F(b,Exception))return null;throw b;}},"~S");c(b,"getPdbID",function(){return this.ms.getInfo(this.am.cmi,JV.JC.getBoolName(4))===Boolean.TRUE?this.ms.getInfo(this.am.cmi,"pdbID"):null});c(b,"getModelInfo",function(a){return this.ms.getInfo(this.am.cmi,

a)},"~S");c(b,"notifyScriptEditor",function(a,b){null!=this.scriptEditor&&this.scriptEditor.notify(a,b)},"~N,~A");c(b,"sendConsoleMessage",function(a){null!=this.appConsole&&this.appConsole.sendConsoleMessage(a)},"~S");c(b,"getModelkitPropertySafely",function(a){return null==this.modelkit?null:this.modelkit.getProperty(a)},"~S");c(b,"setModelkitPropertySafely",function(a,b){return null==this.modelkit?null:this.modelkit.setProperty(a,b)},"~S,~O");c(b,"isModelKitOption",function(a,b){return null!=this.modelkit&&

this.modelkit.checkOption(a,b)},"~S,~S");c(b,"getSymmetryInfo",function(a,b,c,f,e,h,j,m,n,p,q,r){try{return this.getSymTemp().getSymmetryInfoAtom(this.ms,a,b,c,f,e,h,m,j,n,p,q,r)}catch(s){if(F(s,Exception))return System.out.println("Exception in Viewer.getSymmetryInfo: "+s),JV.Viewer.isJS||s.printStackTrace(),null;throw s;}},"~N,~S,~N,JU.P3,JU.P3,JU.P3,~N,~S,~N,~N,~N,~A");c(b,"getMacro",function(a){if(null==this.macros||this.macros.isEmpty())try{var b=this.getAsciiFileOrNull(this.g.macroDirectory+

"/macros.json");this.macros=this.parseJSON(b)}catch(c){if(F(c,Exception))this.macros=new java.util.Hashtable;else throw c;}if(null==a){var b=new JU.SB,f;for(a=this.macros.keySet().iterator();a.hasNext()&&((f=a.next())||1);){var e=this.macros.get(f);b.append(f).append("\t").appendO(e).append("\n")}return b.toString()}a=a.toLowerCase();return this.macros.containsKey(a)?this.macros.get(a).get("path").toString():null},"~S");c(b,"getConsoleFontScale",function(){return this.consoleFontScale});c(b,"setConsoleFontScale",

function(a){this.consoleFontScale=a},"~N");c(b,"confirm",function(a,b){return this.apiPlatform.confirm(a,b)},"~S,~S");c(b,"evalStringGUI",function(a){this.evalStringQuiet(a+"; ## GUI ##")},"~S");c(b,"selectStatus",function(a,b,c,f,e){this.select(a,b,c,f);e&&this.setStatusSelect(a)},"JU.BS,~B,~N,~B,~B");c(b,"setStatusSelect",function(a){this.hasSelected=!1;this.sm.setStatusSelect(null==a?this.bsA():a)},"JU.BS");c(b,"wasmInchiHack",function(a){(JV.Viewer.isJS&&(0<=a.indexOf("inchi")||0<=a.indexOf("INCHI"))||

0<=a.indexOf("TAUTOMER")||0<=a.indexOf("tautomer"))&&this.getInchi(null,null,null);return a},"~S");c(b,"getInchi",function(a,b,c){try{var f=this.apiPlatform.getInChI();if(null==a&&null==b)return"";if("string"==typeof b){var e=b;e.startsWith("$")||e.startsWith(":")?b=this.getFileAsString4(e,-1,!1,!1,!0,"script"):!e.startsWith("InChI=")&&0>e.indexOf(" ")&&(e=this.setLoadFormat(!1,"$"+b,"$",!1),b=this.getFileAsString4(e,-1,!1,!1,!0,"script"))}return f.getInchi(this,a,b,c)}catch(h){return""}},"JU.BS,~O,~S");

c(b,"findSpaceGroup",function(a,b,c,f,e,h,j){var m=null;if(null==b&&null==c||0!=(j&2))b=this.getThisModelAtoms();null==c?b.isEmpty()||(a=null==a?this.getOperativeSymmetry():a,m=null==a?null:a.findSpaceGroup(this,b,null,f,null,h,j)):m=this.getSymTemp().findSpaceGroup(this,b,c,f,e,h,j);return null==m&&0!=(j&1)?"":m},"J.api.SymmetryInterface,JU.BS,~S,~A,JU.T3,~A,~N");c(b,"restrictToModel",function(a,b){null==a&&(a=this.bsA());var c=a.isEmpty();if(c&&0<=b)return a;-1==b&&(b=this.am.cmi);if(0>b){if(c)return this.getThisModelAtoms();

b=this.ms.at[a.nextSetBit(0)].getModelIndex()}c=this.getModelUndeletedAtomsBitSet(b);c.and(a);return c},"JU.BS,~N");c(b,"getThisModelAtoms",function(){return this.getModelUndeletedAtomsBitSet(this.getVisibleFramesBitSet().nextSetBit(0))});c(b,"getSymmetryEquivPoints",function(a,b){var c=this.getCurrentUnitCell();return null==c?new JU.Lst:c.getEquivPoints(null,a,b)},"JU.P3,~S");c(b,"getSymmetryEquivPointList",function(a,b){var c=this.getCurrentUnitCell();if(null==c)return new JU.Lst;c.getEquivPointList(a,

0,b.toLowerCase(),null);return a},"JU.Lst,~S");c(b,"getOperativeSymmetry",function(){var a=this.getCurrentUnitCell();return null==a||null==a.getSymmetryOperations()?null:a});c(b,"formatText",function(a){if(0>a.indexOf("@{")&&0>a.indexOf("%{"))return a;var b=a,c=0<=b.indexOf("\\");c&&(b=JU.PT.rep(b,"\\%","\u0001"),b=JU.PT.rep(b,"\\@","\u0002"),c=!b.equals(a));for(var b=JU.PT.rep(b,"%{","@{"),f;0<=(a=b.indexOf("@{"));){a++;var e=a+1;f=b.length;for(var h=1,j="\x00",m="\x00";0<h&&++a<f;){var n=b.charAt(a);

if("\x00"!=j)"\\"==m?n="\x00":n==j&&(j="\x00"),m=n;else switch(n.charCodeAt(0)){case 39:case 34:j=n;break;case 123:h++;break;case 125:h--}}if(a>=f)return b;f=b.substring(e,a);if(0==f.length)return b;f=this.evaluateExpression(f);y(f,"JU.P3")&&(f=JU.Escape.eP(f));b=b.substring(0,e-2)+f.toString()+b.substring(a+1)}c&&(b=JU.PT.rep(b,"\u0002","@"),b=JU.PT.rep(b,"\u0001","%"));return b},"~S");c(b,"getScaleText",function(a,b,c,f){a=JM.Measurement.fixUnits(0<a.length?(a.startsWith("//")?a.substring(2):a).toLowerCase():

this.g.measureDistanceUnits.equals("vdw")?"angstroms":this.g.measureDistanceUnits);0==JM.Measurement.fromUnits(1,a)&&(a=JM.Measurement.fixUnits(this.g.measureDistanceUnits));if(null==f)return a;var e=this.tm.modelRadius*this.tm.scaleDefaultPixelsPerAngstrom/this.tm.scalePixelsPerAngstrom/4,h=b?2:1,j=0,m=b=0,n=0;for(c=2*(c*this.imageFontScaling/h);b<c;)m=JM.Measurement.toUnits(e,a,!1),j=B(Math.floor(Math.log10(m))),n=Math.pow(10,j),m=JM.Measurement.fromUnits(n+1E-6,a),b=D(m*this.tm.scalePixelsPerAngstrom/

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c(b,"checkConsoleScript",function(a){return 0==a.indexOf("JSCONSOLE")?(this.html5Applet._showInfo(0>a.indexOf("CLOSE")),0<=a.indexOf("CLEAR")&&this.html5Applet._clearConsole(),!0):!1},"~S");c(b,"haveAccessInternal",function(a){if(null==a)return this.access===JV.Viewer.ACCESS.INTERNAL;if(JV.Viewer.isJS)return!0;a=a.$replace("\\","/");var b=this.access!==JV.Viewer.ACCESS.NONE&&(null==this.internalAccessPath||this.access!==JV.Viewer.ACCESS.INTERNAL||a.startsWith(this.internalAccessPath));b||System.err.println("Viewer: Internal file access in "+

this.internalAccessPath+" denied for "+a);return b},"~S");c(b,"setAccessInternal",function(a){JV.Viewer.isJS||(null==a?this.access=this.access0:this.access!==JV.Viewer.ACCESS.INTERNAL&&(this.access=JV.Viewer.ACCESS.INTERNAL),this.internalAccessPath=a)},"~S");c(b,"getItaNumberFor",function(a){a=this.getSymStatic().getSpaceGroupInfoObj("itaNumber",a,!1,!1);return null==a?-1:JU.PT.parseInt(a)},"~S");b.$Viewer$1$=function(){var a=aa(JV,"Viewer$1",null,Runnable);j(a,"run",function(){this.f$.me.dragMinimizeAtom(this.f$.iAtom)})};

var a=H(JV.Viewer,"ACCESS",Enum);I(a,"NONE",0,[]);I(a,"READSPT",1,[]);I(a,"ALL",2,[]);I(a,"INTERNAL",3,[]);self.Jmol&&Jmol.extend&&Jmol.extend("vwr",JV.Viewer.prototype);b.isJS=!1;b.isSwingJS=!1;b.appletDocumentBase="";b.appletCodeBase="";b.appletIdiomaBase=null;b.jsDocumentBase="";b.jmolObject=null;b.strJavaVendor="Java: "+System.getProperty("java.vendor","j2s");b.strOSName=System.getProperty("os.name","");b.strJavaVersion="Java "+System.getProperty("java.version","");b.version_date=null;b.staticFunctions=

new java.util.Hashtable;b.nProcessors=1;b.isHighPrecision=!1;b.symStatic=null})}fa._coreLoaded=!0})(Clazz,Clazz.getClassName,Clazz.newLongArray,Clazz.doubleToByte,Clazz.doubleToInt,Clazz.doubleToLong,Clazz.declarePackage,Clazz.instanceOf,Clazz.load,Clazz.instantialize,Clazz.decorateAsClass,Clazz.floatToInt,Clazz.floatToLong,Clazz.makeConstructor,Clazz.defineEnumConstant,Clazz.exceptionOf,Clazz.newIntArray,Clazz.newFloatArray,Clazz.declareType,Clazz.prepareFields,Clazz.superConstructor,Clazz.newByteArray,

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Clazz.getStackTrace,Clazz.inheritArgs,Clazz.alert,Clazz.defineMethod,Clazz.overrideMethod,Clazz.declareAnonymous,Clazz.cloneFinals);

0 function(file, file0, js, isLoaded)

1 function (node, file, why, ignoreOnload, fSuccess, _loadScript)

2 function (file, fSuccess)

3 function(file, file0, js, isLoaded)

4 function (node, file, why, ignoreOnload, fSuccess, _loadScript)

5 function (file, fSuccess)

6 function(file, file0, js, isLoaded)

7 function (node, file, why, ignoreOnload, fSuccess, _loadScript)

8 function (file, fSuccess)

9 function(file, file0, js, isLoaded)

10 function (node, file, why, ignoreOnload, fSuccess, _loadScript)

11 function (file, fSuccess)

12 function(file, file0, js, isLoaded)

13 function (node, file, why, ignoreOnload, fSuccess, _loadScript)

14 function (file, fSuccess)

15 function(file, file0, js, isLoaded)

16 function (node, file, why, ignoreOnload, fSuccess, _loadScript)

17 function (file, fSuccess)

18 function(file, file0, js, isLoaded)

19 function (node, file, why, ignoreOnload, fSuccess, _loadScript)

20 function (file, fSuccess)

21 function(file, file0, js, isLoaded)

22 function (node, file, why, ignoreOnload, fSuccess, _loadScript)

23 function (file, fSuccess)

24 function(file, file0, js, isLoaded)

file cmd: popup

functions on this page:

Jmol Examples: PREDEFINED SETS