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07 May 2006 - 26 Feb 2024

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Node Object

Description:

A Node object is the basic building block of CDX chemical objects. At its most basic level, a Node is "a thing at the end of a bond." Most commonly, a Node will represent a single atom, but it may have other chemical meanings according to the value of the kCDXProp_Node_Type property.

When looking at a Node, there are really two places to find most types of information. Consider a node with the atom label (a contained Text object) CH₂. The Text object contains the three characters 'C', 'H', and '2'. You could take the Text object itself and -- with no other information -- figure out that this node represents a carbon atom and two attached hydrogens. For such a simple case, that sort of analysis is easy, but things can get very complicated very quickly.

For that reason, ChemDraw will always write redundant information. It is always safe to ignore the label entirely when interpreting ChemDraw-generated files. Instead, you can find out that this node is a carbon by looking at the kCDXProp_Node_Element property, and you can find the number of attached hydrogens by looking at the kCDXProp_Atom_NumHydrogens property.

All Nodes must be contained in Fragment objects; they cannot be stored directly in Page or Fragment objects. This redundancy extends across all node types.

When reading files, ChemDraw does two things. If a contained Text object is present, ChemDraw uses that object as is as the Node's label, and ignores the chemical properties entirely. If a Text object is not present, ChemDraw then looks to the chemical properties and creates an atom label on the fly, if appropriate. Accordingly, programs writing their own CDX files are welcome to write either a Text object or a collection of chemical properties, whichever is most convenient. Of course, they can write out both, too, just like ChemDraw does -- but they do not have to do so.

Most Node objects have no required properties or objects, but nodes representing multicenter attachments or variable attachment points require the kCDXProp_Node_Attachments property.

Subobjects:

Value	Name	CDXML Name
0x8003	kCDXObj_Fragment	fragment
	A collection of nodes and their connectivity (bonds).
0x8006	kCDXObj_Text	t
	An arbitrary block of (possibly styled) text.
0x8011	kCDXObj_ObjectTag	objecttag
	Arbitrarily named property, one or more of which can be attached to any ChemDraw object.

Properties:

Value	Name	CDXML Name	Type
n/a	n/a	id	UINT16
	A unique identifier for an object, used when other objects refer to it.
0x000A	kCDXProp_ZOrder	Z	INT16
	Back-to-front ordering index in 2D drawing.
0x000F	kCDXProp_IgnoreWarnings	IgnoreWarnings	CDXBooleanImplied
	Signifies whether chemical warnings should be suppressed on this object.
0x0010	kCDXProp_ChemicalWarning	Warning	CDXString
	A warning concerning possible chemical problems with this object.
0x0011	kCDXProp_Visible	Visible	CDXBoolean
	The object is visible if non-zero.
0x0200	kCDXProp_2DPosition	p	CDXPoint2D
	The 2D location (in the order of vertical and horizontal locations) of an object.
0x0201	kCDXProp_3DPosition	xyz	CDXPoint3D
	The 3D location (in the order of X-, Y-, and Z-locations in right-handed coordinate system) of an object in CDX coordinate units. The precise meaning of this attribute varies depending on the type of object.
0x0301	kCDXProp_ForegroundColor	color	UINT16
	The foreground color of an object represented as the two-based index into the object's color table.
0x0302	kCDXProp_BackgroundColor	bgcolor	INT16
	The background color of an object represented as the two-based index into the object's color table.
0x0400	kCDXProp_Node_Type	NodeType	INT16
	The type of a node object. This is an enumerated property.
0x0401	kCDXProp_Node_LabelDisplay	LabelDisplay	INT8
	The characteristics of node label display. This is an enumerated property.
0x0402	kCDXProp_Node_Element	Element	INT16
	The atomic number of the atom representing this node.
0x0403	kCDXProp_Atom_ElementList	ElementList	CDXElementList
	A list of atomic numbers.
0x0404	kCDXProp_Atom_Formula	Formula	CDXFormula
	The composition of a node representing a fragment whose composition is known, but whose connectivity is not. For example, C4H9 represents a mixture of the 4 butyl isomers.
0x0420	kCDXProp_Atom_Isotope	Isotope	INT16
	The absolute isotopic mass of an atom (2 for deuterium, 14 for carbon-14).
0x0421	kCDXProp_Atom_Charge	Charge	INT8
	The atomic charge of an atom.
0x0422	kCDXProp_Atom_Radical	Radical	UINT8
	The atomic radical attribute of an atom. This is an enumerated property.
0x0423	kCDXProp_Atom_RestrictFreeSites	FreeSites	UINT8
	Indicates that up to the specified number of additional substituents are permitted on this atom.
0x0424	kCDXProp_Atom_RestrictImplicitHydrogens	ImplicitHydrogens	CDXBooleanImplied
	Signifies that implicit hydrogens are not allowed on this atom.
0x0425	kCDXProp_Atom_RestrictRingBondCount	RingBondCount	INT8
	The number of ring bonds attached to an atom. This is an enumerated property.
0x0426	kCDXProp_Atom_RestrictUnsaturatedBonds	UnsaturatedBonds	INT8
	Indicates whether unsaturation should be present or absent. This is an enumerated property.
0x0427	kCDXProp_Atom_RestrictRxnChange	RxnChange	CDXBooleanImplied
	If present, signifies that the reaction change of an atom must be as specified.
0x0428	kCDXProp_Atom_RestrictRxnStereo	RxnStereo	INT8
	The change of stereochemistry of an atom during a reaction. This is an enumerated property.
0x0429	kCDXProp_Atom_AbnormalValence	AbnormalValence	CDXBooleanImplied
	Signifies that an abnormal valence for an atom is permitted.
0x042B	kCDXProp_Atom_NumHydrogens	NumHydrogens	UINT16
	The number of (explicit) hydrogens in a labeled atom consisting of one heavy atom and (optionally) the symbol H (e.g., CH3).
0x042E	kCDXProp_Atom_HDot	HDot	CDXBooleanImplied
	Signifies the presence of an implicit hydrogen with stereochemistry specified equivalent to an explicit H atom with a wedged bond.
0x042F	kCDXProp_Atom_HDash	HDash	CDXBooleanImplied
	Signifies the presence of an implicit hydrogen with stereochemistry specified equivalent to an explicit H atom with a hashed bond.
0x0430	kCDXProp_Atom_Geometry	Geometry	INT8
	The geometry of the bonds about this atom. This is an enumerated property.
0x0431	kCDXProp_Atom_BondOrdering	BondOrdering	CDXObjectIDArray
	An ordering of the bonds to this node, used for stereocenters, fragments, and named alternative groups with more than one attachment.
0x0432	kCDXProp_Node_Attachments	Attachments	CDXObjectIDArrayWithCounts
	Required for multi- and variable attached nodes. For multicenter attachment nodes or variable attachment nodes, a list of IDs of the nodes which are multiply or variably attached to this node.
0x0433	kCDXProp_Atom_GenericNickname	GenericNickname	CDXString
	The name of the generic nickname.
0x0434	kCDXProp_Atom_AltGroupID	AltGroupID	CDXObjectID
	The ID of the alternative group object that describes this node.
0x0435	kCDXProp_Atom_RestrictSubstituentsUpTo	SubstituentsUpTo	UINT8
	Indicates that substitution is restricted to no more than the specified value.
0x0436	kCDXProp_Atom_RestrictSubstituentsExactly	SubstituentsExactly	UINT8
	Indicates that exactly the specified number of substituents must be present.
0x0437	kCDXProp_Atom_CIPStereochemistry	AS	INT8
	The node's absolute stereochemistry according to the Cahn-Ingold-Prelog system. This is an enumerated property.
0x0438	kCDXProp_Atom_Translation	Translation	INT8
	Provides for restrictions on whether a given node may match other more- or less-general nodes. This is an enumerated property.
0x0439	kCDXProp_Atom_AtomNumber	AtomNumber	CDXString
	Atom number, as text.
0x043A	kCDXProp_Atom_ShowQuery	ShowAtomQuery	CDXBoolean
	Show the query indicator if non-zero.
0x043B	kCDXProp_Atom_ShowStereo	ShowAtomStereo	CDXBoolean
	Show the stereochemistry indicator if non-zero.
0x043C	kCDXProp_Atom_ShowAtomNumber	ShowAtomNumber	CDXBoolean
	Show the atom number if non-zero.
0x043D	kCDXProp_Atom_LinkCountLow	LinkCountLow	INT16
	Low end of repeat count for link nodes.
0x043E	kCDXProp_Atom_LinkCountHigh	LinkCountHigh	INT16
	High end of repeat count for link nodes.
0x043F	kCDXProp_Atom_IsotopicAbundance	IsotopicAbundance	INT8
	Isotopic abundance of this atom's isotope. This is an enumerated property.
0x0440	kCDXProp_Atom_ExternalConnectionType	ExternalConnectionType	INT8
	Type of external connection, for atoms of type kCDXNodeType_ExternalConnectionPoint. This is an enumerated property.
0x0441	kCDXProp_Atom_GenericList	GenericList	CDXGenericList
	A list of generic nicknames.
0x0445	kCDXProp_Atom_ShowEnhancedStereo	ShowAtomEnhancedStereo	CDXBoolean
	Show the enhanced stereochemistry indicator if non-zero.
0x0446	kCDXProp_Atom_EnhancedStereoType	EnhancedStereoType	UINT8
	The type of enhanced stereochemistry present on this atom. This is an enumerated property.
0x0447	kCDXProp_Atom_EnhancedStereoGroupNum	EnhancedStereoGroupNum	UINT16
	The group number associated with Or and And enhanced stereochemistry types.
0x0807	kCDXProp_LineWidth	LineWidth	CDXCoordinate
	The default line width.
0x080A	kCDXProp_LabelStyle	(not used)	CDXFontStyle
	The default style for atom labels..
0x081A	kCDXProp_LabelStyleFont	LabelFont	INT16
	The default font family for atom labels.
0x081C	kCDXProp_LabelStyleSize	LabelSize	INT16
	The default font size for atom labels.
0x081E	kCDXProp_LabelStyleFace	LabelFace	INT16
	The default font style for atom labels.