# ~groups.txt  Jmol jmol.sourceforge.net script file
# Bob Hanson hansonr@stolaf.edu 2:29 PM 04/13/2006
# intended for files that have all H atoms explicit (not typical PDB files)
# this script must be loaded AFTER each "load" command -- it does not persist.

define ~methylC carbon and connected(4) and connected(3,hydrogen)
define ~methylH hydrogen and connected(~methylC)
define ~CH3 ~methylC or ~methylH

define ~methyleneC carbon and connected(4) and connected(2,hydrogen)
define ~methyleneH hydrogen and connected(~methyleneC)
define ~CH2 ~methyleneC or ~methyleneH

define ~methineC carbon and connected(4) and connected(1,hydrogen)
define ~methineH hydrogen and connected(~methineC)
define ~CH ~methineC or ~methineH

define ~CR4 carbon and connected(4,carbon)

define ~sp2C carbon and connected(3)
define ~spC carbon and connected(2)
define ~sp2O oxygen and connected(1)

define ~carbonylC ~sp2C and connected(~sp2O)
define ~carbonylO ~sp2O and connected(~carbonylC)
define ~CO ~carbonylC or ~carbonylO

define ~alkyne ~spC and connected(~spC)

define ~keteneC ~spC and connected(1, ~sp2O)
define ~keteneO ~sp2O and connected(~keteneC)
define ~ketene ~keteneC or ~keteneO

define ~hydroxylO oxygen and connected(hydrogen) and connected(carbon and not ~carbonylC)
define ~hydroxylH hydrogen and connected(~hydroxylO)
define ~OH ~hydroxylO or ~hydroxylH

define ~exchangableH hydrogen and connected(oxygen or nitrogen)

define ~carboxylicacidC ~carbonylC and connected(carbon) and connected(2,oxygen) and connected(1,oxygen and connected(hydrogen))
define ~carboxylicacidO oxygen and connected(~carboxylicacidC)
define ~carboxylicacidOH hydrogen and connected(~carboxylicacidO)
define ~carboxylicacidH hydrogen and connected(~carboxylicacidO)
define ~RCO2H ~carboxylicacidC or ~carboxylicacidO or ~carboxylicacidH

define ~esterC ~carbonylC and connected(carbon) and connected(2,oxygen) and not connected(oxygen and connected(hydrogen))
define ~esterO oxygen and connected(~esterC)
define ~RCO2R ~esterC or ~esterO

define ~aldehydeC ~carbonylC and connected(1,carbon) and connected(1,hydrogen)
define ~aldehydeH hydrogen and connected(~carbonylC)
define ~RCHO ~aldehydeC or ~aldehydeH

define ~ketoneC ~carbonylC and connected(2,carbon)
define ~ketoneO ~carbonylO and connected(~ketoneC) 
define ~R2CO ~ketoneC or ~ketoneO

define ~etherO oxygen and connected(2,carbon) and not ~carbonylO
define ~ROR ~etherO