Chemoinformatics: A way to reconstruct an RMG mol from an obmol.

gistfile1.txt

#!/usr/bin/python

import openbabel as ob

"""

This gist shows how to create a molecule from an OB mol.
OpenBabel does not have the obmol.GetAtomByIdx(int) method.

"""

def createOBMol():
	inchistr = "InChI=1S/CH4/h1H4"
	obConversion = ob.OBConversion()
	obConversion.SetInAndOutFormats("inchi", "smi")
	obmol = ob.OBMol()
	obConversion.ReadString(obmol, inchistr)
	obmol.AddHydrogens()
	return obmol

def main():
	print 'creating OBMol: '
	obmol = createOBMol()

	print 'creating mol: '

	vertices = []

	# iterate through atoms in obmol
	for obatom in ob.OBMolAtomIter(obmol):
		idx = obatom.GetIdx()#openbabel idx starts at 1!
		print 'idx: ', idx
	   
		atom = 'Mock atom'
		vertices.append(atom)#array index corresponds to idx of obatom!
	
	# iterate through bonds in obmol
	for obbond in ob.OBMolBondIter(obmol):
		atom1 = vertices[obbond.GetBeginAtomIdx() - 1]
		atom2 = vertices[obbond.GetEndAtomIdx() - 1]
		order = obbond.GetBondOrder()
		bond = 'Mock bond'#python array indices start at 0

if __name__ == '__main__':
	main()