Chemoinformatics: Differences between OB and RDKit IDx

ob_test.py

import openbabel as ob

from rdkit import Chem

"""

This snippet shows that the IDx getter of OpenBabel and RDKit differ in implementation.

Openbabel IDx: starts at 1
RDKit IDx: starts at 0

"""
def main():

	inchistr = "InChI=1S/CH4/h1H4"
	print  'OpenBabel:' 
	obConversion = ob.OBConversion()
	obConversion.SetInAndOutFormats("inchi", "smi")
	obmol = ob.OBMol()
	obConversion.ReadString(obmol, inchistr)
	obmol.AddHydrogens()
	for obatom in ob.OBMolAtomIter(obmol): 
		print 'Openbabel IDx: ', obatom.GetIdx()

	print  'RDKit: '
	rdkitmol = Chem.inchi.MolFromInchi(inchistr, removeHs=False)
	rdkitmol = Chem.AddHs(rdkitmol)
	for rdatom in rdkitmol.GetAtoms():
		print 'RDKit IDx: ', rdatom.GetIdx()


if __name__ == '__main__':
	main()