[Rdkit-discuss] atom mapping using GetSubstructMatch

[Jan H. J. <jhj...@ch...>]

I am trying to map atoms in one molecule to those of another using GetSubstructMatch, but have a problem with molecule pairs like the two below

The problem is that GetSubstructMatch ignored the H on the n, so that the protonated “n" in mol1 is mapped to the deprotonated “n”
in mol2, and vice versa

Is there a way to fix this?

Best regards, Jan



smiles1 = "ClCc1[nH]c(c2n1)cccc2"
smiles2 = "c1(I)cc(I)c2c(c1)nc(CCl)[nH]2"

mol1 = Chem.MolFromSmiles(smiles1)
mol2 = Chem.MolFromSmiles(smiles2)

order_mol1 = list(mol1.GetSubstructMatch(mol1))
order_mol2 = list(mol2.GetSubstructMatch(mol1))

print order_mol2

atom_map = dict(zip(order_mol1,order_mol2))
print atom_map

Draw.DrawingOptions.includeAtomNumbers=True
img = Draw.MolsToGridImage([mol1,mol2],molsPerRow=4,subImgSize=(200,200),useSVG=False)
img