Re: [Rdkit-discuss] atom mapping using GetSubstructMatch

[Paolo T. <pao...@un...>]

Dear Jan,

this gist shows a way to do what you need:

https://gist.github.com/ptosco/9b4a637a2814426846fe181f15aa8cdc

Basically, you'll need to convert explicit Hs into real atoms. Please 
note that indices in the tuple obtained in the match with hydrogens 
still apply to the original molecules without hydrogens, as hydrogens 
are added after all heavy atoms.

Hope that helps, kind regards
Paolo

On 01/29/18 08:23, Jan Halborg Jensen wrote:
> 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
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