Hi Rdkit community,
I have a case where I have pairs of molecules that are very similar, but
have different atom indices. I would like to figure out what is the best
way to get pairs of analogous atom indices:
For example, a dictionary that maps each probe atom index to a reference
atom index:
match_dict = {0:4,1:7,2:10...} Maybe with some tolerance for what is
considered a usable match.
I have experimented with calculating a fingerprint distance matrix focused
on all pairs of atoms, and then finding the minimum, but this doesn't seem
to work so well for molecules with repeating structure. Does anyone have
any pointers on the right way to do this?
Thanks so much for any suggestions.
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