What about something like this?
https://gist.github.com/PatWalters/15352d9007c33a214ac13d3dda814624
On Wed, Jun 9, 2021 at 9:28 PM Christopher Schlicksup <cjschlick...@lbl.gov>
wrote:
> 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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