Hi, I’ve done this sort of comparison many times I actually use a SVL script within Moe and there is an example here (http://www.cambridgemedchemconsulting.com/resources/hit_identification/fragment_collection_profiles.html <http://www.cambridgemedchemconsulting.com/resources/hit_identification/fragment_collection_profiles.html>)
However I’ve found that the success is very much dependent on the fact 1 described by Greg, get all the structures standardised then comparison using canonical SMILES or InChi seems to work fine. Cheers, Chris > On 29 Nov 2016, at 17:24, rdkit-discuss-requ...@lists.sourceforge.net wrote: > > fact 1: if the structures are coming from different sources, they need to > be standardized/normalized before you compare them. This is true regardless > of how you want to compare them. The details of the standardization process > are not incredibly important, but it does need to take care of the things > you care about when comparing molecules. For example, if you don't care > about differences between salts, it should strip salts. If you don't care > about differences between tautomers, it should normalize tautomers.
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