Hi Steve, I think it would be better to use a similarity metric based on fingerprints.
Regards, Christos Christos Kannas Researcher Ph.D Student [image: View Christos Kannas's profile on LinkedIn] <http://cy.linkedin.com/in/christoskannas> On 28 November 2016 at 18:25, Stephen O'hagan <soha...@manchester.ac.uk> wrote: > Has anyone come up with fool-proof way of matching structurally equivalent > molecules? > > > > Unique Smiles or InChI String comparisons don’t appear to work presumable > because there are different but equivalent structures, e.g. explicit vs > non-explicit H’s, Kekule vs Aromatic, isomeric forms vs non-isomeric form, > tautomers etc. > > > > I also expect that comparing InChI strings might need something more than > just a simple string comparison, such as masking off stereo information > when you don’t care about stereo isomers. > > > > I assume there are suitable tools within RDKit that can do this? > > > > N.B. I need to collate tables from several sources that have a mix of > smiles / InChI / sdf molecular representations. > > > > I usually use RDKit via Python and/or Knime. > > > > Cheers, > > Steve. > > > > ------------------------------------------------------------ > ------------------ > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > >
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