The Layered InChI (LyChi), developed by Trung Nguyen at NCATS was designed to directly address the problem you describe. I don't have any first hand experience with this method (yet), but it looks intriguing.
https://github.com/ncats/lychi Pat On Mon, Nov 28, 2016 at 11:25 AM, 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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