Hi Tom, Can you open an issue on GitHub and I will fix it. Andrew has given a good explanation. My view is the simple fix is we add the flag in (1), or I could write a better canonicalisation algorithm (2). I did recently present to inchi the “how” on inorganic stereochemistry (octahedral etc) perhaps I should practise what I preach so to speak.
- John > On 25 May 2023, at 20:14, Tom Hubbard <cubb...@gmail.com> wrote: > > > Hi, > > I am trying to read in an SDF using IteratingSDFReader and extract properties > and create SMILES from the structure. For the most part this works fine, > however I seem to be running into an issue with large molecules (>1000 heavy > atoms) with the errors: > > An InChI could not be generated and used to canonise SMILES: null > > Could not generate InChI Numbers: Too many atoms [did you forget > 'LargeMolecules' switch?] > > I've had a good look through all the documentation and cannot find anything > on Large Molecules. Does CDK have a heavy atom limit and/or is there a way to > convert these large molecules to InChi and subsequently to SMILES? > > Any help would be much appreciated! > > Tom > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
