Thank you Andrew for your excellent explanation, I spent a long time looking for that info without much success! I think that gives me a potential workaround for large molecules for the time being.
John, issue opened on github: InChi LargeMolecules Switch · Issue #974 · cdk/cdk (github.com) <https://github.com/cdk/cdk/issues/974> Thanks Tom On Fri, 26 May 2023 at 08:22, John May <john.wilkinson...@gmail.com> wrote: > 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 >
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