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
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