Error handling and non-aromatic rings

Computer-Aided Drug Design at the Durrant Lab › Forums › Gypsum-DL › Error handling and non-aromatic rings

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    • March 17, 2022 at 11:55 am #75927
      Stephan Schott
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      Hi,
      Thanks for the nice tool.
      I have face some issues with 2 particular molecules that break the workflow:

      COc1ccc(NC(/N=C(\O)Cc2ccc(OC)c(OC)c2)=N\c2nc(C)cc(C)n2)cc1
      Causes a Runtime error with RDKit:
      RuntimeError: Pre-condition Violation
      bad bond type
      Violation occurred on line 125 in file Code/GraphMol/Canon.cpp
      Failed Expression: bond->getBondType() == Bond::SINGLE || bond->getIsAromatic()
      RDKIT: 2021.09.5
      BOOST: 1_74
      I am handling it by just adding an additional exception.

      CCc1c2c(cc(=O)n1CCOC)NN@@H+C2=O
      Causes the workflow to break because the list of ring indeces is empty. With the brief time I looked at it I am not sure why they have to have at least 1 non-aromatic atom, but that condition seems to fail.

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