Error handling and non-aromatic rings

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

  • This topic is empty.
Viewing 0 reply threads
  • Author
    • #75927 Reply
      Stephan Schott

      Thanks for the nice tool.
      I have face some issues with 2 particular molecules that break the workflow:

      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.

      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.

Viewing 0 reply threads
Reply To: Error handling and non-aromatic rings
Your information: