Bond order not present in ouput smiles

Computer-Aided Drug Design at the Durrant Lab Forums DeepFrag Bond order not present in ouput smiles

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    • #95731 Reply
      Patricio Chinestrad
      Guest

      Hello everyone,

      I’m trying to use the DeepFrag output to generate .pdbqt files for docking. However, the SMILES output does not keep the correct bond order. For example, aromatic rings lose the double bonds and therefore are deformed when trying to generate the 3D coordinates from the SMILE string.

      Is there a way to prevent this?
      Thanks!

    • #95805 Reply
      Patricio Chinestrad
      Guest

      In case its relevant, I’ve noticed that the SMILES output from the WebApp do contain the correct bonds, it seems only the CLI output is missing the double bonds.

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