Bond order not present in ouput smiles

[Patricio Chinestrad]

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!

[Patricio Chinestrad]

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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