RuntimeError: Can't handle 3 explicit H for each heavy atomin noH mol.

forlilab / Meeko

Interfacing RDKit and AutoDock

GNU Lesser General Public License v2.1

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RuntimeError: Can't handle 3 explicit H for each heavy atomin noH mol. #14

Closed davidyanglee closed 1 year ago

davidyanglee commented 2 years ago

In a batch mode for mk_prepare_ligand, how may one solve the following problem in batch mode?

RuntimeError: Can't handle 3 explicit H for each heavy atomin noH mol. Was expecting only imines [H]N=

Thank you. David

diogomart commented 2 years ago

Can you share the molecule that produces the error?

We'll need to raise a warning instead of an error, at least in batch mode. Meanwhile one way to fix it is to remove the problematic molecule. Sorry about that...

Thank you

diogomart commented 1 year ago

Probably fixed in #39. Feel free to open a new issue, or re-open this one if necessary.