Meeko fails to recognize `A` atom type from PDBQT

forlilab / Meeko

Interfacing RDKit and AutoDock

GNU Lesser General Public License v2.1

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Meeko fails to recognize `A` atom type from PDBQT #93

Closed althea-hansel closed 3 months ago

althea-hansel commented 3 months ago

When passing in a PDBQT receptor for mk_prepare_receptor.py, the following error is raised from RDKit:

****
Post-condition Violation
Element 'A' not found
Violation occurred on line 93 in file /project/build/temp.linux-x86_64-cpython-311/rdkit/Code/GraphMol/PeriodicTable.h
Failed Expression: anum > -1
****

I have encountered this before, since RDKit cannot recognize the A atom type.

diogomart commented 3 months ago

Maybe we shouldn't support PDBQT as input. Can you find a workaround or do you absolutely need this feature?

althea-hansel commented 3 months ago

I have always manually converted between the AD atom types and elements, I forget if the method used to live in Meeko or Ringtail or not. I think functionally it doesn't make a difference if we drop the feature (it is easy to convert in pymol, etc). We would just need to update the command-line help

diogomart commented 3 months ago

Thanks, I'll update command line help then.