Closed pducrot closed 1 year ago
Hi,
RDKitMolCreate.from_pdbqt_mol
returns None
objects, instead of RDKit molecules, if the REMARK SMILES line is missing in the DLG/PDBQT file (see code). This would happen if meeko was not used to prepare the PDBQT inputs for docking.
Hi, thank you for your feedback. Actually, I prepared pdbqt files with Meeko, ran AutoDock/vina and the output .dlg files contain the smiles
DOCKED: REMARK SMILES Cn1cc(-c2cncc...
DOCKED: REMARK SMILES IDX 5 1 25 2 9 3 8...
DOCKED: REMARK SMILES IDX 28 14 29 15 30...
DOCKED: REMARK SMILES IDX 15 25 16 26 22...
I see in your code line 175 of molecule_pdbqt.py that SMILES is expected in lines starting with REMARK SMILES, whereas the output dlg files from autodock start with DOCKED:
The "DOCKED:" keyword is remove with is_dlg=True
, so your DLG should work fine. I have no clue what is going on. Can you share the DLG?
AS you can see above, I indeed set is_dlg to True. I'll generate a file with a public compound for you and share, cannot share this one.
Sounds good, I'll then try to reproduce the problem
After thorough investigation, I found the files that were blocking and addressed. It's all fine, thanks for you time and help.
Hi, I'm trying to use Meeko from python to convert a list of .dlg files to a single sdf file.
RDkit returns an error at the above commented "m.SetProp()" line: AttributeError: 'NoneType' object has no attribute 'SetProp'
Does RDKitMolCreate.from_pdbqt_mol return a list of regular RDkit molecular object, or is there a need to convert those and how? Reading the Meeko code, it seems that the molecule was generate using Chem.MolFromSmiles() and should therefore have a SetProp attribute. Thanks, Pierre