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forlilab / Meeko

Interfacing RDKit and AutoDock
GNU Lesser General Public License v2.1
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write_pdbqt_string error for large molecules (protein) #42

Closed QJ-Chen closed 1 year ago

QJ-Chen commented 1 year ago

For class RDKitMoleculeSetup in molsetup.py:

def find_pattern(self, smarts):
    p = Chem.MolFromSmarts(smarts)
    return self.mol.GetSubstructMatches(p)

mol.GetSubstructMatches has a default parameter maxMatches=1000. For mol with more than 1000 same element, e.g. C, excess atoms will not be setup.

diogomart commented 1 year ago

Yeah, large molecules or polymers are not really the main focus of the RDKit or Meeko.

diogomart commented 1 year ago

Meeko will start writing PDBQT strings for the receptor as well when we release v0.5, but it won't rely on RDKit. Instead, it will rely on tabulated AD4 atom types and Gasteiger charges and indexed by residue and atom names according to Amber naming. So, it will be limited to a subset of stardard residues, at least in the beggining.