Commit 6f89e63f authored by Levi Pierce's avatar Levi Pierce
Browse files

PDBBind Dataset Load Error #562 

Added fix to handle missing atoms in residues before assigning protonation
parent 76012de4

deepchem/utils/rdkit_util.py

+3 −0
Original line number Diff line number Diff line
@@ -51,6 +51,9 @@ def add_hydrogens_to_mol(mol): 
    pdb_stringio.write(pdbblock)

    pdb_stringio.seek(0)

    fixer = pdbfixer.PDBFixer(pdbfile=pdb_stringio)

    fixer.findMissingResidues()

    fixer.findMissingAtoms()

    fixer.addMissingAtoms()

    fixer.addMissingHydrogens(7.4)



    hydrogenated_io = StringIO()

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