86698c801848975de9a21fb17093e045b6271ea3,rdkit_fixer.py,,PreparePDBMol,#,94

Before Change

    // check if we have all templates
    for resname in unique_resname:
        if resname not in residue_mols and resname not in ["HOH"]:
            raise ValueError("There is no template for residue "%s"" % resname)

    // reset B.O. using templates
    for resname in residue_mols.keys():
        template = residue_mols[resname]
        new_mol = AssignPDBResidueBondOrdersFromTemplate(template, new_mol)

After Change

    for atom in new_mol.GetAtoms():
        if atom.GetAtomicNum() == 8 and atom.GetPDBResidueInfo().GetName().strip() == "OXT":
            bonds = atom.GetBonds()
            if len(bonds) > 0: // this should not happen at all
                bonds[0].SetBondType(BondType.SINGLE)

    return new_mol

Instances