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

Before Change

    residue_mols = OrderedDict(sorted(residue_mols.items(), key=lambda x: x[1].GetNumAtoms()))

    // 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

    // Deal with residue lists
    if residue_whitelist is None:
        // Get templates for all residues in molecules
        unique_resname = set(resnames)
    else:
        unique_resname = set(residue_whitelist)
    if residue_blacklist is not None:
        unique_resname = unique_resname.difference(set(residue_blacklist))

Instances