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]

After Change

    
    new_mol = Chem.RWMol(mol)
    removal_queue = []
    resnames = []
    for aix, atom in enumerate(new_mol.GetAtoms()):
        atomicnum = atom.GetAtomicNum()
        info = atom.GetPDBResidueInfo()
        resname = info.GetResidueName().strip().upper()
        resnames.append(resname)
        // Remove Hs by hard, Chem.RemoveHs does not remove double bonded Hs
        if removeHs and atomicnum == 1:
            removal_queue.append(aix)
        // Remove waters

Instances