61b518a2a177dbcd193d96a6f87797afaea0fc5d,rdkit_fixer.py,,AddMissingAtoms,#,364

Before Change

    // TODO: add backbone peptide bonds, if they were missing
    // TODO: try to better guess the types of atoms (if possible)

    try:
        fixed_residue = ConstrainedEmbed(template, residue)
    except ValueError as e:
        residue2 = SimplifyMol(Chem.Mol(residue))
        template2 = SimplifyMol(Chem.Mol(template))
        fixed_residue = ConstrainedEmbed(template2, residue2)
    assert fixed_residue is not None
    matched_atoms = fixed_residue.__sssAtoms
    assert len(matched_atoms) > 0

After Change

    // TODO: add backbone peptide bonds, if they were missing
    // TODO: try to better guess the types of atoms (if possible)

    matched_atoms = template.GetSubstructMatch(residue)
    if matched_atoms:  // instead of catching ValueError
        fixed_residue = ConstrainedEmbed(template, residue)
    else:
        residue2 = SimplifyMol(Chem.Mol(residue))
        template2 = SimplifyMol(Chem.Mol(template))
        matched_atoms = template2.GetSubstructMatch(residue2)
        if matched_atoms:
            fixed_residue = ConstrainedEmbed(template2, residue2)
        else:
            raise ValueError("No matching found at missing atom stage.",
                             template.GetProp("_Name"),
                             Chem.MolToSmiles(template),
                             Chem.MolToSmiles(residue),
                             )

    new_amap = []
    for i in range(fixed_residue.GetNumAtoms()):
        if i not in matched_atoms:
            atom = fixed_residue.GetAtomWithIdx(i)

Instances