a10212a69685b846f0fa45a4458697b3cb55a9b2,rdkit_fixer.py,,PreparePDBMol,#,136

Before Change

    if visited_bonds:  // probably we dont want to delete all
        new_mol = Chem.RWMol(new_mol)
        visited_bonds = set(visited_bonds)
        for a1_ix, a2_ix in product(range(new_mol.GetNumAtoms()), repeat=2):
            bond = new_mol.GetBondBetweenAtoms(a1_ix, a2_ix)
            if bond is None or (a1_ix, a2_ix) in visited_bonds or (a1_ix, a2_ix) in visited_bonds:
                continue

After Change

        new_mol = Chem.RWMol(new_mol)
        visited_bonds = set(visited_bonds)
        bonds_queue = []
        for bond in new_mol.GetBonds():
            a1 = bond.GetBeginAtomIdx()
            a2 = bond.GetEndAtomIdx()
            if (a1, a2) not in visited_bonds and (a1, a2) not in visited_bonds:
                bonds_queue.append((a1, a2))
        for a1_ix, a2_ix in bonds_queue:
            bond = new_mol.GetBondBetweenAtoms(a1_ix, a2_ix)
            if bond is None or (a1_ix, a2_ix) in visited_bonds or (a1_ix, a2_ix) in visited_bonds:
                continue

Instances