def get_atom_with_map_num(mol, map_num, expected_results):
atom = utils.get_atom_with_map_num(mol, map_num)
symbol, num_hydrogens = expected_results
assert (atom.GetSymbol() == symbol)
assert (atom.GetTotalNumHs() == num_hydrogens)
def _create_reactants(self):
self._process_nucleophile()
map_nums = (self.TEMPLATE_OLIGOMERIZATION_MAP_NUM,
self.BACKBONE_NITROGEN_MAP_NUM)
if isinstance(self.model, models.Sidechain):
monomer = self._create_monomer()
self.reactants = [
utils.connect_mols(monomer,
self.template,
map_nums=map_nums,
clear_map_nums=False)
]
else:
# remove wildcard atom attached to n-terminus added in call to tag_monomer_connection_atom()
wildcard_atom = utils.get_atom_with_map_num(
self.reacting_atom, self.N_TERM_WILDCARD_MAP_NUM)
self.reacting_mol = Chem.RWMol(self.reacting_mol)
self.reacting_mol.RemoveAtom(wildcard_atom.GetIdx())
# connect template to monomer
self.reactants = [
utils.connect_mols(self.reacting_mol,
self.template,
map_nums=map_nums,
clear_map_nums=False)
]
def test_remove_atom(mol, map_num, symbol):
atom = utils.get_atom_with_map_num(mol, map_num)
prev_num_atoms = len(mol.GetAtoms())
mol = utils.remove_atom(mol, atom.GetIdx())
atoms = mol.GetAtoms()
assert (len(atoms) == prev_num_atoms - 1)
for atom in atoms:
assert (atom.GetSymbol() != symbol)
def _validate_sidechain(self):
connection_atom = utils.get_atom_with_map_num(
self.reacting_mol, self.SIDECHAIN_OLIGOMERIZATION_MAP_NUM)
paths = Chem.FindAllPathsOfLengthN(
self.reacting_mol,
3,
useBonds=False,
rootedAtAtom=self.reacting_atom.GetIdx())
atoms = set().union([atom for path in paths for atom in path])
if connection_atom.GetIdx() not in atoms - set(
atom.GetIdx() for atom in connection_atom.GetNeighbors()):
raise InvalidMolecule(
'The attachment point of the reacting sidechain must be two atoms away from the reacting atom in a pictet spangler reaction!'
)
def _validate_monomer(self):
try:
n_term_atom = utils.get_atom_with_map_num(
self.reacting_mol, self.BACKBONE_NITROGEN_MAP_NUM)
paths = Chem.FindAllPathsOfLengthN(
self.reacting_mol,
5,
useBonds=False,
rootedAtAtom=self.reacting_atom.GetIdx())
atoms = set().union([atom for path in paths for atom in path])
if n_term_atom.GetIdx() not in atoms - set(
atom.GetIdx() for atom in n_term_atom.GetNeighbors()):
raise InvalidMolecule(
'The reacting atom in the monomer must be 4 atoms away from the N-terminus!'
)
except (AttributeError, RuntimeError):
raise InvalidMolecule
def get_atom_with_map_num_fail(mol, map_num):
with pytest.raises(RuntimeError):
atom = utils.get_atom_with_map_num(mol, map_num)