def test_fix_stereo(smiles, fragment_smiles):
parent_stereo = Fragmenter._find_stereo(smiles_to_molecule(smiles, True))
fragment = smiles_to_molecule(fragment_smiles, add_atom_map=True)
fixed = Fragmenter._fix_stereo(fragment, parent_stereo)
assert Fragmenter._check_stereo(fixed, parent_stereo) is True
def test_check_stereo(smiles, fragment_smiles, output, warning, caplog):
parent = smiles_to_molecule(smiles, add_atom_map=True)
fragment = smiles_to_molecule(fragment_smiles, add_atom_map=True)
parent_stereo = Fragmenter._find_stereo(parent)
with caplog.at_level(logging.WARNING):
assert Fragmenter._check_stereo(fragment, parent_stereo) == output
if warning is None:
assert len(caplog.records) == 0
else:
assert len(caplog.records) == 1
assert caplog.records[0].message.startswith(warning)
def test_cap_open_valance():
molecule, _, functional_groups, ring_systems = Fragmenter._prepare_molecule(
smiles_to_molecule("CNCCc1ccccc1", True), default_functional_groups(),
False)
expected_atom = get_map_index(
molecule,
molecule.chemical_environment_matches("[#7]-[#6H3:1]")[0][0],
)
# noinspection PyTypeChecker
atoms, bonds = Fragmenter._get_torsion_quartet(
molecule,
tuple(
get_map_index(molecule, i) for i in
molecule.chemical_environment_matches("[#6a:1]-[#6H2:2]")[0]),
)
atoms, bonds = Fragmenter._get_ring_and_fgroups(molecule,
functional_groups,
ring_systems, atoms, bonds)
# Remove the cap atom from the current list to make sure it gets included during
# capping.
atoms -= {expected_atom}
atoms, _ = Fragmenter._cap_open_valence(molecule, functional_groups, atoms,
bonds)
# Check that carbon bonded to N was added
assert expected_atom in atoms
def test_get_ring_and_fgroup_ortho(input_smiles, bond_smarts,
expected_pattern):
"""Ensure that FGs and rings attached to ortho groups are correctly
detected.
The expected values were generated using fragmenter=0.0.7
"""
molecule, _, functional_groups, ring_systems = Fragmenter._prepare_molecule(
smiles_to_molecule(input_smiles, True), default_functional_groups(),
False)
bond = tuple(
get_map_index(molecule, i)
for i in molecule.chemical_environment_matches(bond_smarts)[0])
# noinspection PyTypeChecker
atoms, bonds = Fragmenter._get_torsion_quartet(molecule, bond)
atoms, bonds = Fragmenter._get_ring_and_fgroups(molecule,
functional_groups,
ring_systems, atoms, bonds)
actual_atoms = {
map_index
for map_index in atoms if
molecule.atoms[get_atom_index(molecule, map_index)].atomic_number != 1
}
expected_atoms = {
get_map_index(molecule, atom_index)
for match in molecule.chemical_environment_matches(expected_pattern)
for atom_index in match
}
assert actual_atoms == expected_atoms
def test_atom_bond_set_to_mol(abemaciclib):
molecule = smiles_to_molecule(abemaciclib.to_smiles(mapped=False), True)
atoms = {
get_map_index(molecule, atom_index)
for match in molecule.chemical_environment_matches(
"[C:1][C:2][N:3]1[C:4][C:5][N:6][C:7][C:8]1")
for atom_index in match
}
bonds = {(
get_map_index(molecule, bond.atom1_index),
get_map_index(molecule, bond.atom2_index),
)
for bond in molecule.bonds
if get_map_index(molecule, bond.atom1_index) in atoms
and get_map_index(molecule, bond.atom2_index) in atoms}
fragment, _ = Fragmenter._atom_bond_set_to_mol(molecule, {},
atoms=atoms,
bonds=bonds)
for bond in fragment.bonds:
if bond.atom1.atomic_number == 1 or bond.atom2.atomic_number == 1:
continue
map_index_1 = get_map_index(fragment, bond.atom1_index)
map_index_2 = get_map_index(fragment, bond.atom2_index)
assert tuple(sorted((map_index_1, map_index_2))) in bonds
def test_find_stereo(smiles, output):
molecule = smiles_to_molecule(smiles, add_atom_map=True)
actual_stereo = Fragmenter._find_stereo(molecule)
expected_stereo = key_smarts_to_map_indices(output, molecule)
assert actual_stereo == expected_stereo
def test_ring_fgroups(input_smiles, n_output):
parent = smiles_to_molecule(input_smiles, True)
parent_groups = Fragmenter._find_functional_groups(
parent, default_functional_groups())
parent_rings = Fragmenter._find_ring_systems(parent, parent_groups)
assert len(parent_rings[1][0]) == n_output
def test_keep_non_rotor(keep_non_rotor_ring_substituents, n_output):
ring_systems = Fragmenter._find_ring_systems(
smiles_to_molecule("c1ccccc1C", True),
{},
keep_non_rotor_ring_substituents=keep_non_rotor_ring_substituents,
)
assert len(ring_systems[1][0]) == n_output
def test_compare_wbo():
parent = assign_elf10_am1_bond_orders(
smiles_to_molecule("CCCC", add_atom_map=True))
rotors_wbo = WBOFragmenter._get_rotor_wbo(
parent, WBOFragmenter.find_rotatable_bonds(parent, None))
fragment = smiles_to_molecule("CCCC", add_atom_map=True)
for bond_tuple, value in rotors_wbo.items():
assert numpy.isclose(
WBOFragmenter._compare_wbo(fragment, bond_tuple, value),
0.0,
atol=1.0e-6,
)
assert numpy.isclose(
WBOFragmenter._compare_wbo(fragment, bond_tuple, value + 1.0),
1.0,
atol=1.0e-6,
)
def test_get_torsion_quartet(input_smiles, expected_n_atoms, expected_n_bonds):
molecule = smiles_to_molecule(input_smiles, True)
bond_match = molecule.chemical_environment_matches("C[C:1][C:2]CCCC")[0]
atoms, bonds = Fragmenter._get_torsion_quartet(
molecule,
(
get_map_index(molecule, bond_match[0]),
get_map_index(molecule, bond_match[1]),
),
)
# This also includes explicit hydrogen
assert len(atoms) == expected_n_atoms
assert len(bonds) == expected_n_bonds
def test_build_fragment():
parent = assign_elf10_am1_bond_orders(smiles_to_molecule("CCCCCC", True))
rotors_wbo = WBOFragmenter._get_rotor_wbo(
parent, WBOFragmenter.find_rotatable_bonds(parent, None))
fragments = {
bond: WBOFragmenter._build_fragment(parent, {}, {}, {},
bond,
parent_wbo,
threshold=0.05)
for bond, parent_wbo in rotors_wbo.items()
}
assert len(fragments) == 3
assert (fragments[(3, 5)].to_smiles(explicit_hydrogens=False,
mapped=False) == "CCCCC")
assert (fragments[(4, 6)].to_smiles(explicit_hydrogens=False,
mapped=False) == "CCCCC")
assert (fragments[(5, 6)].to_smiles(explicit_hydrogens=False,
mapped=False) == "CCCCCC")
def test_get_rotor_wbo():
molecule = smiles_to_molecule("CCCC", True)
for bond in molecule.bonds:
bond.fractional_bond_order = 0.986
expected_bonds = {
(
get_map_index(molecule, match[0]),
get_map_index(molecule, match[1]),
)
for match in molecule.chemical_environment_matches("[#6:1]-[#6:2]")
}
rotors_wbo = WBOFragmenter._get_rotor_wbo(
molecule, WBOFragmenter.find_rotatable_bonds(molecule, None))
assert len(rotors_wbo) == 1
rotor_index = next(iter(rotors_wbo))
assert rotor_index in expected_bonds
assert numpy.isclose(rotors_wbo[rotor_index], 0.986, atol=0.001)
def test_get_ring_and_fgroup(input_smiles, bond_smarts, expected):
molecule, _, functional_groups, ring_systems = Fragmenter._prepare_molecule(
smiles_to_molecule(input_smiles, True), default_functional_groups(),
False)
# noinspection PyTypeChecker
atoms, bonds = Fragmenter._get_torsion_quartet(
molecule,
tuple(
get_map_index(molecule, i)
for i in molecule.chemical_environment_matches(bond_smarts)[0]),
)
bonds = {tuple(sorted(bond)) for bond in bonds}
l_atoms = len(atoms)
l_bonds = len(bonds)
atoms_2, bonds_2 = Fragmenter._get_ring_and_fgroups(
molecule, functional_groups, ring_systems, atoms, bonds)
assert (l_atoms == len(atoms_2)) == expected
assert (l_bonds == len(bonds_2)) == expected
def test_find_ring_systems(input_smiles, n_ring_systems):
ring_systems = Fragmenter._find_ring_systems(
smiles_to_molecule(input_smiles, True), {})
assert len(ring_systems) == n_ring_systems
def test_smiles_to_molecule(add_atom_map):
molecule = smiles_to_molecule("CCCC", add_atom_map=add_atom_map)
assert isinstance(molecule, Molecule)
assert ("atom_map" in molecule.properties) == add_atom_map