def test_species_isomorphism():
h2.graph = None
h2_copy = Species(name='H2', atoms=[h_a, h_b], charge=0, mult=1)
h2_copy.graph = None
with pytest.raises(NoMolecularGraph):
assert mol_graphs.species_are_isomorphic(h2, h2_copy)
# With molecular graphs the species should be isomorphic
mol_graphs.make_graph(h2)
mol_graphs.make_graph(h2_copy)
assert mol_graphs.species_are_isomorphic(h2, h2_copy)
# Shift one of the atoms far away and remake the graph
h2_copy.atoms[1].translate(vec=np.array([10, 0, 0]))
mol_graphs.make_graph(h2_copy)
assert mol_graphs.species_are_isomorphic(h2, h2_copy) is False
# Generating a pair of conformers that are isomporhpic should return that
# the species are again isomorphic
h2.conformers = [
Conformer(name='h2_conf', atoms=[h_a, h_b], charge=0, mult=1)
]
h2_copy.conformers = [
Conformer(name='h2_conf', atoms=[h_a, h_b], charge=0, mult=1)
]
assert mol_graphs.species_are_isomorphic(h2, h2_copy)
def test_isomorphic_no_active():
os.chdir(os.path.join(here, 'data'))
ts_syn = Conformer(name='syn_ts', charge=-1, mult=0, atoms=xyz_file_to_atoms('E2_ts_syn.xyz'))
mol_graphs.make_graph(ts_syn)
mol_graphs.set_active_mol_graph(ts_syn, active_bonds=[(8, 5), (0, 5), (1, 2)])
ts_anti = Conformer(name='anti_ts', charge=-1, mult=0, atoms=xyz_file_to_atoms('E2_ts.xyz'))
mol_graphs.make_graph(ts_anti)
assert mol_graphs.is_isomorphic(ts_syn.graph, ts_anti.graph, ignore_active_bonds=True)
os.chdir(here)
def test_conformers():
methane = Molecule(name='methane', smiles='C')
# Function requiring a molecule having a conformer attribute
@utils.requires_conformers()
def test(mol):
print(mol.conformers[0].n_atoms)
with pytest.raises(NoConformers):
test(methane)
# Populating a species conformers should allow this function to be called
methane.conformers = [Conformer(name='conf0', atoms=methane.atoms)]
test(methane)
def test_species_conformers_isomorphic():
h2_a = Molecule(name='H2', atoms=[Atom('H'), Atom('H', x=0.7)])
h2_b = Molecule(name='H2', atoms=[Atom('H'), Atom('H', x=1.5)])
assert not mol_graphs.species_are_isomorphic(h2_a, h2_b)
# Should raise an exception for two non-isomorphic graphs
with pytest.raises(NoMapping):
mol_graphs.get_mapping(h2_a.graph, h2_b.graph)
h2_a.conformers = None
h2_b.conformers = [
Conformer(name='H2', atoms=[Atom('H'), Atom('H', x=0.7)])
]
assert mol_graphs.species_are_isomorphic(h2_a, h2_b)
from autode.input_output import xyz_file_to_atoms
from autode.conformers import conf_gen, Conformer
from autode.methods import XTB
# Initialise the complex from a .xyz file containing a square planar structure
vaskas = Molecule(name='vaskas', atoms=xyz_file_to_atoms('vaskas.xyz'))
# Set up some distance constraints where the keys are the atom indexes and
# the value the distance in Å. Fixing the Cl-P, Cl-P and Cl-C(=O) distances
# enforces a square planar geometry
distance_constraints = {
(1, 2): vaskas.get_distance(1, 2),
(1, 3): vaskas.get_distance(1, 3),
(1, 4): vaskas.get_distance(1, 4)
}
# Generate 5 conformers
for n in range(5):
# Apply random displacements to each atom and minimise under a bonded +
# repulsive forcefield including the distance constraints
atoms = conf_gen.get_simanl_atoms(species=vaskas,
dist_consts=distance_constraints,
conf_n=n)
# Generate a conformer from these atoms then optimise with XTB
conformer = Conformer(name=f'vaskas_conf{n}', atoms=atoms)
conformer.optimise(method=XTB())
conformer.print_xyz_file()