def test_combined_molecule():
core_mol = CoreMolecule(atoms=atoms, atoms_to_del=[2])
# Ethane
mol = CombinedMolecule(core_mol=core_mol, frag_smiles='C[*]')
assert coordinates_are_resonable(coords=mol.get_coordinates())
assert mol.n_atoms == 8
mol = CombinedMolecule(core_mol=core_mol, frag_smiles_list=['C[*]'])
assert coordinates_are_resonable(coords=mol.get_coordinates())
assert mol.n_atoms == 8
fragment_mol = FragmentMolecule(smiles='C[*]')
mol = CombinedMolecule(core_mol=core_mol, fragment=fragment_mol)
assert coordinates_are_resonable(coords=mol.get_coordinates())
assert mol.n_atoms == 8
mol = CombinedMolecule(core_mol=core_mol, fragments=[fragment_mol])
assert coordinates_are_resonable(coords=mol.get_coordinates())
assert mol.n_atoms == 8
# Delete two hydrogens from methae
core_mol = CoreMolecule(atoms=atoms, atoms_to_del=[2, 3])
# Propane
mol = CombinedMolecule(core_mol=core_mol, frag_smiles='C[*]')
assert coordinates_are_resonable(coords=mol.get_coordinates())
assert mol.n_atoms == 11
def test_benzene_func():
benzene_xyz_path = os.path.join(here, 'data', 'benzene.xyz')
# Every hydrogen atom in benzene should be able to be functionalised
for atom_to_del in [7, 8, 9, 10, 11, 12]:
benzene = CoreMolecule(name='benzene',
xyz_filename=benzene_xyz_path,
atoms_to_del=[atom_to_del])
toluene = CombinedMolecule(benzene, frag_smiles='C[*]')
assert toluene.n_atoms == 15
# Likewise if the atoms are reordered so the H atoms are first
benzene_xyz_path = os.path.join(here, 'data', 'benzene_reordered.xyz')
for atom_to_del in [1, 2, 3, 4, 5, 6]:
benzene = CoreMolecule(name='benzene',
xyz_filename=benzene_xyz_path,
atoms_to_del=[atom_to_del])
toluene = CombinedMolecule(benzene, frag_smiles='C[*]')
assert toluene.n_atoms == 15
def test_combined_molecule_no_nn():
methane = CoreMolecule(atoms=atoms)
methane.datom_idxs = [2]
with pytest.raises(CombinationFailed):
_ = CombinedMolecule(core_mol=methane,
frag_smiles='C[*]')
def test_bad_core_molecule():
atoms_far_h = [Atom('C', 1.24788, 0.56457, -1.79703),
Atom('H', 9, 9, 9),
Atom('H', 0.87808, 0.86789, -2.79804),
Atom('H', 0.87807, 1.27982, -1.03385),
Atom('H', 0.87807, -0.45398, -1.55920)]
# Core molecule with a atom to delete that doesn't have a nearest neighbour
core_mol = CoreMolecule(atoms=atoms_far_h)
with pytest.raises(DatomsNotValid):
core_mol.get_datom_nn(datom_idx=1)
def test_combined_molecule_diff_fragements():
core_mol = CoreMolecule(atoms=atoms, atoms_to_del=[2])
# Can't add two fragments to a molecule with one atom to delete
with pytest.raises(CombinationFailed):
_ = CombinedMolecule(core_mol=core_mol,
frag_smiles_list=['C[*]', 'C[*]'])
# Similarly with two atoms to delete and a fragment smiles list of only
# one fragment
core_mol = CoreMolecule(atoms=atoms, atoms_to_del=[2, 3])
with pytest.raises(CombinationFailed):
_ = CombinedMolecule(core_mol=core_mol, frag_smiles_list=['C[*]'])
def test_pme3():
ph3 = CoreMolecule(xyz_filename=os.path.join(here, 'data', 'PH3.xyz'),
atoms_to_del=[2, 3, 4])
pme3 = CombinedMolecule(core_mol=ph3, frag_smiles='C[*]', name='PMe3')
assert coordinates_are_resonable(coords=pme3.get_coordinates())
def test_combined_molecule_no_fragments():
core_mol = CoreMolecule(atoms=atoms, atoms_to_del=[2])
# Should be able to make a combined molecule from a core that has no
# atoms to delete, but will add no atoms (Is this the clearest behaviour?)
mol = CombinedMolecule(core_mol=core_mol)
assert mol.n_atoms == 0
def test_combined_molecule_ortho_subst():
methane = CoreMolecule(atoms=atoms, atoms_to_del=[2, 3])
# Submitting two tBu groups onto methane should be possible (generate a
# sensible structure if the optimisation includes the previously added
# fragment
subt = CombinedMolecule(core_mol=methane,
frag_smiles='CC(C)([*])C')
assert coordinates_are_resonable(coords=subt.get_coordinates())
def test_core_molecule():
core_mol = CoreMolecule(atoms=atoms)
# Core molecule with no atoms to delete should retain all atoms
assert core_mol.n_atoms == 5
core_mol = CoreMolecule(atoms=atoms, atoms_to_del=[2])
assert core_mol.n_atoms == 4
# atoms_to_del list is indexed from 1, so atom 0 is not valid
with pytest.raises(DatomsNotValid):
_ = CoreMolecule(atoms=atoms, atoms_to_del=[0])
with pytest.raises(DatomsNotValid):
_ = CoreMolecule(atoms=atoms, atoms_to_del=[6])
# Cannot use a carbon atom in ethane as the atom to delete
xyz_path = os.path.join(here, 'data', 'ethane.xyz')
with pytest.raises(DatomsNotValid):
_ = CoreMolecule(name='ethane', xyz_filename=xyz_path, atoms_to_del=[1])
def test_tpp():
for name in ['Ph', 'phenyl', 'C6H5']:
ph3 = CoreMolecule(xyz_filename='examples/PH3.xyz',
atoms_to_del=[2, 3, 4])
# Fragments are added with aliases so any of {Ph, pheynl, C5H6} are
# possible
fragment = get_fragment_molecule(name=name)
assert fragment is not None
tpp = CombinedMolecule(core_mol=ph3, fragment=fragment, name='TPP')
assert coordinates_are_resonable(coords=tpp.get_coordinates())
assert tpp.n_atoms == 34
def test_fragment_from_file():
benzene = CoreMolecule(xyz_filename=os.path.join(here, 'data',
'benzene.xyz'),
atoms_to_del=[7])
methyl = FragmentMolecule(name='methyl',
xyz_filename=os.path.join(
here, 'data', 'methyl.xyz'))
toluene = CombinedMolecule(core_mol=benzene,
fragment=methyl,
name='toluene')
assert toluene.n_atoms == 15
assert coordinates_are_resonable(coords=toluene.get_coordinates())
def test_dmhp():
ph3 = CoreMolecule(xyz_filename=os.path.join(here, 'data', 'PH3.xyz'),
atoms_to_del=[2, 3, 4])
dimphp = CombinedMolecule(
core_mol=ph3,
frag_smiles_list=['C[*]', 'C[*]', '[*]C1=CC=CC=C1'],
name='dimphp')
# Check that the geometry is fairly sensible
assert coordinates_are_resonable(coords=dimphp.get_coordinates())
dimphp.make_graph()
assert dimphp.graph.number_of_edges() == 20
def test_example():
benzene_file_path = os.path.join(here, 'data', 'benzene.xyz')
benzene = CoreMolecule(xyz_filename=benzene_file_path, atoms_to_del=[7])
toluene = CombinedMolecule(core_mol=benzene,
frag_smiles='C[*]',
name='toluene')
toluene.print_xyz_file()
assert os.path.exists('toluene.xyz')
gen_toluene_atoms = xyz_file_to_atoms('toluene.xyz')
os.remove('toluene.xyz')
# Toluene has 15 atoms
assert len(gen_toluene_atoms) == 15
def test_fragment_molecule2():
core_mol = CoreMolecule(atoms=atoms, atoms_to_del=[2])
# Fragment molecules can also be initialised from [Fr] SMILES strings as
# well as ['*']
fragment_mol = FragmentMolecule(name='HOR', smiles='O[*]')
assert fragment_mol.n_atoms == 2 # OH atoms
mol = CombinedMolecule(core_mol=core_mol, fragment=fragment_mol)
assert mol.n_atoms == 6
assert coordinates_are_resonable(coords=mol.get_coordinates())
# Should also work directly from the SMILES string
mol = CombinedMolecule(core_mol=core_mol, frag_smiles='O[*]')
assert mol.n_atoms == 6
assert coordinates_are_resonable(coords=mol.get_coordinates())
def test_combined_molecule_no_core():
core_mol = CoreMolecule(atoms=atoms)
with pytest.raises(CombinationFailed):
_ = CombinedMolecule(core_mol=core_mol, frag_smiles='C[*]')
from molfunc import CoreMolecule, CombinedMolecule
fragments = {
'NMe2': 'CN([Fr])C',
'NH2': 'N[Fr]',
'OH': 'O[Fr]',
'Me': 'C[Fr]',
'F': 'F[Fr]'
}
methane = CoreMolecule(xyz_filename='CH4.xyz', atoms_to_del=[2])
for name, smiles in fragments.items():
combined = CombinedMolecule(core_mol=methane,
frag_smiles=smiles,
name=f'CH3_{name}')
combined.print_xyz_file()