def test_broken_xyz_file():
with pytest.raises(XYZfileDidNotExist):
_ = xyz_file_to_atoms(filename='XXXXXX')
with pytest.raises(NotXYZfile):
path = os.path.join(here, 'data', 'wrong_extension_xyz_file.mol')
_ = xyz_file_to_atoms(filename=path)
with pytest.raises(XYZfileMalformatted):
path = os.path.join(here, 'data', 'wrong_format_xyz_file.xyz')
_ = xyz_file_to_atoms(filename=path)
with pytest.raises(XYZfileMalformatted):
path = os.path.join(here, 'data', 'no_data_xyz_file.xyz')
_ = xyz_file_to_atoms(filename=path)
def test_okay_xyz_file():
atoms = xyz_file_to_atoms(os.path.join(here, 'data', 'hydrocarbon.xyz'))
assert len(atoms) == 20
for atom in atoms:
assert isinstance(atom, Atom)
# String representation should be concise
assert len(str(atoms[0])) < 50
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_cli():
join = Popen(['molfunc', xyz_path, '-a', '7', '-s', 'C[*]'])
join.wait()
toluene_path = os.path.join(here, 'data', 'benzene_mod.xyz')
assert os.path.exists(toluene_path)
toluene_atoms = xyz_file_to_atoms(filename=toluene_path)
assert len(toluene_atoms) == 15
toluene = Molecule(atoms=toluene_atoms)
# Geometry should be sensible.. i.e. min pairwise distance > 0.8 Å
# and the maximum < 5 Å
toluene_coords = toluene.get_coordinates()
dist_mat = distance_matrix(toluene_coords, toluene_coords)
assert 0.8 < np.min(dist_mat+np.identity(15)) < 5.0
os.remove(toluene_path)
def __init__(self, name='mol', xyz_filename=None, smiles=None, atoms=None):
"""
Base molecule class. Initialised in order of priority: SMILES string,
xyz file, atoms
------------------------ Keyword Arguments ----------------------------
:param name: (str)
:param xyz_filename: (str) .xyz filename (or filepath) from which atoms
will be extracted
:param smiles: (str) SMILES string defining the molecule from which a
3D structure as atoms are extracted using RDKit
:param atoms: (list(molfunc.atom.Atom)) List of atoms used to
initialise the molecule
"""
self.name = str(name)
self.n_atoms = 0
self.graph = None
self.atoms = None
if smiles is not None:
# Use RDKit to convert SMILES -> atoms
self.set_atoms(atoms=smiles_to_atoms(smiles))
if xyz_filename is not None:
# Initialisation with an xyz file takes precedence over SMILES
self.set_atoms(atoms=xyz_file_to_atoms(xyz_filename))
if atoms is not None:
self.set_atoms(atoms)
if self.n_atoms != 0:
# If there are atoms in the molecule set the graph and valancies
self.make_graph()
self.set_atomic_valancies()