def test_sum_mep():
reactant = ReactantComplex(Molecule(smiles='C', charge=0, mult=1))
product = ProductComplex(Molecule(smiles='C', charge=0, mult=1))
product.graph.remove_edge(0, 1)
product.graph.remove_edge(0, 2)
# Fictitious PES
pes = PES2d(reactant,
product,
r1s=np.linspace(1, 2, 3),
r1_idxs=(0, 1),
r2s=np.linspace(1, 2, 3),
r2_idxs=(0, 2))
# Energies are all 0 apart from at the 'saddle point' (1, 1)
for i in range(3):
for j in range(3):
pes.species[i, j] = deepcopy(reactant)
pes.species[i, j].energy = 0
if i == j == 2:
pes.species[i, j].graph = product.graph
pes.species[1, 1].energy = 1
mep_sum = mep.get_sum_energy_mep(saddle_point_r1r2=(1.5, 1.5), pes_2d=pes)
# Energy over the saddle point is 1 both sides -> 2 Ha
assert mep_sum == 2
def test_2b2f():
reac = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 0.6, 0, 0), Atom('N', 10, 0, 0), Atom('O', 10.6, 0, 0)])
prod = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 10, 0, 0), Atom('N', 0.6, 0, 0), Atom('O', 10.6, 0, 0)])
assert br.get_fbonds_bbonds_2b2f(reac, prod, [], [[(0, 1)], [(2, 3)]], [[(0, 2)], [(1, 3)]], [], [], []) == [
br.BondRearrangement(forming_bonds=[(0, 2), (1, 3)], breaking_bonds=[(0, 1), (2, 3)])]
reac = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 0.6, 0, 0), Atom('H', 10, 0, 0),
Atom('N', 10.6, 0, 0), Atom('O', 20, 0, 0)])
prod = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 10, 0, 0), Atom('H', 1.2, 0, 0),
Atom('N', 20, 0, 0), Atom('O', 0.6, 0, 0)])
assert br.get_fbonds_bbonds_2b2f(reac, prod, [], [[(0, 1)], [(2, 3)]], [[(0, 4), (2, 4)]], [], [], []) == [
br.BondRearrangement(forming_bonds=[(0, 4), (2, 4)], breaking_bonds=[(0, 1), (2, 3)])]
reac = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 0.6, 0, 0), Atom('H', 1.2, 0, 0), Atom('O', 10, 0, 0)])
prod = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 10, 0, 0), Atom('H', 11.2, 0, 0), Atom('O', 10.6, 0, 0)])
assert br.get_fbonds_bbonds_2b2f(reac, prod, [], [[(0, 1), (1, 2)]], [[(0, 3), (2, 3)], [(1, 3)]], [], [], []) == [
br.BondRearrangement(forming_bonds=[(0, 3), (1, 3)], breaking_bonds=[(0, 1), (1, 2)]),
br.BondRearrangement(forming_bonds=[(1, 3), (2, 3)], breaking_bonds=[(0, 1), (1, 2)])]
reac = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 0.6, 0, 0), Atom('H', 1.2, 0, 0), Atom('O', 10, 0, 0)])
prod = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 10, 0, 0), Atom('H', 1.2, 0, 0), Atom('O', 0.6, 0, 0)])
assert br.get_fbonds_bbonds_2b2f(reac, prod, [], [[(0, 1), (1, 2)]], [[(0, 3), (2, 3)]], [], [], []) == [
br.BondRearrangement(forming_bonds=[(0, 3), (2, 3)], breaking_bonds=[(0, 1), (1, 2)])]
reac = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 0.6, 0, 0), Atom('N', 1.2, 0, 0), Atom('C', 10, 0, 0)])
prod = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('C', 10, 0, 0), Atom('N', 1.2, 0, 0), Atom('C', 0.6, 0, 0)])
assert br.get_fbonds_bbonds_2b2f(reac, prod, [], [], [], [[[(0, 1)], [(0, 3)]], [[(1, 2)], [(2, 3)]]], [], []) == [br.BondRearrangement(forming_bonds=[(0, 3), (2, 3)], breaking_bonds=[(0, 1), (1, 2)])]
def test_butene(tmpdir):
os.chdir(tmpdir)
butene = Molecule(name='z-but-2-ene',
charge=0,
mult=1,
atoms=[
Atom('C', -1.69185, -0.28379, -0.01192),
Atom('C', -0.35502, -0.40751, 0.01672),
Atom('C', -2.39437, 1.04266, -0.03290),
Atom('H', -2.13824, 1.62497, 0.87700),
Atom('H', -3.49272, 0.88343, -0.05542),
Atom('H', -2.09982, 1.61679, -0.93634),
Atom('C', 0.57915, 0.76747, 0.03048),
Atom('H', 0.43383, 1.38170, -0.88288),
Atom('H', 1.62959, 0.40938, 0.05452),
Atom('H', 0.39550, 1.39110, 0.93046),
Atom('H', -2.29700, -1.18572, -0.02030),
Atom('H', 0.07422, -1.40516, 0.03058)
])
butene.graph.nodes[0]['stereo'] = True
butene.graph.nodes[1]['stereo'] = True
# Conformer generation should retain the stereochemistry
atoms = conf_gen.get_simanl_atoms(species=butene)
regen = Molecule(name='regenerated_butene', atoms=atoms, charge=0, mult=1)
regen.print_xyz_file()
regen_coords = regen.coordinates
# The Z-butene isomer has a r(C_1 C_2) < 3.2 Å where C_1C=CC_2
assert np.linalg.norm(regen_coords[6] - regen_coords[2]) < 3.6
os.chdir(here)
def test_get_bond_rearrangs():
if os.path.exists('test_bond_rearrangs.txt'):
os.remove('test_bond_rearrangs.txt')
# ethane --> Ch3 + Ch3
reac = Molecule(smiles='CC')
prod = Molecule(atoms=[Atom('C', -8.3, 1.4, 0.0),
Atom('C', 12, 1.7, -0.0),
Atom('H', -8.6, 0.5, -0.5),
Atom('H', -8.6, 2.3, -0.4),
Atom('H', -8.6, 1.3, 1),
Atom('H', 12.3, 1.7, -1.0),
Atom('H', 12.4, 0.8, 0.4),
Atom('H', 12.3, 2.5, 0.5)])
assert br.get_bond_rearrangs(ReactantComplex(reac), ProductComplex(prod), name='test') == [br.BondRearrangement(breaking_bonds=[(0, 1)])]
# Rerunning the get function should read test_bond_rearrangs.txt, so modify it, swapping 0 and 1 in the breaking
# bond then reopen
with open('test_bond_rearrangs.txt', 'w') as rearr_file:
print('fbond\n'
'bbonds\n'
'1 0\n'
'end', file=rearr_file)
rearr = br.get_bond_rearrangs(ReactantComplex(reac), ProductComplex(prod), name='test')[0]
assert rearr == BondRearrangement(breaking_bonds=[(1, 0)])
assert br.get_bond_rearrangs(ReactantComplex(prod), ProductComplex(reac), name='test2') is None
# If reactants and products are identical then the rearrangement is undetermined
assert br.get_bond_rearrangs(ReactantComplex(reac), ProductComplex(reac), name='test3') is None
os.remove('test_bond_rearrangs.txt')
def get_optimised_species(calc, method, direction, atoms):
"""Get the species that is optimised from an initial set of atoms"""
species = Molecule(name=f'{calc.name}_{direction}',
atoms=atoms,
charge=calc.molecule.charge,
mult=calc.molecule.mult)
# Note that for the surface to be the same the keywords.opt and keywords.hess need to match in the level of theory
calc = Calculation(name=f'{calc.name}_{direction}',
molecule=species,
method=method,
keywords=method.keywords.opt,
n_cores=Config.n_cores)
calc.run()
try:
species.set_atoms(atoms=calc.get_final_atoms())
species.energy = calc.get_energy()
make_graph(species)
except AtomsNotFound:
logger.error(f'{direction} displacement calculation failed')
return species
def test_grad():
h2 = Molecule(name='h2', atoms=[Atom('H'), Atom('H', x=0.5)])
grad_calc = Calculation(name='h2_grad',
molecule=h2,
method=method,
keywords=Config.MOPAC.keywords.grad)
grad_calc.run()
energy = grad_calc.get_energy()
assert energy is not None
gradients = grad_calc.get_gradients()
assert gradients.shape == (2, 3)
delta_r = 1E-5
h2_disp = Molecule(name='h2_disp',
atoms=[Atom('H'), Atom('H', x=0.5 + delta_r)])
h2_disp.single_point(method)
delta_energy = h2_disp.energy - energy # Ha]
grad = delta_energy / delta_r # Ha A^-1
# Difference between the absolute and finite difference approximation
assert np.abs(gradients[1, 0] - grad) < 1E-1
# Broken gradient file
grad_calc.output.filename = 'h2_grad_broken.out'
grad_calc.output.file_lines = open('h2_grad_broken.out', 'r').readlines()
with pytest.raises(CouldNotGetProperty):
_ = grad_calc.get_gradients()
def test_3b():
reac = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('H', 0.6, 0, 0), Atom('H', 1.2, 0, 0), Atom('H', 1.8, 0, 0)])
make_graph(reac, allow_invalid_valancies=True)
prod = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('H', 10, 0, 0), Atom('H', 20, 0, 0), Atom('H', 30, 0, 0)])
# Reactants to products must break three bonds but this is not yet supported in any form
assert br.get_bond_rearrangs(ReactantComplex(reac), ProductComplex(prod), name='3b_test') is None
def test_1b1f():
reac = Molecule(atoms=[Atom('C', 0, 0, 0), Atom('H', 0.6, 0, 0), Atom('H', 10, 0, 0)])
prod = Molecule(atoms=[Atom('C', 0, 0, 0), Atom('H', 10, 0, 0), Atom('H', 10.6, 0, 0)])
assert br.get_fbonds_bbonds_1b1f(reac, prod, [], [[(0, 1)]], [[(1, 2)]], [], [], []) == [br.BondRearrangement(forming_bonds=[(1, 2)], breaking_bonds=[(0, 1)])]
reac = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('H', 0.6, 0, 0), Atom('H', 10, 0, 0)])
prod = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('H', 10, 0, 0), Atom('H', 10.6, 0, 0)])
assert br.get_fbonds_bbonds_1b1f(reac, prod, [], [], [], [[[(0, 1)], [(1, 2)]]], [], []) == [br.BondRearrangement(forming_bonds=[(1, 2)], breaking_bonds=[(0, 1)])]
def test_ts_conformer(tmpdir):
os.chdir(tmpdir)
ch3cl = Reactant(charge=0,
mult=1,
atoms=[
Atom('Cl', 1.63664, 0.02010, -0.05829),
Atom('C', -0.14524, -0.00136, 0.00498),
Atom('H', -0.52169, -0.54637, -0.86809),
Atom('H', -0.45804, -0.50420, 0.92747),
Atom('H', -0.51166, 1.03181, -0.00597)
])
f = Reactant(charge=-1, mult=1, atoms=[Atom('F', 4.0, 0.0, 0.0)])
ch3f = Product(charge=0,
mult=1,
atoms=[
Atom('C', -0.05250, 0.00047, -0.00636),
Atom('F', 1.31229, -0.01702, 0.16350),
Atom('H', -0.54993, -0.04452, 0.97526),
Atom('H', -0.34815, 0.92748, -0.52199),
Atom('H', -0.36172, -0.86651, -0.61030)
])
cl = Reactant(charge=-1, mult=1, atoms=[Atom('Cl', 4.0, 0.0, 0.0)])
f_ch3cl_tsguess = TSguess(reactant=ReactantComplex(f, ch3cl),
product=ProductComplex(ch3f, cl),
atoms=[
Atom('F', -2.66092, -0.01426, 0.09700),
Atom('Cl', 1.46795, 0.05788, -0.06166),
Atom('C', -0.66317, -0.01826, 0.02488),
Atom('H', -0.78315, -0.58679, -0.88975),
Atom('H', -0.70611, -0.54149, 0.97313),
Atom('H', -0.80305, 1.05409, 0.00503)
])
f_ch3cl_tsguess.bond_rearrangement = BondRearrangement(breaking_bonds=[
(2, 1)
],
forming_bonds=[(0,
2)])
f_ch3cl_ts = TransitionState(ts_guess=f_ch3cl_tsguess)
atoms = conf_gen.get_simanl_atoms(
species=f_ch3cl_ts, dist_consts=get_distance_constraints(f_ch3cl_ts))
regen = Molecule(name='regenerated_ts', charge=-1, mult=1, atoms=atoms)
# regen.print_xyz_file()
# Ensure the making/breaking bonds retain their length
regen_coords = regen.get_coordinates()
assert are_coords_reasonable(regen_coords) is True
assert 1.9 < np.linalg.norm(regen_coords[0] - regen_coords[2]) < 2.1
assert 2.0 < np.linalg.norm(regen_coords[1] - regen_coords[2]) < 2.2
os.chdir(here)
def test_2b():
reac = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('H', 0.6, 0, 0), Atom('H', 1.2, 0, 0)])
make_graph(reac, allow_invalid_valancies=True)
prod = Molecule(atoms=[Atom('H', 0, 0, 0), Atom('H', 10, 0, 0), Atom('H', 20, 0, 0)])
# Reactants to products must break two bonds
assert len(br.get_bond_rearrangs(ReactantComplex(reac), ProductComplex(prod), name='2b_test')) == 1
os.remove('2b_test_bond_rearrangs.txt')
assert br.get_fbonds_bbonds_2b(reac, prod, [], [[(0, 1), (1, 2)]], [], [], [(0, 2)], []) == [br.BondRearrangement(breaking_bonds=[(0, 1), (1, 2)])]
def test_molecule_from_xyz():
os.chdir(os.path.join(here, 'data'))
h2 = Molecule('h2_conf0.xyz')
assert h2.name == 'h2_conf0'
assert h2.n_atoms == 2
assert h2.formula() == 'H2'
os.chdir(here)
def test_siman_conf_gen(tmpdir):
os.chdir(tmpdir)
rh_complex = Molecule(name='[RhH(CO)3(ethene)]',
smiles='O=C=[Rh]1(=C=O)(CC1)([H])=C=O')
assert are_coords_reasonable(coords=rh_complex.get_coordinates())
assert rh_complex.n_atoms == 14
assert 12 < rh_complex.graph.number_of_edges() < 15 # What is a bond even
os.chdir(here)
def test_metal_eta_complex(tmpdir):
os.chdir(tmpdir)
# eta-6 benzene Fe2+ complex used in the molassembler paper
m = Molecule(smiles='[C@@H]12[C@H]3[C@H]4[C@H]5[C@H]6[C@@H]1[Fe]265437N'
'(C8=CC=CC=C8)C=CC=[N+]7C9=CC=CC=C9')
m.print_xyz_file()
assert are_coords_reasonable(coords=m.get_coordinates())
os.chdir(here)
def calc_mult():
h = Molecule(name='H', smiles='[H]')
assert calc_multiplicity(h, n_radical_electrons=1) == 2
# Setting the multiplicity manually should override the number of radical electrons derived from the SMILES string
# note: H with M=3 is obviously not possible
h.mult = 3
assert calc_multiplicity(h, n_radical_electrons=1) == 3
# Diradicals should default to singlets..
assert calc_multiplicity(h, n_radical_electrons=2) == 1
def test_find_lowest_energy_conformer():
# Spoof XTB availability
xtb.path = here
propane = Molecule(name='propane', smiles='CCC')
propane.find_lowest_energy_conformer(lmethod=xtb)
assert len(propane.conformers) > 0
# Finding low energy conformers should set the energy of propane
assert propane.energy is not None
assert propane.atoms is not None
def test_two_possibles():
ch2ch3f = Molecule(name='radical', charge=0, mult=2,
smiles='FC[C]([H])[H]')
ch3ch2f = Molecule(name='radical', charge=0, mult=2,
smiles='C[C]([H])F')
rearrs = br.get_bond_rearrangs(ReactantComplex(ch2ch3f), ProductComplex(ch3ch2f),
name='H_migration')
# There are two possibilities for H migration by they should be considered the same
assert len(rearrs) == 1
os.remove('H_migration_bond_rearrangs.txt')
def test_molecule_opt():
mol = Molecule(name='H2', smiles='[H][H]')
# Set the orca path to something that exists
orca.path = here
mol.optimise(method=orca)
assert mol.energy == -1.160687049941
assert mol.n_atoms == 2
opt_coords = mol.get_coordinates()
# H2 bond length ~ 0.767 Å at PBE/def2-SVP
assert 0.766 < np.linalg.norm(opt_coords[0] - opt_coords[1]) < 0.768
def test_gradients():
os.chdir(os.path.join(here, 'data', 'xtb'))
h2 = Molecule(name='h2', atoms=[Atom('H'), Atom('H', x=1.0)])
h2.single_point(method)
delta_r = 1E-5
h2_disp = Molecule(name='h2_disp',
atoms=[Atom('H'), Atom('H', x=1.0 + delta_r)])
h2_disp.single_point(method)
delta_energy = h2_disp.energy - h2.energy # Ha
grad = delta_energy / delta_r # Ha A^-1
calc = Calculation(name='h2_grad',
molecule=h2,
method=method,
keywords=method.keywords.grad)
calc.run()
diff = calc.get_gradients()[1, 0] - grad # Ha A^-1
# Difference between the absolute and finite difference approximation
assert np.abs(diff) < 1E-5
# Older xtb version
with open('gradient', 'w') as gradient_file:
print(
'$gradient\n'
'cycle = 1 SCF energy = -4.17404780397 |dE/dxyz| = 0.027866\n'
'3.63797523123375 -1.13138130908142 -0.00032759661848 C \n'
'5.72449332438353 -1.13197561185651 0.00028950521969 H \n'
' 2.94133258016711 0.22776472016180 -1.42078243039077 H \n'
' 2.94175598539510 -0.58111835182372 1.88747566982948 H \n'
'2.94180792167968 -3.04156357656436 -0.46665514803992 H \n'
'-1.7221823521705E-05 7.9930724499610E-05 -1.1737079840097E-04\n'
' 1.4116296505865E-02 -4.0359524399270E-05 3.9719638516747E-05\n'
'-4.7199424681741E-03 9.0086220034949E-03 -9.4114548523723E-03\n'
'-4.6956970257351E-03 3.6356853660431E-03 1.2558467871909E-02\n'
' -4.6834351884340E-03 -1.2683878569638E-02 -3.0693618596526E-03\n'
'$end',
file=gradient_file)
calc = Calculation(name='methane',
molecule=Molecule(name='methane', smiles='C'),
method=method,
keywords=method.keywords.grad)
gradients = method.get_gradients(calc)
assert gradients.shape == (5, 3)
assert np.abs(gradients[0, 0]) < 1E-3
os.chdir(here)
def test_fix_angle_error():
os.chdir(os.path.join(here, 'data', 'g09'))
mol = Molecule(smiles='CC/C=C/CO')
mol.name = 'molecule'
calc = Calculation(name='angle_fail', molecule=mol, method=method,
keywords=opt_keywords)
calc.run()
assert os.path.exists('angle_fail_g09_cartesian.com') is True
assert os.path.exists('angle_fail_g09_internal.com') is True
assert calc.output.filename == 'angle_fail_g09_internal.log'
assert calc.terminated_normally()
def test_multiple_possibilities():
r1 = Molecule(name='h_dot', smiles='[H]')
r2 = Molecule(name='methane', smiles='C')
p1 = Molecule(name='h2', smiles='[HH]')
p2 = Molecule(name='ch3_dot', smiles='[CH3]')
reac = ReactantComplex(r1, r2)
reac.print_xyz_file()
rearrs = br.get_bond_rearrangs(reac, ProductComplex(p1, p2),
name='H_subst')
os.remove('H_subst_bond_rearrangs.txt')
# All H abstractions are the same
assert len(rearrs) == 1
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_constrained_opt():
os.chdir(os.path.join(here, 'data'))
mol = Molecule(name='h3',
mult=2,
charge=0,
atoms=[
Atom('H', 0.0, 0.0, 0.0),
Atom('H', 0.7, 0.0, 0.0),
Atom('H', 1.7, 0.0, 0.0)
])
Config.XTB.path = here # A path that exists
ts_guess = get_ts_guess_constrained_opt(
reactant=ReactantComplex(mol),
distance_consts={(0, 1): 1.0},
method=orca,
keywords=Config.ORCA.keywords.low_opt,
name='template_ts_guess',
product=ProductComplex(mol))
assert ts_guess.n_atoms == 3
os.remove('xcontrol_template_ts_guess_constrained_opt_ll_xtb')
os.remove('template_ts_guess_constrained_opt_ll_xtb.xyz')
os.remove('template_ts_guess_constrained_opt_orca.inp')
os.chdir(here)
def test_psi4_opt_calculation():
methylchloride = Molecule(name='CH3Cl',
smiles='[H]C([H])(Cl)[H]',
solvent_name='water')
calc = Calculation(name='opt',
molecule=methylchloride,
method=method,
keywords=opt_keywords)
calc.run()
assert os.path.exists('opt_psi4.inp') is True
assert os.path.exists('opt_orca.out') is True
assert len(calc.get_final_atoms()) == 5
assert -499.735 < calc.get_energy() < -499.730
assert calc.output.exists()
assert calc.output.file_lines is not None
assert calc.get_imaginary_freqs() == []
assert calc.input.filename == 'opt_psi4.inp'
assert calc.output.filename == 'opt_psi4.out'
assert calc.terminated_normally()
assert calc.optimisation_converged()
calc = Calculation(name='opt',
molecule=methylchloride,
method=method,
keywords=opt_keywords)
# If the calculation is not run with calc.run() then there should be no
# input and the calc should raise that there is no input
with pytest.raises(NoInputError):
execute_calc(calc)
def test_calc_bad_mol():
class Mol:
pass
mol = Mol()
with pytest.raises(AssertionError):
Calculation(name='bad_mol_object',
molecule=mol,
method=method,
keywords=opt_keywords)
mol.atoms = None
mol.mult = 1
mol.n_atoms = 0
mol.charge = 0
mol.solvent = None
with pytest.raises(NoInputError):
Calculation(name='no_atoms_mol',
molecule=mol,
method=method,
keywords=opt_keywords)
mol = Molecule(name='methane', smiles='C')
mol.solvent = Solvent(name='xx', smiles='X', aliases=['X'])
with pytest.raises(SolventUnavailable):
Calculation(name='no_atoms_mol',
molecule=mol,
method=method,
keywords=opt_keywords)
def test_solvation():
methane = Molecule(name='solvated_methane', smiles='C',
solvent_name='water')
with pytest.raises(UnsuppportedCalculationInput):
# Should raise on unsupported calculation type
method.implicit_solvation_type = 'xxx'
calc = Calculation(name='broken_solvation', molecule=methane,
method=method, keywords=sp_keywords)
calc.run()
method.implicit_solvation_type = 'CPCM'
calc = Calculation(name='methane_cpcm', molecule=methane,
method=method, keywords=sp_keywords)
calc.generate_input()
assert any('cpcm' in line.lower() for line in open('methane_cpcm_orca.inp', 'r'))
os.remove('methane_cpcm_orca.inp')
method.implicit_solvation_type = 'SMD'
calc = Calculation(name='methane_smd', molecule=methane,
method=method, keywords=sp_keywords)
calc.generate_input()
assert any('smd' in line.lower() for line in open('methane_smd_orca.inp', 'r'))
os.remove('methane_smd_orca.inp')
def test_graph_without_active_edges():
mol = Molecule(name='H2', atoms=[Atom('H'), Atom('H', x=0.7)])
mol.graph.edges[(0, 1)]['active'] = True
graph = mol_graphs.get_graph_no_active_edges(mol.graph)
# Should now have no edges if the one bond was defined as active
assert graph.number_of_edges() == 0
def test_chiral_rotation(tmpdir):
os.chdir(tmpdir)
chiral_ethane = Molecule(name='chiral_ethane',
charge=0,
mult=1,
atoms=[
Atom('C', -0.26307, 0.59858, -0.07141),
Atom('C', 1.26597, 0.60740, -0.09729),
Atom('Cl', -0.91282, 2.25811, 0.01409),
Atom('F', -0.72365, -0.12709, 1.01313),
Atom('H', -0.64392, 0.13084, -1.00380),
Atom('Cl', 1.93888, 1.31880, 1.39553),
Atom('H', 1.61975, 1.19877, -0.96823),
Atom('Br', 1.94229, -1.20011, -0.28203)
])
chiral_ethane.graph.nodes[0]['stereo'] = True
chiral_ethane.graph.nodes[1]['stereo'] = True
atoms = conf_gen.get_simanl_atoms(chiral_ethane)
regen = Molecule(name='regenerated_ethane', charge=0, mult=1, atoms=atoms)
regen_coords = regen.coordinates
coords = chiral_ethane.coordinates
# Atom indexes of the C(C)(Cl)(F)(H) chiral centre
ccclfh = [0, 1, 2, 3, 4]
# Atom indexes of the C(C)(Cl)(Br)(H) chiral centre
ccclbrh = [1, 0, 5, 7, 6]
for centre_idxs in [ccclfh, ccclbrh]:
# Ensure the fragmented centres map almost identically
# if calc_rmsd(template_coords=coords[centre_idxs], coords_to_
# fit=regen_coords[centre_idxs]) > 0.5:
# chiral_ethane.print_xyz_file(filename=os.path.join(here,
# 'chiral_ethane.xyz'))
# regen.print_xyz_file(filename=os.path.join(here, 'regen.xyz'))
# RMSD on the 5 atoms should be < 0.5 Å
assert calc_rmsd(coords1=coords[centre_idxs],
coords2=regen_coords[centre_idxs]) < 0.5
os.chdir(here)
def test_nci_complex():
water = Molecule(name='water', smiles='O')
f = Molecule(name='formaldehyde', smiles='C=O')
nci_complex = NCIComplex(f, water)
assert nci_complex.n_atoms == 7
# Set so the number of conformers doesn't explode
Config.num_complex_sphere_points = 6
Config.num_complex_random_rotations = 4
nci_complex._generate_conformers()
assert len(nci_complex.conformers) == 24
for conformer in nci_complex.conformers:
# conformer.print_xyz_file()
assert geom.are_coords_reasonable(coords=conformer.get_coordinates())
def test_basic_attributes():
with pytest.raises(NoAtomsInMolecule):
Molecule(atoms=[])
Molecule()
methane = Molecule(name='methane', smiles='C')
assert methane.name == 'methane'
assert methane.smiles == 'C'
assert methane.energy is None
assert methane.n_atoms == 5
assert methane.graph.number_of_edges() == 4
assert methane.graph.number_of_nodes() == methane.n_atoms
assert methane.conformers is None
assert methane.charge == 0
assert methane.mult == 1
assert isinstance(methane.rdkit_mol_obj, Mol)
def test_find_lowest_energy_conformer():
os.chdir(os.path.join(here, 'data'))
# Spoof XTB availability
xtb.path = here
xtb.available = True
propane = Molecule(name='propane', smiles='CCC')
propane.find_lowest_energy_conformer(lmethod=xtb)
assert len(propane.conformers) > 0
# Finding low energy conformers should set the energy of propane
assert propane.energy is not None
assert propane.atoms is not None
os.chdir(here)