def test_find_tss():
Config.num_conformers = 1
# Spoof ORCA install
Config.ORCA.path = here
# Don't run the calculation without a working XTB install
if shutil.which('xtb') is None or not shutil.which('xtb').endswith('xtb'):
return
if os.path.exists('/dev/shm'):
Config.ll_tmp_dir = '/dev/shm'
Config.XTB.path = shutil.which('xtb')
Config.ORCA.implicit_solvation_type = cpcm
Config.make_ts_template = False
Config.num_complex_sphere_points = 2
Config.num_complex_random_rotations = 1
# SN2 example
flouride = Reactant(name='F-', smiles='[F-]')
methyl_chloride = Reactant(name='CH3Cl', smiles='ClC')
chloride = Product(name='Cl-', smiles='[Cl-]')
methyl_flouride = Product(name='CH3F', smiles='CF')
reaction = Reaction(flouride,
methyl_chloride,
chloride,
methyl_flouride,
name='sn2',
solvent_name='water')
# Will work in data/locate_ts/transition_states
reaction.locate_transition_state()
assert reaction.ts is not None
os.chdir('transition_states')
assert reaction.ts.is_true_ts()
os.chdir('..')
reaction.ts.save_ts_template(folder_path=os.getcwd())
assert os.path.exists('template0.txt')
# There should now be a saved template
templates = get_ts_templates(folder_path=os.getcwd())
assert len(templates) == 1
template = templates[0]
assert template.solvent.name == 'water'
assert template.mult == 1
assert template.charge == -1
assert template.graph.number_of_nodes() == 6
# Reset the configuration
Config.ll_tmp_dir = None
def test_isomorphic_reactant_product():
r_water = Reactant(name='h2o', smiles='O')
r_methane = Reactant(name='methane', smiles='C')
p_water = Product(name='h2o', smiles='O')
p_methane = Product(name='methane', smiles='C')
# Reaction where the reactant and product complexes are isomorphic
# should return no TS
reaction = Reaction(r_water, r_methane, p_water, p_methane)
reaction.locate_transition_state()
assert reaction.ts is None
def test_find_tss():
os.chdir(os.path.join(here, 'data', 'locate_ts'))
Config.num_conformers = 1
# Spoof ORCA install
Config.ORCA.path = here
# Don't run the calculation without a working XTB install
if shutil.which('xtb') is None or not shutil.which('xtb').endswith('xtb'):
return
Config.XTB.path = shutil.which('xtb')
Config.ORCA.implicit_solvation_type = 'cpcm'
Config.make_ts_template = False
Config.num_complex_sphere_points = 2
Config.num_complex_random_rotations = 1
# SN2 example
flouride = Reactant(name='F-', smiles='[F-]')
methyl_chloride = Reactant(name='CH3Cl', smiles='ClC')
chloride = Product(name='Cl-', smiles='[Cl-]')
methyl_flouride = Product(name='CH3F', smiles='CF')
reaction = Reaction(flouride,
methyl_chloride,
chloride,
methyl_flouride,
name='sn2',
solvent_name='water')
# Will work in data/locate_ts/transition_states
reaction.locate_transition_state()
assert reaction.ts is not None
os.chdir(os.path.join(here, 'data', 'locate_ts', 'transition_states'))
for filename in os.listdir(os.getcwd()):
if filename.endswith(('.inp', '.png')):
os.remove(filename)
assert reaction.ts.is_true_ts()
reaction.ts.save_ts_template(folder_path=os.getcwd())
assert os.path.exists('template0.obj')
# There should now be a saved template
templates = get_ts_templates(folder_path=os.getcwd())
assert len(templates) == 1
template = templates[0]
assert template.solvent.name == 'water'
assert template.mult == 1
assert template.charge == -1
assert template.graph.number_of_nodes() == 6
# Tidy the generated files
os.remove('template0.obj')
os.chdir(here)