def test_ts_templates_find():
templates = get_ts_templates(folder_path='/a/path/that/doesnt/exist')
assert len(templates) == 0
# Create a incorrectly formatted file, i.e. blank
open('wrong_template.txt', 'w').close()
templates = get_ts_templates(folder_path=os.getcwd())
assert len(templates) == 0
os.remove('wrong_template.txt')
def get_template_ts_guess(reactant, product, bond_rearrangement, name, method, dist_thresh=4.0):
"""Get a transition state guess object by searching though the stored TS
templates
Arguments:
reactant (autode.complex.ReactantComplex):
bond_rearrangement (autode.bond_rearrangement.BondRearrangement):
product (autode.complex.ProductComplex):
method (autode.wrappers.base.ElectronicStructureMethod):
name (str):
keywords (list(str)): Keywords to use for the ElectronicStructureMethod
Keyword Arguments:
dist_thresh (float): distance above which a constrained optimisation
probably won't work due to the initial geometry
being too far away from the ideal (default: {4.0})
Returns:
TSGuess object: ts guess object
"""
logger.info('Getting TS guess from stored TS template')
active_bonds_and_dists_ts = {}
# This will add edges so don't modify in place
mol_graph = get_truncated_active_mol_graph(graph=reactant.graph,
active_bonds=bond_rearrangement.all)
ts_guess_templates = get_ts_templates()
for ts_template in ts_guess_templates:
if not template_matches(reactant=reactant, ts_template=ts_template,
truncated_graph=mol_graph):
continue
# Get the mapping from the matching template
mapping = get_mapping_ts_template(larger_graph=mol_graph,
smaller_graph=ts_template.graph)
for active_bond in bond_rearrangement.all:
i, j = active_bond
try:
active_bonds_and_dists_ts[active_bond] = ts_template.graph.edges[mapping[i],
mapping[j]]['distance']
except KeyError:
logger.warning(f'Couldn\'t find a mapping for bond {i}-{j}')
if len(active_bonds_and_dists_ts) == len(bond_rearrangement.all):
logger.info('Found a TS guess from a template')
if any([reactant.get_distance(*bond) > dist_thresh for bond in bond_rearrangement.all]):
logger.info(f'TS template has => 1 active bond distance larger than {dist_thresh}. Passing')
pass
else:
return get_ts_guess_constrained_opt(reactant, method=method, keywords=method.keywords.opt, name=name,
distance_consts=active_bonds_and_dists_ts, product=product)
logger.info('Could not find a TS guess from a template')
return None
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 has_matching_ts_templates(reactant, bond_rearr):
"""
See if there are any templates suitable to get a TS guess from a template
Arguments:
reactant (autode.complex.ReactantComplex):
bond_rearr (autode.bond_rearrangement.BondRearrangement):
Returns:
bool:
"""
mol_graph = get_truncated_active_mol_graph(graph=reactant.graph,
active_bonds=bond_rearr.all)
ts_guess_templates = get_ts_templates()
for ts_template in ts_guess_templates:
if template_matches(reactant=reactant, ts_template=ts_template,
truncated_graph=mol_graph):
return True
return False
def test_ts_template():
# Spoof XTB install
Config.XTB.path = here
Config.ts_template_folder_path = os.path.join(here, 'data', 'ts_guess')
bond_rearr = BondRearrangement(breaking_bonds=[(2, 1)],
forming_bonds=[(0, 2)])
reac_shift = reac_complex.copy()
reac_shift.set_atoms(atoms=[
Atom('F', -3.0587, -0.8998, -0.2180),
Atom('Cl', 0.3842, 0.86572, -1.65507),
Atom('C', -1.3741, -0.0391, -0.9719),
Atom('H', -1.9151, -0.0163, -1.9121),
Atom('H', -1.6295, 0.6929, -0.2173),
Atom('H', -0.9389, -0.9786, -0.6534)
])
reac_shift.print_xyz_file()
templates = get_ts_templates()
assert len(templates) == 1
assert templates[0].graph.number_of_nodes() == 6
tsg_template = get_template_ts_guess(reac_shift,
product_complex,
name='template',
bond_rearr=bond_rearr,
method=XTB(),
dist_thresh=4.0)
# Reset the folder path to the default
Config.ts_template_folder_path = None
assert tsg_template is not None
def test_ts_templates():
templates = get_ts_templates(folder_path='/a/path/that/doesnt/exist')
assert len(templates) == 0
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)