def test_grid_multi_conformers():
"Test generating grid multiconformer"
smiles = 'HC(H)(C(H)(H)OH)OH'
mapped_smiles = '[H:5][C:1]([H:6])([C:2]([H:7])([H:8])[O:4][H:10])[O:3][H:9]'
mol = cmiles.utils.load_molecule(smiles)
mapped_mol = cmiles.utils.load_molecule(mapped_smiles)
dihedrals = [(2, 0, 1, 3), (0, 1, 3, 9), (1, 0, 2, 8)]
intervals = [60, 60, 60]
with pytest.raises(ValueError):
chemi.generate_grid_conformers(mol, dihedrals, intervals)
mult_conf = chemi.generate_grid_conformers(mapped_mol, dihedrals,
intervals)
def generate_grid_conformers():
mol = chemi.smiles_to_oemol('CCCC')
dihedrals = [(0, 2, 3, 1), (3, 2, 0, 4)]
intervals = [30, 90]
grid = chemi.generate_grid_conformers(mol,
dihedrals=dihedrals,
intervals=intervals)
assert grid.GetMaxConfIdx() == 48
def teat_qcschema_to_xyz():
smiles = 'HC(H)(C(H)(H)OH)OH'
mapped_smiles = '[H:5][C:1]([H:6])([C:2]([H:7])([H:8])[O:4][H:10])[O:3][H:9]'
mol = cmiles.utils.load_molecule(smiles)
mapped_mol = cmiles.utils.load_molecule(mapped_smiles)
dihedrals = [(2, 0, 1, 3), (0, 1, 3, 9), (1, 0, 2, 8)]
intervals = [90, 90, 90]
mult_conf = chemi.generate_grid_conformers(mapped_mol, dihedrals,
intervals)
# generate list of qcschema molecules
qcschema_molecules = [
cmiles.utils.mol_to_map_ordered_qcschema(conf, mol_id)
for conf in multi_conf.GetConfs()
]
def generate_torsiondrive_input(self, frag, json_filename=None):
"""
Generate input for torsiondrive QCFractal portal
Parameters
----------
fragment_dict: dict
dictionary with fragment identifiers and provenance
workflow_id: str
workflow to use for options
options: dict, optional, default None
Keyword options. If None will use options defined in workflow
json_filename: str, optional, default None
If given will write jobs to json file
Returns
-------
torsiondrive_inputs: dictionary defining the molecule and torsiondrive job options.
"""
options = self.off_workflow.get_options('torsiondrive_input')
provenance = _get_provenance(workflow_id=self.workflow_id,
routine='torsiondrive_input')
frag['provenance']['routine']['torsiondrive_input'] = provenance[
'routine']['torsiondrive_input']
provenance = frag['provenance']
mol_id = frag['identifiers']
mapped_smiles = mol_id[
'canonical_isomeric_explicit_hydrogen_mapped_smiles']
mapped_mol = chemi.smiles_to_oemol(mapped_smiles)
needed_torsions = torsions.find_torsions(mapped_mol,
options['restricted'])
if options['multiple_confs']:
# Generate grid of multiple conformers
dihedrals = []
for torsion_type in needed_torsions:
for tor in needed_torsions[torsion_type]:
dihedrals.append(needed_torsions[torsion_type][tor])
intervals = options['initial_conf_grid_resolution']
if not isinstance(intervals, list):
intervals = [intervals] * len(dihedrals)
try:
conformers = chemi.generate_grid_conformers(
mapped_mol, dihedrals=dihedrals, intervals=intervals)
except RuntimeError:
utils.logger().warning(
"{} does not have coordinates. This can happen for several reasons related to Omega. "
"{} will not be included in fragments dictionary".format(
mol_id['canonical_isomeric_smiles'],
mol_id['canonical_isomeric_smiles']))
return False
chemi.resolve_clashes(conformers)
qcschema_molecules = [
mol_to_map_ordered_qcschema(conf, mol_id)
for conf in conformers.GetConfs()
]
try:
conformer = chemi.generate_conformers(mapped_mol, max_confs=1)
# resolve clashes
qcschema_molecule = mol_to_map_ordered_qcschema(conformer, mol_id)
except RuntimeError:
utils.logger().warning(
"{} does not have coordinates. This can happen for several reasons related to Omega. "
"{} will not be included in fragments dictionary".format(
mol_id['canonical_isomeric_smiles'],
mol_id['canonical_isomeric_smiles']))
return False
identifier = mol_id[
'canonical_isomeric_explicit_hydrogen_mapped_smiles']
torsiondrive_inputs = {
identifier: {
'torsiondrive_input': {},
'provenance': provenance
}
}
restricted_torsions = needed_torsions.pop('restricted')
optimization_jobs = torsions.generate_constraint_opt_input(
qcschema_molecule, restricted_torsions,
**options['restricted_optimization_options'])
torsiondrive_inputs[identifier][
'optimization_input'] = optimization_jobs
torsiondrive_jobs = torsions.define_torsiondrive_jobs(
needed_torsions, **options['torsiondrive_options'])
if options['multiple_confs']:
qcschema_molecule = qcschema_molecules
# Currently, all jobs are started from same initial conformation
# ToDo Start later job from optimized conformers from last job
for i, job in enumerate(torsiondrive_jobs):
torsiondrive_input = {'type': 'torsiondrive_input'}
torsiondrive_input['initial_molecule'] = qcschema_molecule
#torsiondrive_input['initial_molecule']['identifiers'] = mol_id
torsiondrive_input['dihedrals'] = torsiondrive_jobs[job][
'dihedrals']
torsiondrive_input['grid_spacing'] = torsiondrive_jobs[job][
'grid_spacing']
job_name = ''
for i, torsion in enumerate(torsiondrive_input['dihedrals']):
if i > 0:
job_name += '_{}'.format(torsion)
else:
job_name += '{}'.format(torsion)
torsiondrive_inputs[identifier]['torsiondrive_input'][
job_name] = torsiondrive_input
if json_filename:
with open(json_filename, 'w') as f:
json.dump(torsiondrive_inputs, f, indent=2, sort_keys=True)
return torsiondrive_inputs