def coordinates_validator(cls, value, values):
"""Species.coordinates validator"""
label = f' for species "{values["label"]}"' if 'label' in values and values['label'] is not None else ''
converter.add_common_isotopes_to_coords(value)
is_valid, err = common.is_valid_coordinates(value)
if not is_valid:
raise ValueError(f'The following coordinates dictionary{label} is invalid:\n{value}\nReason:\n{err}')
return value
def irc_trajectories_validator(cls, value, values):
"""Species.irc_trajectories validator"""
label = f' for species "{values["label"]}"' if 'label' in values and values['label'] is not None else ''
if 'is_ts' in values and values['is_ts'] and value is None:
raise ValueError(f'IRC trajectories must be given{label} if the species is a TS.')
if 'is_ts' in values and not values['is_ts'] and value is not None:
raise ValueError(f'IRC trajectories were given{label}, but the species is not defined as a TS.\n'
f'(Set the "is_ts" attribute to True if the species is meant to be a TS.)')
if value is not None:
for i, traj in enumerate(value):
for j, frame in enumerate(traj):
converter.add_common_isotopes_to_coords(frame)
is_valid, err = common.is_valid_coordinates(frame)
if not is_valid:
raise ValueError(f'Frame {j} in IRC trajectory {i}{label} is invalid:\n'
f'{frame}\nReason:\n{err}')
return value
def trajectory_validator(cls, value, values):
"""TorsionsBase.trajectory validator"""
label = f' for species "{values["label"]}"' if 'label' in values and values['label'] is not None else ''
trajectory_dimension = 0
entry = value
while not isinstance(entry, dict):
if isinstance(entry, (list, tuple)):
entry = entry[0]
trajectory_dimension += 1
elif isinstance(entry, dict):
is_valid, err = common.is_valid_coordinates(entry)
if not is_valid:
raise ValueError(f"Not all coordinates in the torsion trajectory{label} are valid."
f"Reason:\n{err}\nGot:\n{entry}.")
else:
raise ValueError(f"Lowest level trajectory entries in a torsion must be coordinates "
f"dictionaries, got {entry}{label} which is a {type(entry)}.")
if 'dimension' in values and values['dimension'] and trajectory_dimension != values['dimension']:
raise ValueError(f"Got a {trajectory_dimension}D trajectory attribute for a declared dimension "
f"of {values['dimension']}{label}:\n{value}")
return value
def conformers_validator(cls, value, values):
"""Species.conformers validator"""
label = f' for species "{values["label"]}"' if 'label' in values and values['label'] is not None else ''
if 'torsions' in values and values['torsions']:
raise ValueError(f'Either torsions or conformers must be given, got both{label}.')
for conformer in value:
is_valid, err = common.is_valid_coordinates(conformer, allowed_keys=['energy', 'degeneracy'])
if not is_valid:
raise ValueError(f"Not all conformers{label} are valid. Reason:\n{err}\n"
f"Got:\n{conformer}\nin:\n{value}.")
if 'energy' not in conformer:
raise ValueError(f'A conformer entry in the conformers argument{label} must have an "energy" key.')
if not isinstance(conformer['energy'], float):
raise ValueError(f"A conformer energy must be a float, got {conformer['energy']} which is a "
f"{type(conformer['energy'])}{label}.")
if 'degeneracy' not in conformer:
conformer['degeneracy'] = 1
if conformer['degeneracy'] % 1:
# The degeneracy is converted to float, cannot check isinstance for int
raise ValueError(f"A conformer degeneracy must be a float, got {conformer['degeneracy']} which is a "
f"{type(conformer['degeneracy'])}{label}.")
return value
def test_is_valid_coordinates():
"""Test whether a coordinates dictionary is valid"""
assert common.is_valid_coordinates(ch4_coords)[0]
assert not common.is_valid_coordinates(n3h5_xyz)[0]
converter.add_common_isotopes_to_coords(n3h5_xyz)
assert common.is_valid_coordinates(n3h5_xyz)[0]