def test_to_and_from_dict(self):
mm = MoleculeMatcher(tolerance=0.5,
mapper=InchiMolAtomMapper(angle_tolerance=50.0))
d = mm.as_dict()
mm2 = MoleculeMatcher.from_dict(d)
self.assertEqual(d, mm2.as_dict())
mm = MoleculeMatcher(tolerance=0.5, mapper=IsomorphismMolAtomMapper())
d = mm.as_dict()
mm2 = MoleculeMatcher.from_dict(d)
self.assertEqual(d, mm2.as_dict())
def test_fit(self):
self.fit_with_mapper(IsomorphismMolAtomMapper())
self.fit_with_mapper(InchiMolAtomMapper())
def __init__(self, redundancy_parameters, geometry):
'''
Makes a RedundancyGuard, and sets default parameter values if
necessary.
TODO: currently using pymatgen's structure matcher for comparing bulk
and sheet structures, both pymatgen's structure matcher and
molecule matcher for comparing wires, and only the molecule matcher
for clusters. The sheet and wire cases aren't ideal, since the
structure matcher assumes periodicity in all three dimensions, and
the molecule matcher assumes no periodicity.
Args:
redundancy parameters: a dictionary of parameters
geometry: the Geometry object
'''
# defaults
#
# lattice length tolerance, in fractional coordinates
self.default_lattice_length_tol = 0.05
# lattice angle tolerance, in degrees
self.default_lattice_angle_tol = 2
# site tolerance, in fraction of average free length per atom
self.default_site_tol = 0.1
# whether to transform to primitive cells before comparing
self.default_use_primitive_cell = True
# whether to check if structures are equal to supercells of each other
self.default_attempt_supercell = True
# RMSD tolerance for comparing clusters
self.default_rmsd_tol = 0.1
# the epa difference interval
self.default_epa_diff = 0.0
# set to defaults
if redundancy_parameters in (None, 'default'):
self.set_all_to_defaults()
# parse the parameters, and set to defaults if necessary
else:
# lattice length tolerance
if 'lattice_length_tol' not in redundancy_parameters:
self.lattice_length_tol = self.default_lattice_length_tol
elif redundancy_parameters['lattice_length_tol'] in (None,
'default'):
self.lattice_length_tol = self.default_lattice_length_tol
else:
self.lattice_length_tol = redundancy_parameters[
'lattice_length_tol']
# lattice angle tolerance
if 'lattice_angle_tol' not in redundancy_parameters:
self.lattice_angle_tol = self.default_lattice_angle_tol
elif redundancy_parameters['lattice_angle_tol'] in (None,
'default'):
self.lattice_angle_tol = self.default_lattice_angle_tol
else:
self.lattice_angle_tol = redundancy_parameters[
'lattice_angle_tol']
# site tolerance
if 'site_tol' not in redundancy_parameters:
self.site_tol = self.default_site_tol
elif redundancy_parameters['site_tol'] in (None, 'default'):
self.site_tol = self.default_site_tol
else:
self.site_tol = redundancy_parameters['site_tol']
# whether to use primitive cells
if 'use_primitive_cell' not in redundancy_parameters:
self.use_primitive_cell = self.default_use_primitive_cell
elif redundancy_parameters['use_primitive_cell'] in (None,
'default'):
self.use_primitive_cell = self.default_use_primitive_cell
else:
self.use_primitive_cell = redundancy_parameters[
'use_primitive_cell']
# whether to try matching supercells
if 'attempt_supercell' not in redundancy_parameters:
self.attempt_supercell = self.default_attempt_supercell
elif redundancy_parameters['attempt_supercell'] in (None,
'default'):
self.attempt_supercell = self.default_attempt_supercell
else:
self.attempt_supercell = redundancy_parameters[
'attempt_supercell']
# RMSD tolerance
if 'rmsd_tol' not in redundancy_parameters:
self.rmsd_tol = self.default_rmsd_tol
elif redundancy_parameters['rmsd_tol'] in (None, 'default'):
self.rmsd_tol = self.default_rmsd_tol
else:
self.rmsd_tol = redundancy_parameters['rmsd_tol']
# epa difference
if 'epa_diff' not in redundancy_parameters:
self.epa_diff = self.default_epa_diff
elif redundancy_parameters['epa_diff'] in (None, 'default'):
self.epa_diff = self.default_epa_diff
else:
self.epa_diff = redundancy_parameters['epa_diff']
# make the StructureMatcher object
#
# the first False is to prevent the matcher from scaling the volumes,
# and the second False is to prevent subset matching
self.structure_matcher = StructureMatcher(
self.lattice_length_tol, self.site_tol, self.lattice_angle_tol,
self.use_primitive_cell, False, self.attempt_supercell, False,
ElementComparator())
# make the MoleculeMatcher object
if geometry.shape == 'cluster' or geometry.shape == 'wire':
iso_mol_atom_mapper = IsomorphismMolAtomMapper()
self.molecule_matcher = MoleculeMatcher(self.rmsd_tol,
iso_mol_atom_mapper)
ob.obErrorLog.SetOutputLevel(0) # to suppress openbabel warnings