def fit_with_mapper(self, mapper):
coords = [[0.000000, 0.000000, 0.000000],
[0.000000, 0.000000, 1.089000],
[1.026719, 0.000000, -0.363000],
[-0.513360, -0.889165, -0.363000],
[-0.513360, 0.889165, -0.363000]]
mol1 = Molecule(["C", "H", "H", "H", "H"], coords)
op = SymmOp.from_origin_axis_angle([0, 0, 0], [0.1, 0.2, 0.3], 60)
rotcoords = [op.operate(c) for c in coords]
mol2 = Molecule(["C", "H", "H", "H", "H"], rotcoords)
mm = MoleculeMatcher(mapper=mapper)
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "benzene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "benzene2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "benzene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t2.xyz"))
self.assertFalse(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "c1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "c2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t4.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "j1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "j2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "ethene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "ethene2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "toluene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "toluene2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "cyclohexane1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "cyclohexane2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "oxygen1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "oxygen2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mm = MoleculeMatcher(tolerance=0.001, mapper=mapper)
mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t4.xyz"))
self.assertFalse(mm.fit(mol1, mol2))
def test_thiane_ethynyl(self):
mm = MoleculeMatcher(tolerance=0.05, mapper=InchiMolAtomMapper())
mol1 = Molecule.from_file(os.path.join(test_dir, "thiane_ethynyl1.sdf"))
mol2 = Molecule.from_file(os.path.join(test_dir, "thiane_ethynyl2.sdf"))
self.assertFalse(mm.fit(mol1, mol2))
def test_cdi_23(self):
mm = MoleculeMatcher(tolerance=0.05, mapper=InchiMolAtomMapper())
mol1 = Molecule.from_file(os.path.join(test_dir, "cdi_23_1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "cdi_23_2.xyz"))
self.assertFalse(mm.fit(mol1, mol2))
def test_thiane(self):
mm = MoleculeMatcher(tolerance=0.05, mapper=InchiMolAtomMapper())
mol1 = read_mol(os.path.join(test_dir, "thiane1.sdf"))
mol2 = read_mol(os.path.join(test_dir, "thiane2.sdf"))
self.assertFalse(mm.fit(mol1, mol2))
def test_strange_inchi(self):
mm = MoleculeMatcher(tolerance=0.05, mapper=InchiMolAtomMapper())
mol1 = Molecule.from_file(os.path.join(test_dir, "k1.sdf"))
mol2 = Molecule.from_file(os.path.join(test_dir, "k2.sdf"))
self.assertTrue(mm.fit(mol1, mol2))
def test_strange_inchi(self):
mm = MoleculeMatcher(tolerance=0.05, mapper=InchiMolAtomMapper())
mol1 = Molecule.from_file(os.path.join(test_dir, "k1.sdf"))
mol2 = Molecule.from_file(os.path.join(test_dir, "k2.sdf"))
self.assertTrue(mm.fit(mol1, mol2))
def fit_with_mapper(self, mapper):
coords = [[0.000000, 0.000000, 0.000000],
[0.000000, 0.000000, 1.089000],
[1.026719, 0.000000, -0.363000],
[-0.513360, -0.889165, -0.363000],
[-0.513360, 0.889165, -0.363000]]
mol1 = Molecule(["C", "H", "H", "H", "H"], coords)
op = SymmOp.from_origin_axis_angle([0, 0, 0], [0.1, 0.2, 0.3], 60)
rotcoords = [op.operate(c) for c in coords]
mol2 = Molecule(["C", "H", "H", "H", "H"], rotcoords)
mm = MoleculeMatcher(mapper=mapper)
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "benzene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "benzene2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "benzene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t2.xyz"))
self.assertFalse(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "c1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "c2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t4.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "j1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "j2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "ethene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "ethene2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "toluene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "toluene2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "cyclohexane1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "cyclohexane2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mol1 = Molecule.from_file(os.path.join(test_dir, "oxygen1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "oxygen2.xyz"))
self.assertTrue(mm.fit(mol1, mol2))
mm = MoleculeMatcher(tolerance=0.001, mapper=mapper)
mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t4.xyz"))
self.assertFalse(mm.fit(mol1, mol2))
def test_cdi_23(self):
mm = MoleculeMatcher(tolerance=0.05, mapper=InchiMolAtomMapper())
mol1 = Molecule.from_file(os.path.join(test_dir, "cdi_23_1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "cdi_23_2.xyz"))
self.assertFalse(mm.fit(mol1, mol2))
def test_thiane(self):
mm = MoleculeMatcher(tolerance=0.05, mapper=InchiMolAtomMapper())
mol1 = Molecule.from_file(os.path.join(test_dir, "thiane1.sdf"))
mol2 = Molecule.from_file(os.path.join(test_dir, "thiane2.sdf"))
self.assertFalse(mm.fit(mol1, mol2))
class RedundancyGuard(object):
'''
A RedundancyGuard object is used to check if an Organism is redundant with
other organisms already seen by the algorithm.
'''
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
def set_all_to_defaults(self):
'''
Sets all the redundancy parameters to default values.
'''
self.lattice_length_tol = self.default_lattice_length_tol
self.lattice_angle_tol = self.default_lattice_angle_tol
self.site_tol = self.default_site_tol
self.use_primitive_cell = self.default_use_primitive_cell
self.attempt_supercell = self.default_attempt_supercell
self.rmsd_tol = self.default_rmsd_tol
self.epa_diff = self.default_epa_diff
def check_redundancy(self, new_organism, orgs_list, geometry):
'''
Checks for redundancy, both structural and if specified, epa (d-value).
Returns the organism with which new_organism is redundant, or None if
no redundancy.
Args:
new_organism: the Organism to check for redundancy
orgs_list: the list containing all Organisms to check against
geometry: the Geometry of the search
'''
# if new_organism isn't relaxed, then just check structures
if new_organism.epa is None:
for organism in orgs_list:
if new_organism.id != organism.id: # just in case
# check if their structures match
if self.check_structures(new_organism, organism, geometry):
print('Organism {} failed structural redundancy - '
'looks like organism {} '.format(
new_organism.id, organism.id))
return organism
# if new_organism is relaxed, only check against relaxed organisms
else:
for organism in orgs_list:
if new_organism.id != organism.id and organism.epa is not None:
# check if their structures match
if self.check_structures(new_organism, organism, geometry):
print('Organism {} failed structural redundancy - '
'looks like organism {} '.format(
new_organism.id, organism.id))
return organism
# check how close their epa's are
if abs(new_organism.epa - organism.epa) < self.epa_diff:
print('Organism {} failed energy per atom redundancy '
'- looks like organism {} '.format(
new_organism.id, organism.id))
return organism
return None
def check_structures(self, org1, org2, geometry):
'''
Compares the structures of two organisms to determine if they are
redundant.
Returns a boolean indicating whether the structures of the two
organisms are redundant.
Args:
org1: the first Organism
org2: the second Organism
geometry: the Geometry of the search
'''
# use the molecule matcher for cluster searches
if geometry.shape == 'cluster':
return self.match_molecules(org1.cell, org2.cell)
elif geometry.shape == 'wire':
molecules_match = self.match_molecules(org1.cell, org2.cell)
structures_match = self.structure_matcher.fit(org1.cell, org2.cell)
return molecules_match or structures_match
else:
return self.structure_matcher.fit(org1.cell, org2.cell)
def match_molecules(self, cell1, cell2):
'''
Compares two cells to determine if they are redundant using pymatgen's
comparison algorithm that assumes no periodicity in any direction.
Returns a boolean indicating whether the cells are redundant.
Args:
cell1: the first Cell
cell2: the second Cell
'''
mol1 = Molecule(cell1.species, cell1.cart_coords)
mol2 = Molecule(cell2.species, cell2.cart_coords)
return self.molecule_matcher.fit(mol1, mol2)