def test_mismatched_atom_composition(self):
mol1 = Molecule.from_file(os.path.join(test_dir, "benzene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t2.xyz"))
mm = HungarianOrderMatcher(mol1)
with self.assertRaises(ValueError):
_, rmsd = mm.fit(mol2)
def test_to_and_from_dict(self):
mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
mm_source = HungarianOrderMatcher(mol1)
d_source = mm_source.as_dict()
mm_target = HungarianOrderMatcher.from_dict(d_source)
self.assertDictEqual(d_source, mm_target.as_dict())
def test_get_rmsd(self):
mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t4.xyz"))
mm = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 0.002825344731118855, places=6)
def test_rotated_molecule(self):
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]]
op = SymmOp.from_origin_axis_angle([0, 0, 0], [0.1, 0.2, 0.3], 60)
rotcoords = [op.operate(c) for c in coords]
mol1 = Molecule(["C", "H", "H", "H", "H"], coords)
mol2 = Molecule(["C", "H", "H", "H", "H"], rotcoords)
mm = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 0., places=6)
def _align_slot(self,
slot: Fragment,
fragment: Fragment
) -> Tuple[Fragment, float]:
"""
[summary]
Parameters
----------
slot : Fragment
[description]
fragment : Fragment
[description]
Returns
-------
Tuple[Fragment, float]
[description]
"""
# m0 = slot.atoms.copy()
m0 = slot.extract_dummies()
m0.perturb(distance=0.01)
m0.replace_species({"X": "H"})
m1 = fragment.extract_dummies()
m1.perturb(distance=0.01)
m1.replace_species({"X": "H"})
_, U, V, rmsd = HungarianOrderMatcher(m0).match(m1)
new_coords = fragment.atoms.cart_coords.dot(U) + V
fragment.atoms = Molecule(fragment.atoms.species, coords=new_coords)
fragment_tags = numpy.array([-1, ] * len(fragment.atoms))
for j, frag_tag in enumerate(fragment_tags):
fragment.atoms[j].properties["tags"] = frag_tag
slot_tags = slot.atoms.site_properties["tags"]
for i, slot_tag in enumerate(slot_tags):
tag_by_dist = []
for j in fragment.atoms.indices_from_symbol("X"):
d = slot.atoms[i].coords - fragment.atoms[j].coords
tag_by_dist.append((numpy.linalg.norm(d), j))
_, best_match = sorted(tag_by_dist)[0]
fragment.atoms[best_match].properties["tags"] = slot_tag
return fragment, rmsd
def setUpClass(cls):
cls.mol1 = Molecule.from_file(os.path.join(test_dir, "Si2O_cluster.xyz"))
cls.mm = HungarianOrderMatcher(cls.mol1)
def test_to_and_from_dict(self):
d = self.mm.as_dict()
mm = HungarianOrderMatcher.from_dict(d)
self.assertDictEqual(d, mm.as_dict())
def test_fit(self):
mol1 = Molecule.from_file(os.path.join(test_dir, "benzene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "benzene2.xyz"))
mm = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 1.4171601659148593e-05, places=6)
mol1 = Molecule.from_file(os.path.join(test_dir, "c1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "c2.xyz"))
mm = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 9.479012116064961e-05, places=6)
mol1 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "t4.xyz"))
mm = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 0.002825344731118855, places=6)
mol1 = Molecule.from_file(os.path.join(test_dir, "j1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "j2.xyz"))
mm = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 9.28245597473488e-05, places=6)
mol1 = Molecule.from_file(os.path.join(test_dir, "ethene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "ethene2.xyz"))
mm = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 0.00021150729609276233, places=6)
mol1 = Molecule.from_file(os.path.join(test_dir, "toluene1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "toluene2.xyz"))
mm = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 0.0001445787263551832, places=6)
mol1 = Molecule.from_file(os.path.join(test_dir, "cyclohexane1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "cyclohexane2.xyz"))
mm = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 0.00012447269440740117, places=6)
mol1 = Molecule.from_file(os.path.join(test_dir, "oxygen1.xyz"))
mol2 = Molecule.from_file(os.path.join(test_dir, "oxygen2.xyz"))
mm = HungarianOrderMatcher(mol1)
_, rmsd = mm.fit(mol2)
self.assertAlmostEqual(rmsd, 0., places=6)