def uniform_labels(self, mol1, mol2):
obmol1 = BabelMolAdaptor(mol1).openbabel_mol
obmol2 = BabelMolAdaptor(mol2).openbabel_mol
ilabel1, iequal_atom1, inchi1 = self._inchi_labels(obmol1)
ilabel2, iequal_atom2, inchi2 = self._inchi_labels(obmol2)
if inchi1 != inchi2:
return None, None # Topoligically different
if iequal_atom1 != iequal_atom2:
raise Exception("Design Error! Equavilent atoms are inconsistent")
vmol1 = self._virtual_molecule(obmol1, ilabel1, iequal_atom1)
vmol2 = self._virtual_molecule(obmol2, ilabel2, iequal_atom2)
if vmol1.NumAtoms() < 3 or self._is_molecule_linear(vmol1) \
or self._is_molecule_linear(vmol2):
# using isomorphism for difficult (actually simple) molecules
clabel1, clabel2 = self._assistant_mapper.uniform_labels(mol1, mol2)
else:
heavy_atom_indices2 = self._align_heavy_atoms(obmol1, obmol2,
vmol1, vmol2, ilabel1,
ilabel2, iequal_atom1)
clabel1, clabel2 = self._align_hydrogen_atoms(obmol1, obmol2,
ilabel1,
heavy_atom_indices2)
elements1 = self._get_elements(obmol1, clabel1)
elements2 = self._get_elements(obmol2, clabel2)
if elements1 != elements2:
raise Exception("Design Error! Atomic elements are inconsistent")
return clabel1, clabel2
def test_init(self):
adaptor = BabelMolAdaptor(self.mol)
obmol = adaptor.openbabel_mol
self.assertEqual(obmol.NumAtoms(), 5)
adaptor = BabelMolAdaptor(adaptor.openbabel_mol)
self.assertEqual(adaptor.pymatgen_mol.formula, "H4 C1")
def test_localopt(self):
self.mol[1] = "H", [0, 0, 1.05]
adaptor = BabelMolAdaptor(self.mol)
adaptor.localopt()
optmol = adaptor.pymatgen_mol
for site in optmol[1:]:
self.assertAlmostEqual(site.distance(optmol[0]), 1.09216, 2)
def test_get_rmsd(self):
mm = MoleculeMatcher()
mol1 = BabelMolAdaptor.from_file(os.path.join(test_dir,
"t3.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir,
"t4.xyz")).pymatgen_mol
self.assertEqual('{0:7.3}'.format(mm.get_rmsd(mol1, mol2)), "0.00488")
def test_localopt(self):
self.mol[1] = "H", [0, 0, 1.05]
adaptor = BabelMolAdaptor(self.mol)
adaptor.localopt()
optmol = adaptor.pymatgen_mol
for site in optmol[1:]:
self.assertAlmostEqual(site.distance(optmol[0]), 1.09216, 2)
def get_molecule_hash(self, mol):
"""
Return inchi as molecular hash
"""
obmol = BabelMolAdaptor(mol).openbabel_mol
inchi = self._inchi_labels(obmol)[2]
return inchi
def test_from_string(self):
if not babelio.babel_loaded:
raise SkipTest("OpenBabel not present. Skipping...")
xyz = XYZ(self.mol)
adaptor = BabelMolAdaptor.from_string(str(xyz), "xyz")
mol = adaptor.pymatgen_mol
self.assertEqual(mol.formula, "H4 C1")
def write_mol(mol, filename):
"""
Write a molecule to a file based on file extension. For example, anything
ending in a "xyz" is assumed to be a XYZ file. Supported formats include
xyz, Gaussian input (gjf|g03|g09|com|inp), and pymatgen's JSON serialized
molecules.
Args:
mol (Molecule/IMolecule): Molecule to write
filename (str): A filename to write to.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.xyz*"):
return XYZ(mol).write_file(filename)
elif any([
fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["gjf", "g03", "g09", "com", "inp"]
]):
return GaussianInput(mol).write_file(filename)
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename, "w") as f:
return json.dump(mol, f, cls=PMGJSONEncoder)
else:
m = re.search("\.(pdb|mol|mdl|sdf|sd|ml2|sy2|mol2|cml|mrv)",
filename.lower())
if m:
return BabelMolAdaptor(mol).write_file(filename, m.group(1))
raise ValueError("Unrecognized file extension!")
def test_from_file(self):
if not babelio.babel_loaded:
raise SkipTest("OpenBabel not present. Skipping...")
adaptor = BabelMolAdaptor.from_file(os.path.join(test_dir,
"Ethane_e.pdb"),
"pdb")
mol = adaptor.pymatgen_mol
self.assertEqual(mol.formula, "H6 C2")
def uniform_labels(self, mol1, mol2):
"""
Pair the geometrically equivalent atoms of the molecules.
Calculate RMSD on all possible isomorphism mappings and return mapping
with the least RMSD
Args:
mol1: First molecule. OpenBabel OBMol or pymatgen Molecule object.
mol2: Second molecule. OpenBabel OBMol or pymatgen Molecule object.
Returns:
(list1, list2) if uniform atom order is found. list1 and list2
are for mol1 and mol2, respectively. Their length equal
to the number of atoms. They represents the uniform atom order
of the two molecules. The value of each element is the original
atom index in mol1 or mol2 of the current atom in uniform atom
order.
(None, None) if unform atom is not available.
"""
obmol1 = BabelMolAdaptor(mol1).openbabel_mol
obmol2 = BabelMolAdaptor(mol2).openbabel_mol
h1 = self.get_molecule_hash(obmol1)
h2 = self.get_molecule_hash(obmol2)
if h1 != h2:
return None, None
query = ob.CompileMoleculeQuery(obmol1)
isomapper = ob.OBIsomorphismMapper.GetInstance(query)
isomorph = ob.vvpairUIntUInt()
isomapper.MapAll(obmol2, isomorph)
sorted_isomorph = [sorted(x, key=lambda morp: morp[0])
for x in isomorph]
label2_list = tuple([tuple([p[1] + 1 for p in x])
for x in sorted_isomorph])
vmol1 = obmol1
aligner = ob.OBAlign(True, False)
aligner.SetRefMol(vmol1)
least_rmsd = float("Inf")
best_label2 = None
label1 = list(range(1, obmol1.NumAtoms() + 1))
# noinspection PyProtectedMember
elements1 = InchiMolAtomMapper._get_elements(vmol1, label1)
for label2 in label2_list:
# noinspection PyProtectedMember
elements2 = InchiMolAtomMapper._get_elements(obmol2, label2)
if elements1 != elements2:
continue
vmol2 = ob.OBMol()
for i in label2:
vmol2.AddAtom(obmol2.GetAtom(i))
aligner.SetTargetMol(vmol2)
aligner.Align()
rmsd = aligner.GetRMSD()
if rmsd < least_rmsd:
least_rmsd = rmsd
best_label2 = copy.copy(label2)
return label1, best_label2
def test_group_molecules(self):
mm = MoleculeMatcher(tolerance=0.001)
filename_list = None
with open(os.path.join(test_dir, "mol_list.txt")) as f:
filename_list = [line.strip() for line in f.readlines()]
mol_list = [BabelMolAdaptor.from_file(os.path.join(test_dir, f)).pymatgen_mol\
for f in filename_list]
mol_groups = mm.group_molecules(mol_list)
filename_groups = [[filename_list[mol_list.index(m)] for m in g] for g \
in mol_groups]
grouped_text = None
with open(os.path.join(test_dir, "grouped_mol_list.txt")) as f:
grouped_text = f.read().strip()
self.assertEqual(str(filename_groups), grouped_text)
def test_group_molecules(self):
mm = MoleculeMatcher(tolerance=0.001)
filename_list = None
with open(os.path.join(test_dir, "mol_list.txt")) as f:
filename_list = [line.strip() for line in f.readlines()]
mol_list = [BabelMolAdaptor.from_file(os.path.join(test_dir, f)).pymatgen_mol\
for f in filename_list]
mol_groups = mm.group_molecules(mol_list)
filename_groups = [[filename_list[mol_list.index(m)] for m in g] for g \
in mol_groups]
grouped_text = None
with open(os.path.join(test_dir, "grouped_mol_list.txt")) as f:
grouped_text = f.read().strip()
self.assertEqual(str(filename_groups), grouped_text)
def read_mol(filename):
"""
Reads a molecule based on file extension. For example, anything ending in
a "xyz" is assumed to be a XYZ file. Supported formats include xyz,
gaussian input (gjf|g03|g09|com|inp), Gaussian output (.out|and
pymatgen's JSON serialized molecules. Using openbabel,
many more extensions are supported but requires openbabel to be installed.
Args:
filename:
A filename to read from.
Returns:
A Molecule object.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.xyz*"):
return XYZ.from_file(filename).molecule
elif any([
fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["gjf", "g03", "g09", "com", "inp"]
]):
return GaussianInput.from_file(filename).molecule
elif any([
fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["out", "lis", "log"]
]):
return GaussianOutput(filename).final_structure
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename) as f:
s = json.load(f, cls=PMGJSONDecoder)
if type(s) != Molecule:
raise IOError("File does not contain a valid serialized "
"molecule")
return s
else:
m = re.search("\.(pdb|mol|mdl|sdf|sd|ml2|sy2|mol2|cml|mrv)",
filename.lower())
if m:
return BabelMolAdaptor.from_file(filename, m.group(1)).pymatgen_mol
raise ValueError("Unrecognized file extension!")
def read_mol(filename):
"""
Reads a molecule based on file extension. For example, anything ending in
a "xyz" is assumed to be a XYZ file. Supported formats include xyz,
gaussian input (gjf|g03|g09|com|inp), Gaussian output (.out|and
pymatgen's JSON serialized molecules. Using openbabel,
many more extensions are supported but requires openbabel to be installed.
Args:
filename:
A filename to read from.
Returns:
A Molecule object.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.xyz*"):
return XYZ.from_file(filename).molecule
elif any([fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["gjf", "g03", "g09", "com", "inp"]]):
return GaussianInput.from_file(filename).molecule
elif any([fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["out", "lis", "log"]]):
return GaussianOutput(filename).final_structure
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename) as f:
s = json.load(f, cls=PMGJSONDecoder)
if type(s) != Molecule:
raise IOError("File does not contain a valid serialized "
"molecule")
return s
else:
m = re.search("\.(pdb|mol|mdl|sdf|sd|ml2|sy2|mol2|cml|mrv)",
filename.lower())
if m:
return BabelMolAdaptor.from_file(filename,
m.group(1)).pymatgen_mol
raise ValueError("Unrecognized file extension!")
def _calc_rms(self, mol1, mol2, clabel1, clabel2):
"""
Calculate the RMSD.
Args:
mol1:
The first molecule. OpenBabel OBMol or pymatgen Molecule object
mol2:
The second molecule. OpenBabel OBMol or pymatgen Molecule
object
clabel1:
The atom indices that can reorder the first molecule to
uniform atom order
clabel1:
The atom indices that can reorder the second molecule to
uniform atom order
Returns:
The RMSD.
"""
obmol1 = BabelMolAdaptor(mol1).openbabel_mol
obmol2 = BabelMolAdaptor(mol2).openbabel_mol
cmol1 = ob.OBMol()
for i in clabel1:
oa1 = obmol1.GetAtom(i)
a1 = cmol1.NewAtom()
a1.SetAtomicNum(oa1.GetAtomicNum())
a1.SetVector(oa1.GetVector())
cmol2 = ob.OBMol()
for i in clabel2:
oa2 = obmol2.GetAtom(i)
a2 = cmol2.NewAtom()
a2.SetAtomicNum(oa2.GetAtomicNum())
a2.SetVector(oa2.GetVector())
aligner = ob.OBAlign(True, False)
aligner.SetRefMol(cmol1)
aligner.SetTargetMol(cmol2)
aligner.Align()
return aligner.GetRMSD()
def test_from_string(self):
xyz = XYZ(self.mol)
adaptor = BabelMolAdaptor.from_string(str(xyz), "xyz")
mol = adaptor.pymatgen_mol
self.assertEqual(mol.formula, "H4 C1")
def test_from_file(self):
adaptor = BabelMolAdaptor.from_file(
os.path.join(test_dir, "Ethane_e.pdb"), "pdb")
mol = adaptor.pymatgen_mol
self.assertEqual(mol.formula, "H6 C2")
def test_from_string(self):
xyz = XYZ(self.mol)
adaptor = BabelMolAdaptor.from_string(str(xyz), "xyz")
mol = adaptor.pymatgen_mol
self.assertEqual(mol.formula, "H4 C1")
def test_from_file(self):
adaptor = BabelMolAdaptor.from_file(
os.path.join(test_dir, "Ethane_e.pdb"), "pdb")
mol = adaptor.pymatgen_mol
self.assertEqual(mol.formula, "H6 C2")
def test_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 = BabelMolAdaptor.from_file(os.path.join(test_dir, "benzene1.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir, "benzene2.xyz")).pymatgen_mol
self.assertTrue(mm.fit(mol1, mol2))
mol1 = BabelMolAdaptor.from_file(os.path.join(test_dir, "benzene1.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir, "t2.xyz")).pymatgen_mol
self.assertFalse(mm.fit(mol1, mol2))
mol1 = BabelMolAdaptor.from_file(os.path.join(test_dir, "c1.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir, "c2.xyz")).pymatgen_mol
self.assertTrue(mm.fit(mol1, mol2))
mol1 = BabelMolAdaptor.from_file(os.path.join(test_dir, "t3.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir, "t4.xyz")).pymatgen_mol
self.assertTrue(mm.fit(mol1, mol2))
mol1 = BabelMolAdaptor.from_file(os.path.join(test_dir, "j1.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir, "j2.xyz")).pymatgen_mol
self.assertTrue(mm.fit(mol1, mol2))
mol1 = BabelMolAdaptor.from_file(os.path.join(test_dir, "ethene1.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir, "ethene2.xyz")).pymatgen_mol
self.assertTrue(mm.fit(mol1, mol2))
mol1 = BabelMolAdaptor.from_file(os.path.join(test_dir, "toluene1.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir, "toluene2.xyz")).pymatgen_mol
self.assertTrue(mm.fit(mol1, mol2))
mol1 = BabelMolAdaptor.from_file(os.path.join(test_dir, "cyclohexane1.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir, "cyclohexane2.xyz")).pymatgen_mol
self.assertTrue(mm.fit(mol1, mol2))
mol1 = BabelMolAdaptor.from_file(os.path.join(test_dir, "oxygen1.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir, "oxygen2.xyz")).pymatgen_mol
self.assertTrue(mm.fit(mol1, mol2))
mm = MoleculeMatcher(tolerance=0.001, mapper=mapper)
mol1 = BabelMolAdaptor.from_file(os.path.join(test_dir, "t3.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir, "t4.xyz")).pymatgen_mol
self.assertFalse(mm.fit(mol1, mol2))
def test_get_rmsd(self):
mm = MoleculeMatcher()
mol1 = BabelMolAdaptor.from_file(os.path.join(test_dir, "t3.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir, "t4.xyz")).pymatgen_mol
self.assertEqual('{0:7.3}'.format(mm.get_rmsd(mol1, mol2)), "0.00488")
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 = BabelMolAdaptor.from_file(os.path.join(
test_dir, "benzene1.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(
test_dir, "benzene2.xyz")).pymatgen_mol
self.assertTrue(mm.fit(mol1, mol2))
mol1 = BabelMolAdaptor.from_file(os.path.join(
test_dir, "benzene1.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir,
"t2.xyz")).pymatgen_mol
self.assertFalse(mm.fit(mol1, mol2))
mol1 = BabelMolAdaptor.from_file(os.path.join(test_dir,
"c1.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir,
"c2.xyz")).pymatgen_mol
self.assertTrue(mm.fit(mol1, mol2))
mol1 = BabelMolAdaptor.from_file(os.path.join(test_dir,
"t3.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir,
"t4.xyz")).pymatgen_mol
self.assertTrue(mm.fit(mol1, mol2))
mol1 = BabelMolAdaptor.from_file(os.path.join(test_dir,
"j1.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir,
"j2.xyz")).pymatgen_mol
self.assertTrue(mm.fit(mol1, mol2))
mol1 = BabelMolAdaptor.from_file(os.path.join(
test_dir, "ethene1.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(
test_dir, "ethene2.xyz")).pymatgen_mol
self.assertTrue(mm.fit(mol1, mol2))
mol1 = BabelMolAdaptor.from_file(os.path.join(
test_dir, "toluene1.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(
test_dir, "toluene2.xyz")).pymatgen_mol
self.assertTrue(mm.fit(mol1, mol2))
mol1 = BabelMolAdaptor.from_file(
os.path.join(test_dir, "cyclohexane1.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(
os.path.join(test_dir, "cyclohexane2.xyz")).pymatgen_mol
self.assertTrue(mm.fit(mol1, mol2))
mol1 = BabelMolAdaptor.from_file(os.path.join(
test_dir, "oxygen1.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(
test_dir, "oxygen2.xyz")).pymatgen_mol
self.assertTrue(mm.fit(mol1, mol2))
mm = MoleculeMatcher(tolerance=0.001, mapper=mapper)
mol1 = BabelMolAdaptor.from_file(os.path.join(test_dir,
"t3.xyz")).pymatgen_mol
mol2 = BabelMolAdaptor.from_file(os.path.join(test_dir,
"t4.xyz")).pymatgen_mol
self.assertFalse(mm.fit(mol1, mol2))