def setUp(self):
warnings.simplefilter("ignore")
self.file = os.path.join(test_dir, "func_group_test.mol")
self.mol = Molecule.from_file(self.file)
self.strat = OpenBabelNN()
self.mg = MoleculeGraph.with_local_env_strategy(self.mol, self.strat)
self.extractor = FunctionalGroupExtractor(self.mg)
def test_init(self):
# Ensure that instantiation is equivalent for all valid input types
extractor_str = FunctionalGroupExtractor(self.file)
extractor_mol = FunctionalGroupExtractor(self.mol)
extractor_mg = self.extractor
self.assertEqual(extractor_str.molgraph, extractor_mol.molgraph)
self.assertEqual(extractor_str.molgraph, extractor_mg.molgraph)
self.assertEqual(extractor_str.species, extractor_mol.species)
self.assertEqual(extractor_str.species, extractor_mg.species)
# Test optimization
file_no_h = os.path.join(test_dir, "func_group_test_no_h.mol")
extractor_no_h = FunctionalGroupExtractor(file_no_h, optimize=True)
self.assertEqual(len(extractor_no_h.molecule), len(extractor_mol.molecule))
self.assertEqual(extractor_no_h.species, extractor_mol.species)
def setUp(self):
warnings.simplefilter("ignore")
self.file = os.path.join(test_dir, "func_group_test.mol")
self.mol = Molecule.from_file(self.file)
self.strat = OpenBabelNN()
self.mg = MoleculeGraph.with_local_env_strategy(self.mol, self.strat,
reorder=False,
extend_structure=False)
self.extractor = FunctionalGroupExtractor(self.mg)
class FunctionalGroupExtractorTest(unittest.TestCase):
def setUp(self):
warnings.simplefilter("ignore")
self.file = os.path.join(test_dir, "func_group_test.mol")
self.mol = Molecule.from_file(self.file)
self.strat = OpenBabelNN()
self.mg = MoleculeGraph.with_local_env_strategy(self.mol,
self.strat,
reorder=False,
extend_structure=False)
self.extractor = FunctionalGroupExtractor(self.mg)
def tearDown(self):
warnings.simplefilter("default")
del self.extractor
del self.mg
del self.strat
del self.mol
del self.file
def test_init(self):
# Ensure that instantiation is equivalent for all valid input types
extractor_str = FunctionalGroupExtractor(self.file)
extractor_mol = FunctionalGroupExtractor(self.mol)
extractor_mg = self.extractor
self.assertEqual(extractor_str.molgraph, extractor_mol.molgraph)
self.assertEqual(extractor_str.molgraph, extractor_mg.molgraph)
self.assertEqual(extractor_str.species, extractor_mol.species)
self.assertEqual(extractor_str.species, extractor_mg.species)
# Test optimization
file_no_h = os.path.join(test_dir, "func_group_test_no_h.mol")
extractor_no_h = FunctionalGroupExtractor(file_no_h, optimize=True)
self.assertEqual(len(extractor_no_h.molecule),
len(extractor_mol.molecule))
self.assertEqual(extractor_no_h.species, extractor_mol.species)
def test_get_heteroatoms(self):
heteroatoms = self.extractor.get_heteroatoms()
hetero_species = [self.extractor.species[x] for x in heteroatoms]
self.assertEqual(len(heteroatoms), 3)
self.assertEqual(sorted(hetero_species), ["N", "O", "O"])
# Test with limitation
hetero_no_o = self.extractor.get_heteroatoms(elements=["N"])
self.assertEqual(len(hetero_no_o), 1)
def test_get_special_carbon(self):
special_cs = self.extractor.get_special_carbon()
self.assertEqual(len(special_cs), 4)
# Test with limitation
special_cs_no_o = self.extractor.get_special_carbon(elements=["N"])
self.assertEqual(len(special_cs_no_o), 2)
def test_link_marked_atoms(self):
heteroatoms = self.extractor.get_heteroatoms()
special_cs = self.extractor.get_special_carbon()
link = self.extractor.link_marked_atoms(heteroatoms.union(special_cs))
self.assertEqual(len(link), 1)
self.assertEqual(len(link[0]), 9)
# Exclude Oxygen-related functional groups
heteroatoms_no_o = self.extractor.get_heteroatoms(elements=["N"])
special_cs_no_o = self.extractor.get_special_carbon(elements=["N"])
all_marked = heteroatoms_no_o.union(special_cs_no_o)
link_no_o = self.extractor.link_marked_atoms(all_marked)
self.assertEqual(len(link_no_o), 2)
def test_get_basic_functional_groups(self):
basics = self.extractor.get_basic_functional_groups()
# Molecule has one methyl group which will be caught.
self.assertEqual(len(basics), 1)
self.assertEqual(len(basics[0]), 4)
basics_no_methyl = self.extractor.get_basic_functional_groups(
func_groups=["phenyl"])
self.assertEqual(len(basics_no_methyl), 0)
def test_get_all_functional_groups(self):
heteroatoms = self.extractor.get_heteroatoms()
special_cs = self.extractor.get_special_carbon()
link = self.extractor.link_marked_atoms(heteroatoms.union(special_cs))
basics = self.extractor.get_basic_functional_groups()
all_func = self.extractor.get_all_functional_groups()
self.assertEqual(len(all_func), (len(link) + len(basics)))
self.assertEqual(sorted(all_func), sorted(link + basics))
def test_categorize_functional_groups(self):
all_func = self.extractor.get_all_functional_groups()
categorized = self.extractor.categorize_functional_groups(all_func)
self.assertTrue("O=C1C=CC(=O)[N]1" in categorized.keys())
self.assertTrue("[CH3]" in categorized.keys())
total_count = sum([c["count"] for c in categorized.values()])
self.assertEqual(total_count, 2)
class FunctionalGroupExtractorTest(unittest.TestCase):
def setUp(self):
warnings.simplefilter("ignore")
self.file = os.path.join(test_dir, "func_group_test.mol")
self.mol = Molecule.from_file(self.file)
self.strat = OpenBabelNN()
self.mg = MoleculeGraph.with_local_env_strategy(self.mol, self.strat,
reorder=False,
extend_structure=False)
self.extractor = FunctionalGroupExtractor(self.mg)
def tearDown(self):
warnings.simplefilter("default")
del self.extractor
del self.mg
del self.strat
del self.mol
del self.file
def test_init(self):
# Ensure that instantiation is equivalent for all valid input types
extractor_str = FunctionalGroupExtractor(self.file)
extractor_mol = FunctionalGroupExtractor(self.mol)
extractor_mg = self.extractor
self.assertEqual(extractor_str.molgraph, extractor_mol.molgraph)
self.assertEqual(extractor_str.molgraph, extractor_mg.molgraph)
self.assertEqual(extractor_str.species, extractor_mol.species)
self.assertEqual(extractor_str.species, extractor_mg.species)
# Test optimization
file_no_h = os.path.join(test_dir, "func_group_test_no_h.mol")
extractor_no_h = FunctionalGroupExtractor(file_no_h, optimize=True)
self.assertEqual(len(extractor_no_h.molecule), len(extractor_mol.molecule))
self.assertEqual(extractor_no_h.species, extractor_mol.species)
def test_get_heteroatoms(self):
heteroatoms = self.extractor.get_heteroatoms()
hetero_species = [self.extractor.species[x] for x in heteroatoms]
self.assertEqual(len(heteroatoms), 3)
self.assertEqual(sorted(hetero_species), ["N", "O", "O"])
# Test with limitation
hetero_no_o = self.extractor.get_heteroatoms(elements=["N"])
self.assertEqual(len(hetero_no_o), 1)
def test_get_special_carbon(self):
special_cs = self.extractor.get_special_carbon()
self.assertEqual(len(special_cs), 4)
# Test with limitation
special_cs_no_o = self.extractor.get_special_carbon(elements=["N"])
self.assertEqual(len(special_cs_no_o), 2)
def test_link_marked_atoms(self):
heteroatoms = self.extractor.get_heteroatoms()
special_cs = self.extractor.get_special_carbon()
link = self.extractor.link_marked_atoms(heteroatoms.union(special_cs))
self.assertEqual(len(link), 1)
self.assertEqual(len(link[0]), 9)
# Exclude Oxygen-related functional groups
heteroatoms_no_o = self.extractor.get_heteroatoms(elements=["N"])
special_cs_no_o = self.extractor.get_special_carbon(elements=["N"])
all_marked = heteroatoms_no_o.union(special_cs_no_o)
link_no_o = self.extractor.link_marked_atoms(all_marked)
self.assertEqual(len(link_no_o), 2)
def test_get_basic_functional_groups(self):
basics = self.extractor.get_basic_functional_groups()
# Molecule has one methyl group which will be caught.
self.assertEqual(len(basics), 1)
self.assertEqual(len(basics[0]), 4)
basics_no_methyl = self.extractor.get_basic_functional_groups(func_groups=["phenyl"])
self.assertEqual(len(basics_no_methyl), 0)
def test_get_all_functional_groups(self):
heteroatoms = self.extractor.get_heteroatoms()
special_cs = self.extractor.get_special_carbon()
link = self.extractor.link_marked_atoms(heteroatoms.union(special_cs))
basics = self.extractor.get_basic_functional_groups()
all_func = self.extractor.get_all_functional_groups()
self.assertEqual(len(all_func), (len(link) + len(basics)))
self.assertEqual(sorted(all_func), sorted(link + basics))
def test_categorize_functional_groups(self):
all_func = self.extractor.get_all_functional_groups()
categorized = self.extractor.categorize_functional_groups(all_func)
self.assertTrue("O=C1C=CC(=O)[N]1" in categorized.keys())
self.assertTrue("[CH3]" in categorized.keys())
total_count = sum([c["count"] for c in categorized.values()])
self.assertEqual(total_count, 2)
def get_molecule_data(self, mol_id):
"""
Compile all useful molecular data for analysis, including molecule size
(number of atoms), molecular weight, enthalpy, entropy, and functional
groups.
NOTE: This function automatically converts energy, enthalpy, and entropy
into SI units (J/mol and J/mol*K)
:param mol_id: Unique ID associated with the molecule.
:return: dict of relevant molecule data.
"""
mol_data = {"mol_id": mol_id}
if self.db is None:
raise RuntimeError("Cannot query database; connection is invalid."
" Try to connect again.")
collection = self.db.db["molecules"]
mol_entry = collection.find_one({"mol_id": mol_id})
for calc in mol_entry["calcs_reversed"]:
if calc["task"]["name"] in ["freq", "frequency"]:
mol_data["enthalpy"] = calc["enthalpy"] * 4.184 * 1000
mol_data["entropy"] = calc["entropy"] * 4.184
if calc["task"]["name"] == "sp":
mol_data["energy"] = calc[
"final_energy_sp"] * 627.509 * 4.184 * 1000
if calc["task"]["name"] in ["opt", "optimization"]:
mol_dict = calc["molecule_from_optimized_geometry"]
mol_data["molecule"] = Molecule.from_dict(mol_dict)
adaptor = BabelMolAdaptor(mol_data["molecule"])
pbmol = adaptor.pybel_mol
mol_data["number_atoms"] = len(mol_data["molecule"])
mol_data["molecular_weight"] = pbmol.molwt
mol_data["tpsa"] = pbmol.calcdesc()["TPSA"]
extractor = FunctionalGroupExtractor(mol_data["molecule"])
molgraph = extractor.molgraph
func_grps = extractor.get_all_functional_groups()
mol_data["functional_groups"] = extractor.categorize_functional_groups(
func_grps)
weights = nx.get_edge_attributes(molgraph.graph, "weight")
bonds_checked = set()
double_bonds = 0
triple_bonds = 0
for bond, weight in weights.items():
# Remove index from multidigraph
bond = (bond[0], bond[1])
if int(weight) == 2 and bond not in bonds_checked:
double_bonds += 1
elif int(weight) == 3 and bond not in bonds_checked:
triple_bonds += 1
bonds_checked.add(bond)
mol_data["double_bonds"] = double_bonds
mol_data["triple_bonds"] = triple_bonds
species = [str(s.specie) for s in mol_data["molecule"].sites]
mol_data["species"] = dict(Counter(species))
return mol_data