def test_in_database_with_actual_database(self):
db_file = os.path.join(db_dir, "db.json")
dir2620 = os.path.join(module_dir, "..", "..", "test_files",
"2620_complete")
mol2620 = QCOutput(os.path.join(
dir2620, "mol.qout.opt_0")).data["initial_molecule"]
parse_firetask = QChemToDb(calc_dir=dir2620, db_file=db_file)
parse_firetask.run_task({})
with patch("atomate.qchem.firetasks.fragmenter.FWAction"
) as FWAction_patch:
ft = FragmentMolecule(
molecule=self.neg_tfsi,
db_file=db_file,
depth=0,
additional_charges=[-2, 1],
do_triplets=False,
)
ft.run_task({})
self.assertEqual(ft.check_db, True)
self.assertEqual(ft.charges, [-1, 0, -2, 1])
self.assertEqual(len(FWAction_patch.call_args[1]["additions"]),
623)
self.assertEqual(ft._in_database(mol2620), True)
mol2620.set_charge_and_spin(charge=0)
self.assertEqual(ft._in_database(mol2620), False)
def test_babel_PC_depth_0_vs_depth_10(self):
with patch("atomate.qchem.firetasks.fragmenter.FWAction"
) as FWAction_patch:
ft = FragmentMolecule(molecule=self.pc,
depth=0,
open_rings=False,
do_triplets=False)
ft.run_task({})
self.assertEqual(ft.check_db, False)
depth0frags = ft.unique_fragments
self.assertEqual(len(depth0frags), 295)
self.assertEqual(len(FWAction_patch.call_args[1]["additions"]),
295 * 3)
with patch("atomate.qchem.firetasks.fragmenter.FWAction"
) as FWAction_patch:
ft = FragmentMolecule(molecule=self.pc,
depth=10,
open_rings=False,
do_triplets=False)
ft.run_task({})
self.assertEqual(ft.check_db, False)
depth10frags = ft.unique_fragments
self.assertEqual(len(depth10frags), 63)
self.assertEqual(len(FWAction_patch.call_args[1]["additions"]),
63 * 3)
for fragment10 in depth10frags:
found = False
for fragment0 in depth0frags:
if fragment0.isomorphic_to(fragment10):
found = True
self.assertEqual(found, True)
def test_babel_PC_depth_0_vs_depth_10(self):
with patch("atomate.qchem.firetasks.fragmenter.FWAction"
) as FWAction_patch:
ft = FragmentMolecule(molecule=self.pc, depth=0, open_rings=False, do_triplets=False)
ft.run_task({})
self.assertEqual(ft.check_db,False)
depth0frags = ft.unique_fragments
self.assertEqual(len(depth0frags), 295)
self.assertEqual(
len(FWAction_patch.call_args[1]["additions"]), 295*3)
with patch("atomate.qchem.firetasks.fragmenter.FWAction"
) as FWAction_patch:
ft = FragmentMolecule(molecule=self.pc, depth=10, open_rings=False, do_triplets=False)
ft.run_task({})
self.assertEqual(ft.check_db,False)
depth10frags = ft.unique_fragments
self.assertEqual(len(depth10frags), 63)
self.assertEqual(
len(FWAction_patch.call_args[1]["additions"]), 63*3)
for fragment10 in depth10frags:
found = False
for fragment0 in depth0frags:
if fragment0.isomorphic_to(fragment10):
found = True
self.assertEqual(found, True)
def test_neg_TFSI_with_additional_charges(self):
with patch("atomate.qchem.firetasks.fragmenter.FWAction"
) as FWAction_patch:
ft = FragmentMolecule(
molecule=self.neg_tfsi,
depth=0,
additional_charges=[-2, 1],
do_triplets=False,
)
ft.run_task({})
self.assertEqual(ft.check_db, False)
self.assertEqual(ft.charges, [-1, 0, -2, 1])
self.assertEqual(len(FWAction_patch.call_args[1]["additions"]),
624)
with patch("atomate.qchem.firetasks.fragmenter.FWAction"
) as FWAction_patch:
ft = FragmentMolecule(
molecule=self.neg_tfsi,
depth=0,
additional_charges=[0, 1],
do_triplets=False,
)
ft.run_task({})
self.assertEqual(ft.check_db, False)
self.assertEqual(len(FWAction_patch.call_args[1]["additions"]),
468)
def test_babel_TFSI(self):
with patch("atomate.qchem.firetasks.fragmenter.FWAction"
) as FWAction_patch:
ft = FragmentMolecule(molecule=self.tfsi, depth=0, do_triplets=False)
ft.run_task({})
self.assertEqual(ft.check_db,False)
self.assertEqual(ft.charges,[-1,0,1])
self.assertEqual(
len(FWAction_patch.call_args[1]["additions"]), 468)
def test_edges_given_PC(self):
with patch("atomate.qchem.firetasks.fragmenter.FWAction"
) as FWAction_patch:
ft = FragmentMolecule(molecule=self.pc, edges=self.pc_edges, depth=0, open_rings=False, do_triplets=False)
ft.run_task({})
self.assertEqual(ft.check_db,False)
self.assertEqual(ft.charges,[-1,0,1])
self.assertEqual(
len(FWAction_patch.call_args[1]["additions"]), 295 * 3)
def test_babel_TFSI(self):
with patch("atomate.qchem.firetasks.fragmenter.FWAction"
) as FWAction_patch:
ft = FragmentMolecule(molecule=self.tfsi, depth=0, do_triplets=False)
ft.run_task({})
self.assertEqual(ft.check_db,False)
self.assertEqual(ft.charges,[-1,0,1])
self.assertEqual(
len(FWAction_patch.call_args[1]["additions"]), 468)
def test_edges_given_PC(self):
with patch("atomate.qchem.firetasks.fragmenter.FWAction"
) as FWAction_patch:
ft = FragmentMolecule(molecule=self.pc, edges=self.pc_edges, depth=0, open_rings=False, do_triplets=False)
ft.run_task({})
self.assertEqual(ft.check_db,False)
self.assertEqual(ft.charges,[-1,0,1])
self.assertEqual(
len(FWAction_patch.call_args[1]["additions"]), 295 * 3)
def test_EC_neg(self):
with patch("atomate.qchem.firetasks.fragmenter.FWAction"
) as FWAction_patch:
ft = FragmentMolecule(molecule=self.neg_ec, depth=1, check_db=False)
ft.run_task({})
self.assertEqual(ft.check_db,False)
frags = ft.unique_fragments
self.assertEqual(len(frags), 7)
self.assertEqual(
len(FWAction_patch.call_args[1]["additions"]), 15)
def test_EC_neg(self):
with patch("atomate.qchem.firetasks.fragmenter.FWAction"
) as FWAction_patch:
ft = FragmentMolecule(molecule=self.neg_ec, depth=1, check_db=False)
ft.run_task({})
self.assertEqual(ft.check_db,False)
frags = ft.unique_fragments
self.assertEqual(len(frags), 7)
self.assertEqual(
len(FWAction_patch.call_args[1]["additions"]), 14)
def test_in_database_with_actual_database(self):
db_file=os.path.join(db_dir, "db.json")
dir2620=os.path.join(module_dir, "..", "..", "test_files", "2620_complete")
mol2620=QCOutput(os.path.join(dir2620,"mol.qout.opt_0")).data["initial_molecule"]
parse_firetask = QChemToDb(calc_dir=dir2620, db_file=db_file)
parse_firetask.run_task({})
with patch("atomate.qchem.firetasks.fragmenter.FWAction"
) as FWAction_patch:
ft = FragmentMolecule(molecule=self.neg_tfsi, db_file=db_file, depth=0, additional_charges=[-2,1], do_triplets=False)
ft.run_task({})
self.assertEqual(ft.check_db,True)
self.assertEqual(ft.charges,[-1,0,-2,1])
self.assertEqual(
len(FWAction_patch.call_args[1]["additions"]), 623)
self.assertEqual(ft._in_database(mol2620),True)
mol2620.set_charge_and_spin(charge=0)
self.assertEqual(ft._in_database(mol2620),False)
def test_in_database_and_EC_neg_frag(self):
db_file = os.path.join(db_dir, "db.json")
mmdb = QChemCalcDb.from_db_file(db_file, admin=True)
with open(os.path.join(module_dir, "..", "..", "test_files","sb40.json")) as f:
tmp = json.load(f)
for entry in tmp:
mmdb.insert(entry)
with patch("atomate.qchem.firetasks.fragmenter.FWAction"
) as FWAction_patch:
ft = FragmentMolecule(molecule=self.neg_ec, depth=1, qchem_input_params={"pcm_dielectric": 40.0}, check_db=True, db_file=db_file)
ft.run_task({})
self.assertEqual(ft.check_db,True)
frags = ft.unique_fragments
self.assertEqual(len(frags), 7)
self.assertEqual(
len(FWAction_patch.call_args[1]["additions"]), 0)
mmdb.reset()
def test_in_database_and_EC_neg_frag(self):
db_file = os.path.join(db_dir, "db.json")
mmdb = QChemCalcDb.from_db_file(db_file, admin=True)
with open(os.path.join(module_dir, "..", "..", "test_files","sb40.json")) as f:
tmp = json.load(f)
for entry in tmp:
mmdb.insert(entry)
with patch("atomate.qchem.firetasks.fragmenter.FWAction"
) as FWAction_patch:
ft = FragmentMolecule(molecule=self.neg_ec, depth=1, qchem_input_params={"pcm_dielectric": 40.0}, check_db=True, db_file=db_file)
ft.run_task({})
self.assertEqual(ft.check_db,True)
frags = ft.unique_fragments
self.assertEqual(len(frags), 7)
self.assertEqual(
len(FWAction_patch.call_args[1]["additions"]), 0)
mmdb.reset()