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_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_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_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_FragmentFW_not_defaults(self):
firework = FragmentFW(molecule=self.act_mol,
depth=0,
open_rings=False,
additional_charges=[2],
do_triplets=False,
name="fragmenting a thing",
qchem_cmd="qchem -slurm",
multimode="mpi",
max_cores=12,
qchem_input_params={"pcm_dielectric": 10.0},
db_file=os.path.join(db_dir, "db.json"),
check_db=False)
self.assertEqual(
firework.tasks[0].as_dict(),
FragmentMolecule(molecule=self.act_mol,
depth=0,
open_rings=False,
additional_charges=[2],
do_triplets=False,
max_cores=12,
qchem_input_params={
"pcm_dielectric": 10.0
},
db_file=os.path.join(db_dir, "db.json"),
check_db=False).as_dict())
self.assertEqual(firework.parents, [])
self.assertEqual(firework.name, "fragmenting a thing")
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()
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_FragmentFW_defaults(self):
firework = FragmentFW(molecule=self.act_mol)
self.assertEqual(
firework.tasks[0].as_dict(),
FragmentMolecule(molecule=self.act_mol,
depth=1,
open_rings=True,
additional_charges=[],
do_triplets=True,
max_cores=">>max_cores<<",
qchem_input_params={},
db_file=None,
check_db=True).as_dict())
self.assertEqual(firework.parents, [])
self.assertEqual(firework.name, "fragment and optimize")
def test_build_unique_relevant_molecules(self):
ft = FragmentMolecule(molecule=self.pc,
edges=self.pc_edges,
depth=0,
opt_steps=1000)
ft.mol = ft.get("molecule")
ft.depth = ft.get("depth")
ft.charges = [-1, 0, 1]
ft.do_triplets = False
edges = {(e[0], e[1]): None for e in self.pc_edges}
mol_graph = MoleculeGraph.with_edges(self.pc, edges)
ft.unique_fragments = mol_graph.build_unique_fragments()
ft._build_unique_relevant_molecules()
self.assertEqual(len(ft.unique_molecules), 295 * 3)
#dumpfn(ft.unique_molecules, os.path.join(module_dir,"pc_mols.json"))
ref_mols = loadfn(os.path.join(module_dir, "pc_mols.json"))
self.assertEqual(ft.unique_molecules, ref_mols)
ft = FragmentMolecule(molecule=self.pos_pc,
edges=self.pc_edges,
depth=0,
opt_steps=1000)
ft.mol = ft.get("molecule")
ft.depth = ft.get("depth")
ft.charges = [-1, 0, 1, 2]
ft.do_triplets = False
mol_graph = MoleculeGraph.with_edges(self.pos_pc, edges)
ft.unique_fragments = mol_graph.build_unique_fragments()
ft._build_unique_relevant_molecules()
self.assertEqual(len(ft.unique_molecules), 295 * 4)
#dumpfn(ft.unique_molecules, os.path.join(module_dir,"pos_pc_mols.json"))
ref_mols = loadfn(os.path.join(module_dir, "pos_pc_mols.json"))
self.assertEqual(ft.unique_molecules, ref_mols)
ft = FragmentMolecule(molecule=self.pc_frag1,
edges=self.pc_frag1_edges,
depth=0)
ft.mol = ft.get("molecule")
ft.depth = ft.get("depth")
ft.charges = [-1, 0, 1]
ft.do_triplets = False
pc_frag1_edges = {(e[0], e[1]): None for e in self.pc_frag1_edges}
mol_graph = MoleculeGraph.with_edges(self.pc_frag1, pc_frag1_edges)
ft.unique_fragments = mol_graph.build_unique_fragments()
ft._build_unique_relevant_molecules()
self.assertEqual(len(ft.unique_molecules), 12 * 3)
#dumpfn(ft.unique_molecules, os.path.join(module_dir,"pc_frag1_mols.json"))
ref_mols = loadfn(os.path.join(module_dir, "pc_frag1_mols.json"))
self.assertEqual(ft.unique_molecules, ref_mols)
def test_build_new_FWs(self):
ft = FragmentMolecule(molecule=self.pc_frag1,
edges=self.pc_frag1_edges,
depth=0)
ft.mol = ft.get("molecule")
ft.depth = ft.get("depth")
ft.charges = [-1, 0, 1]
ft.do_triplets = False
ft.linked = False
ft.qchem_input_params = {}
pc_frag1_edges = {(e[0], e[1]): None for e in self.pc_frag1_edges}
mol_graph = MoleculeGraph.with_edges(self.pc_frag1, pc_frag1_edges)
unique_frag_dict = mol_graph.build_unique_fragments()
unique_frag_list = []
for key in unique_frag_dict:
for frag in unique_frag_dict[key]:
unique_frag_list.append(frag)
ft.unique_fragments = unique_frag_list
ft._build_unique_relevant_molecules()
ft.all_relevant_docs = list()
new_FWs = ft._build_new_FWs()
self.assertEqual(len(new_FWs), 36)
def test_in_database_through_build_new_FWs(self):
ft = FragmentMolecule(molecule=self.pc_frag1,
edges=self.pc_frag1_edges,
depth=0)
ft.mol = ft.get("molecule")
ft.depth = ft.get("depth")
ft.charges = [-1, 0, 1]
ft.do_triplets = False
ft.linked = False
ft.qchem_input_params = {}
pc_frag1_edges = {(e[0], e[1]): None for e in self.pc_frag1_edges}
mol_graph = MoleculeGraph.with_edges(self.pc_frag1, pc_frag1_edges)
unique_frag_dict = mol_graph.build_unique_fragments()
unique_frag_list = []
for key in unique_frag_dict:
for frag in unique_frag_dict[key]:
unique_frag_list.append(frag)
ft.unique_fragments = unique_frag_list
ft._build_unique_relevant_molecules()
docs = loadfn(os.path.join(module_dir, "doc.json"))
for doc in docs:
doc["input"]["initial_molecule"] = doc["input"][
"initial_molecule"].as_dict()
ft.all_relevant_docs = docs
new_FWs = ft._build_new_FWs()
self.assertEqual(len(new_FWs), 29)
def test_build_unique_relevant_molecules_with_triplets(self):
ft = FragmentMolecule(molecule=self.pc,
edges=self.pc_edges,
depth=0,
opt_steps=1000)
ft.mol = ft.get("molecule")
ft.depth = ft.get("depth")
ft.charges = [-1, 0, 1]
ft.do_triplets = True
edges = {(e[0], e[1]): None for e in self.pc_edges}
mol_graph = MoleculeGraph.with_edges(self.pc, edges)
unique_frag_dict = mol_graph.build_unique_fragments()
unique_frag_list = []
for key in unique_frag_dict:
for frag in unique_frag_dict[key]:
unique_frag_list.append(frag)
ft.unique_fragments = unique_frag_list
ft._build_unique_relevant_molecules()
self.assertEqual(len(ft.unique_molecules), 1323)
# dumpfn(ft.unique_molecules, os.path.join(module_dir,"pc_mols_with_trips.json"))
loadfn(os.path.join(module_dir, "pc_mols_with_trips.json"))
# self.assertEqual(ft.unique_molecules, ref_mols)
ft = FragmentMolecule(molecule=self.pos_pc,
edges=self.pc_edges,
depth=0,
opt_steps=1000)
ft.mol = ft.get("molecule")
ft.depth = ft.get("depth")
ft.charges = [-1, 0, 1, 2]
ft.do_triplets = True
mol_graph = MoleculeGraph.with_edges(self.pos_pc, edges)
unique_frag_dict = mol_graph.build_unique_fragments()
unique_frag_list = []
for key in unique_frag_dict:
for frag in unique_frag_dict[key]:
unique_frag_list.append(frag)
ft.unique_fragments = unique_frag_list
ft._build_unique_relevant_molecules()
self.assertEqual(len(ft.unique_molecules), 1770)
# dumpfn(ft.unique_molecules, os.path.join(module_dir,"pos_pc_mols_with_trips.json"))
loadfn(os.path.join(module_dir, "pos_pc_mols_with_trips.json"))
# self.assertEqual(ft.unique_molecules, ref_mols)
ft = FragmentMolecule(molecule=self.pc_frag1,
edges=self.pc_frag1_edges,
depth=0)
ft.mol = ft.get("molecule")
ft.depth = ft.get("depth")
ft.charges = [-1, 0, 1]
ft.do_triplets = True
pc_frag1_edges = {(e[0], e[1]): None for e in self.pc_frag1_edges}
mol_graph = MoleculeGraph.with_edges(self.pc_frag1, pc_frag1_edges)
unique_frag_dict = mol_graph.build_unique_fragments()
unique_frag_list = []
for key in unique_frag_dict:
for frag in unique_frag_dict[key]:
unique_frag_list.append(frag)
ft.unique_fragments = unique_frag_list
ft._build_unique_relevant_molecules()
self.assertEqual(len(ft.unique_molecules), 54)
# dumpfn(ft.unique_molecules, os.path.join(module_dir,"pc_frag1_mols_with_trips.json"))
loadfn(os.path.join(module_dir, "pc_frag1_mols_with_trips.json"))
def __init__(self,
molecule=None,
depth=1,
open_rings=True,
additional_charges=None,
do_triplets=True,
name="fragment and optimize",
qchem_cmd=">>qchem_cmd<<",
multimode=">>multimode<<",
max_cores=">>max_cores<<",
qchem_input_params=None,
db_file=None,
check_db=True,
parents=None,
**kwargs):
"""
Fragment the given structure and optimize all unique fragments
Args:
molecule (Molecule): Input molecule.
depth (int): Fragmentation depth. Defaults to 1. See fragmenter firetask for more details.
open_rings (bool): Whether or not to open any rings encountered during fragmentation.
Defaults to True. See fragmenter firetask for more details.
additional_charges (list): List of additional charges besides the defaults. See fragmenter
firetask for more details.
do_triplets (bool): Whether to simulate triplets as well as singlets for molecules with an
even number of electrons. Defaults to True.
name (str): Name for the Firework.
qchem_cmd (str): Command to run QChem. Supports env_chk.
multimode (str): Parallelization scheme, either openmp or mpi. Supports env_chk.
max_cores (int): Maximum number of cores to parallelize over. Supports env_chk.
qchem_input_params (dict): Specify kwargs for instantiating the input set parameters.
Basic uses would be to modify the default inputs of the set,
such as dft_rung, basis_set, pcm_dielectric, scf_algorithm,
or max_scf_cycles. See pymatgen/io/qchem/sets.py for default
values of all input parameters. For instance, if a user wanted
to use a more advanced DFT functional, include a pcm with a
dielectric of 30, and use a larger basis, the user would set
qchem_input_params = {"dft_rung": 5, "pcm_dielectric": 30,
"basis_set": "6-311++g**"}. However, more advanced customization
of the input is also possible through the overwrite_inputs key
which allows the user to directly modify the rem, pcm, smd, and
solvent dictionaries that QChemDictSet passes to inputs.py to
print an actual input file. For instance, if a user wanted to
set the sym_ignore flag in the rem section of the input file
to true, then they would set qchem_input_params = {"overwrite_inputs":
"rem": {"sym_ignore": "true"}}. Of course, overwrite_inputs
could be used in conjuction with more typical modifications,
as seen in the test_double_FF_opt workflow test.
db_file (str): Path to file specifying db credentials to place output parsing.
check_db (bool): Whether or not to check the database for equivalent structures
before adding new fragment fireworks. Defaults to True.
parents ([Firework]): Parents of this particular Firework.
**kwargs: Other kwargs that are passed to Firework.__init__.
"""
qchem_input_params = qchem_input_params or {}
additional_charges = additional_charges or []
t = []
t.append(
FragmentMolecule(molecule=molecule,
depth=depth,
open_rings=open_rings,
additional_charges=additional_charges,
do_triplets=do_triplets,
max_cores=max_cores,
qchem_input_params=qchem_input_params,
db_file=db_file,
check_db=check_db))
super(FragmentFW, self).__init__(t,
parents=parents,
name=name,
**kwargs)
def test_build_unique_relevant_molecules_with_triplets(self):
ft = FragmentMolecule(molecule=self.pc, edges=self.pc_edges, depth=0, opt_steps=1000)
ft.mol = ft.get("molecule")
ft.depth = ft.get("depth")
ft.charges = [-1, 0, 1]
ft.do_triplets = True
edges = {(e[0], e[1]): None for e in self.pc_edges}
mol_graph = MoleculeGraph.with_edges(self.pc, edges)
ft.unique_fragments = mol_graph.build_unique_fragments()
ft._build_unique_relevant_molecules()
self.assertEqual(len(ft.unique_molecules), 1323)
#dumpfn(ft.unique_molecules, os.path.join(module_dir,"pc_mols_with_trips.json"))
ref_mols = loadfn(os.path.join(module_dir, "pc_mols_with_trips.json"))
self.assertEqual(ft.unique_molecules, ref_mols)
ft = FragmentMolecule(molecule=self.pos_pc, edges=self.pc_edges, depth=0, opt_steps=1000)
ft.mol = ft.get("molecule")
ft.depth = ft.get("depth")
ft.charges = [-1, 0, 1, 2]
ft.do_triplets = True
mol_graph = MoleculeGraph.with_edges(self.pos_pc, edges)
ft.unique_fragments = mol_graph.build_unique_fragments()
ft._build_unique_relevant_molecules()
self.assertEqual(len(ft.unique_molecules), 1770)
#dumpfn(ft.unique_molecules, os.path.join(module_dir,"pos_pc_mols_with_trips.json"))
ref_mols = loadfn(os.path.join(module_dir, "pos_pc_mols_with_trips.json"))
self.assertEqual(ft.unique_molecules, ref_mols)
ft = FragmentMolecule(molecule=self.pc_frag1, edges=self.pc_frag1_edges, depth=0)
ft.mol = ft.get("molecule")
ft.depth = ft.get("depth")
ft.charges = [-1, 0, 1]
ft.do_triplets = True
pc_frag1_edges = {(e[0], e[1]): None for e in self.pc_frag1_edges}
mol_graph = MoleculeGraph.with_edges(self.pc_frag1, pc_frag1_edges)
ft.unique_fragments = mol_graph.build_unique_fragments()
ft._build_unique_relevant_molecules()
self.assertEqual(len(ft.unique_molecules), 54)
#dumpfn(ft.unique_molecules, os.path.join(module_dir,"pc_frag1_mols_with_trips.json"))
ref_mols = loadfn(os.path.join(module_dir, "pc_frag1_mols_with_trips.json"))
self.assertEqual(ft.unique_molecules, ref_mols)
def test_build_new_FWs(self):
ft = FragmentMolecule(molecule=self.pc_frag1, edges=self.pc_frag1_edges, depth=0)
ft.mol = ft.get("molecule")
ft.depth = ft.get("depth")
ft.charges = [-1, 0, 1]
ft.do_triplets = False
ft.qchem_input_params = {}
pc_frag1_edges = {(e[0], e[1]): None for e in self.pc_frag1_edges}
mol_graph = MoleculeGraph.with_edges(self.pc_frag1, pc_frag1_edges)
ft.unique_fragments = mol_graph.build_unique_fragments()
ft._build_unique_relevant_molecules()
ft.all_relevant_docs = list()
new_FWs = ft._build_new_FWs()
self.assertEqual(len(new_FWs), 36)
def test_in_database_through_build_new_FWs(self):
ft = FragmentMolecule(molecule=self.pc_frag1, edges=self.pc_frag1_edges, depth=0)
ft.mol = ft.get("molecule")
ft.depth = ft.get("depth")
ft.charges = [-1, 0, 1]
ft.do_triplets = False
ft.qchem_input_params = {}
pc_frag1_edges = {(e[0], e[1]): None for e in self.pc_frag1_edges}
mol_graph = MoleculeGraph.with_edges(self.pc_frag1, pc_frag1_edges)
ft.unique_fragments = mol_graph.build_unique_fragments()
ft._build_unique_relevant_molecules()
docs = loadfn(os.path.join(module_dir, "doc.json"))
for doc in docs:
doc["input"]["initial_molecule"] = doc["input"]["initial_molecule"].as_dict()
ft.all_relevant_docs = docs
new_FWs = ft._build_new_FWs()
self.assertEqual(len(new_FWs), 29)