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"))
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)
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"))
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)
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"))
ref_mols = loadfn(os.path.join(module_dir, "pc_frag1_mols_with_trips.json"))
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_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)
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_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)