def test_free_energy(self):
reaction = RedoxReaction(self.EC_0_entry, self.EC_1_entry)
reaction.electron_free_energy = -2.15
reaction.free_energy()
self.assertEqual(reaction.free_energy_A, 6.231346035181195)
self.assertEqual(reaction.free_energy_B, -6.231346035181195)
def test_energy(self):
reaction = RedoxReaction(self.EC_0_entry, self.EC_1_entry)
reaction.electron_free_energy = -2.15
reaction.energy()
self.assertEqual(reaction.energy_A, 0.3149076465170424)
self.assertEqual(reaction.energy_B, -0.3149076465170424)
def test_graph_representation(self):
reaction = RedoxReaction(entries["EC_0"], entries["EC_1"])
reaction.electron_free_energy = -2.15
graph = reaction.graph_representation()
EC_0_ind = entries["EC_0"].parameters["ind"]
EC_1_ind = entries["EC_1"].parameters["ind"]
self.assertCountEqual(
list(graph.nodes),
[
EC_0_ind,
EC_1_ind,
str(EC_0_ind) + "," + str(EC_1_ind),
str(EC_1_ind) + "," + str(EC_0_ind),
],
)
self.assertEqual(len(graph.edges), 4)
self.assertEqual(
graph.get_edge_data(EC_0_ind,
str(EC_0_ind) + "," +
str(EC_1_ind))["softplus"],
5.629805462349386,
)
def test_add_reactions(self):
# set up RN
RN = ReactionNetwork.from_input_entries(
self.LiEC_reextended_entries, electron_free_energy=-2.15
)
# set up input variables
EC_0_entry = None
EC_minus_entry = None
# print(RN.entries["C3 H4 O3"].keys())
for entry in RN.entries["C3 H4 O3"][10][0]:
if self.EC_mg.isomorphic_to(entry.mol_graph):
EC_0_entry = entry
break
for entry in RN.entries["C3 H4 O3"][10][-1]:
if self.EC_mg.isomorphic_to(entry.mol_graph):
EC_minus_entry = entry
break
redox = RedoxReaction(EC_0_entry, EC_minus_entry)
redox.electron_free_energy = -2.15
redox_graph = redox.graph_representation()
# run calc
RN.add_reaction(redox_graph)
# assert
self.assertEqual(list(RN.graph.nodes), ["456,455", 456, 455, "455,456"])
self.assertEqual(
list(RN.graph.edges),
[("456,455", 455), (456, "456,455"), (455, "455,456"), ("455,456", 456)],
)
def test_generate(self):
reactions = RedoxReaction.generate(entries["RN"].entries)
self.assertEqual(len(reactions), 273)
for r in reactions:
if r.reactant == entries["EC_0"]:
self.assertEqual(r.product.entry_id, entries["EC_1"].entry_id)
if r.reactant == entries["EC_-1"]:
self.assertEqual(r.product.entry_id, entries["EC_0"].entry_id)
def test_graph_representation(self):
RN = ReactionNetwork.from_input_entries(self.LiEC_reextended_entries)
EC_0_ind = None
EC_1_ind = None
EC_0_RN_entry = None
EC_1_RN_entry = None
for entry in RN.entries["C3 H4 O3"][10][0]:
if self.EC_mg.isomorphic_to(entry.mol_graph):
EC_0_ind = entry.parameters["ind"]
EC_0_RN_entry = entry
break
for entry in RN.entries["C3 H4 O3"][10][1]:
if self.EC_mg.isomorphic_to(entry.mol_graph):
EC_1_ind = entry.parameters["ind"]
EC_1_RN_entry = entry
break
reaction = RedoxReaction(EC_0_RN_entry, EC_1_RN_entry)
reaction.electron_free_energy = -2.15
graph = reaction.graph_representation()
self.assertCountEqual(
list(graph.nodes),
[
EC_0_ind,
EC_1_ind,
str(EC_0_ind) + "," + str(EC_1_ind),
str(EC_1_ind) + "," + str(EC_0_ind),
],
)
self.assertEqual(len(graph.edges), 4)
self.assertEqual(
graph.get_edge_data(EC_0_ind,
str(EC_0_ind) + "," +
str(EC_1_ind))["softplus"],
5.629805462349386,
)
def test_atom_mapping(self):
entries = bucket_mol_entries(
[self.EC_minus_entry, self.EC_0_entry, self.EC_1_entry])
reactions, families = RedoxReaction.generate(entries)
self.assertEqual(len(reactions), 2)
for r in reactions:
self.assertEqual(
r.reactants_atom_mapping,
[{
0: 0,
1: 1,
2: 2,
3: 3,
4: 4,
5: 5,
6: 6,
7: 7,
8: 8,
9: 9
}],
)
self.assertEqual(
r.products_atom_mapping,
[{
0: 0,
1: 1,
2: 2,
3: 3,
4: 4,
5: 5,
6: 6,
7: 7,
8: 8,
9: 9
}],
)
def test_atom_mapping(self):
ents = bucket_mol_entries(
[entries["EC_-1"], entries["EC_0"], entries["EC_1"]])
reactions = RedoxReaction.generate(ents)
self.assertEqual(len(reactions), 2)
for r in reactions:
self.assertEqual(
r.reactants_atom_mapping,
[{
0: 0,
1: 1,
2: 2,
3: 3,
4: 4,
5: 5,
6: 6,
7: 7,
8: 8,
9: 9
}],
)
self.assertEqual(
r.products_atom_mapping,
[{
0: 0,
1: 1,
2: 2,
3: 3,
4: 4,
5: 5,
6: 6,
7: 7,
8: 8,
9: 9
}],
)
def test_reaction_type(self):
reaction = RedoxReaction(self.EC_0_entry, self.EC_1_entry)
self.assertEqual(reaction.rxn_type_A, "One electron oxidation")
self.assertEqual(reaction.rxn_type_B, "One electron reduction")
def test_generate(self):
RN = ReactionNetwork.from_input_entries(self.LiEC_reextended_entries)
reactions, families = RedoxReaction.generate(RN.entries)
self.assertEqual(len(reactions), 273)
def test_reaction_type(self):
reaction = RedoxReaction(entries["EC_0"], entries["EC_1"])
self.assertEqual(reaction.__class__.__name__, "RedoxReaction")
self.assertEqual(reaction.rxn_type_A, "One electron oxidation")
self.assertEqual(reaction.rxn_type_B, "One electron reduction")
def test_energy(self):
reaction = RedoxReaction(entries["EC_0"], entries["EC_1"])
reaction.electron_free_energy = -2.15
self.assertEqual(reaction.energy_A, 0.3149076465170424)
self.assertEqual(reaction.energy_B, -0.3149076465170424)
def test_free_energy(self):
reaction = RedoxReaction(entries["EC_0"], entries["EC_1"])
reaction.electron_free_energy = -2.15
reaction.set_free_energy()
self.assertEqual(reaction.free_energy_A, 6.231346035181195)
self.assertEqual(reaction.free_energy_B, -6.231346035181195)