def test_free_energy(self):
reaction = IntramolSingleBondChangeReaction(self.LiEC_entry,
self.LiEC_RO_entry)
reaction.free_energy()
self.assertEqual(reaction.free_energy_A, -1.1988634269218892)
self.assertEqual(reaction.free_energy_B, 1.1988634269218892)
def test_energy(self):
reaction = IntramolSingleBondChangeReaction(self.LiEC_entry,
self.LiEC_RO_entry)
reaction.energy()
self.assertEqual(reaction.energy_A, -0.03746218086303088)
self.assertEqual(reaction.energy_B, 0.03746218086303088)
def test_graph_representation(self):
LiEC_RN_entry = entries["LiEC"]
LiEC_RO_RN_entry = entries["LiEC_RO"]
LiEC_ind = LiEC_RN_entry.parameters["ind"]
LiEC_RO_ind = LiEC_RO_RN_entry.parameters["ind"]
reaction = IntramolSingleBondChangeReaction(LiEC_RN_entry,
LiEC_RO_RN_entry)
reaction.electron_free_energy = -2.15
graph = reaction.graph_representation()
# print(graph.nodes, graph.edges)
# print(graph.get_edge_data(LiEC_ind, str(LiEC_ind) + "," + str(LiEC_RO_ind)))
self.assertCountEqual(
list(graph.nodes),
[
LiEC_ind,
LiEC_RO_ind,
str(LiEC_ind) + "," + str(LiEC_RO_ind),
str(LiEC_RO_ind) + "," + str(LiEC_ind),
],
)
self.assertEqual(len(graph.edges), 4)
self.assertEqual(
graph.get_edge_data(LiEC_ind,
str(LiEC_ind) + "," +
str(LiEC_RO_ind))["softplus"],
0.15092362164364986,
)
def test_generate(self):
RN = ReactionNetwork.from_input_entries(self.LiEC_reextended_entries)
reactions, families = IntramolSingleBondChangeReaction.generate(
RN.entries)
self.assertEqual(len(reactions), 93)
for r in reactions:
# TODO (mjwen) this is never run for two reasons:
# 1. It should be:
# if r.reactant == self.LiEC_RO_entry:
# self.assertEqual(r.product.entry_id, self.LiEC_entry.entry_id)
# since this class generates bond formation reactions
# Even, after fixing 1, there is still another problem.
# 2. There are multiple MoleculeEntry with the same `formula`,`Nbonds`,
# and `charge` as self.LiEC_entry. In `setUpClass`, one of such
# MoleculeEntry is set to self.LiEC_entry,
# but in IntramolSingleBondChangeReaction, another MoleculeEntry will be
# used as the reactant. This happens because in both `setUpClass` and
# `IntramolSingleBondChangeReaction`, the code `break` when one entry is
# found.
# To fix this, we can either clean the input data to make sure there is
# only one LiEC, or we do some bookkeeping in `setUpClass` and then make
# the correct check.
# if r.reactant == self.LiEC_entry:
# self.assertEqual(r.product.entry_id, self.LiEC_RO_entry.entry_id)
pass
def test_generate(self):
reactions = IntramolSingleBondChangeReaction.generate(
entries["entries_box"].entries_dict)
self.assertEqual(len(reactions), 73)
reaction_set = set()
for reaction in reactions:
reaction_set.add(
frozenset(
[reaction.reactant.entry_id, reaction.product.entry_id]))
self.assertEqual(len(reaction_set), 73)
for r in reactions:
# TODO (mjwen) this is never run for two reasons:
# 1. It should be:
# if r.reactant == self.LiEC_RO_entry:
# self.assertEqual(r.product.entry_id, self.LiEC_entry.entry_id)
# since this class generates bond formation reactions
# Even, after fixing 1, there is still another problem.
# 2. There are multiple MoleculeEntry with the same `formula`,`Nbonds`,
# and `charge` as self.LiEC_entry. In `setUpClass`, one of such
# MoleculeEntry is set to self.LiEC_entry,
# but in IntramolSingleBondChangeReaction, another MoleculeEntry will be
# used as the reactant. This happens because in both `setUpClass` and
# `IntramolSingleBondChangeReaction`, the code `break` when one entry is
# found.
# To fix this, we can either clean the input data to make sure there is
# only one LiEC, or we do some bookkeeping in `setUpClass` and then make
# the correct check.
if r.reactant == entries["LiEC_RO"]:
self.assertEqual(r.product.entry_id, entries["LiEC"].entry_id)
def test_reaction_type(self):
reaction = IntramolSingleBondChangeReaction(self.LiEC_entry,
self.LiEC_RO_entry)
self.assertEqual(reaction.rxn_type_A,
"Intramolecular single bond formation")
self.assertEqual(reaction.rxn_type_B,
"Intramolecular single bond breakage")
def test_graph_representation(self):
RN = ReactionNetwork.from_input_entries(self.LiEC_reextended_entries)
# print(RN.entries["C3 H4 Li1 O3"][11][0][0].molecule)
LiEC_ind = None
LiEC_RO_ind = None
LiEC_RN_entry = None
LiEC_RO_RN_entry = None
for entry in RN.entries["C3 H4 Li1 O3"][12][0]:
if self.LiEC_mg.isomorphic_to(entry.mol_graph):
LiEC_ind = entry.parameters["ind"]
LiEC_RN_entry = entry
break
for entry in RN.entries["C3 H4 Li1 O3"][11][0]:
if self.LiEC_RO_mg.isomorphic_to(entry.mol_graph):
LiEC_RO_ind = entry.parameters["ind"]
LiEC_RO_RN_entry = entry
break
reaction = IntramolSingleBondChangeReaction(LiEC_RN_entry,
LiEC_RO_RN_entry)
reaction.electron_free_energy = -2.15
graph = reaction.graph_representation()
print(graph.nodes, graph.edges)
print(
graph.get_edge_data(LiEC_ind,
str(LiEC_ind) + "," + str(LiEC_RO_ind)))
self.assertCountEqual(
list(graph.nodes),
[
LiEC_ind,
LiEC_RO_ind,
str(LiEC_ind) + "," + str(LiEC_RO_ind),
str(LiEC_RO_ind) + "," + str(LiEC_ind),
],
)
self.assertEqual(len(graph.edges), 4)
self.assertEqual(
graph.get_edge_data(LiEC_ind,
str(LiEC_ind) + "," +
str(LiEC_RO_ind))["softplus"],
0.15092362164364986,
)
def test_reaction_type(self):
reaction = IntramolSingleBondChangeReaction(entries["LiEC"],
entries["LiEC_RO"])
self.assertEqual(reaction.__class__.__name__,
"IntramolSingleBondChangeReaction")
self.assertEqual(reaction.rxn_type_A,
"Intramolecular single bond formation")
self.assertEqual(reaction.rxn_type_B,
"Intramolecular single bond breakage")
def test_atom_mapping(self):
entries = bucket_mol_entries([self.LiEC_RO_entry, self.LiEC_entry])
reactions, families = IntramolSingleBondChangeReaction.generate(
entries)
self.assertEqual(len(reactions), 1)
rxn = reactions[0]
self.assertEqual(rxn.reactant_ids[0], self.LiEC_RO_entry.entry_id)
self.assertEqual(rxn.product_ids[0], self.LiEC_entry.entry_id)
self.assertEqual(
rxn.reactants_atom_mapping,
[{
0: 0,
1: 1,
2: 2,
3: 3,
4: 4,
5: 5,
6: 6,
7: 7,
8: 8,
9: 9,
10: 10
}],
)
self.assertEqual(
rxn.products_atom_mapping,
[{
0: 0,
1: 1,
2: 2,
3: 3,
4: 4,
5: 5,
6: 6,
7: 7,
8: 8,
9: 9,
10: 10
}],
)
def test_atom_mapping(self):
ents = bucket_mol_entries([entries["LiEC_RO"], entries["LiEC"]])
reactions = IntramolSingleBondChangeReaction.generate(ents)
self.assertEqual(len(reactions), 1)
rxn = reactions[0]
self.assertEqual(rxn.reactant.entry_id, entries["LiEC_RO"].entry_id)
self.assertEqual(rxn.product.entry_id, entries["LiEC"].entry_id)
self.assertEqual(
rxn.reactants_atom_mapping,
[{
0: 0,
1: 1,
2: 2,
3: 3,
4: 4,
5: 5,
6: 6,
7: 7,
8: 8,
9: 9,
10: 10
}],
)
self.assertEqual(
rxn.products_atom_mapping,
[{
0: 2,
1: 3,
2: 1,
3: 4,
4: 5,
5: 0,
6: 6,
7: 9,
8: 10,
9: 7,
10: 8
}],
)
def test_energy(self):
reaction = IntramolSingleBondChangeReaction(entries["LiEC"],
entries["LiEC_RO"])
self.assertEqual(reaction.energy_A, -0.0377282729020294)
self.assertEqual(reaction.energy_B, 0.0377282729020294)
def test_free_energy(self):
reaction = IntramolSingleBondChangeReaction(entries["LiEC"],
entries["LiEC_RO"])
reaction.set_free_energy()
self.assertEqual(reaction.free_energy_A, -1.2094343722765188)
self.assertEqual(reaction.free_energy_B, 1.2094343722765188)
