def test_generate_node_string(self):
react_prod = [
([19, 32], [673]),
([41], [992]),
([1, 652], [40, 53]),
([4], [5, 6]),
]
node_strings = []
for rxn in react_prod:
node_str = ReactionNetwork.generate_node_string(rxn[0], rxn[1])
node_strings.append(node_str)
self.assertListEqual(node_strings,
["19+32,673", "41,992", "1+652,40+53", "4,5+6"])
def test_identify_concerted_rxns_via_intermediates(self):
# v1 and v2 comparison
# load reactions from v1 of concerted reactions
v1 = loadfn(
os.path.join(test_dir,
"identify_concerted_intermediate_list_v1.json"))
# load RN
with open(
os.path.join(
test_dir,
"identify_concerted_via_intermediate_unittest_RN.pkl"),
"rb",
) as input:
RN_loaded = pickle.load(input)
# process reaction list from v1 of concerted reaction such that Nones are removed,
# A+B>B+A and repeated reactions are removed
v1_processed = []
for r_old in v1:
a = r_old[0]
b = r_old[1]
if None in b:
b.remove(None)
if len(a) == 2 and len(b) == 2:
inter = 0
inter = set(a).intersection(set(b))
for i in inter:
a.remove(i)
b.remove(i)
a.sort()
b.sort()
c = [a, b]
v1_processed.append(c)
with open(
os.path.join(
test_dir,
"identify_concerted_intermediate_list_v2_iter1.pkl"),
"rb",
) as handle:
v2_unique = pickle.load(handle)
v1_set = set(map(lambda x: repr(x), v1_processed))
v2_set = set(map(lambda x: repr(x), v2_unique))
inter = list(v1_set.intersection(v2_set))
v1_v2 = list(map(lambda y: literal_eval(y), v1_set - v2_set))
v2_v1 = list(map(lambda y: literal_eval(y), v2_set - v1_set))
# check if v2 missed any reactions found by v1
missed_by_v2 = []
for r in v1_v2:
node_str = ReactionNetwork.generate_node_string(r[0], r[1])
if node_str not in RN_loaded.graph.nodes:
missed_by_v2.append(r)
# checks number of same reactions in v1 and v2, number of reactions missed by v2,
# and number of new reactions found by v2
self.assertEqual(len(missed_by_v2), 0)
self.assertEqual(len(v1_v2), 11)
self.assertEqual(len(v2_v1), 0)
self.assertEqual(len(inter), 29214)
self.assertEqual(len(v2_unique), 29214)
with open(
os.path.join(
test_dir,
"identify_concerted_intermediate_list_v2_iter2.pkl"),
"rb",
) as handle:
v2_unique_iter2 = pickle.load(handle)
v2_set_iter2 = set(map(lambda x: repr(x), v2_unique_iter2))
inter_iter2 = list(v1_set.intersection(v2_set_iter2))
self.assertEqual(len(inter_iter2), 0)
self.assertEqual(len(v2_unique_iter2), 2100)
# v2 and v3 comparison
RN_loaded.matrix = None
(
v3_unique_iter1,
v3_all_iter1,
) = RN_loaded.identify_concerted_rxns_via_intermediates(
RN_loaded, single_elem_interm_ignore=[], update_matrix=True)
v3_set = set(map(lambda x: repr(x), v3_unique_iter1))
inter_v2_v3 = list(v2_set.intersection(v3_set))
v2_v3 = list(map(lambda y: literal_eval(y), v2_set - v3_set))
v3_v2 = list(map(lambda y: literal_eval(y), v3_set - v2_set))
self.assertEqual(len(v3_unique_iter1), 29225)
self.assertEqual(len(v2_v3), 0)
self.assertEqual(len(v3_v2), 11)
self.assertEqual(len(inter_v2_v3), 29214)
new_by_v3 = []
for r in v3_v2:
node_str = ReactionNetwork.generate_node_string(r[0], r[1])
if node_str not in RN_loaded.graph.nodes:
new_by_v3.append(r)
self.assertEqual(len(new_by_v3), 0)