def test_characterize_path(self):
# set up input variables
with open(
os.path.join(test_dir, "unittest_RN_before_characterize_path.pkl"), "rb"
) as input:
RN = pickle.load(input)
path = loadfn(os.path.join(test_dir, "unittest_characterize_path_path_IN.json"))
solved_PRs = loadfn(
os.path.join(test_dir, "unittest_characterize_path_old_solved_PRs_IN.json")
)
with open(
os.path.join(test_dir, "unittest_characterize_path_PRs_IN.pkl"), "rb"
) as input:
PR_paths = pickle.load(input)
# run calc
path_instance = ReactionPath.characterize_path(
path,
"softplus",
RN.min_cost,
RN.graph,
solved_PRs,
RN.PR_byproducts,
PR_paths,
)
# assert
self.assertEqual(path_instance.byproducts, [356, 182, 548])
self.assertEqual(path_instance.unsolved_prereqs, [])
self.assertEqual(path_instance.solved_prereqs, [556, 46])
self.assertEqual(path_instance.cost, 12.592087913497771)
self.assertEqual(path_instance.pure_cost, 0.0)
self.assertEqual(path_instance.hardest_step_deltaG, None)
self.assertEqual(
path_instance.path,
[
456,
"456+PR_556,424",
424,
"424,423",
423,
"423,420",
420,
"420,356+543",
543,
"543+PR_46,15",
15,
"15,13",
13,
"13,1+548",
1,
"1,2",
2,
],
)
def test_characterize_path_final(self):
# set up input variables
with open(os.path.join(test_dir, "unittest_RN_pr_solved.pkl"),
"rb") as input:
RN_pr_solved = pickle.load(input)
# perform calc
# print(RN_pr_solved.PRs[2], RN_pr_solved.PRs[2])
path_class = ReactionPath.characterize_path_final(
RN_pr_solved.PRs[2][456].path,
RN_pr_solved.weight,
RN_pr_solved.graph,
RN_pr_solved.solved_PRs,
RN_pr_solved.PRs,
RN_pr_solved.PR_byproducts,
)
# assert
self.assertEqual(path_class.byproducts, [356, 548, 182])
self.assertEqual(path_class.solved_prereqs, [556, 46])
self.assertEqual(path_class.all_prereqs, [556, 46])
self.assertEqual(path_class.cost, 12.592087913497771)
self.assertEqual(
path_class.path,
[
456,
"456+556,424",
424,
"424,423",
423,
"423,420",
420,
"420,356+543",
543,
"46+543,15",
15,
"15,13",
13,
"13,1+548",
1,
"1,2",
2,
],
)
self.assertEqual(path_class.overall_free_energy_change,
10.868929712195717)
self.assertEqual(path_class.pure_cost, 12.592087913497771)
self.assertEqual(path_class.hardest_step_deltaG, 4.018404627691188)