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Added helper functions to check the parameters of the generated TS guess
 And added minor adjustments for the test functions of the different reaction families
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‎arc/job/adapters/ts/heuristics_test.py‎

Lines changed: 98 additions & 87 deletions
Original file line numberDiff line numberDiff line change
@@ -32,14 +32,10 @@
3232
hydrolysis
3333
)
3434
from arc.reaction import ARCReaction
35-
from arc.species.converter import str_to_xyz, zmat_to_xyz, xyz_to_str,zmat_from_xyz
35+
from arc.species.converter import str_to_xyz, zmat_to_xyz, xyz_to_str
3636
from arc.species.species import ARCSpecies
37-
from arc.species.zmat import _compare_zmats
3837
from arc.species.vectors import calculate_param
39-
40-
FAMILY_SETS = {'set_1': ['ester_hydrolysis', 'imine_hydrolysis','ether_hydrolysis'],
41-
'set_2': ['nitrile_hydrolysis']} #sub-groups of hydrolysis reaction families
42-
38+
from arc.species.zmat import _compare_zmats
4339

4440
class TestHeuristicsAdapter(unittest.TestCase):
4541
"""
@@ -2326,17 +2322,6 @@ def test_are_h_abs_wells_reversed(self):
23262322
self.assertFalse(r_reversed)
23272323
self.assertFalse(p_reversed)
23282324

2329-
2330-
2331-
@classmethod
2332-
def tearDownClass(cls):
2333-
"""
2334-
A function that is run ONCE after all unit tests in this class.
2335-
Delete all project directories created during these unit tests.
2336-
"""
2337-
shutil.rmtree(os.path.join(ARC_PATH, 'arc', 'testing', 'heuristics'), ignore_errors=True)
2338-
shutil.rmtree(os.path.join(ARC_PATH, 'arc', 'testing', 'heuristics_1'), ignore_errors=True)
2339-
23402325
def test_is_water(self):
23412326
"""Test the is_water() function."""
23422327
water = self.water
@@ -2488,6 +2473,29 @@ def test_check_dao_angle(self):
24882473
result = check_dao_angle(d2_indices, initial_xyz)
24892474
self.assertFalse(result)
24902475

2476+
# Validation Helper Functions
2477+
def check_distance(self, coords, atoms, expected, places=0):
2478+
"""Checks if the calculated distance between atoms is close to the expected value."""
2479+
value = calculate_param(coords=coords, atoms=atoms)
2480+
self.assertAlmostEqual(value, expected, places=places)
2481+
2482+
def check_angle(self, coords, atoms, expected, places=None, delta=None):
2483+
"""Checks if the calculated angle is within the acceptable deviation."""
2484+
value = calculate_param(coords=coords, atoms=atoms)
2485+
if delta:
2486+
self.assertAlmostEqual(value, expected, delta=delta)
2487+
elif places:
2488+
self.assertAlmostEqual(value, expected, places=places)
2489+
2490+
def check_dihedral(self, coords, atoms, expected, places=None, delta=None):
2491+
"""Checks if the calculated dihedral angle is within the acceptable deviation."""
2492+
value = calculate_param(coords=coords, atoms=atoms)
2493+
normalized = abs((value + 180) % 360 - 180)
2494+
if delta:
2495+
self.assertAlmostEqual(normalized, expected, delta=delta)
2496+
elif places:
2497+
self.assertAlmostEqual(normalized, expected, places=places)
2498+
24912499
def test_ester_hydrolysis(self):
24922500
"""Test ester hydrolysis reactions."""
24932501
water = self.water
@@ -2544,27 +2552,27 @@ def test_ester_hydrolysis(self):
25442552
self.assertIn('ester_hydrolysis', families)
25452553
xyz_guesses_total, zmats_total = hydrolysis(tested_rxn)
25462554

2547-
for i in xyz_guesses_total:
2548-
family=i['family']
2555+
for guess_block in xyz_guesses_total:
2556+
family=guess_block['family']
25492557
print(family)
2550-
a,b,f,d,O,H1= i['indices'][0], i['indices'][1], i['indices'][2], i['indices'][3], i['indices'][4], i['indices'][5]
2551-
for j in i['xyz_guesses']:
2552-
xyz_str = xyz_to_str(j)
2558+
a,b,f,O,H1,d= guess_block['indices'][0], guess_block['indices'][1], guess_block['indices'][2], guess_block['indices'][3], guess_block['indices'][4], guess_block['indices'][5]
2559+
print(a,b,f,d,O,H1)
2560+
for guess in guess_block['xyz_guesses']:
2561+
xyz_str = xyz_to_str(guess)
25532562
print(xyz_str)
25542563
print()
25552564
if family== 'ester_hydrolysis':#the parameters of ether hydrolysis are checked in the following test section
25562565
distance_ab=(calculate_param(coords=initial_xyz['coords'], atoms=[b, a]))*1.3
2557-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[b, a]), distance_ab, places=0)
2558-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[a, O]), 1.8, places=0)
2559-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[O, H1]), 1.21, places=0)
2560-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[O, H1+1]), 0.97, places=2)
2561-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[b, a, O]), 77, places=0)
2562-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[a, O, H1]), 71, places=0)
2563-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[H1, O, H1+1]), 111, places=0)
2564-
self.assertAlmostEqual(abs((calculate_param(coords=j['coords'], atoms=[f, d, a, O]) + 180) % 360 - 180), 140, places=0)
2565-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[b, a, O, H1]), 1.64, places=1)
2566-
self.assertAlmostEqual(abs((calculate_param(coords=j['coords'], atoms=[a, H1, O, H1+1]) + 180) % 360 - 180), 103, places=0)
2567-
2566+
self.check_distance(coords=guess['coords'], atoms=[b, a], expected=distance_ab, places=0)
2567+
self.check_distance(coords=guess['coords'], atoms=[a, O], expected=1.8, places=0)
2568+
self.check_distance(coords=guess['coords'], atoms=[O, H1], expected=1.21, places=0)
2569+
self.check_distance(coords=guess['coords'], atoms=[O, H1 + 1], expected=0.97,places=0)
2570+
self.check_angle(coords=guess['coords'], atoms=[b, a, O], expected=77, delta=5)
2571+
self.check_angle(coords=guess['coords'], atoms=[a, O, H1], expected=71, delta=5)
2572+
self.check_angle(coords=guess['coords'], atoms=[H1, O, H1 + 1], expected=111, delta=5)
2573+
self.check_dihedral(coords=guess['coords'], atoms=[f, d, a, O], expected=140, delta=5)
2574+
self.check_dihedral(coords=guess['coords'], atoms=[b, a, O, H1], expected=1.64, delta=3)
2575+
self.check_dihedral(coords=guess['coords'], atoms=[a, H1, O, H1 + 1], expected=103, delta=5)
25682576
def test_ether_hydrolysis(self):
25692577
"""Test ether hydrolysis reactions."""
25702578
water = self.water
@@ -2598,27 +2606,25 @@ def test_ether_hydrolysis(self):
25982606
families = [entry['family'] for entry in product_dicts]
25992607
self.assertIn('ether_hydrolysis', families)
26002608
xyz_guesses_total, zmats_total = hydrolysis(tested_rxn)
2601-
for i in xyz_guesses_total:
2602-
print(i['family'])
2603-
a, b, f, d, O, H1 = i['indices'][0], i['indices'][1], i['indices'][2], i['indices'][3], i['indices'][4], i['indices'][5]
2609+
for guess_block in xyz_guesses_total:
2610+
print(guess_block['family'])
2611+
a, b, f, O, H1, d = guess_block['indices'][0], guess_block['indices'][1], guess_block['indices'][2], guess_block['indices'][3], guess_block['indices'][4], guess_block['indices'][5]
26042612
print(a, b, f, d, O, H1)
2605-
for j in i['xyz_guesses']:
2606-
xyz_str = xyz_to_str(j)
2613+
for guess in guess_block['xyz_guesses']:
2614+
xyz_str = xyz_to_str(guess)
26072615
print(xyz_str)
26082616
print()
26092617
distance_ab = (calculate_param(coords=initial_xyz['coords'], atoms=[b, a])) * 1.5
2610-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[b, a]), distance_ab, places=0)
2611-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[a, O]), 2.1, places=0)
2612-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[O, H1]), 1.21, places=0)
2613-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[O, H1 + 1]), 0.97, places=0)
2614-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[b, a, O]), 65, places=0)
2615-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[a, O, H1]), 72, places=0)
2616-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[H1, O, H1 + 1]), 106, places=0)
2617-
self.assertAlmostEqual(abs((calculate_param(coords=j['coords'], atoms=[f, d, a, O]) + 180) % 360 - 180),
2618-
98.25, places=0)
2619-
self.assertAlmostEqual((calculate_param(coords=j['coords'], atoms=[b, a, O, H1]) + 180) % 360 - 180, -0.72, places=1)
2620-
self.assertAlmostEqual(
2621-
abs((calculate_param(coords=j['coords'], atoms=[a, H1, O, H1 + 1]) + 180) % 360 - 180), 103, places=0)
2618+
self.check_distance(coords=guess['coords'], atoms=[b, a], expected=distance_ab, places=0)
2619+
self.check_distance(coords=guess['coords'], atoms=[a, O], expected=2.1, places=0)
2620+
self.check_distance(coords=guess['coords'], atoms=[O, H1], expected=1.21, places=0)
2621+
self.check_distance(coords=guess['coords'], atoms=[O, H1 + 1], expected=0.97, places=0)
2622+
self.check_angle(coords=guess['coords'], atoms=[b, a, O], expected=65, delta=5)
2623+
self.check_angle(coords=guess['coords'], atoms=[a, O, H1], expected=72, delta=5)
2624+
self.check_angle(coords=guess['coords'], atoms=[H1, O, H1 + 1], expected=106, delta=6)
2625+
self.check_dihedral(coords=guess['coords'], atoms=[f, d, a, O], expected=98.25, delta=10)
2626+
self.check_dihedral(coords=guess['coords'], atoms=[b, a, O, H1], expected=-0.72, delta=10)
2627+
self.check_dihedral(coords=guess['coords'], atoms=[a, H1, O, H1 + 1], expected=103, delta=10)
26222628

26232629
def test_imine_hydrolysis(self):
26242630
"""Test imine hydrolysis reactions."""
@@ -2640,7 +2646,7 @@ def test_imine_hydrolysis(self):
26402646
phenylalaninol=self.phenylalaninol
26412647
rxn4=ARCReaction(r_species=[phenylethanimine, water], p_species=[phenylalaninol])
26422648

2643-
tested_rxn = rxn4
2649+
tested_rxn = rxn3
26442650
reactant = tested_rxn.r_species[0]
26452651
initial_xyz = reactant.get_xyz()
26462652
product_dicts = get_reaction_family_products(
@@ -2652,28 +2658,25 @@ def test_imine_hydrolysis(self):
26522658
families = [entry['family'] for entry in product_dicts]
26532659
self.assertIn('imine_hydrolysis', families)
26542660
xyz_guesses_total, zmats_total = hydrolysis(reaction=tested_rxn)
2655-
for i in xyz_guesses_total:
2656-
print(i['family'])
2657-
a, b, f, d, O, H1 = i['indices'][0], i['indices'][1], i['indices'][2], i['indices'][3], i['indices'][4], i['indices'][5]
2661+
for block in xyz_guesses_total:
2662+
print(block['family'])
2663+
a, b, f, O, H1, d = block['indices'][0], block['indices'][1], block['indices'][2], block['indices'][3], block['indices'][4], block['indices'][5]
26582664
print(a, b, f, d, O, H1)
2659-
for j in i['xyz_guesses']:
2660-
xyz_str = xyz_to_str(j)
2665+
for guess in block['xyz_guesses']:
2666+
xyz_str = xyz_to_str(guess)
26612667
print(xyz_str)
26622668
print()
26632669
distance_ab = (calculate_param(coords=initial_xyz['coords'], atoms=[b, a])) * 1.3
2664-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[b, a]), distance_ab, places=0)
2665-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[a, O]), 1.8, places=0)
2666-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[O, H1]), 1.21, places=0)
2667-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[O, H1 + 1]), 0.97, places=0)
2668-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[b, a, O]), 78, places=0)
2669-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[a, O, H1]), 70, places=0)
2670-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[H1, O, H1 + 1]), 111, places=0)
2671-
self.assertAlmostEqual(abs((calculate_param(coords=j['coords'], atoms=[f, d, a, O]) + 180) % 360 - 180),
2672-
108, places=0)
2673-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[b, a, O, H1]),12, places=0)
2674-
self.assertAlmostEqual(
2675-
abs((calculate_param(coords=j['coords'], atoms=[a, H1, O, H1 + 1]) + 180) % 360 - 180), 113,
2676-
places=0)
2670+
self.check_distance(coords=guess['coords'], atoms=[b, a], expected=distance_ab, places=0)
2671+
self.check_distance(coords=guess['coords'], atoms=[a, O], expected=1.8, places=0)
2672+
self.check_distance(coords=guess['coords'], atoms=[O, H1], expected=1.21, places=0)
2673+
self.check_distance(coords=guess['coords'], atoms=[O, H1 + 1], expected=0.97, places=0)
2674+
self.check_angle(coords=guess['coords'], atoms=[b, a, O], expected=78, delta=5)
2675+
self.check_angle(coords=guess['coords'], atoms=[a, O, H1], expected=70, delta=5)
2676+
self.check_angle(coords=guess['coords'], atoms=[H1, O, H1 + 1], expected=111, delta=5)
2677+
self.check_dihedral(coords=guess['coords'], atoms=[f, d, a, O], expected=108, delta=5)
2678+
self.check_dihedral(coords=guess['coords'], atoms=[b, a, O, H1], expected=12, delta=5)
2679+
self.check_dihedral(coords=guess['coords'], atoms=[a, H1, O, H1 + 1], expected=113, delta=5)
26772680

26782681
def test_nitrile_hydrolysis(self):
26792682
"""Test nitrile hydrolysis reactions."""
@@ -2707,27 +2710,35 @@ def test_nitrile_hydrolysis(self):
27072710
families = [entry['family'] for entry in product_dicts]
27082711
self.assertIn('nitrile_hydrolysis', families)
27092712
xyz_guesses_total, zmats_total = hydrolysis(tested_rxn)
2710-
for i in xyz_guesses_total:
2711-
a, b, f, O, H1 = i['indices'][0], i['indices'][1], i['indices'][2], i['indices'][4], i['indices'][5]
2712-
print(i['family'])
2713-
for j in i['xyz_guesses']:
2714-
xyz_str = xyz_to_str(j)
2713+
for block in xyz_guesses_total:
2714+
a, b, f, O, H1 = block['indices'][0], block['indices'][1], block['indices'][2], block['indices'][4], block['indices'][5]
2715+
print(block['family'])
2716+
for guess in block['xyz_guesses']:
2717+
xyz_str = xyz_to_str(guess)
27152718
print(xyz_str)
27162719
print()
27172720
distance_ab = (calculate_param(coords=initial_xyz['coords'], atoms=[b, a])) * 1.1
2718-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[b, a]), distance_ab, places=2)
2719-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[a, O]), 1.8, places=2)
2720-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[O, H1]), 1.21, places=2)
2721-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[O, H1 + 1]), 0.97, places=2)
2722-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[b, a, O]), 97, places=1)
2723-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[a, O, H1]), 58, places=1)
2724-
self.assertAlmostEqual(calculate_param(coords=j['coords'], atoms=[H1, O, H1 + 1]), 111, places=1)
2725-
self.assertAlmostEqual(abs((calculate_param(coords=j['coords'], atoms=[f, b, a, O]) + 180) % 360 - 180),
2726-
174, places=1)
2727-
self.assertAlmostEqual((calculate_param(coords=j['coords'], atoms=[b, a, O, H1]) + 180) % 360 - 180, -0.0154, places=1)
2728-
self.assertAlmostEqual(
2729-
abs((calculate_param(coords=j['coords'], atoms=[a, H1, O, H1 + 1]) + 180) % 360 - 180), 104,
2730-
places=1)
2721+
self.check_distance(coords=guess['coords'], atoms=[b, a], expected=distance_ab, places=0)
2722+
self.check_distance(coords=guess['coords'], atoms=[a, O], expected=1.8, places=0)
2723+
self.check_distance(coords=guess['coords'], atoms=[O, H1], expected=1.21, places=0)
2724+
self.check_distance(coords=guess['coords'], atoms=[O, H1 + 1], expected=0.97, places=0)
2725+
self.check_angle(coords=guess['coords'], atoms=[b, a, O], expected=97, delta=5)
2726+
self.check_angle(coords=guess['coords'], atoms=[a, O, H1], expected=58, delta=5)
2727+
self.check_angle(coords=guess['coords'], atoms=[H1, O, H1 + 1], expected=111, delta=5)
2728+
self.check_dihedral(coords=guess['coords'], atoms=[f, b, a, O], expected=174, delta=5)
2729+
self.check_dihedral(coords=guess['coords'], atoms=[b, a, O, H1], expected=-0.0154, delta=5)
2730+
self.check_dihedral(coords=guess['coords'], atoms=[a, O, H1, H1 + 1], expected=104, delta=5)
2731+
2732+
@classmethod
2733+
def tearDownClass(cls):
2734+
"""
2735+
A function that is run ONCE after all unit tests in this class.
2736+
Delete all project directories created during these unit tests.
2737+
"""
2738+
shutil.rmtree(os.path.join(ARC_PATH, 'arc', 'testing', 'heuristics'), ignore_errors=True)
2739+
shutil.rmtree(os.path.join(ARC_PATH, 'arc', 'testing', 'heuristics_1'), ignore_errors=True)
2740+
2741+
27312742

27322743
if __name__ == '__main__':
27332744
unittest.main(testRunner=unittest.TextTestRunner(verbosity=2))

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