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WBO testing #430

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Oct 31, 2019
Merged

WBO testing #430

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a096787
test
Sep 30, 2019
9a5ff04
test
sukanyasasmal Oct 25, 2019
bf3a323
added test for wbo
sukanyasasmal Oct 25, 2019
fab711d
test for wbo
sukanyasasmal Oct 25, 2019
a2624cd
molecules for testing wiberg bond order
sukanyasasmal Oct 25, 2019
68e16f4
added wbo testing
sukanyasasmal Oct 28, 2019
618ce63
Delete test_wbo.py
sukanyasasmal Oct 28, 2019
b0eda6b
Rename new test molecules with pubchem CID
j-wags Oct 29, 2019
6f28473
Remove WBO calculation from ToolkitAM1BCCHandler.create_forces
j-wags Oct 29, 2019
5adccf9
Merge branch 'master' into wbo
sukanyasasmal Oct 30, 2019
d1b283b
updated release history
sukanyasasmal Oct 30, 2019
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50 changes: 50 additions & 0 deletions openforcefield/data/molecules/molecule_anion.sdf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,50 @@

-OEChem-10251911083D

21 22 0 0 0 0 0 0 0999 V2000
2.5846 -1.9672 -3.6367 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0132 -0.9725 -4.3521 N 0 0 0 0 0 0 0 0 0 0 0 0
1.3994 0.0009 -3.6427 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3301 0.0263 -2.2591 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9298 -1.0142 -1.5584 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5710 -2.0339 -2.2528 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8851 -1.0363 -0.1124 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9210 -1.6309 0.6081 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8783 -1.6520 2.0022 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7997 -1.0786 2.6757 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7638 -0.4841 1.9551 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8066 -0.4630 0.5610 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7601 -1.0977 3.9561 O 0 5 0 0 0 0 0 0 0 0 0 0
3.0702 -2.7390 -4.2250 H 0 0 0 0 0 0 0 0 0 0 0 0
0.9485 0.7897 -4.2356 H 0 0 0 0 0 0 0 0 0 0 0 0
0.8212 0.8393 -1.7512 H 0 0 0 0 0 0 0 0 0 0 0 0
3.0493 -2.8630 -1.7412 H 0 0 0 0 0 0 0 0 0 0 0 0
3.7679 -2.0828 0.0975 H 0 0 0 0 0 0 0 0 0 0 0 0
3.6997 -2.1226 2.5403 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0895 -0.0300 2.4565 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0086 0.0041 0.0131 H 0 0 0 0 0 0 0 0 0 0 0 0
1 6 1 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
5 7 1 0 0 0 0
7 12 1 0 0 0 0
7 8 2 0 0 0 0
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9 10 2 0 0 0 0
10 11 1 0 0 0 0
11 12 2 0 0 0 0
10 13 1 0 0 0 0
1 14 1 0 0 0 0
3 15 1 0 0 0 0
4 16 1 0 0 0 0
6 17 1 0 0 0 0
8 18 1 0 0 0 0
9 19 1 0 0 0 0
11 20 1 0 0 0 0
12 21 1 0 0 0 0
M CHG 1 13 -1
M END
$$$$
51 changes: 51 additions & 0 deletions openforcefield/data/molecules/molecule_neutral.sdf
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Original file line number Diff line number Diff line change
@@ -0,0 +1,51 @@

-OEChem-10251911073D

22 23 0 0 0 0 0 0 0999 V2000
2.5824 -1.9679 -3.6368 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0102 -0.9737 -4.3521 N 0 0 0 0 0 0 0 0 0 0 0 0
1.3965 -0.0002 -3.6425 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3282 0.0255 -2.2588 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9287 -1.0146 -1.5582 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5698 -2.0343 -2.2529 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8851 -1.0363 -0.1124 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9210 -1.6309 0.6081 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8783 -1.6520 2.0022 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7997 -1.0786 2.6757 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7638 -0.4841 1.9551 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8066 -0.4630 0.5610 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7583 -1.0986 4.0360 O 0 0 0 0 0 0 0 0 0 0 0 0
3.0678 -2.7397 -4.2253 H 0 0 0 0 0 0 0 0 0 0 0 0
0.9449 0.7882 -4.2352 H 0 0 0 0 0 0 0 0 0 0 0 0
0.8194 0.8385 -1.7508 H 0 0 0 0 0 0 0 0 0 0 0 0
3.0487 -2.8631 -1.7414 H 0 0 0 0 0 0 0 0 0 0 0 0
3.7685 -2.0817 0.0975 H 0 0 0 0 0 0 0 0 0 0 0 0
3.6885 -2.1157 2.5587 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0783 -0.0356 2.4747 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.0086 0.0048 0.0140 H 0 0 0 0 0 0 0 0 0 0 0 0
2.5449 -1.5434 4.3899 H 0 0 0 0 0 0 0 0 0 0 0 0
1 6 1 0 0 0 0
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3 4 2 0 0 0 0
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6 17 1 0 0 0 0
8 18 1 0 0 0 0
9 19 1 0 0 0 0
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12 21 1 0 0 0 0
13 22 1 0 0 0 0
M END
$$$$
65 changes: 63 additions & 2 deletions openforcefield/tests/test_toolkits.py
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Expand Up @@ -451,6 +451,68 @@ def test_compute_wiberg_bond_orders(self):
print([bond.fractional_bond_order for bond in molecule.bonds])
# TODO: Add test for equivalent Wiberg orders for equivalent bonds



@pytest.mark.skipif(not OpenEyeToolkitWrapper.is_available(), reason='OpenEye Toolkit not available')
def test_compute_wiberg_bond_orders_neutral_charge_mol(self):
"""Test OpenEyeToolkitWrapper compute_wiberg_bond_orders() for neutral and charged molecule"""

toolkit_wrapper = OpenEyeToolkitWrapper()
# Reading neutral molecule from file
filename = get_data_file_path('molecules/molecule_neutral.sdf')
molecule1 = Molecule.from_file(filename)
# Reading negative molecule from file
filename = get_data_file_path('molecules/molecule_anion.sdf')
molecule2 = Molecule.from_file(filename)

# Checking that only one additional bond is present ihe neutral molecule
assert (len(molecule1.bonds)==len(molecule2.bonds)+1)

for charge_model in ['am1', 'pm3']:
molecule1.compute_wiberg_bond_orders(toolkit_registry=toolkit_wrapper, charge_model=charge_model)

for i in molecule1.bonds:
if i.is_aromatic:
# Checking aromatic bonds
assert (1.15 < i.fractional_bond_order < 1.60)
elif (i.atom1.atomic_number == 1 or i.atom2.atomic_number == 1):
# Checking bond order of C-H or O-H bonds are around 1
assert (0.85 < i.fractional_bond_order < 1.05)
elif (i.atom1.atomic_number == 8 or i.atom2.atomic_number == 8):
# Checking C-O single bond
wbo_C_O_neutral = i.fractional_bond_order
assert (1.0 < wbo_C_O_neutral < 1.5)
else:
# Should be C-C single bond
assert (i.atom1_index == 4 and i.atom2_index == 6) or (i.atom1_index == 6 and i.atom2_index == 4)
wbo_C_C_neutral = i.fractional_bond_order
assert (1.0 < wbo_C_C_neutral < 1.3)

molecule2.compute_wiberg_bond_orders(toolkit_registry=toolkit_wrapper, charge_model=charge_model)
for i in molecule2.bonds:
if i.is_aromatic:
# Checking aromatic bonds
assert (1.0 < i.fractional_bond_order < 1.6)
elif (i.atom1.atomic_number == 1 or i.atom2.atomic_number == 1):
# Checking bond order of C-H or O-H bonds are around 1
assert (0.85 < i.fractional_bond_order < 1.05)
elif (i.atom1.atomic_number == 8 or i.atom2.atomic_number == 8):
# Checking C-O single bond
wbo_C_O_anion = i.fractional_bond_order
assert (1.3 < wbo_C_O_anion < 1.8)
else:
# Should be C-C single bond
assert(i.atom1_index == 4 and i.atom2_index == 6) or (i.atom1_index == 6 and i.atom2_index == 4)
wbo_C_C_anion = i.fractional_bond_order
assert (1.0 < wbo_C_C_anion < 1.3)

# Wiberg bond order of C-C single bond is higher in the anion
assert (wbo_C_C_anion > wbo_C_C_neutral)
# Wiberg bond order of C-O bond is higher in the anion
assert (wbo_C_O_anion > wbo_C_O_neutral)



@pytest.mark.skipif(not OpenEyeToolkitWrapper.is_available(), reason='OpenEye Toolkit not available')
def test_compute_wiberg_bond_orders_charged(self):
"""Test OpenEyeToolkitWrapper compute_wiberg_bond_orders() on a molecule with net charge +1"""
Expand All @@ -463,8 +525,7 @@ def test_compute_wiberg_bond_orders_charged(self):
molecule.compute_wiberg_bond_orders(toolkit_registry=toolkit_wrapper, charge_model=charge_model)
# TODO: Add test for equivalent Wiberg orders for equivalent bonds

@pytest.mark.skipif(not OpenEyeToolkitWrapper.is_available(),
reason='OpenEye Toolkit not available')
@pytest.mark.skipif(not OpenEyeToolkitWrapper.is_available(), reason='OpenEye Toolkit not available')
def test_compute_wiberg_bond_orders_double_bond(self):
"""Test OpenEyeToolkitWrapper compute_wiberg_bond_orders() on a molecule with a double bond"""

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2 changes: 1 addition & 1 deletion openforcefield/typing/engines/smirnoff/parameters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2676,7 +2676,7 @@ def create_force(self, system, topology, **kwargs):
#temp_mol.compute_partial_charges(quantum_chemical_method=self._quantum_chemical_method,
# partial_charge_method=self._partial_charge_method)
temp_mol.compute_partial_charges_am1bcc(toolkit_registry=toolkit_registry)

temp_mol.compute_wiberg_bond_orders(toolkit_registry=toolkit_registry)
# Assign charges to relevant atoms
for topology_molecule in topology._reference_molecule_to_topology_molecules[ref_mol]:

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