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Changed the default forcefield to OPLSAA #38

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merged 4 commits into from
Dec 15, 2024
Merged

Changed the default forcefield to OPLSAA #38

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2cf5ffc
Changed the default forcefield to OPLSAA
paulsaxe Oct 25, 2024
59ccb1f
Updated for changes in SMILES handling
paulsaxe Dec 15, 2024
ec995b8
Not sure what the problem is!
paulsaxe Dec 15, 2024
1a027b0
Not sure what the problem is!
paulsaxe Dec 15, 2024
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6 changes: 6 additions & 0 deletions HISTORY.rst
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Original file line number Diff line number Diff line change
@@ -1,6 +1,12 @@
=======
History
=======
2024.12.14 -- Updated for changes in SMILES handling
* Changes in the handling of SMILES in MolSystem required small changes in the tests
to continue using Open Babel for SMILES.

2024.10.25 -- Changed the default forcefield to OPLSAA

2024.6.30 -- Bugfix: Error submitting jobs with local forcefield files.

2024.6.29 -- Bugfix: factor of 2 for dihedrals and impropers in ligpargen
Expand Down
2 changes: 1 addition & 1 deletion forcefield_step/forcefield_parameters.py
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Expand Up @@ -66,7 +66,7 @@ class ForcefieldParameters(seamm.Parameters):
"help_text": "What to do with the forcefield.",
},
"forcefield_file": {
"default": forcefields[0],
"default": "oplsaa.frc",
"kind": "enumeration",
"default_units": "",
"enumeration": tuple(forcefields),
Expand Down
64 changes: 33 additions & 31 deletions tests/test_oplsaa_assignment.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
When the default for SMILES was changed to RDKit, tests with explicit
hydrogens in the SMILES failed because RDKit produces a different order
of atoms than OpenBabel in these cases. For the time being, in these tests
the call to configuration.smiles adds the argument 'rdkit=False' to continue
the call to configuration.smiles adds the argument 'flavor="openbabel"' to continue
using OpenBabel.
"""

Expand Down Expand Up @@ -322,7 +322,7 @@ def test_opls_113(oplsaa_assigner, configuration):
+ ["opls_115", "opls_113", "opls_114"]
+ 5 * ["opls_118"]
)
configuration.from_smiles("C(O[H])C(O[H])CO[H]", rdkit=False)
configuration.from_smiles("C(O[H])C(O[H])CO[H]", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand All @@ -337,7 +337,7 @@ def test_opls_113(oplsaa_assigner, configuration):
+ 3 * ["opls_118"]
+ 6 * ["opls_85"]
)
configuration.from_smiles("C(O[H])C(O[H])C(O[H])(C)C", rdkit=False)
configuration.from_smiles("C(O[H])C(O[H])C(O[H])(C)C", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -937,7 +937,7 @@ def test_opls_160(oplsaa_assigner, configuration):
+ 2 * ["opls_85"]
+ 5 * ["opls_91"]
)
configuration.from_smiles("[H]OCc1ccccc1", rdkit=False)
configuration.from_smiles("[H]OCc1ccccc1", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand All @@ -954,7 +954,7 @@ def test_opls_161(oplsaa_assigner, configuration):
+ 4 * ["opls_85"]
+ 5 * ["opls_91"]
)
configuration.from_smiles("[H]OC(C)c1ccccc1", rdkit=False)
configuration.from_smiles("[H]OC(C)c1ccccc1", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand All @@ -971,7 +971,7 @@ def test_opls_162(oplsaa_assigner, configuration):
+ 6 * ["opls_85"]
+ 5 * ["opls_91"]
)
configuration.from_smiles("[H]OC(C)(C)c1ccccc1", rdkit=False)
configuration.from_smiles("[H]OC(C)(C)c1ccccc1", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -1063,7 +1063,7 @@ def test_opls_174(oplsaa_assigner, configuration):
correct = (
["opls_221", "opls_174", "opls_220"] + 6 * ["opls_90"] + 5 * ["opls_91"]
)
configuration.from_smiles("[H]C(=O)c1ccccc1", rdkit=False)
configuration.from_smiles("[H]C(=O)c1ccccc1", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -1093,7 +1093,7 @@ def test_opls_219(oplsaa_assigner, configuration):
opls 221, hydrogen in aldehyde -CH=O
"""
correct = ["opls_221", "opls_219", "opls_220", "opls_80"] + 3 * ["opls_85"]
configuration.from_smiles("[H]C(=O)C", rdkit=False)
configuration.from_smiles("[H]C(=O)C", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -1350,7 +1350,7 @@ def test_opls_198(oplsaa_assigner, configuration):
+ 2 * ["opls_194", "opls_195", "opls_198"]
+ 6 * ["opls_85"]
)
configuration.from_smiles("N([H])(C(=O)C)C(=O)C", rdkit=False)
configuration.from_smiles("N([H])(C(=O)C)C(=O)C", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -1383,7 +1383,7 @@ def test_opls_199(oplsaa_assigner, configuration):
+ 2 * ["opls_194", "opls_195", "opls_199", "opls_80"]
+ 10 * ["opls_85"]
)
configuration.from_smiles("N([H])(C(=O)CC)C(=O)CC", rdkit=False)
configuration.from_smiles("N([H])(C(=O)CC)C(=O)CC", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -1416,7 +1416,7 @@ def test_opls_200(oplsaa_assigner, configuration):
+ 2 * (["opls_194", "opls_195", "opls_200"] + 2 * ["opls_80"])
+ 14 * ["opls_85"]
)
configuration.from_smiles("N([H])(C(=O)C(C)C)C(=O)C(C)C", rdkit=False)
configuration.from_smiles("N([H])(C(=O)C(C)C)C(=O)C(C)C", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -1449,7 +1449,9 @@ def test_opls_201(oplsaa_assigner, configuration):
+ 2 * (["opls_194", "opls_195", "opls_201"] + 3 * ["opls_80"])
+ 18 * ["opls_85"]
)
configuration.from_smiles("N([H])(C(=O)C(C)(C)C)C(=O)C(C)(C)C", rdkit=False)
configuration.from_smiles(
"N([H])(C(=O)C(C)(C)C)C(=O)C(C)(C)C", flavor="openbabel"
)
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -1497,7 +1499,7 @@ def test_opls_207(oplsaa_assigner, configuration):
+ 3 * ["opls_85"]
+ 5 * ["opls_91"]
)
configuration.from_smiles("CC(=O)N([H])c1ccccc1", rdkit=False)
configuration.from_smiles("CC(=O)N([H])c1ccccc1", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand All @@ -1513,15 +1515,15 @@ def test_opls_209(oplsaa_assigner, configuration):
correct = ["opls_80", "opls_209", "opls_210", "opls_211", "opls_212"] + 3 * [
"opls_85"
]
configuration.from_smiles("CC(=O)O[H]", rdkit=False)
configuration.from_smiles("CC(=O)O[H]", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
raise AssertionError(f"\n result: {result}\ncorrect: {correct}")

# Formic acid is an edge case
correct = ["opls_221", "opls_209", "opls_210", "opls_211", "opls_212"]
configuration.from_smiles("[H]C(=O)O[H]", rdkit=False)
configuration.from_smiles("[H]C(=O)O[H]", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand All @@ -1534,7 +1536,7 @@ def test_opls_213(oplsaa_assigner, configuration):
opls 221, hydrogen in aldehydes, formic acid, formamide...
"""
correct = ["opls_221", "opls_213", "opls_214", "opls_214"]
configuration.from_smiles("[H]C(=O)[O-]", rdkit=False)
configuration.from_smiles("[H]C(=O)[O-]", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -1616,7 +1618,7 @@ def test_opls_225(oplsaa_assigner, configuration):
+ ["opls_183", "opls_177", "opls_178", "opls_80", "opls_212"]
+ 7 * ["opls_85"]
)
configuration.from_smiles("O=C(O)C(C)N([H])C(=O)C", rdkit=False)
configuration.from_smiles("O=C(O)C(C)N([H])C(=O)C", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand All @@ -1631,7 +1633,7 @@ def test_opls_226(oplsaa_assigner, configuration):
+ ["opls_183", "opls_177", "opls_178", "opls_80", "opls_212"]
+ 5 * ["opls_85"]
)
configuration.from_smiles("O=C(O)CN([H])C(=O)C", rdkit=False)
configuration.from_smiles("O=C(O)CN([H])C(=O)C", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand All @@ -1646,7 +1648,7 @@ def test_opls_227(oplsaa_assigner, configuration):
+ ["opls_180", "opls_183", "opls_177", "opls_178", "opls_80", "opls_212"]
+ 9 * ["opls_85"]
)
configuration.from_smiles("O=C(O)C(C)(C)N([H])C(=O)C", rdkit=False)
configuration.from_smiles("O=C(O)C(C)(C)N([H])C(=O)C", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -2006,7 +2008,7 @@ def test_opls_411(oplsaa_assigner, configuration):
+ ["opls_411", "opls_210", "opls_211", "opls_212"]
+ 5 * ["opls_91"]
)
configuration.from_smiles("c1ccccc1C(=O)O[H]", rdkit=False)
configuration.from_smiles("c1ccccc1C(=O)O[H]", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -2523,7 +2525,7 @@ def test_opls_528(oplsaa_assigner, configuration):
+ ["opls_538", "opls_539", "opls_540", "opls_541"]
+ ["opls_542", "opls_543"]
)
configuration.from_smiles("n1([H])ccc2ccccc21", rdkit=False)
configuration.from_smiles("n1([H])ccc2ccccc21", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -2582,7 +2584,7 @@ def test_opls_561(oplsaa_assigner, configuration):
+ ["opls_566", "opls_567", "opls_568", "opls_569"]
+ ["opls_573", "opls_570", "opls_571", "opls_572"]
)
configuration.from_smiles("n1cnc2c(c1)ncn2[H]", rdkit=False)
configuration.from_smiles("n1cnc2c(c1)ncn2[H]", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -2651,7 +2653,7 @@ def test_opls_585(oplsaa_assigner, configuration):
+ 2 * ["opls_739"]
+ ["opls_540", "opls_542", "opls_543"]
)
configuration.from_smiles("n1([H])cc(CCN)c2cc(O[H])ccc21", rdkit=False)
configuration.from_smiles("n1([H])cc(CCN)c2cc(O[H])ccc21", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -3551,7 +3553,7 @@ def test_opls_820(oplsaa_assigner, configuration):
+ ["opls_824"]
+ 3 * ["opls_85"]
)
configuration.from_smiles("CC(=O)N(O[H])[H]", rdkit=False)
configuration.from_smiles("CC(=O)N(O[H])[H]", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand All @@ -3572,7 +3574,7 @@ def test_opls_821(oplsaa_assigner, configuration):
+ ["opls_824"]
+ 5 * ["opls_91"]
)
configuration.from_smiles("c1ccccc1C(=O)N(O[H])[H]", rdkit=False)
configuration.from_smiles("c1ccccc1C(=O)N(O[H])[H]", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand All @@ -3591,7 +3593,7 @@ def test_opls_820a(oplsaa_assigner, configuration):
+ ["opls_185"]
+ 6 * ["opls_85"]
)
configuration.from_smiles("CC(=O)N(O[H])C", rdkit=False)
configuration.from_smiles("CC(=O)N(O[H])C", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -3780,7 +3782,7 @@ def test_opls_853(oplsaa_assigner, configuration):
+ 5 * ["opls_852"]
+ 3 * ["opls_85"]
)
configuration.from_smiles("[H]C(=O)N(C)CC", rdkit=False)
configuration.from_smiles("[H]C(=O)N(C)CC", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand All @@ -3803,7 +3805,7 @@ def test_opls_850b(oplsaa_assigner, configuration):
+ 4 * ["opls_852"]
+ 6 * ["opls_85"]
)
configuration.from_smiles("[H]C(=O)N(C)C(C)C", rdkit=False)
configuration.from_smiles("[H]C(=O)N(C)C(C)C", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -3927,7 +3929,7 @@ def test_opls_900(oplsaa_assigner, configuration):
opls_903: central C =C=
"""
correct = ["opls_900", "opls_903", "opls_900"] + 4 * ["opls_899"]
configuration.from_smiles("C=C=C")
configuration.from_smiles("C=C=C", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down Expand Up @@ -3994,7 +3996,7 @@ def test_opls_902(oplsaa_assigner, configuration):
+ 2 * ["opls_899"]
+ 6 * ["opls_85"]
)
configuration.from_smiles("C=C=C(C)C")
configuration.from_smiles("C=C=C(C)C", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand All @@ -4006,7 +4008,7 @@ def test_opls_902(oplsaa_assigner, configuration):
+ ["opls_80", "opls_80"]
+ 12 * ["opls_85"]
)
configuration.from_smiles("CC(C)=C=C(C)C")
configuration.from_smiles("CC(C)=C=C(C)C", flavor="openbabel")
result = oplsaa_assigner.assign(configuration)
if result != correct:
print(f"Incorrect typing. Should be:\n {correct}\nnot\n {result}")
Expand Down
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