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OpenFreeEnergy · Feb 3, 2025 · b8062f0 · b8062f0
1 parent 9330a15
commit b8062f0
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Showing 3 changed files with 6 additions and 9 deletions.
diff --git a/src/pontibus/tests/protocols/solvation/test_tokenization.py b/src/pontibus/tests/protocols/solvation/test_tokenization.py
@@ -91,9 +91,7 @@ def test_repr(self, instance):
 
 class TestVacuumUnit(GufeTokenizableTestsMixin):
     cls = ASFEVacuumUnit
-    repr = (
-        "ASFEVacuumUnit(Absolute Solvation, benzene vacuum leg"
-    )
+    repr = "ASFEVacuumUnit(Absolute Solvation, benzene vacuum leg"
     key = None
 
     @pytest.fixture()

diff --git a/src/pontibus/tests/utils/test_interchange_packmol.py b/src/pontibus/tests/utils/test_interchange_packmol.py
@@ -118,10 +118,10 @@ def test_check_deduplicate_charged_mols(smc_components_benzene_unnamed):
     different conformer.
     """
     benzene1 = list(smc_components_benzene_unnamed.values())[0]
-    benzene1.assign_partial_charges(partial_charge_method='gasteiger')
-    benzene2 = Molecule.from_smiles('c1ccccc1')
+    benzene1.assign_partial_charges(partial_charge_method="gasteiger")
+    benzene2 = Molecule.from_smiles("c1ccccc1")
     benzene2.generate_conformers(n_conformers=1)
-    benzene2.assign_partial_charges(partial_charge_method='gasteiger')
+    benzene2.assign_partial_charges(partial_charge_method="gasteiger")
 
     assert all(benzene1.partial_charges == benzene2.partial_charges)
     assert np.any(benzene1.conformers[0] != benzene2.conformers[0])

diff --git a/src/pontibus/utils/system_creation.py b/src/pontibus/utils/system_creation.py
@@ -108,7 +108,7 @@ def _check_library_charges(
 
 
 def _check_and_deduplicate_charged_mols(
-    molecules: list[OFFMolecule]
+    molecules: list[OFFMolecule],
 ) -> list[OFFMolecule]:
     """
     Checks list of molecules with charges and removes any isomorphic
@@ -143,8 +143,7 @@ def _check_and_deduplicate_charged_mols(
 
     for moli in molecules:
         isomorphic_mols = [
-            molj for molj in unique_mols
-            if moli.is_isomorphic_with(molj)
+            molj for molj in unique_mols if moli.is_isomorphic_with(molj)
         ]
 
         if isomorphic_mols: