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OpenBioSim · Oct 29, 2024 · 11f3ccb · 11f3ccb
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commit 11f3ccb
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Showing 2 changed files with 12 additions and 6 deletions.
diff --git a/python/BioSimSpace/Sandpit/Exscientia/FreeEnergy/_restraint_search.py b/python/BioSimSpace/Sandpit/Exscientia/FreeEnergy/_restraint_search.py
@@ -687,7 +687,6 @@ def analyse(
                 "The decoupled molecule has more than one residue and is likely a macromolecule. Ensure that this is intended."
             )
 
-
         ligand_selection_str = f"((resname {decoupled_resname}) and (not name H*))"
         if append_to_ligand_selection:
             ligand_selection_str += " and "
@@ -1033,10 +1032,12 @@ def _findOrderedPairs(u, ligand_selection_str, receptor_selection_str, cutoff):
         """
 
         lig_selection = u.select_atoms(ligand_selection_str)
-        
+
         # Ensure that there are no shared atoms between the ligand selection and all possible receptor selections.
         all_possible_receptor_selection = u.select_atoms(receptor_selection_str)
-        shared_atoms = [atom for atom in lig_selection if atom in all_possible_receptor_selection]
+        shared_atoms = [
+            atom for atom in lig_selection if atom in all_possible_receptor_selection
+        ]
         if shared_atoms:
             raise _AnalysisError(
                 "Shared atoms between ligand and receptor selections detected. "
@@ -1521,7 +1522,9 @@ def _findOrderedBoresch(
                             dtheta = abs(val - circmean)
                             corrected_values.append(min(dtheta, 2 * _np.pi - dtheta))
                         corrected_values = _np.array(corrected_values)
-                        boresch_dof_data[pair][dof]["var"] = _np.mean(corrected_values ** 2)
+                        boresch_dof_data[pair][dof]["var"] = _np.mean(
+                            corrected_values**2
+                        )
 
                     # Assume Gaussian distributions and calculate force constants for harmonic potentials
                     # so as to reproduce these distributions at 298 K

diff --git a/tests/Sandpit/Exscientia/FreeEnergy/test_restraint_search.py b/tests/Sandpit/Exscientia/FreeEnergy/test_restraint_search.py
@@ -136,6 +136,7 @@ def test_top(self, restraint_search):
         with open(outdir / "BoreschRestraint.top", "r") as f:
             assert "intermolecular_interactions" in f.read()
 
+
 @pytest.mark.skipif(
     (has_gromacs is False or has_mdanalysis is False),
     reason="Requires MDAnalysis and Gromacs to be installed.",
@@ -177,7 +178,7 @@ def _restraint_search(self, tmp_path_factory):
     @pytest.fixture(scope="class")
     def _restraint_search_protein(self, tmp_path_factory):
         # Select the protein as the ligand.
-        return partial(self._restraint_search_general, tmp_path_factory,ligand_idx=0)()
+        return partial(self._restraint_search_general, tmp_path_factory, ligand_idx=0)()
 
     @staticmethod
     @pytest.fixture(scope="class")
@@ -280,7 +281,9 @@ def test_analysis_failure_boresch(self, _restraint_search):
                 cutoff=0.1 * angstrom,
             )
 
-    def test_non_overlapping_anchor_selections_forbidden(self, _restraint_search_protein):
+    def test_non_overlapping_anchor_selections_forbidden(
+        self, _restraint_search_protein
+    ):
         """
         Ensure that anchor atoms cannot be in the same molecule
         (the protein has been selected as the ligand, so we are