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openforcefield · Jan 13, 2025 · 71e37a0 · 71e37a0
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diff --git a/openff/interchange/_tests/_openmm.py b/openff/interchange/_tests/_openmm.py
@@ -144,9 +144,9 @@ def _compare_nonbonded_parameters(force1, force2):
         q2, sig2, eps2 = force2.getParticleParameters(i)
         assert abs(q2 - q1) < 1e-8 * openmm.unit.elementary_charge, f"charge mismatch in particle {i}: {q1} vs {q2}"
         assert abs(sig2 - sig1) < 1e-12 * openmm.unit.nanometer, f"sigma mismatch in particle {i}: {sig1} vs {sig2}"
-        assert (
-            abs(eps2 - eps1) < 1e-12 * openmm.unit.kilojoule_per_mole
-        ), f"epsilon mismatch in particle {i}: {eps1} vs {eps2}"
+        assert abs(eps2 - eps1) < 1e-12 * openmm.unit.kilojoule_per_mole, (
+            f"epsilon mismatch in particle {i}: {eps1} vs {eps2}"
+        )
 
 
 @requires_package("openmm")

diff --git a/openff/interchange/_tests/interoperability_tests/test_openmm.py b/openff/interchange/_tests/interoperability_tests/test_openmm.py
@@ -785,9 +785,9 @@ def test_preserve_per_residue_unique_atom_names(self, explicit_arg, sage):
 
         # Assert the test's assumptions
         _ace, ala1, ala2, _nme = off_topology.hierarchy_iterator("residues")
-        assert [a.name for a in ala1.atoms] == [
-            a.name for a in ala2.atoms
-        ], "Test assumes both alanines have same atom names"
+        assert [a.name for a in ala1.atoms] == [a.name for a in ala2.atoms], (
+            "Test assumes both alanines have same atom names"
+        )
 
         for res in off_topology.hierarchy_iterator("residues"):
             res_atomnames = [atom.name for atom in res.atoms]

diff --git a/openff/interchange/_tests/test_issues.py b/openff/interchange/_tests/test_issues.py
@@ -132,9 +132,9 @@ def test_issue_1049():
 
     # the same index in system should also be a virtual site in the topology
     for particle_index, particle in enumerate(openmm_topology.atoms()):
-        assert openmm_system.isVirtualSite(particle_index) == (
-            particle.element is None
-        ), f"particle index {particle_index} is a virtual site in the system OR topology but not both"
+        assert openmm_system.isVirtualSite(particle_index) == (particle.element is None), (
+            f"particle index {particle_index} is a virtual site in the system OR topology but not both"
+        )
 
 
 def test_issue_1052(sage, ethanol):

diff --git a/openff/interchange/_tests/unit_tests/interop/openmm/_import/test_compat.py b/openff/interchange/_tests/unit_tests/interop/openmm/_import/test_compat.py
@@ -29,8 +29,7 @@ def test_error_topology_mismatch(self, monkeypatch, sage_unconstrained, ethanol)
         with pytest.raises(
             UnsupportedImportError,
             match=re.escape(
-                "The number of particles in the system (9) and "
-                "the number of atoms in the topology (3) do not match.",
+                "The number of particles in the system (9) and the number of atoms in the topology (3) do not match.",
             ),
         ):
             from_openmm(

diff --git a/openff/interchange/components/mdconfig.py b/openff/interchange/components/mdconfig.py
@@ -71,8 +71,7 @@ class MDConfig(_BaseModel):
     coul_cutoff: _DistanceQuantity = Field(
         Quantity(9.0, unit.angstrom),
         description=(
-            "The distance at which electrostatic interactions are truncated or transition from "
-            "short- to long-range."
+            "The distance at which electrostatic interactions are truncated or transition from short- to long-range."
         ),
     )
 

diff --git a/openff/interchange/interop/gromacs/export/_export.py b/openff/interchange/interop/gromacs/export/_export.py
@@ -141,13 +141,13 @@ def _get_new_entry_name(atom_type_list) -> str:
                     mapping_to_reduced_atom_types[atom_type.name] = _at_name
             else:
                 top.write(
-                    f"{atom_type.name :<11s}\t"
-                    f"{atom_type.atomic_number :6d}\t"
-                    f"{atom_type.mass.m :.16g}\t"
-                    f"{atom_type.charge.m :.16f}\t"
-                    f"{atom_type.particle_type :5s}\t"
-                    f"{atom_type.sigma.m :.16g}\t"
-                    f"{atom_type.epsilon.m :.16g}\n",
+                    f"{atom_type.name:<11s}\t"
+                    f"{atom_type.atomic_number:6d}\t"
+                    f"{atom_type.mass.m:.16g}\t"
+                    f"{atom_type.charge.m:.16f}\t"
+                    f"{atom_type.particle_type:5s}\t"
+                    f"{atom_type.sigma.m:.16g}\t"
+                    f"{atom_type.epsilon.m:.16g}\n",
                 )
 
         if not merge_atom_types:
@@ -156,13 +156,13 @@ def _get_new_entry_name(atom_type_list) -> str:
 
         for atom_type_name, atom_type in reduced_atom_types:
             top.write(
-                f"{atom_type_name :<11s}\t"
-                f"{atom_type.atomic_number :6d}\t"
-                f"{atom_type.mass.m :.16g}\t"
-                f"{atom_type.charge.m :.16f}\t"
-                f"{atom_type.particle_type :5s}\t"
-                f"{atom_type.sigma.m :.16g}\t"
-                f"{atom_type.epsilon.m :.16g}\n",
+                f"{atom_type_name:<11s}\t"
+                f"{atom_type.atomic_number:6d}\t"
+                f"{atom_type.mass.m:.16g}\t"
+                f"{atom_type.charge.m:.16f}\t"
+                f"{atom_type.particle_type:5s}\t"
+                f"{atom_type.sigma.m:.16g}\t"
+                f"{atom_type.epsilon.m:.16g}\n",
             )
         top.write("\n")
         return mapping_to_reduced_atom_types
@@ -225,25 +225,25 @@ def _write_atoms(
         for atom in molecule_type.atoms:
             if merge_atom_types:
                 top.write(
-                    f"{atom.index :6d} "
-                    f"{mapping_to_reduced_atom_types[atom.atom_type] :6s}"
-                    f"{atom.residue_index % 100_000 :8d} "
-                    f"{atom.residue_name :8s} "
-                    f"{atom.name :6s}"
-                    f"{atom.charge_group_number :6d}"
-                    f"{atom.charge.m :20.12f}"
-                    f"{atom.mass.m :20.12f}\n",
+                    f"{atom.index:6d} "
+                    f"{mapping_to_reduced_atom_types[atom.atom_type]:6s}"
+                    f"{atom.residue_index % 100_000:8d} "
+                    f"{atom.residue_name:8s} "
+                    f"{atom.name:6s}"
+                    f"{atom.charge_group_number:6d}"
+                    f"{atom.charge.m:20.12f}"
+                    f"{atom.mass.m:20.12f}\n",
                 )
             else:
                 top.write(
-                    f"{atom.index :6d} "
-                    f"{atom.atom_type :6s}"
-                    f"{atom.residue_index % 100_000 :8d} "
-                    f"{atom.residue_name :8s} "
-                    f"{atom.name :6s}"
-                    f"{atom.charge_group_number :6d}"
-                    f"{atom.charge.m :20.12f}"
-                    f"{atom.mass.m :20.12f}\n",
+                    f"{atom.index:6d} "
+                    f"{atom.atom_type:6s}"
+                    f"{atom.residue_index % 100_000:8d} "
+                    f"{atom.residue_name:8s} "
+                    f"{atom.name:6s}"
+                    f"{atom.charge_group_number:6d}"
+                    f"{atom.charge.m:20.12f}"
+                    f"{atom.mass.m:20.12f}\n",
                 )
 
         top.write("\n")
@@ -256,7 +256,7 @@ def _write_pairs(self, top, molecule_type):
 
         for pair in molecule_type.pairs:
             top.write(
-                f"{pair.atom1 :6d}\t{pair.atom2 :6d}\t{function :6d}\n",
+                f"{pair.atom1:6d}\t{pair.atom2:6d}\t{function:6d}\n",
             )
 
         top.write("\n")
@@ -269,11 +269,7 @@ def _write_bonds(self, top, molecule_type):
 
         for bond in molecule_type.bonds:
             top.write(
-                f"{bond.atom1 :6d} "
-                f"{bond.atom2 :6d} "
-                f"{function :6d}"
-                f"{bond.length.m :20.12f} "
-                f"{bond.k.m :20.12f} ",
+                f"{bond.atom1:6d} {bond.atom2:6d} {function:6d}{bond.length.m:20.12f} {bond.k.m:20.12f} ",
             )
 
             top.write("\n")
@@ -288,12 +284,12 @@ def _write_angles(self, top, molecule_type):
 
         for angle in molecule_type.angles:
             top.write(
-                f"{angle.atom1 :6d} "
-                f"{angle.atom2 :6d} "
-                f"{angle.atom3 :6d} "
-                f"{function :6d} "
-                f"{angle.angle.m :20.12f} "
-                f"{angle.k.m :20.12f} ",
+                f"{angle.atom1:6d} "
+                f"{angle.atom2:6d} "
+                f"{angle.atom3:6d} "
+                f"{function:6d} "
+                f"{angle.angle.m:20.12f} "
+                f"{angle.k.m:20.12f} ",
             )
 
             top.write("\n")
@@ -314,26 +310,26 @@ def _write_dihedrals(self, top, molecule_type):
             function = functions[type(dihedral)]
 
             top.write(
-                f"{dihedral.atom1 :6d}"
-                f"{dihedral.atom2 :6d}"
-                f"{dihedral.atom3 :6d}"
-                f"{dihedral.atom4 :6d}"
-                f"{functions[type(dihedral)] :6d}",
+                f"{dihedral.atom1:6d}"
+                f"{dihedral.atom2:6d}"
+                f"{dihedral.atom3:6d}"
+                f"{dihedral.atom4:6d}"
+                f"{functions[type(dihedral)]:6d}",
             )
 
             if function in [1, 4]:
                 top.write(
-                    f"{dihedral.phi.m :20.12f}{dihedral.k.m :20.12f}{dihedral.multiplicity :18d}",
+                    f"{dihedral.phi.m:20.12f}{dihedral.k.m:20.12f}{dihedral.multiplicity:18d}",
                 )
 
             elif function == 3:
                 top.write(
-                    f"{dihedral.c0.m :20.12f}"
-                    f"{dihedral.c1.m :20.12f}"
-                    f"{dihedral.c2.m :20.12f}"
-                    f"{dihedral.c3.m :20.12f}"
-                    f"{dihedral.c4.m :20.12f}"
-                    f"{dihedral.c5.m :20.12f}",
+                    f"{dihedral.c0.m:20.12f}"
+                    f"{dihedral.c1.m:20.12f}"
+                    f"{dihedral.c2.m:20.12f}"
+                    f"{dihedral.c3.m:20.12f}"
+                    f"{dihedral.c4.m:20.12f}"
+                    f"{dihedral.c5.m:20.12f}",
                 )
 
             else:
@@ -397,11 +393,11 @@ def _write_exclusions(self, top, molecule_type):
 
         for exclusion in molecule_type.exclusions:
             top.write(
-                f"{exclusion.first_atom :6d}",
+                f"{exclusion.first_atom:6d}",
             )
             for other_atom in exclusion.other_atoms:
                 top.write(
-                    f"{other_atom :6d}",
+                    f"{other_atom:6d}",
                 )
 
             top.write("\n")
@@ -416,9 +412,9 @@ def _write_settles(self, top, molecule_type):
 
         for settle in molecule_type.settles:
             top.write(
-                f"{settle.first_atom :6d}\t"
-                f"{function :6d}\t"
-                f"{settle.oxygen_hydrogen_distance.m_as(unit.nanometer) :20.12f}\t"
+                f"{settle.first_atom:6d}\t"
+                f"{function:6d}\t"
+                f"{settle.oxygen_hydrogen_distance.m_as(unit.nanometer):20.12f}\t"
                 f"{settle.hydrogen_hydrogen_distance.m_as(unit.nanometer):20.12f}\n",
             )
 

diff --git a/plugins/nonbonded_plugins/nonbonded.py b/plugins/nonbonded_plugins/nonbonded.py
@@ -136,7 +136,7 @@ class SMIRNOFFBuckinghamCollection(_SMIRNOFFNonbondedCollection):
 
     acts_as: str = "vdW"
 
-    expression: str = "a*exp(-b*r)-c*r^-6;" "a=sqrt(a1*a2);" "b=2/(1/b1+1/b2);" "c=sqrt(c1*c2);"
+    expression: str = "a*exp(-b*r)-c*r^-6;a=sqrt(a1*a2);b=2/(1/b1+1/b2);c=sqrt(c1*c2);"
 
     periodic_method: str = "cutoff"
     nonperiodic_method: str = "no-cutoff"
@@ -177,9 +177,9 @@ def pre_computed_terms(self) -> dict[str, float]:
     @classmethod
     def check_openmm_requirements(cls, combine_nonbonded_forces: bool) -> None:
         """Run through a list of assertions about what is compatible when exporting this to OpenMM."""
-        assert (
-            not combine_nonbonded_forces
-        ), "Custom non-bonded functional forms require `combine_nonbonded_forces=False`."
+        assert not combine_nonbonded_forces, (
+            "Custom non-bonded functional forms require `combine_nonbonded_forces=False`."
+        )
 
     def store_potentials(self, parameter_handler: BuckinghamHandler) -> None:
         """
@@ -331,9 +331,9 @@ def modify_parameters(
     @classmethod
     def check_openmm_requirements(cls, combine_nonbonded_forces: bool) -> None:
         """Run through a list of assertions about what is compatible when exporting this to OpenMM."""
-        assert (
-            not combine_nonbonded_forces
-        ), "Custom non-bonded functional forms require `combine_nonbonded_forces=False`."
+        assert not combine_nonbonded_forces, (
+            "Custom non-bonded functional forms require `combine_nonbonded_forces=False`."
+        )
 
     def store_potentials(self, parameter_handler: DoubleExponentialHandler) -> None:
         """