[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

feflow/utils/vendored.py

@@ -11,7 +11,8 @@
 Copyright (c) 2025 Open Free Energy
 """
 
-from typing import Optional, Iterable
+from typing import Optional
+from collections.abc import Iterable
 
 import numpy as np
 import numpy.typing as npt
@@ -28,8 +29,8 @@ def get_omm_modeller(
     protein_comps: Optional[Iterable[ProteinComponent] | ProteinComponent],
     solvent_comps: Optional[Iterable[SolventComponent] | SolventComponent],
     small_mols: Optional[Iterable[SmallMoleculeComponent] | SmallMoleculeComponent],
-    omm_forcefield : ForceField,
-    solvent_settings : OpenMMSolvationSettings
+    omm_forcefield: ForceField,
+    solvent_settings: OpenMMSolvationSettings,
 ) -> ModellerReturn:
     """
     Generate an OpenMM Modeller class based on a potential input ProteinComponent,
@@ -58,19 +59,15 @@ def get_omm_modeller(
     """
     component_resids = {}
 
-    def _add_small_mol(comp,
-                       mol,
-                       system_modeller: Modeller,
-                       comp_resids: dict[Component, npt.NDArray]):
+    def _add_small_mol(
+        comp, mol, system_modeller: Modeller, comp_resids: dict[Component, npt.NDArray]
+    ):
         """
         Helper method to add OFFMol to an existing Modeller object and
         update a dictionary tracking residue indices for each component.
         """
         omm_top = mol.to_topology().to_openmm()
-        system_modeller.add(
-            omm_top,
-            ensure_quantity(mol.conformers[0], 'openmm')
-        )
+        system_modeller.add(omm_top, ensure_quantity(mol.conformers[0], "openmm"))
 
         nres = omm_top.getNumResidues()
         resids = [res.index for res in system_modeller.topology.residues()]
@@ -86,19 +83,20 @@ def _add_small_mol(comp,
         except TypeError:
             protein_comps = {protein_comps}  # make it a set/iterable with the comp
         for protein_comp in protein_comps:
-            system_modeller.add(protein_comp.to_openmm_topology(),
-                                protein_comp.to_openmm_positions())
+            system_modeller.add(
+                protein_comp.to_openmm_topology(), protein_comp.to_openmm_positions()
+            )
             # add missing virtual particles (from crystal waters)
             system_modeller.addExtraParticles(omm_forcefield)
             component_resids[protein_comp] = np.array(
-              [r.index for r in system_modeller.topology.residues()]
+                [r.index for r in system_modeller.topology.residues()]
             )
             # if we solvate temporarily rename water molecules to 'WAT'
             # see openmm issue #4103
             if solvent_comps is not None:
                 for r in system_modeller.topology.residues():
-                    if r.name == 'HOH':
-                        r.name = 'WAT'
+                    if r.name == "HOH":
+                        r.name = "WAT"
 
     # Now loop through small mols
     if small_mols:
@@ -107,8 +105,12 @@ def _add_small_mol(comp,
         except TypeError:
             small_mols = {small_mols}  # make it a set/iterable with the comp
         for small_mol_comp in small_mols:
-            _add_small_mol(small_mol_comp, small_mol_comp.to_openff(), system_modeller,
-                           component_resids)
+            _add_small_mol(
+                small_mol_comp,
+                small_mol_comp.to_openff(),
+                system_modeller,
+                component_resids,
+            )
 
     # Add solvent if neeeded
     if solvent_comps:
@@ -120,7 +122,9 @@ def _add_small_mol(comp,
         # TODO: Support multiple solvent components? Is there a use case for it?
         # Error out when we iter(have more than one solvent component in the states/systems
         if len(solvent_comps) > 1:
-            raise ValueError("More than one solvent component found in systems. Only one supported.")
+            raise ValueError(
+                "More than one solvent component found in systems. Only one supported."
+            )
         solvent_comp = solvent_comps[0]  # Get the first (and only?) solvent component
         # Do unit conversions if necessary
         solvent_padding = None
@@ -150,20 +154,16 @@ def _add_small_mol(comp,
             numAdded=solvent_settings.number_of_solvent_molecules,
         )
 
-        all_resids = np.array(
-            [r.index for r in system_modeller.topology.residues()]
-        )
+        all_resids = np.array([r.index for r in system_modeller.topology.residues()])
 
         existing_resids = np.concatenate(
             [resids for resids in component_resids.values()]
         )
 
-        component_resids[solvent_comp] = np.setdiff1d(
-            all_resids, existing_resids
-        )
+        component_resids[solvent_comp] = np.setdiff1d(all_resids, existing_resids)
         # undo rename of pre-existing waters
         for r in system_modeller.topology.residues():
-            if r.name == 'WAT':
-                r.name = 'HOH'
+            if r.name == "WAT":
+                r.name = "HOH"
 
-    return system_modeller, component_resids
+    return system_modeller, component_resids