Pre-commit hooks formatting

Author: JMorado

src/fes_ml/alchemical/alchemist.py

@@ -100,8 +100,10 @@ def add_modification_to_graph(
             The value of the alchemical state parameter.
         """
         if modification.NAME in self._graph.nodes and lambda_value is None:
-            lambda_value = self._graph.nodes[modification.NAME].get("lambda_value", None)
-            
+            lambda_value = self._graph.nodes[modification.NAME].get(
+                "lambda_value", None
+            )
+
         self._graph.add_node(
             modification.NAME, modification=modification, lambda_value=lambda_value
         )

src/fes_ml/alchemical/modifications/custom_lj.py

@@ -1,15 +1,17 @@
-from .lj_softcore import LJSoftCoreModification
-import openmm.unit as _unit
+import logging
+from typing import List, Optional, Union
+
 import openmm as _mm
-from openff.toolkit.typing.engines.smirnoff import ForceField as _ForceField
+import openmm.unit as _unit
 from openff.toolkit.topology import Topology as _Topology
+from openff.toolkit.typing.engines.smirnoff import ForceField as _ForceField
 
 from .base_modification import BaseModification, BaseModificationFactory
-import logging
-from typing import List, Optional, Union
+from .lj_softcore import LJSoftCoreModification
 
 logger = logging.getLogger(__name__)
 
+
 class CustomLJModificationFactory(BaseModificationFactory):
     """Factory for creating CustomLJModification instances."""
 
@@ -54,7 +56,7 @@ def apply(
         alchemical_atoms : List[int]
             A list of the indices of the alchemical atoms.
         lambda_value : float
-            The value of the alchemical state parameter. 
+            The value of the alchemical state parameter.
         original_offxml : List[str]
             A list of paths to the original OFFXML files.
         lj_offxml : str
@@ -77,21 +79,26 @@ def apply(
         opt_params = {}
         for p in force_field_opt.get_parameter_handler("vdW"):
             opt_params[p.id] = {
-                "epsilon": p.epsilon.to_openmm().value_in_unit(_unit.kilojoules_per_mole), 
-                "sigma": p.sigma.to_openmm().value_in_unit(_unit.nanometer)
-                }
+                "epsilon": p.epsilon.to_openmm().value_in_unit(
+                    _unit.kilojoules_per_mole
+                ),
+                "sigma": p.sigma.to_openmm().value_in_unit(_unit.nanometer),
+            }
 
-        # Update the Lennard-Jones parameters in the CustomNonbondedForce 
+        # Update the Lennard-Jones parameters in the CustomNonbondedForce
         force_field = _ForceField(*original_offxml)
         labels = force_field.label_molecules(topology_off)
         index = 0
         for mol in labels:
             for _, val in mol["vdW"].items():
                 atom_type = val.id
                 # Get the original Lennard-Jones parameters
-                parameters = [opt_params[atom_type]["sigma"], opt_params[atom_type]["epsilon"]]
+                parameters = [
+                    opt_params[atom_type]["sigma"],
+                    opt_params[atom_type]["epsilon"],
+                ]
                 # Update the Lennard-Jones parameters
                 custom_nb_force.setParticleParameters(index, parameters)
                 index += 1
 
-        return system
+        return system