diff --git a/opencadd/databases/klifs/core.py b/opencadd/databases/klifs/core.py
index c3def060..59650479 100644
--- a/opencadd/databases/klifs/core.py
+++ b/opencadd/databases/klifs/core.py
@@ -1321,7 +1321,6 @@ class CoordinatesProvider(BaseProvider):
     """
 
     def __init__(self, *args, **kwargs):
-
         self.options = {
             "entities": ["complex", "ligand", "pocket", "protein", "water"],
             "extensions": ["mol2", "pdb"],
diff --git a/opencadd/databases/klifs/local.py b/opencadd/databases/klifs/local.py
index e38f5cea..1c5d2b7d 100644
--- a/opencadd/databases/klifs/local.py
+++ b/opencadd/databases/klifs/local.py
@@ -52,7 +52,6 @@ class LocalInitializer:
     """
 
     def __init__(self, database, path_to_klifs_download, *args, **kwargs):
-
         self._database = database
         self._path_to_klifs_download = path_to_klifs_download
 
@@ -70,7 +69,6 @@ class _LocalDatabaseGenerator:
     """
 
     def __init__(self):
-
         self.path_to_klifs_download = None
 
     @classmethod
@@ -317,7 +315,6 @@ def _add_filepaths(klifs_metadata):
         filepaths = []
 
         for _, row in klifs_metadata.iterrows():
-
             # Depending on whether alternate model and chain ID is given build file path:
             filepath = metadata_to_filepath(
                 ".",
@@ -394,7 +391,6 @@ class Kinases(LocalInitializer, KinasesProvider):
     """
 
     def all_kinase_groups(self):
-
         # Get local database
         kinase_groups = self._database.copy()
         # Standardize DataFrame
@@ -404,7 +400,6 @@ def all_kinase_groups(self):
         return kinase_groups
 
     def all_kinase_families(self, groups=None):
-
         # Get local database and select rows
         kinase_families = self._database.copy()
         groups = self._ensure_list(groups)
@@ -417,7 +412,6 @@ def all_kinase_families(self, groups=None):
         return kinase_families
 
     def all_kinases(self, groups=None, families=None, species=None):
-
         # Get local database and select rows
         kinases = self._database.copy()
         groups = self._ensure_list(groups)
@@ -433,7 +427,6 @@ def all_kinases(self, groups=None, families=None, species=None):
         return kinases
 
     def by_kinase_klifs_id(self, kinase_klifs_ids):
-
         kinase_klifs_ids = self._ensure_list(kinase_klifs_ids)
         # Get local database and select rows
         kinases = self._database.copy()
@@ -443,7 +436,6 @@ def by_kinase_klifs_id(self, kinase_klifs_ids):
         return kinases
 
     def by_kinase_name(self, kinase_names, species=None):
-
         kinase_names = self._ensure_list(kinase_names)
         # Get local database and select rows
         kinases = self._database.copy()
@@ -469,7 +461,6 @@ class Ligands(LocalInitializer, LigandsProvider):
     """
 
     def all_ligands(self):
-
         # Get local database
         ligands = self._database.copy()
         # Standardize DataFrame
@@ -477,7 +468,6 @@ def all_ligands(self):
         return ligands
 
     def by_kinase_klifs_id(self, kinase_klifs_ids):
-
         kinase_klifs_ids = self._ensure_list(kinase_klifs_ids)
         # Get local database and select rows
         ligands = self._database.copy()
@@ -498,7 +488,6 @@ def by_kinase_klifs_id(self, kinase_klifs_ids):
         return ligands
 
     def by_kinase_name(self, kinase_names):
-
         kinase_names = self._ensure_list(kinase_names)
         # Get local database and select rows
         ligands = self._database.copy()
@@ -532,7 +521,6 @@ def by_kinase_name(self, kinase_names):
         return ligands
 
     def by_ligand_expo_id(self, ligand_expo_ids):
-
         ligand_expo_ids = self._ensure_list(ligand_expo_ids)
         # Get local database and select rows
         ligands = self._database.copy()
@@ -553,7 +541,6 @@ class Structures(LocalInitializer, StructuresProvider):
     """
 
     def all_structures(self):
-
         # Get local database
         structures = self._database.copy()
         # Standardize DataFrame
@@ -564,7 +551,6 @@ def all_structures(self):
         return structures
 
     def by_structure_klifs_id(self, structure_klifs_ids):
-
         structure_klifs_ids = self._ensure_list(structure_klifs_ids)
         # Get local database and select rows
         structures = self._database.copy()
@@ -582,7 +568,6 @@ def by_structure_klifs_id(self, structure_klifs_ids):
         return structures
 
     def by_kinase_klifs_id(self, kinase_klifs_ids):
-
         kinase_klifs_ids = self._ensure_list(kinase_klifs_ids)
         # Get local database and select rows
         structures = self._database.copy()
@@ -597,7 +582,6 @@ def by_kinase_klifs_id(self, kinase_klifs_ids):
     def by_structure_pdb_id(
         self, structure_pdb_ids, structure_alternate_model=None, structure_chain=None
     ):
-
         structure_pdb_ids = self._ensure_list(structure_pdb_ids)
         # Get local database and select rows
         structures = self._database.copy()
@@ -615,7 +599,6 @@ def by_structure_pdb_id(
         return structures
 
     def by_ligand_expo_id(self, ligand_expo_ids):
-
         ligand_expo_ids = self._ensure_list(ligand_expo_ids)
         # Get local database and select rows
         structures = self._database.copy()
@@ -628,7 +611,6 @@ def by_ligand_expo_id(self, ligand_expo_ids):
         return structures
 
     def by_kinase_name(self, kinase_names):
-
         kinase_names = self._ensure_list(kinase_names)
         # Get local database and select rows (search in all available kinase names)
         structures = self._database.copy()
@@ -662,7 +644,6 @@ class Interactions(LocalInitializer, InteractionsProvider):
     """
 
     def all_interactions(self):
-
         # Get local database
         interactions = self._database.copy()
         # Standardize DataFrame
@@ -673,7 +654,6 @@ def all_interactions(self):
         return interactions
 
     def by_structure_klifs_id(self, structure_klifs_ids):
-
         structure_klifs_ids = self._ensure_list(structure_klifs_ids)
         # Get local database and select rows
         interactions = self._database.copy()
@@ -686,7 +666,6 @@ def by_structure_klifs_id(self, structure_klifs_ids):
         return interactions
 
     def by_kinase_klifs_id(self, kinase_klifs_ids):
-
         kinase_klifs_ids = self._ensure_list(kinase_klifs_ids)
         # Get local database and select rows
         interactions = self._database.copy()
@@ -713,7 +692,6 @@ class Pockets(LocalInitializer, PocketsProvider):
     """
 
     def by_structure_klifs_id(self, structure_klifs_id, extension="mol2"):  # pylint: disable=W0221
-
         # Get kinase pocket from structure ID
         structures_local = Structures(self._database, self._path_to_klifs_download)
         structure = structures_local.by_structure_klifs_id(structure_klifs_id).squeeze()
@@ -786,7 +764,6 @@ class Coordinates(LocalInitializer, CoordinatesProvider):
     def to_text(
         self, structure_klifs_id_or_filepath, entity="complex", extension="mol2"
     ):  # pylint: disable=W0221
-
         filepath = self._to_filepath(structure_klifs_id_or_filepath, entity, extension)
         with open(filepath, "r") as f:
             text = f.read()
@@ -795,7 +772,6 @@ def to_text(
     def to_dataframe(
         self, structure_klifs_id_or_filepath, entity="complex", extension="mol2"
     ):  # pylint: disable=W0221
-
         filepath = self._to_filepath(structure_klifs_id_or_filepath, entity, extension)
         dataframe = DataFrame.from_file(filepath)
         dataframe = self._add_residue_klifs_ids(dataframe, filepath)
@@ -804,7 +780,6 @@ def to_dataframe(
     def to_rdkit(
         self, structure_klifs_id_or_filepath, entity="complex", extension="mol2", compute2d=True
     ):  # pylint: disable=W0221
-
         filepath = self._to_filepath(structure_klifs_id_or_filepath, entity, extension)
         rdkit_mol = Rdkit.from_file(filepath, compute2d)
         return rdkit_mol
@@ -893,7 +868,6 @@ class Drugs(LocalInitializer, DrugsProvider):
     """
 
     def all_drugs(self):
-
         raise NotImplementedError(
             "Information on drugs is not available locally! Please use a remote session."
         )
@@ -907,13 +881,11 @@ class StructureConformations(LocalInitializer, StructureConformationsProvider):
     """
 
     def all_conformations(self):
-
         raise NotImplementedError(
             "Information on conformations is not available locally! Please use a remote session."
         )
 
     def by_structure_klifs_id(self, structure_klifs_id):
-
         raise NotImplementedError(
             "Information on conformations is not available locally! Please use a remote session."
         )
@@ -927,7 +899,6 @@ class StructureModifiedResidues(LocalInitializer, StructureModifiedResiduesProvi
     """
 
     def by_structure_klifs_id(self, structure_klifs_id):
-
         raise NotImplementedError(
             "Information on modified residues is not available locally! Please use a remote session."
         )
diff --git a/opencadd/databases/klifs/remote.py b/opencadd/databases/klifs/remote.py
index b8e1450d..5eb4f832 100644
--- a/opencadd/databases/klifs/remote.py
+++ b/opencadd/databases/klifs/remote.py
@@ -65,7 +65,6 @@ class RemoteInitializer:
     """
 
     def __init__(self, client, *args, **kwargs):
-
         self._client = client
 
 
@@ -77,7 +76,6 @@ class Kinases(RemoteInitializer, KinasesProvider):
     """
 
     def all_kinase_groups(self):
-
         # Use KLIFS API
         result = self._client.Information.get_kinase_groups().response().result
         # Convert list to DataFrame (1 column)
@@ -87,7 +85,6 @@ def all_kinase_groups(self):
         return kinase_groups
 
     def all_kinase_families(self, groups=None):
-
         groups = self._ensure_list(groups)
         # Use KLIFS API
         result = (
@@ -100,7 +97,6 @@ def all_kinase_families(self, groups=None):
         return kinase_families
 
     def all_kinases(self, groups=None, families=None, species=None):
-
         groups = self._ensure_list(groups)
         families = self._ensure_list(families)
         # Use KLIFS API
@@ -122,7 +118,6 @@ def all_kinases(self, groups=None, families=None, species=None):
         return kinases
 
     def by_kinase_klifs_id(self, kinase_klifs_ids):
-
         kinase_klifs_ids = self._ensure_list(kinase_klifs_ids)
         # Use KLIFS API
         result = (
@@ -139,7 +134,6 @@ def by_kinase_klifs_id(self, kinase_klifs_ids):
         return kinases
 
     def by_kinase_name(self, kinase_names, species=None):
-
         kinase_names = self._ensure_list(kinase_names)
         # Use KLIFS API
         result = (
@@ -164,7 +158,6 @@ class Ligands(RemoteInitializer, LigandsProvider):
     """
 
     def all_ligands(self):
-
         # Use KLIFS API: Get all kinase KLIFS IDs
         kinases_remote = Kinases(self._client)
         kinases = kinases_remote.all_kinases()
@@ -182,7 +175,6 @@ def all_ligands(self):
         return ligands
 
     def by_kinase_klifs_id(self, kinase_klifs_ids):
-
         # Use KLIFS API (send requests iteratively)
         ligands = self._multiple_remote_requests(self._by_kinase_klifs_id, kinase_klifs_ids)
         # Standardize DataFrame
@@ -223,7 +215,6 @@ def _by_kinase_klifs_id(self, kinase_klifs_id):
         return ligands
 
     def by_kinase_name(self, kinase_names):
-
         kinase_names = self._ensure_list(kinase_names)
         # Use KLIFS API: Get kinase KLIFS IDs for input kinase names (remotely)
         # Note: One kinase name can be linked to multiple kinase KLIFS IDs (due to multiple species)
@@ -252,7 +243,6 @@ def by_kinase_name(self, kinase_names):
         return ligands
 
     def by_ligand_klifs_id(self, ligand_klifs_ids):
-
         ligand_klifs_ids = self._ensure_list(ligand_klifs_ids)
         # Use KLIFS API: Get all ligands
         ligands = self.all_ligands()
@@ -265,7 +255,6 @@ def by_ligand_klifs_id(self, ligand_klifs_ids):
         return ligands
 
     def by_ligand_expo_id(self, ligand_expo_ids):
-
         ligand_expo_ids = self._ensure_list(ligand_expo_ids)
         # Use KLIFS API: Get all ligands
         ligands = self.all_ligands()
@@ -286,7 +275,6 @@ class Structures(RemoteInitializer, StructuresProvider):
     """
 
     def all_structures(self):
-
         # Use KLIFS API: Get all kinase KLIFS IDs
         kinases_remote = Kinases(self._client)
         kinases = kinases_remote.all_kinases()
@@ -302,7 +290,6 @@ def all_structures(self):
         return structures
 
     def by_structure_klifs_id(self, structure_klifs_ids):
-
         structure_klifs_ids = self._ensure_list(structure_klifs_ids)
         # Use KLIFS API
         result = (
@@ -321,7 +308,6 @@ def by_structure_klifs_id(self, structure_klifs_ids):
         return structures
 
     def by_ligand_klifs_id(self, ligand_klifs_ids):
-
         ligand_klifs_ids = self._ensure_list(ligand_klifs_ids)
         # Use KLIFS API: Get all structures
         structures = self.all_structures()
@@ -336,7 +322,6 @@ def by_ligand_klifs_id(self, ligand_klifs_ids):
         return structures
 
     def by_kinase_klifs_id(self, kinase_klifs_ids):
-
         kinase_klifs_ids = self._ensure_list(kinase_klifs_ids)
         # Use KLIFS API
         result = (
@@ -357,7 +342,6 @@ def by_kinase_klifs_id(self, kinase_klifs_ids):
     def by_structure_pdb_id(
         self, structure_pdb_ids, structure_alternate_model=None, structure_chain=None
     ):
-
         structure_pdb_ids = self._ensure_list(structure_pdb_ids)
         # Use KLIFS API
         result = (
@@ -381,7 +365,6 @@ def by_structure_pdb_id(
         return structures
 
     def by_ligand_expo_id(self, ligand_expo_ids):
-
         ligand_expo_ids = self._ensure_list(ligand_expo_ids)
         # Use KLIFS API: Get all structures
         structures = self.all_structures()
@@ -396,7 +379,6 @@ def by_ligand_expo_id(self, ligand_expo_ids):
         return structures
 
     def by_kinase_name(self, kinase_names):
-
         kinase_names = self._ensure_list(kinase_names)
         # Use KLIFS API: Get all structures
         structures = self.all_structures()
@@ -419,7 +401,6 @@ class Bioactivities(RemoteInitializer, BioactivitiesProvider):
     """
 
     def all_bioactivities(self, _top_n=None):
-
         # Use KLIFS API: Get all kinase KLIFS IDs
         ligands_remote = Ligands(self._client)
         ligands = ligands_remote.all_ligands()
@@ -441,7 +422,6 @@ def all_bioactivities(self, _top_n=None):
         return bioactivities
 
     def by_kinase_klifs_id(self, kinase_klifs_ids):
-
         kinase_klifs_ids = self._ensure_list(kinase_klifs_ids)
         # Use KLIFS API: Get all kinase KLIFS IDs
         ligands_remote = Ligands(self._client)
@@ -458,7 +438,6 @@ def by_kinase_klifs_id(self, kinase_klifs_ids):
         return bioactivities
 
     def by_ligand_klifs_id(self, ligand_klifs_ids):
-
         # Use KLIFS API (send requests iteratively)
         bioactivities = self._multiple_remote_requests(self._by_ligand_klifs_id, ligand_klifs_ids)
         # Standardize DataFrame
@@ -470,7 +449,6 @@ def by_ligand_klifs_id(self, ligand_klifs_ids):
         return bioactivities
 
     def by_ligand_expo_id(self, ligand_expo_id):
-
         # Use KLIFS API (send requests iteratively)
         bioactivities = self._multiple_remote_requests(self._by_ligand_expo_id, ligand_expo_id)
         # Standardize DataFrame
@@ -557,7 +535,6 @@ class Interactions(RemoteInitializer, InteractionsProvider):
 
     @property
     def interaction_types(self):
-
         # Use KLIFS API
         result = self._client.Interactions.get_interactions_get_types().response().result
         # Convert list of ABC objects to DataFrame
@@ -571,7 +548,6 @@ def interaction_types(self):
         return interaction_types
 
     def all_interactions(self):
-
         # Use KLIFS API: Get all structure KLIFS IDs
         structures_remote = Structures(self._client)
         structures = structures_remote.all_structures()
@@ -587,7 +563,6 @@ def all_interactions(self):
         return interactions
 
     def by_structure_klifs_id(self, structure_klifs_ids):
-
         structure_klifs_ids = self._ensure_list(structure_klifs_ids)
         # Use KLIFS API
         result = (
@@ -606,7 +581,6 @@ def by_structure_klifs_id(self, structure_klifs_ids):
         return interactions
 
     def by_ligand_klifs_id(self, ligand_klifs_ids):
-
         ligand_klifs_ids = self._ensure_list(ligand_klifs_ids)
         # Use KLIFS API: Get structure KLIFS IDs from ligand KLIFS IDs
         structures_remote = Structures(self._client)
@@ -623,7 +597,6 @@ def by_ligand_klifs_id(self, ligand_klifs_ids):
         return interactions
 
     def by_kinase_klifs_id(self, kinase_klifs_ids):
-
         kinase_klifs_ids = self._ensure_list(kinase_klifs_ids)
         # Use KLIFS API: Get structure KLIFS IDs from ligand KLIFS IDs
         structures_remote = Structures(self._client)
@@ -648,7 +621,6 @@ class Pockets(RemoteInitializer, PocketsProvider):
     """
 
     def by_structure_klifs_id(self, structure_klifs_id):
-
         # Use KLIFS API
         result = (
             self._client.Interactions.get_interactions_match_residues(
@@ -677,7 +649,6 @@ class Coordinates(RemoteInitializer, CoordinatesProvider):
     """
 
     def to_text(self, structure_klifs_id, entity="complex", extension="mol2"):
-
         self._raise_invalid_extension(extension)
 
         if entity == "complex" and extension == "mol2":
@@ -721,14 +692,12 @@ def to_text(self, structure_klifs_id, entity="complex", extension="mol2"):
             raise ValueError(f"Data could not be fetched.")
 
     def to_dataframe(self, structure_klifs_id, entity="complex", extension="mol2"):
-
         text = self.to_text(structure_klifs_id, entity, extension)
         dataframe = DataFrame.from_text(text, extension)
         dataframe = self._add_residue_klifs_ids(dataframe, structure_klifs_id)
         return dataframe
 
     def to_rdkit(self, structure_klifs_id, entity="complex", extension="mol2", compute2d=True):
-
         text = self.to_text(structure_klifs_id, entity, extension)
         rdkit_mol = Rdkit.from_text(text, extension, compute2d)
         return rdkit_mol
@@ -882,7 +851,6 @@ class Drugs(RemoteInitializer, DrugsProvider):
     """
 
     def all_drugs(self):
-
         # Use KLIFS API
         result = self._client.Ligands.get_drug_list().response().result
         # Convert list of ABC objects to DataFrame
@@ -902,7 +870,6 @@ class StructureConformations(RemoteInitializer, StructureConformationsProvider):
     """
 
     def all_conformations(self):
-
         # Use KLIFS API: Get all structure KLIFS IDs
         structures_remote = Structures(self._client)
         structures = structures_remote.all_structures()
@@ -918,7 +885,6 @@ def all_conformations(self):
         return conformations
 
     def by_structure_klifs_id(self, structure_klifs_ids):
-
         structure_klifs_ids = self._ensure_list(structure_klifs_ids)
         # Use KLIFS API
         result = (
@@ -945,7 +911,6 @@ class StructureModifiedResidues(RemoteInitializer, StructureModifiedResiduesProv
     """
 
     def by_structure_klifs_id(self, structure_klifs_id):
-
         # Use KLIFS API
         result = (
             self._client.Structures.get_structure_modified_residues(
diff --git a/opencadd/databases/klifs/session.py b/opencadd/databases/klifs/session.py
index 2f61c250..dad3d3f8 100644
--- a/opencadd/databases/klifs/session.py
+++ b/opencadd/databases/klifs/session.py
@@ -46,7 +46,6 @@ class Session:
     """
 
     def __init__(self):
-
         # Not None in local only
         self._path_to_klifs_download = None
         self._database = None
diff --git a/opencadd/io/dataframe.py b/opencadd/io/dataframe.py
index 736cc74c..abdda8c8 100644
--- a/opencadd/io/dataframe.py
+++ b/opencadd/io/dataframe.py
@@ -319,10 +319,8 @@ def _format_dataframe(cls, dataframe, verbose=False):
             dataframe_columns = DATAFRAME_COLUMNS["default"]
 
         # If default column names are missing, add empty columns
-        for (column_name, column_dtype) in dataframe_columns:
-
+        for column_name, column_dtype in dataframe_columns:
             if column_name not in dataframe.columns:
-
                 if column_dtype == "string":
                     dataframe.insert(len(dataframe.columns), column_name, None)
                 elif column_dtype == "float32":
diff --git a/opencadd/structure/pocket/base.py b/opencadd/structure/pocket/base.py
index 05174654..6a818c49 100644
--- a/opencadd/structure/pocket/base.py
+++ b/opencadd/structure/pocket/base.py
@@ -18,7 +18,6 @@ class PocketBase:
     """
 
     def __init__(self):
-
         self.name = None
         self._residue_ids = None
         self._residue_ixs = None
diff --git a/opencadd/structure/pocket/core.py b/opencadd/structure/pocket/core.py
index 6895a5fd..4f45c335 100644
--- a/opencadd/structure/pocket/core.py
+++ b/opencadd/structure/pocket/core.py
@@ -56,7 +56,6 @@ class Pocket(PocketBase):
     """
 
     def __init__(self):
-
         self.name = None
         self.data = None
         self.center = None
diff --git a/opencadd/structure/pocket/features/region.py b/opencadd/structure/pocket/features/region.py
index b5a8868b..05f9081c 100644
--- a/opencadd/structure/pocket/features/region.py
+++ b/opencadd/structure/pocket/features/region.py
@@ -24,7 +24,6 @@ class Region:
     """
 
     def __init__(self, name, residue_ids, residue_ixs=None, color="blue"):
-
         self.name = name
         self.color = color
         self.residue_ids = residue_ids
diff --git a/opencadd/structure/pocket/klifs.py b/opencadd/structure/pocket/klifs.py
index 4fbc7b8c..5cc1f032 100644
--- a/opencadd/structure/pocket/klifs.py
+++ b/opencadd/structure/pocket/klifs.py
@@ -79,7 +79,6 @@ def from_structure_klifs_id(
 
     @staticmethod
     def add_klifs_regions(pocket, pocket_residues):
-
         for (region, color), group in pocket_residues.groupby(
             ["residue.klifs_region", "residue.klifs_color"]
         ):
@@ -93,7 +92,6 @@ def add_klifs_regions(pocket, pocket_residues):
 
     @staticmethod
     def add_klifs_subpockets(pocket, pocket_residues, subpockets):
-
         # Map residue KLIFS IDs > residue ID
         if subpockets is not None:
             subpockets = pd.DataFrame(subpockets)
diff --git a/opencadd/structure/pocket/viewer.py b/opencadd/structure/pocket/viewer.py
index 3f75b9d1..f846e1b7 100644
--- a/opencadd/structure/pocket/viewer.py
+++ b/opencadd/structure/pocket/viewer.py
@@ -51,7 +51,6 @@ class PocketViewer:
     """
 
     def __init__(self):
-
         self.viewer = nglview.NGLWidget()
         self.viewer._remote_call("setSize", target="Widget", args=["1000px", "600px"])
         self.pockets_residue_ngl_ixs = {}
@@ -204,12 +203,10 @@ def _map_residue_ids_names_nglixs(self, pocket):
         residue_id2ix = dataframe[["residue.name", "residue.id"]].drop_duplicates()
 
         if pocket._extension == "mol2":
-
             # Map residue names to nglview index (starting from 1)
             residue_id2ix["residue.ngl_ix"] = [str(i) for i in range(1, len(residue_id2ix) + 1)]
 
         else:
-
             # In this case, residue ID and nglview index are the same
             residue_id2ix["residue.ngl_ix"] = [str(i) for i in residue_id2ix["residue.id"]]
 
diff --git a/opencadd/structure/superposition/engines/mda.py b/opencadd/structure/superposition/engines/mda.py
index 68045d39..3415dcfa 100644
--- a/opencadd/structure/superposition/engines/mda.py
+++ b/opencadd/structure/superposition/engines/mda.py
@@ -75,7 +75,6 @@ def __init__(
         superposition_weights=None,
         superposition_delta_mass_tolerance=0.1,
     ):
-
         self.alignment_strategy = alignment_strategy.lower()
         if self.alignment_strategy == "global":
             self._align_local = False
diff --git a/opencadd/structure/superposition/sequences.py b/opencadd/structure/superposition/sequences.py
index 38ee0fe3..83c79ee1 100644
--- a/opencadd/structure/superposition/sequences.py
+++ b/opencadd/structure/superposition/sequences.py
@@ -12,7 +12,6 @@
 
 
 def matrices(name):
-
     """
     A SubstitutionMatrix maps each possible pairing of a symbol of a first alphabet with
     a symbol of a second alphabet to a score (int)
@@ -42,7 +41,6 @@ def matrices(name):
 
 
 def sequence_alignment(seq1: str, seq2: str, matrix: str, gap: int, local: bool = False) -> str:
-
     """
     Perform a global alignment, based on the Needleman-Wunsch algorithm
 
diff --git a/opencadd/tests/databases/test_klifs_local_remote.py b/opencadd/tests/databases/test_klifs_local_remote.py
index 09413a8a..e82c0ea1 100644
--- a/opencadd/tests/databases/test_klifs_local_remote.py
+++ b/opencadd/tests/databases/test_klifs_local_remote.py
@@ -212,7 +212,6 @@ def test_all_interactions(self):
         check_dataframe(result_local, FIELDS.oc_name_to_type("interactions"))
 
     def test_all_bioactivities(self):
-
         """
         Test request result for all kinases.
         """
diff --git a/opencadd/tests/databases/test_klifs_remote_parallelization.py b/opencadd/tests/databases/test_klifs_remote_parallelization.py
index 479d779f..31a1abef 100644
--- a/opencadd/tests/databases/test_klifs_remote_parallelization.py
+++ b/opencadd/tests/databases/test_klifs_remote_parallelization.py
@@ -18,7 +18,6 @@
     [(REMOTE, [111, 113], 2)],
 )
 def test_remote_parallelization(klifs_session, structure_klifs_ids, n_cores):
-
     pool = Pool(processes=n_cores)
 
     pool.starmap(_parallelize_klifs_session, zip(structure_klifs_ids, repeat(klifs_session)))
diff --git a/opencadd/tests/structure/test_pocket_core.py b/opencadd/tests/structure/test_pocket_core.py
index fc54dd30..b3ceb315 100644
--- a/opencadd/tests/structure/test_pocket_core.py
+++ b/opencadd/tests/structure/test_pocket_core.py
@@ -482,7 +482,6 @@ def test_center_and_ca_atoms(
     def test_format_residue_ids_and_ixs(
         self, residue_ids, residue_ixs, residue_ids_formatted, residue_ixs_formatted
     ):
-
         pocket = Pocket()
         residue_ids, residue_ixs = pocket._format_residue_ids_and_ixs(
             residue_ids, residue_ixs, "text"
diff --git a/opencadd/tests/structure/test_pocket_region.py b/opencadd/tests/structure/test_pocket_region.py
index 40fb71c0..7174681e 100644
--- a/opencadd/tests/structure/test_pocket_region.py
+++ b/opencadd/tests/structure/test_pocket_region.py
@@ -18,7 +18,6 @@ class TestRegion:
         [("example", [1, 2], [10, 20], "blue")],
     )
     def test_attributes_and_properties(self, name, residue_ids, residue_ixs, color):
-
         region = Region(name, residue_ids, residue_ixs, color)
         assert region.name == name
         assert region.residue_ids == residue_ids
diff --git a/opencadd/utils.py b/opencadd/utils.py
index d9eae239..266616a4 100644
--- a/opencadd/utils.py
+++ b/opencadd/utils.py
@@ -44,7 +44,6 @@ def __init__(self, fmt="%(levelname)d: %(message)s", datefmt=None, style="%", **
         super().__init__(fmt=fmt, datefmt=datefmt, style=style, **kwargs)
 
     def format(self, record):
-
         # Save the original format configured by the user
         # when the logger formatter was instantiated
         format_orig = self._style._fmt