chore: lint

Author: Ninjani

src/plinder/data/pipeline/io.py

@@ -105,9 +105,7 @@ def download_affinity_data(
     papyrus_raw_affinity_path = (
         data_dir / "dbs" / "affinity" / "papyrus_affinity_raw.tar.gz"
     )
-    bindingdb_raw_affinity_path = (
-        data_dir / "dbs" / "affinity" / "BindingDB_All.tsv"
-    )
+    bindingdb_raw_affinity_path = data_dir / "dbs" / "affinity" / "BindingDB_All.tsv"
     moad_raw_affinity_path = data_dir / "dbs" / "affinity" / "moad_affinity.csv"
 
     # Make sub directories

src/plinder/data/pipeline/utils.py

@@ -154,7 +154,7 @@ def load_entries_from_zips(
                         reduced[pdb_id] = Entry.model_validate_json(obj.read()).prune(
                             load_for_scoring=load_for_scoring,
                             max_protein_chains=max_protein_chains,
-                            max_ligand_chains=max_ligand_chains
+                            max_ligand_chains=max_ligand_chains,
                         )
                 except Exception as e:
                     LOG.error(f"failed to read name={name} failed with {repr(e)}")

src/plinder/data/utils/annotations/aggregate_annotations.py

@@ -163,7 +163,9 @@ def num_pocket_residues(self) -> int:
         for ligand in self.ligands:
             ligand_pocket_residues = ligand.pocket_residues
             for chain in ligand_pocket_residues:
-                pocket_residues |= set((chain, residue) for residue in ligand_pocket_residues[chain])
+                pocket_residues |= set(
+                    (chain, residue) for residue in ligand_pocket_residues[chain]
+                )
         return len(pocket_residues)
 
     @cached_property
@@ -534,9 +536,11 @@ def ligand_max_molecular_weight(self) -> float:
         """
         Maximum molecular weight of the system ligands
         """
-        max_vals = [ligand.molecular_weight if ligand.molecular_weight is not None else -1.0
+        max_vals = [
+            ligand.molecular_weight if ligand.molecular_weight is not None else -1.0
             for ligand in self.ligands
-            if ligand.molecular_weight is not None]
+            if ligand.molecular_weight is not None
+        ]
         if len(max_vals):
             return max(max_vals)
         else:

src/plinder/data/utils/annotations/get_similarity_scores.py

@@ -426,7 +426,7 @@ def get_score_df(
             if not pdb_id_file.exists():
                 LOG.info(f"get_score_df: pdb_id_file={pdb_id_file} does not exist")
                 continue
-            
+
             # self.entries = {}
             entries_to_load = {pdb_id}
             if search_db != "pred" and pdb_id_file.exists():

src/plinder/data/utils/annotations/ligand_utils.py

@@ -32,7 +32,6 @@
 from plinder.data.utils.annotations.protein_utils import Chain
 from plinder.data.utils.annotations.rdkit_utils import (
     set_smiles_from_ligand_ost,
-    set_smiles_from_ligand_ost_v2,
 )
 from plinder.data.utils.annotations.utils import DocBaseModel