Cleanup ruff linting errors

posebusters/cli.py

@@ -27,7 +27,7 @@ def main():
         logger.error(e)
 
 
-def bust(
+def bust(  # noqa: PLR0913
     mol_pred: list[Path | Mol] = [],
     mol_true: Path | Mol | None = None,
     mol_cond: Path | Mol | None = None,

posebusters/modules/distance_geometry.py

@@ -64,7 +64,7 @@
 }
 
 
-def check_geometry(
+def check_geometry(  # noqa: PLR0913, PLR0915
     mol_pred: Mol,
     threshold_bad_bond_length: float = 0.2,
     threshold_clash: float = 0.2,
@@ -234,8 +234,8 @@ def _two_bonds_to_angle(bond1: tuple[int, int], bond2: tuple[int, int]) -> None
     set1 = set(bond1)
     set2 = set(bond2)
     all_atoms = set1 | set2
-    # angle requires two bonds to share exactly one atom
-    if len(all_atoms) != 3:
+    # angle requires two bonds to share exactly one atom, that is we must have 3 atoms
+    if len(all_atoms) != 3:  # noqa: PLR2004
         return None
     # find shared atom
     shared_atom = set1 & set2

posebusters/modules/intermolecular_distance.py

@@ -12,7 +12,7 @@
 _periodic_table = GetPeriodicTable()
 
 
-def check_intermolecular_distance(
+def check_intermolecular_distance(  # noqa: PLR0913
     mol_pred: Mol,
     mol_cond: Mol,
     radius_type: str = "vdw",

posebusters/modules/rmsd.py

@@ -78,7 +78,7 @@ def check_rmsd(
     return {"results": results}
 
 
-def robust_rmsd(
+def robust_rmsd(  # noqa: PLR0913
     mol_probe: Mol,
     mol_ref: Mol,
     conf_id_probe: int = -1,

posebusters/modules/volume_overlap.py

@@ -13,7 +13,7 @@
 logger = logging.getLogger(__name__)
 
 
-def check_volume_overlap(
+def check_volume_overlap(  # noqa: PLR0913
     mol_pred: Mol,
     mol_cond: Mol,
     clash_cutoff: float = 0.05,

posebusters/posebusters.py

@@ -131,7 +131,7 @@ def _run(self) -> Generator[dict, None, None]:
         """
         self._initialize_modules()
 
-        for i, paths in self.file_paths.iterrows():
+        for _, paths in self.file_paths.iterrows():
             mol_args = {}
             if "mol_cond" in paths and paths["mol_cond"] is not None:
                 mol_cond_load_params = self.config.get("loading", {}).get("mol_cond", {})
@@ -151,15 +151,15 @@ def _run(self) -> Generator[dict, None, None]:
 
                 for name, fname, func, args in zip(self.module_name, self.fname, self.module_func, self.module_args):
                     # pick needed arguments for module
-                    args = {k: v for k, v in mol_args.items() if k in args}
+                    args_needed = {k: v for k, v in mol_args.items() if k in args}
                     # loading takes all inputs
                     if fname == "loading":
-                        args = {k: args.get(k, None) for k in args}
+                        args_needed = {k: args_needed.get(k, None) for k in args_needed}
                     # run module when all needed input molecules are valid Mol objects
-                    if fname != "loading" and not all(args.get(m, None) for m in args):
+                    if fname != "loading" and not all(args_needed.get(m, None) for m in args_needed):
                         module_output: dict[str, Any] = {"results": {}}
                     else:
-                        module_output = func(**args)
+                        module_output = func(**args_needed)
 
                     # save to object
                     self.results[results_key].extend([(name, k, v) for k, v in module_output["results"].items()])

posebusters/tools/loading.py

@@ -68,15 +68,15 @@ def safe_supply_mols(path: Path, load_all=True, sanitize=True, **load_params) ->
     supplier = SDMolSupplier(str(path), sanitize=False, strictParsing=True)
     i = 0
     for mol in supplier:
-        mol = _process_mol(mol, sanitize=sanitize, **load_params)
+        mol_clean = _process_mol(mol, sanitize=sanitize, **load_params)
         i += 1
-        if mol is not None:
-            mol.SetProp("_Path", str(path))
-            mol.SetProp("_Index", str(i))
-        yield mol
+        if mol_clean is not None:
+            mol_clean.SetProp("_Path", str(path))
+            mol_clean.SetProp("_Index", str(i))
+        yield mol_clean
 
 
-def _load_mol(
+def _load_mol(  # noqa: PLR0913
     path: Path,
     load_all=False,
     sanitize=False,
@@ -136,7 +136,7 @@ def _load_and_combine_mols(path: Path, sanitize=True, removeHs=True, strictParsi
     return mol
 
 
-def _process_mol(
+def _process_mol(  # noqa: PLR0913
     mol: Mol | None,
     smiles: str | None = None,
     cleanup=False,

posebusters/tools/molecules.py

@@ -9,23 +9,10 @@
 from rdkit import RDLogger
 from rdkit.Chem.AllChem import AssignBondOrdersFromTemplate
 from rdkit.Chem.Lipinski import HAcceptorSmarts, HDonorSmarts
-from rdkit.Chem.rdchem import (
-    AtomValenceException,
-    Bond,
-    Conformer,
-    GetPeriodicTable,
-    Mol,
-    RWMol,
-)
+from rdkit.Chem.rdchem import AtomValenceException, Bond, Conformer, GetPeriodicTable, Mol, RWMol
 from rdkit.Chem.rdMolAlign import GetBestAlignmentTransform
 from rdkit.Chem.rdmolfiles import MolFromSmarts
-from rdkit.Chem.rdmolops import (
-    AddHs,
-    RemoveHs,
-    RemoveStereochemistry,
-    RenumberAtoms,
-    SanitizeMol,
-)
+from rdkit.Chem.rdmolops import AddHs, RemoveHs, RemoveStereochemistry, RenumberAtoms, SanitizeMol
 from rdkit.Chem.rdMolTransforms import TransformConformer
 
 logger = getLogger(__name__)
@@ -184,7 +171,7 @@ def _get_atomic_number(atomic_symbol: str):
             symbol = "H"
         return _periodic_table.GetAtomicNumber(symbol)
     except Exception:
-        print(atomic_symbol)
+        logger.error("Unknown atomic symbol: %s", atomic_symbol)
         return atomic_symbol
 
 

posebusters/tools/protein.py

@@ -62,7 +62,7 @@ def get_atom_type_mask(mol: Mol, ignore_types: Iterable[str]) -> list[bool]:
     ]
 
 
-def _keep_atom(
+def _keep_atom(  # noqa: PLR0913, PLR0911
     atom: Atom, ignore_h: bool, ignore_protein: bool, ignore_org_cof: bool, ignore_inorg_cof: bool, ignore_water: bool
 ) -> bool:
     """Whether to keep atom for given ignore flags."""

pyproject.toml

@@ -59,6 +59,9 @@ lint.ignore = ["E501"]
 [tool.ruff.format]
 docstring-code-format = true
 
+[tool.ruff.lint.per-file-ignores]
+"tests/*" = ["D", "PLR2004"]
+
 [tool.mypy]
 ignore_missing_imports = true
 

tests/test_posebusters.py

@@ -65,13 +65,13 @@ def test_bust_mol_rdkit() -> None:
     assert df.all(axis=1).values[0]
 
 
-def test_bust_mols_hydrogen() -> None:
+def test_bust_mols_hydrogen(threshold=8) -> None:
     posebusters = PoseBusters("mol")
     df = posebusters.bust([mol_single_h])
-    assert df.sum(axis=1).values[0] >= 8  # energy ratio test fails
+    assert df.sum(axis=1).values[0] >= threshold  # energy ratio test fails
 
 
-def test_bust_mols_consistency() -> None:
+def test_bust_mols_consistency(atol=1e-6) -> None:
     # check that running the same molecule twice gives the same result
 
     posebusters = PoseBusters("mol")
@@ -84,4 +84,4 @@ def test_bust_mols_consistency() -> None:
     for v1, v2 in zip(result_2.values, result_3.values):
         if v1[2] == v2[2] or math.isnan(v1[2]):
             continue
-        assert abs(v1[2] - v2[2]) < 1e-6, f"{v1[0], v1[1]}: {v1[2]} != {v2[2]}"
+        assert abs(v1[2] - v2[2]) < atol, f"{v1[0], v1[1]}: {v1[2]} != {v2[2]}"