fix pylint error

molpipeline/abstract_pipeline_elements/mol2any/mol2bitvector.py

@@ -15,7 +15,7 @@
 import numpy as np
 import numpy.typing as npt
 from rdkit.Chem import rdFingerprintGenerator
-from rdkit.DataStructs import ExplicitBitVect
+from rdkit.DataStructs import ExplicitBitVect  # type: ignore[attr-defined]
 from scipy import sparse
 
 from molpipeline.abstract_pipeline_elements.core import MolToAnyPipelineElement

molpipeline/any2mol/sdf2mol.py

@@ -119,7 +119,7 @@ def pretransform_single(self, value: str) -> OptionalMol:
                 "Invalid SDF string!",
                 self.name,
             )
-        supplier = Chem.SDMolSupplier()
+        supplier = Chem.SDMolSupplier()  # type: ignore[call-arg]
         supplier.SetData(value)
         mol = next(supplier, None)
         if mol is None:

molpipeline/estimators/leader_picker_clustering.py

@@ -8,7 +8,7 @@
 import numpy as np
 import numpy.typing as npt
 from rdkit import DataStructs
-from rdkit.DataStructs import ExplicitBitVect
+from rdkit.DataStructs import ExplicitBitVect  # type: ignore[attr-defined]
 from rdkit.SimDivFilters import rdSimDivPickers
 from sklearn.base import BaseEstimator, ClusterMixin, _fit_context
 from sklearn.utils._param_validation import Interval
@@ -92,7 +92,7 @@ def _assign_points_to_clusters_based_on_centroid(
         max_similarities = np.full(len(fps), -np.inf, dtype=np.float64)
 
         for i, pick_idx in enumerate(picks):
-            similarities = DataStructs.BulkTanimotoSimilarity(fps[pick_idx], fps)
+            similarities = DataStructs.BulkTanimotoSimilarity(fps[pick_idx], fps)  # type: ignore[attr-defined]
             max_mask = similarities > max_similarities
             labels[max_mask] = i
             max_similarities[max_mask] = list(compress(similarities, max_mask))

molpipeline/experimental/explainability/visualization/heatmaps.py

@@ -299,6 +299,6 @@ def color_canvas(canvas: Draw.MolDraw2D, color_grid: ColorGrid) -> None:
 
     for x, y in zip(*mask):
         upper_left, lower_right = color_grid.grid_field_lim(x, y)
-        upper_left, lower_right = Point2D(*upper_left), Point2D(*lower_right)
-        canvas.SetColour(tuple(color_grid.color_grid[x, y]))
+        upper_left, lower_right = Point2D(*upper_left), Point2D(*lower_right)  # type: ignore[assignment]
+        canvas.SetColour(tuple(color_grid.color_grid[x, y]))  # type: ignore[call-arg]
         canvas.DrawRect(upper_left, lower_right)

molpipeline/experimental/explainability/visualization/utils.py

@@ -34,7 +34,7 @@ def get_mol_lims(mol: Chem.Mol) -> tuple[tuple[float, float], tuple[float, float
     coords_list = []
     conf = mol.GetConformer(0)
     for i, _ in enumerate(mol.GetAtoms()):
-        pos = conf.GetAtomPosition(i)
+        pos = conf.GetAtomPosition(i)  # type: ignore[call-arg]
         coords_list.append((pos.x, pos.y))
     coords: npt.NDArray[np.float64] = np.array(coords_list)
     min_p = np.min(coords, axis=0)

molpipeline/mol2any/mol2bin.py

@@ -21,4 +21,4 @@ def pretransform_single(self, value: Chem.Mol) -> str:
         str
             Binary representation of molecule.
         """
-        return value.ToBinary()
+        return value.ToBinary()  # type: ignore[call-overload]

molpipeline/mol2any/mol2maccs_key_fingerprint.py

@@ -3,7 +3,7 @@
 import numpy as np
 from numpy import typing as npt
 from rdkit.Chem import MACCSkeys
-from rdkit.DataStructs import ExplicitBitVect
+from rdkit.DataStructs import ExplicitBitVect  # type: ignore[attr-defined]
 
 from molpipeline.abstract_pipeline_elements.mol2any.mol2bitvector import (
     MolToFingerprintPipelineElement,

molpipeline/mol2any/mol2morgan_fingerprint.py

@@ -163,7 +163,7 @@ def _explain_rdmol(self, mol_obj: RDKitMol) -> dict[int, list[tuple[int, int]]]:
             Dictionary with bit position as key and list of tuples with atom index and radius as value.
         """
         fp_generator = self._get_fp_generator()
-        additional_output = AllChem.AdditionalOutput()
+        additional_output = AllChem.AdditionalOutput()  # type: ignore[attr-defined]
         additional_output.AllocateBitInfoMap()
         # using the dense fingerprint here, to get indices after folding
         _ = fp_generator.GetFingerprint(mol_obj, additionalOutput=additional_output)

molpipeline/mol2any/mol2rdkit_phys_chem.py

@@ -27,7 +27,7 @@
 from molpipeline.utils.molpipeline_types import AnyTransformer, RDKitMol
 
 RDKIT_DESCRIPTOR_DICT: dict[str, Callable[[Chem.Mol], float]]
-RDKIT_DESCRIPTOR_DICT = dict(Descriptors.descList)
+RDKIT_DESCRIPTOR_DICT = dict(Descriptors.descList)  # type: ignore[attr-defined]
 
 # MolWt is removed as ExactMolWt is already included.
 # Ipc is removed because it causes trouble with numpy.

molpipeline/post_prediction.py

@@ -43,7 +43,7 @@ def transform(self, X: Any, **params: Any) -> Any:  # pylint: disable=invalid-na
         """
 
 
-class PostPredictionWrapper(PostPredictionTransformation):
+class PostPredictionWrapper(PostPredictionTransformation):  # pylint: disable=too-many-ancestors
     """Wrapper for post prediction transformations.
 
     This class is used to wrap a PipelineElement in a PostPredictionTransformation.

molpipeline/utils/substructure_handling.py

@@ -70,6 +70,6 @@ def from_mol(
 
         env = Chem.FindAtomEnvironmentOfRadiusN(mol, radius, central_atom_index)
         amap: dict[int, int] = {}
-        _ = Chem.PathToSubmol(mol, env, atomMap=amap)
+        _ = Chem.PathToSubmol(mol, env, atomMap=amap)  # type: ignore[call-arg]
         env_atoms = amap.keys()
         return CircularAtomEnvironment(central_atom_index, radius, set(env_atoms))

tests/test_estimators/test_leader_picker_clustering.py

@@ -20,7 +20,7 @@ class TestLeaderPickerEstimator(unittest.TestCase):
     def test_leader_picker_clustering_estimator(self) -> None:
         """Test LeaderPicker clustering estimator."""
         fingerprint_matrix = [
-            DataStructs.CreateFromBitString(x)
+            DataStructs.CreateFromBitString(x)  # type: ignore[attr-defined]
             for x in [
                 "000",  # 0
                 "100",  # 1

tests/test_estimators/test_similarity_transformation.py

@@ -8,7 +8,7 @@
 import numpy.typing as npt
 from rdkit import Chem
 from rdkit.Chem import rdFingerprintGenerator
-from rdkit.DataStructs import BulkTanimotoSimilarity
+from rdkit.DataStructs import BulkTanimotoSimilarity  # type: ignore[attr-defined]
 from scipy import sparse
 from sklearn.neighbors import KNeighborsClassifier
 

tests/test_experimental/test_explainability/test_visualization/test_visualization.py

@@ -198,15 +198,15 @@ def test_explicit_hydrogens(self) -> None:
         """
         mol_implicit_hydrogens = Chem.MolFromSmiles("C")
         explanations1 = self.test_tree_explainer_clf.explain(
-            [Chem.MolToSmiles(mol_implicit_hydrogens)]
+            [Chem.MolToSmiles(mol_implicit_hydrogens)]  # type: ignore[arg-type]
         )
-        mol_added_hydrogens = Chem.AddHs(mol_implicit_hydrogens)
+        mol_added_hydrogens = Chem.AddHs(mol_implicit_hydrogens)  # type: ignore[arg-type]
         explanations2 = self.test_tree_explainer_clf.explain(
-            [Chem.MolToSmiles(mol_added_hydrogens)]
+            [Chem.MolToSmiles(mol_added_hydrogens)]  # type: ignore[arg-type]
         )
         mol_explicit_hydrogens = Chem.MolFromSmiles("[H]C([H])([H])[H]")
         explanations3 = self.test_tree_explainer_clf.explain(
-            [Chem.MolToSmiles(mol_explicit_hydrogens)]
+            [Chem.MolToSmiles(mol_explicit_hydrogens)]  # type: ignore[arg-type]
         )
 
         # test explanations' atom weights

tests/utils/fingerprints.py

@@ -5,13 +5,18 @@
 import numpy as np
 import numpy.typing as npt
 from rdkit import Chem
-from rdkit.Chem import rdFingerprintGenerator as rdkit_fp
-from rdkit.DataStructs import ExplicitBitVect, UIntSparseIntVect
+from rdkit.Chem import rdFingerprintGenerator
+from rdkit.DataStructs import (  # type: ignore[attr-defined]
+    ExplicitBitVect,
+    UIntSparseIntVect,
+)
 from scipy import sparse
 
 
 def make_sparse_fp(
-    smiles_list: list[str], radius: int, n_bits: int
+    smiles_list: list[str],
+    radius: int,
+    n_bits: int,
 ) -> sparse.csr_matrix:
     """Create a sparse Morgan fingerprint matrix from a list of SMILES.
 
@@ -30,9 +35,10 @@ def make_sparse_fp(
     -------
     sparse.csr_matrix
         Feature matrix.
+
     """
     vector_list = []
-    morgan_fp = rdkit_fp.GetMorganGenerator(radius=radius, fpSize=n_bits)
+    morgan_fp = rdFingerprintGenerator.GetMorganGenerator(radius=radius, fpSize=n_bits)
     for smiles in smiles_list:
         mol = Chem.MolFromSmiles(smiles)
         vector = morgan_fp.GetFingerprintAsNumPy(mol)