mol2morgan_fingerprint: remove deprecated fp function (#83)

* mol2morgan_fingerprint: remove deprecated fp function

    - Remove AllChem.GetMorganFingerprintAsBitVect
      from the code because it is deprecated.
    - Add a test to ensure the bit2atom mapping works
      as intended.

* Error handling sanitize bug (#85)

* fix molsanitize exception error catching

* linting

* isort on other stuff

* Inchitomol (#86)

* fix molsanitize exception error catching

* linting

* isort on other stuff

* add inchitomol element

* Add `--check-only` flag to isort (#88)

* docu: update readme, add image, add feature calc notebook (#90)

* docu: update readme, add image, add feature calc notebook

* readme: add feature calculation example

* readme: add published Molpipeline paper link

* notebooks: add header to feature calculation

* add counted fps to test

---------

Co-authored-by: frederik-sandfort1 <129401811+frederik-sandfort1@users.noreply.github.com>
Co-authored-by: Christian W. Feldmann <128160984+c-w-feldmann@users.noreply.github.com>

molpipeline/mol2any/mol2morgan_fingerprint.py

@@ -151,12 +151,11 @@ def _explain_rdmol(self, mol_obj: RDKitMol) -> dict[int, list[tuple[int, int]]]:
         dict[int, list[tuple[int, int]]]
             Dictionary with bit position as key and list of tuples with atom index and radius as value.
         """
-        bit_info: dict[int, list[tuple[int, int]]] = {}
-        _ = AllChem.GetMorganFingerprintAsBitVect(
-            mol_obj,
-            self.radius,
-            useFeatures=self._use_features,
-            bitInfo=bit_info,
-            nBits=self._n_bits,
+        fp_generator = self._get_fp_generator()
+        additional_output = AllChem.AdditionalOutput()
+        additional_output.AllocateBitInfoMap()
+        _ = fp_generator.GetSparseFingerprint(
+            mol_obj, additionalOutput=additional_output
         )
+        bit_info = additional_output.GetBitInfoMap()
         return bit_info

tests/test_elements/test_mol2any/test_mol2morgan_fingerprint.py

@@ -10,6 +10,7 @@
 from molpipeline import Pipeline
 from molpipeline.any2mol import SmilesToMol
 from molpipeline.mol2any import MolToMorganFP
+from tests.utils.fingerprints import fingerprints_to_numpy
 
 test_smiles = [
     "c1ccccc1",
@@ -128,6 +129,34 @@ def test_setter_getter_error_handling(self) -> None:
         }
         self.assertRaises(ValueError, mol_fp.set_params, **params)
 
+    def test_bit2atom_mapping(self) -> None:
+        """Test that the mapping from bits to atom weights works as intended.
+
+        Notes
+        -----
+        lower n_bit values, e.g. 2048, will lead to a bit clash during folding,
+        for the test smiles "NCCOCCCC(=O)O".
+        We want no folding clashes in this test to check the correct length
+        of the bit-to-atom mapping.
+        """
+        n_bits = 2100
+        sparse_morgan = MolToMorganFP(radius=2, n_bits=n_bits, return_as="sparse")
+        dense_morgan = MolToMorganFP(radius=2, n_bits=n_bits, return_as="dense")
+        explicit_bit_vect_morgan = MolToMorganFP(
+            radius=2, n_bits=n_bits, return_as="explicit_bit_vect"
+        )
+
+        smi2mol = SmilesToMol()
+        for test_smi in test_smiles:
+            for fp_gen in [sparse_morgan, dense_morgan, explicit_bit_vect_morgan]:
+                for counted in [False, True]:
+                    mol = smi2mol.transform([test_smi])[0]
+                    fp_gen.set_params(counted=counted)
+                    fp = fp_gen.transform([mol])
+                    mapping = fp_gen.bit2atom_mapping(mol)
+                    np_fp = fingerprints_to_numpy(fp)
+                    self.assertEqual(np.nonzero(np_fp)[0].shape[0], len(mapping))  # type: ignore
+
 
 if __name__ == "__main__":
     unittest.main()

tests/utils/fingerprints.py

@@ -8,7 +8,7 @@
 
 # pylint: disable=no-name-in-module
 from rdkit.Chem import rdFingerprintGenerator as rdkit_fp
-from rdkit.DataStructs import ExplicitBitVect
+from rdkit.DataStructs import ExplicitBitVect, UIntSparseIntVect
 from scipy import sparse
 
 
@@ -59,6 +59,8 @@ def fingerprints_to_numpy(
     """
     if all(isinstance(fp, ExplicitBitVect) for fp in fingerprints):
         return np.array(fingerprints)
+    if all(isinstance(fp, UIntSparseIntVect) for fp in fingerprints):
+        return np.array([fp.ToList() for fp in fingerprints])
     if isinstance(fingerprints, sparse.csr_matrix):
         return fingerprints.toarray()
     if isinstance(fingerprints, np.ndarray):