Rdmol iterators (#103)

* allow rdkit mols in interators

* pytables 3.9 not compatible with python 3.8

* add simple tests

* fix issue when using generated ids

* version

FPSim2/__init__.py

@@ -5,4 +5,4 @@
 except Exception as e:
     pass
 
-__version__ = "0.4.5"
+__version__ = "0.5.0"

FPSim2/io/chem.py

@@ -94,28 +94,27 @@ def process_fp(fp, mol_id):
     return mol_id, *fp, popcnt
 
 
-def load_molecule(mol_string: str) -> Chem.Mol:
+def load_molecule(molecule: Any) -> Chem.Mol:
     """Reads SMILES, molblock or InChI and returns a RDKit mol.
 
     Parameters
     ----------
-    mol_string : str
-         SMILES, molblock or InChI.
+    molecule : Any
+         Chem.Mol, SMILES, molblock or InChI.
 
     Returns
     -------
     mol: ROMol
         RDKit molecule.
     """
-    if re.search(MOLFILE_RE, mol_string, flags=re.MULTILINE):
-        rdmol = Chem.MolFromMolBlock(mol_string)
-    elif mol_string.startswith("InChI="):
-        try:
-            rdmol = Chem.MolFromInchi(mol_string)
-        except:
-            rdmol = None
+    if isinstance(molecule, Chem.Mol):
+        return molecule
+    if re.search(MOLFILE_RE, molecule, flags=re.MULTILINE):
+        rdmol = Chem.MolFromMolBlock(molecule)
+    elif molecule.startswith("InChI="):
+        rdmol = Chem.MolFromInchi(molecule)
     else:
-        rdmol = Chem.MolFromSmiles(mol_string)
+        rdmol = Chem.MolFromSmiles(molecule)
     return rdmol
 
 
@@ -201,7 +200,7 @@ def it_mol_supplier(
             mol_id = new_mol_id
         else:
             if gen_ids:
-                mol_string = mol[0]
+                mol_string = mol
                 mol_id = new_mol_id
             else:
                 try:

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2019 Eloy Félix Manzanares
+Copyright (c) 2019-2023 Eloy Félix Manzanares
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

setup.py

@@ -134,8 +134,8 @@ def build_extensions(self):
     long_description_content_type="text/markdown",
     ext_modules=ext_modules,
     install_requires=[
-        "rdkit>=2022.3.3",
-        "tables>=3.4.4",
+        "rdkit>=2023.03.2",
+        "tables>=3.4.4,<=3.8.0",
         "numpy >=1.14",
         "sqlalchemy>=1.4.47",
         "scipy",

tests/test_engine.py

@@ -206,8 +206,11 @@ def test_similarity(n_workers):
     in_file = os.path.join(TESTS_DIR, "data/test.h5")
     fpe = FPSim2Engine(in_file, storage_backend="pytables")
     results = fpe.similarity(query_smi, 0.7, n_workers=n_workers)
-    assert results.shape[0] == 4
-    assert list(results[0]) == [1, 1.0]
+    results_romol = fpe.similarity(
+        Chem.MolFromSmiles(query_smi), 0.7, n_workers=n_workers
+    )
+    assert results.shape[0] == results_romol.shape[0] == 4
+    assert list(results[0]) == list(results_romol[0]) == [1, 1.0]
 
 
 @pytest.mark.parametrize("n_workers", (1, 2, 4))

tests/test_io.py

@@ -51,7 +51,18 @@ def test_suppliers():
     it_mols = [
         Chem.MolToSmiles(x[1]) for x in it_mol_supplier(smiles_list, gen_ids=True)
     ]
-    assert smi_mols == sdf_mols == sdfgz_mols == it_mols
+    mols = [Chem.MolFromSmiles(x) for x in smiles_list]
+    rd_it_mols = [Chem.MolToSmiles(x[1]) for x in it_mol_supplier(mols, gen_ids=True)]
+
+    assert smi_mols == sdf_mols == sdfgz_mols == it_mols == rd_it_mols
+    assert (
+        len(smi_mols)
+        == len(sdf_mols)
+        == len(sdfgz_mols)
+        == len(it_mols)
+        == len(rd_it_mols)
+        == len(smiles_list)
+    )
 
 
 def test_get_mol_supplier():