Prepare release (#9)

* prepare release

* fix conflict version and prepare release

Author: TieuLongPhan

Test/SynUtils/test_chemutils.py

@@ -2,13 +2,6 @@
 from rdkit import Chem
 from pathlib import Path
 from syntemp.SynUtils.chemutils import (
-    normalize_molecule,
-    canonicalize_tautomer,
-    salts_remover,
-    reionize_charges,
-    uncharge_molecule,
-    assign_stereochemistry,
-    fragments_remover,
     remove_hydrogens_and_sanitize,
 )
 
@@ -21,45 +14,6 @@ def setUp(self):
         self.caffeine_smiles = "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"
         self.mol = Chem.MolFromSmiles(self.caffeine_smiles)
 
-    def test_normalize_molecule(self):
-        normalized_mol = normalize_molecule(self.mol)
-        self.assertIsInstance(normalized_mol, Chem.Mol)
-
-    def test_canonicalize_tautomer(self):
-        canonical_tautomer = canonicalize_tautomer(self.mol)
-        self.assertIsInstance(canonical_tautomer, Chem.Mol)
-
-    def test_salts_remover(self):
-        # Using a molecule with a known salt
-        mol_with_salt = Chem.MolFromSmiles("CC(=O)O.[Na+]")
-        salt_removed_mol = salts_remover(mol_with_salt)
-        self.assertNotEqual(
-            Chem.MolToSmiles(salt_removed_mol), Chem.MolToSmiles(mol_with_salt)
-        )
-
-    def test_reionize_charges(self):
-        reionized_mol = reionize_charges(self.mol)
-        self.assertIsInstance(reionized_mol, Chem.Mol)
-
-    def test_uncharge_molecule(self):
-        charged_mol = Chem.AddHs(Chem.MolFromSmiles("[NH4+].[Cl-]"))
-        uncharged_mol = uncharge_molecule(charged_mol)
-        self.assertEqual(Chem.rdmolops.GetFormalCharge(uncharged_mol), 0)
-
-    def test_assign_stereochemistry(self):
-        mol_with_stereo = Chem.MolFromSmiles("C[C@H](O)[C@@H](O)C")
-        assign_stereochemistry(mol_with_stereo)
-        self.assertEqual(
-            len(Chem.FindMolChiralCenters(mol_with_stereo, includeUnassigned=True)), 2
-        )
-
-    def test_fragments_remover(self):
-        mol_with_fragments = Chem.MolFromSmiles("CCO.OCC")
-        largest_fragment = fragments_remover(mol_with_fragments)
-        self.assertEqual(
-            largest_fragment.GetNumAtoms(), 3
-        )  # Expecting the ethyl alcohol fragment
-
     def test_remove_hydrogens_and_sanitize(self):
         mol_with_h = Chem.AddHs(self.mol)
         cleaned_mol = remove_hydrogens_and_sanitize(mol_with_h)

pyproject.toml

@@ -27,11 +27,11 @@ dependencies = [
     "chytorch==1.60",
     "chytorch-rxnmap==1.4",
     "torchdata==0.7.1",
-    "rdkit>=2023.9.5",
+    "rdkit>=2024.3.3",
     "networkx>=3.3",
     "seaborn>=0.13.2",
     "joblib>=1.3.2",
-    "synrbl>=0.0.24",
+    "synrbl>=0.0.25",
 ]
 
 [project.urls]

requirements.txt

@@ -8,8 +8,8 @@ chython==1.75
 chytorch==1.60
 chytorch-rxnmap==1.4
 torchdata==0.7.1
-rdkit>=2023.9.5
+rdkit>=2024.3.3
 networkx>=3.3
-seaborn==0.13.2
-joblib==1.3.2
-synrbl>=0.0.24
+seaborn>=0.13.2
+joblib>=1.3.2
+synrbl>=0.0.25

syntemp/SynUtils/chemutils.py

@@ -1,7 +1,5 @@
 import re
 from rdkit import Chem
-from rdkit.Chem.MolStandardize import normalize, tautomer, charge
-from rdkit.Chem.SaltRemover import SaltRemover
 from rdkit.Chem import rdmolops
 from rdkit.Chem.MolStandardize import rdMolStandardize
 from rdkit.Chem.rdMolDescriptors import CalcMolFormula
@@ -10,107 +8,6 @@
 from itertools import combinations_with_replacement
 
 
-def normalize_molecule(mol: Chem.Mol) -> Chem.Mol:
-    """
-    Normalize a molecule using RDKit's Normalizer.
-
-    Args:
-        mol (Chem.Mol): RDKit Mol object to be normalized.
-
-    Returns:
-        Chem.Mol: Normalized RDKit Mol object.
-    """
-    return normalize.Normalizer().normalize(mol)
-
-
-def canonicalize_tautomer(mol: Chem.Mol) -> Chem.Mol:
-    """
-    Canonicalize the tautomer of a molecule using RDKit's TautomerCanonicalizer.
-
-    Args:
-    - mol (Chem.Mol): RDKit Mol object.
-
-    Returns:
-    - Chem.Mol: Mol object with canonicalized tautomer.
-    """
-    return tautomer.TautomerCanonicalizer().canonicalize(mol)
-
-
-def salts_remover(mol: Chem.Mol) -> Chem.Mol:
-    """
-    Remove salt fragments from a molecule using RDKit's SaltRemover.
-
-    Args:
-    - mol (Chem.Mol): RDKit Mol object.
-
-    Returns:
-    - Chem.Mol: Mol object with salts removed.
-    """
-    remover = SaltRemover()
-    return remover.StripMol(mol)
-
-
-def reionize_charges(mol: Chem.Mol) -> Chem.Mol:
-    """
-    Adjust molecule to its most likely ionic state using RDKit's Reionizer.
-
-    Args:
-    - mol: RDKit Mol object.
-
-    Returns:
-    - Mol object with reionized charges.
-    """
-    return charge.Reionizer().reionize(mol)
-
-
-def uncharge_molecule(mol: Chem.Mol) -> Chem.Mol:
-    """
-    Neutralize a molecule by removing counter-ions using RDKit's Uncharger.
-
-    Args:
-        mol: RDKit Mol object.
-
-    Returns:
-        Neutralized Mol object.
-    """
-    uncharger = rdMolStandardize.Uncharger()
-    return uncharger.uncharge(mol)
-
-
-def assign_stereochemistry(
-    mol: Chem.Mol, cleanIt: bool = True, force: bool = True
-) -> None:
-    """
-    Assigns stereochemistry to a molecule using RDKit's AssignStereochemistry.
-
-    Args:
-        mol: RDKit Mol object.
-        cleanIt: Flag indicating whether to clean the molecule.
-                Default is True.
-        force: Flag indicating
-            whether to force stereochemistry assignment.
-            Default is True.
-
-    Returns:
-        None
-    """
-    Chem.AssignStereochemistry(mol, cleanIt=cleanIt, force=force)
-
-
-def fragments_remover(mol: Chem.Mol) -> Chem.Mol:
-    """
-    Remove small fragments from a molecule, keeping only the largest one.
-
-    Args:
-        mol (Chem.Mol): RDKit Mol object.
-
-    Returns:
-        Chem.Mol: Mol object with small fragments removed.
-    """
-    frags = Chem.GetMolFrags(mol, asMols=True, sanitizeFrags=True)
-    return max(frags, default=None, key=lambda m: m.GetNumAtoms())
-
-
 def remove_hydrogens_and_sanitize(mol: Chem.Mol) -> Chem.Mol:
     """
     Remove explicit hydrogens and sanitize a molecule.