Merge pull request #489 from Steinbeck-Lab/development

Development

.github/workflows/dev-build.yml

@@ -36,7 +36,7 @@ jobs:
           password: ${{ env.DOCKER_HUB_PASSWORD  }}
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@v4
+        uses: docker/build-push-action@v5.3.0
         with:
           context: .
           file: ./Dockerfile

.github/workflows/test.yml

@@ -10,7 +10,7 @@ jobs:
       matrix:
         python-version: ["3.10"]
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4.1.4
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v3
       with:

Dockerfile

@@ -45,4 +45,4 @@ RUN pip3 install --no-cache-dir chembl_structure_pipeline --no-deps
 
 COPY ./app /code/app
 
-CMD ["uvicorn", "app.main:app", "--host", "0.0.0.0", "--port", "80", "--workers", "4"]
+CMD ["uvicorn", "app.main:app", "--host", "0.0.0.0", "--port", "80", "--workers", "8"]

app/modules/coconut/preprocess.py

@@ -58,6 +58,7 @@ def get_parent_smiles(molecule: Chem.Mol) -> str:
         parent_mol = Chem.MolFromMolBlock(parent)
 
         if parent_mol:
+            [a.SetAtomMapNum(0) for i, a in enumerate(parent_mol.GetAtoms())]
             parent_smiles = Chem.MolToSmiles(
                 parent_mol, isomericSmiles=False, kekuleSmiles=True
             )
@@ -72,6 +73,62 @@ def get_parent_smiles(molecule: Chem.Mol) -> str:
     return "Error Check input SMILES"
 
 
+def get_smiles(molecule: Chem.Mol, isomeric: bool = True) -> str:
+    """
+    Retrieves the SMILES string (Isomeric or Canonical) for a given RDKit molecule object.
+
+    Args:
+        molecule (Chem.Mol): An RDKit molecule object representing the molecular structure.
+        isomeric (bool, optional): Whether to retrieve the Isomeric SMILES (True) or the Canonical SMILES (False).
+                                   Defaults to True.
+
+    Returns:
+        str: The Isomeric or Canonical SMILES string for the given molecule.
+    """
+    if molecule:
+        [a.SetAtomMapNum(0) for i, a in enumerate(molecule.GetAtoms())]
+        initial_smiles = Chem.MolToSmiles(
+            molecule, isomericSmiles=isomeric, kekuleSmiles=True
+        )
+        canonical_mol = Chem.MolFromSmiles(Chem.CanonSmiles(initial_smiles))
+
+        if canonical_mol:
+            new_smiles = Chem.MolToSmiles(
+                canonical_mol, isomericSmiles=isomeric, kekuleSmiles=True
+            )
+            return new_smiles
+
+    return "Error Check input SMILES"
+
+
+def get_standardized_smiles(standardized_mol_block: str) -> str:
+    """
+    Get the standardized SMILES representation of a molecule.
+
+    This function takes a standardized molecular structure represented as a MolBlock and generates the corresponding
+    standardized SMILES representation.
+
+    Args:
+        standardized_mol_block (str): The standardized molecular structure in MolBlock format.
+
+    Returns:
+        str: The standardized SMILES representation of the molecule.
+    """
+    mol = Chem.MolFromMolBlock(standardized_mol_block)
+    [a.SetAtomMapNum(0) for i, a in enumerate(mol.GetAtoms())]
+    standardized_smiles = Chem.MolToSmiles(
+        mol, kekuleSmiles=True
+    )
+    canonical_mol = Chem.MolFromSmiles(Chem.CanonSmiles(standardized_smiles))
+    if canonical_mol:
+        new_smiles = Chem.MolToSmiles(
+            canonical_mol, isomericSmiles=True, kekuleSmiles=True
+        )
+        return new_smiles
+
+    return "Error Check input SMILES"
+
+
 def get_molecule_hash(molecule: Chem.Mol) -> dict:
     """Return various molecule hashes for the provided SMILES.
 
@@ -83,12 +140,8 @@ def get_molecule_hash(molecule: Chem.Mol) -> dict:
     """
     if molecule:
         Formula = Chem.rdMolDescriptors.CalcMolFormula(molecule)
-        Isomeric_SMILES = Chem.MolToSmiles(molecule, kekuleSmiles=True)
-        Canonical_SMILES = Chem.MolToSmiles(
-            molecule,
-            kekuleSmiles=True,
-            isomericSmiles=False,
-        )
+        Isomeric_SMILES = get_smiles(molecule, isomeric=True)
+        Canonical_SMILES = get_smiles(molecule, isomeric=False)
         Parent_SMILES = get_parent_smiles(molecule)
         return {
             "Formula": Formula,
@@ -152,9 +205,7 @@ def get_COCONUT_preprocessing(
 
         # Standardized molecule
         standardized_mol_block = standardizer.standardize_molblock(original_mol_block)
-        standardized_SMILES = Chem.MolToSmiles(
-            Chem.MolFromMolBlock(standardized_mol_block), kekuleSmiles=True
-        )
+        standardized_SMILES = get_standardized_smiles(standardized_mol_block)
         standardized_mol = parse_input(standardized_SMILES, "rdkit", False)
         standardized_representations = get_representations(standardized_mol)
 

tests/test_classyfire.py

@@ -19,7 +19,8 @@ def test_valid_classyfire(valid_smiles):
     assert result_["query_type"] == "STRUCTURE"
     id_ = result_["id"]
     classified = loop.run_until_complete(result(id_))
-    assert classified["classification_status"] == "In Queue"
+    assert classified["classification_status"] == "Done"
+    assert classified["entities"][0]["class"]["name"] == "Imidazopyrimidines"
 
 
 def test_invalid_classyfire(invalid_smiles):
@@ -28,4 +29,8 @@ def test_invalid_classyfire(invalid_smiles):
     assert result_["query_input"] == "invalid_smiles"
     id_ = result_["id"]
     classified = loop.run_until_complete(result(id_))
-    assert classified["classification_status"] == "In Queue"
+    assert classified["classification_status"] == "Done"
+    assert (
+        classified["invalid_entities"][0]["report"][0]
+        == "Cannot process the input SMILES string, please check again"
+    )