Merge pull request #322 from Steinbeck-Lab/development

Development

app/modules/toolkits/rdkit_wrapper.py

@@ -259,10 +259,10 @@ def getRDKitCXSMILES(smiles: str):
     """This function takes an input as a SMILES string and
     returns a CXSMILES with coordinates.
 
-    Args (str):
-        SMILES string.
-    Returns (str):
-        CXSMILES with coordinates.
+    Args:
+        SMILES string (str): The SMILES string to be converted as input
+    Returns:
+        string: CXSMILES with coordinates.
 
     """
     if any(char.isspace() for char in smiles):
@@ -274,3 +274,30 @@ def getRDKitCXSMILES(smiles: str):
         return Chem.MolToCXSmiles(mol)
     else:
         return "Error reading SMILES string, check again."
+
+
+def getProperties(sdf_file):
+    """
+    Extracts properties from a single molecule contained in an SDF file.
+
+    This function uses the RDKit library to read an SDF (Structure-Data File) and extract properties
+    from the first molecule in the file. It checks if the supplied SDF file contains a valid molecule
+    and retrieves its properties as a dictionary.
+
+    Args:
+        sdf_file (str): The path to the SDF file containing the molecule.
+
+    Returns:
+        dict or None: A dictionary containing the properties of the molecule. If the SDF file contains
+        a valid molecule, the dictionary will have property names as keys and property values as values.
+        If no valid molecule is found, or if there are no properties associated with the molecule, None
+        is returned.
+    """
+    # Create an SDMolSupplier to read the SDF file
+    suppl = Chem.SDMolSupplier(sdf_file)
+
+    # Check if the SDF file contains a valid molecule
+    if len(suppl) == 1 and suppl[0]:
+        # Extract properties as a dictionary
+        properties = suppl[0].GetPropsAsDict()
+        return properties

app/routers/chem.py

@@ -16,6 +16,7 @@
 from app.modules.toolkits.rdkit_wrapper import (
     getTanimotoSimilarityRDKit,
     getRDKitHOSECodes,
+    getProperties,
 )
 from app.modules.coconut.descriptors import getCOCONUTDescriptors
 from app.modules.alldescriptors import getTanimotoSimilarity
@@ -338,7 +339,9 @@ async def standardize_mol(
                 inchi=Chem.inchi.MolToInchi(rdkit_mol),
                 inchikey=Chem.inchi.MolToInchiKey(rdkit_mol),
             )
-            return response
+            original_properties = getProperties(data)
+            return response.update(original_properties)
+
     except Exception as e:
         raise HTTPException(status_code=400, detail=str(e))