feat: Add CXSMILES conversion with CDK #156

app/modules/cdkmodules.py

@@ -376,3 +376,21 @@ def getCIPAnnotation(smiles: str):
             )
 
     return mol
+
+
+def getCXSMILES(smiles: str):
+    """This function takes the user input SMILES and creates a
+    CXSMILES string with 2D atom coordinates
+    Args:
+            smiles (string): SMILES string given by the user.
+    Returns:
+            smiles (string): CXSMILES string.
+
+    """
+    moleculeSDG = getCDKSDG(smiles)
+    SmiFlavor = JClass(cdk_base + ".smiles.SmiFlavor")
+    SmilesGenerator = JClass(cdk_base + ".smiles.SmilesGenerator")(
+        SmiFlavor.Absolute | SmiFlavor.CxSmilesWithCoords
+    )
+    CXSMILES = SmilesGenerator.create(moleculeSDG)
+    return str(CXSMILES)

app/routers/converters.py

@@ -6,7 +6,7 @@
 from rdkit.Chem import AllChem
 from typing import Optional
 from STOUT import translate_forward, translate_reverse
-from app.modules.cdkmodules import getCDKSDGMol
+from app.modules.cdkmodules import getCDKSDGMol, getCXSMILES
 from app.modules.rdkitmodules import get3Dconformers
 
 router = APIRouter(
@@ -122,6 +122,22 @@ async def SMILES_to_InChIKey(smiles: str):
         return "Error reading SMILES string check again."
 
 
+@router.get("/cxsmiles")
+async def SMILES_to_CXSMILES(smiles: str):
+    """
+    Convert SMILES to CXSMILES:
+
+    - **SMILES**: required (query parameter)
+    """
+    if any(char.isspace() for char in smiles):
+        smiles = smiles.replace(" ", "+")
+    if smiles:
+        cxsmiles = getCXSMILES(smiles)
+        return cxsmiles
+    else:
+        return "Error reading SMILES string check again."
+
+
 @router.get("/formats")
 async def SMILES_convert_to_Formats(smiles: str):
     """