feat: CDK and RDKit depict functions

app/modules/cdkmodules.py

@@ -26,24 +26,38 @@
 
 
 def getCDKSDG(smiles: str):
-    """This function takes the user input SMILES and Canonicalize it
-       using the CDK Canonicalisation algorthim.
+    """This function takes the user input SMILES and Creates a
+       Structure Diagram Layout using the CDK.
     Args:
             smiles (string): SMILES string given by the user.
     Returns:
-            mol object (string): CDK Structure Diagram Layout mol block.
+            mol object : mol object with CDK SDG.
     """
     cdk_base = "org.openscience.cdk"
     SCOB = JClass(cdk_base + ".silent.SilentChemObjectBuilder")
-    StringW = JClass("java.io.StringWriter")()
     SmilesParser = JClass(cdk_base + ".smiles.SmilesParser")(SCOB.getInstance())
     molecule = SmilesParser.parseSmiles(smiles)
     StructureDiagramGenerator = JClass(cdk_base + ".layout.StructureDiagramGenerator")()
     StructureDiagramGenerator.generateCoordinates(molecule)
     molecule_ = StructureDiagramGenerator.getMolecule()
 
+    return molecule_
+
+
+def getCDKSDGMol(smiles: str):
+    """This function takes the user input SMILES and returns a mol
+       block as a string with Structure Diagram Layout.
+    Args:
+            smiles (string): SMILES string given by the user.
+    Returns:
+            mol object (string): CDK Structure Diagram Layout mol block.
+    """
+    cdk_base = "org.openscience.cdk"
+    StringW = JClass("java.io.StringWriter")()
+
+    moleculeSDG = getCDKSDG(smiles)
     SDFW = JClass(cdk_base + ".io.SDFWriter")(StringW)
-    SDFW.write(molecule_)
+    SDFW.write(moleculeSDG)
     SDFW.close()
     mol_str = StringW.toString()
     return mol_str

app/modules/depict.py

@@ -0,0 +1,64 @@
+from rdkit import Chem
+from rdkit.Chem.Draw import IPythonConsole
+from rdkit.Chem import rdDepictor
+from rdkit.Chem.Draw import rdMolDraw2D
+import app.modules.cdkmodules as cdkmodules
+from IPython.display import SVG
+
+
+def getCDKDepiction(smiles: str, size=512.0):
+    """This function takes the user input SMILES and Depicts it
+       using the CDK Depiction Generator.
+    Args:
+            smiles (string): SMILES string given by the user.
+    Returns:
+            imag (PIL): CDK Structure Depiction as a pillow image.
+            image (png): CDK Structure Depiction as a PNG image.
+    """
+    cdk_base = "org.openscience.cdk"
+    StandardGenerator = cdkmodules.JClass(
+        cdk_base + ".renderer.generators.standard.StandardGenerator"
+    )
+    DepictionGenerator = cdkmodules.JClass(cdk_base + ".depict.DepictionGenerator")()
+    Color = cdkmodules.JClass("java.awt.Color")
+    UniColor = cdkmodules.JClass(cdk_base + ".renderer.color.UniColor")
+
+    DepictionGenerator.withSize(size, size).withAtomValues().withParam(
+        StandardGenerator.StrokeRatio.class_, 1.5
+    ).withAnnotationColor(Color.BLACK).withParam(
+        StandardGenerator.AtomColor.class_, UniColor(Color.BLACK)
+    ).withBackgroundColor(
+        Color.WHITE
+    ).withZoom(
+        2.0
+    )
+
+    moleculeSDG = cdkmodules.getCDKSDG(smiles)
+    mol_image = DepictionGenerator.depict(moleculeSDG).toSvgStr("px")
+
+    return mol_image.getBytes()
+
+
+def getRDKitDepiction(smiles, molSize=(512, 512), kekulize=True):
+    """This function takes the user input SMILES and Canonicalize it
+       using the RDKit.
+    Args:
+            smiles (string): SMILES string given by the user.
+    Returns:
+            imag (PIL): CDK Structure Depiction as a pillow image.
+            image (png): CDK Structure Depiction as a PNG image.
+    """
+    mol = Chem.MolFromSmiles(smiles)
+    mc = Chem.Mol(mol.ToBinary())
+    if kekulize:
+        try:
+            Chem.Kekulize(mc)
+        except:
+            mc = Chem.Mol(mol.ToBinary())
+    if not mc.GetNumConformers():
+        rdDepictor.Compute2DCoords(mc)
+    drawer = rdMolDraw2D.MolDraw2DSVG(molSize[0], molSize[1])
+    drawer.DrawMolecule(mc)
+    drawer.FinishDrawing()
+    svg = drawer.GetDrawingText()
+    return SVG(svg.replace("svg:", ""))

app/routers/chem.py

@@ -17,7 +17,7 @@
 from app.modules.npscorer import getnp_score
 from app.modules.descriptor_calculator import GetBasicDescriptors
 from app.modules.classyfire import classify, result
-from app.modules.cdkmodules import getCDKSDG
+from app.modules.cdkmodules import getCDKSDGMol
 
 router = APIRouter(
     prefix="/chem",
@@ -141,7 +141,7 @@ async def classyfire_result(id: Optional[str]):
 @router.get("/{smiles}/cdk2d")
 async def cdk2d_coordinates(smiles: Optional[str]):
     if smiles:
-        return getCDKSDG(smiles)
+        return getCDKSDGMol(smiles)
 
 
 # @app.get("/molecules/", response_model=List[schemas.Molecule])