Merge pull request #18 from Steinbeck-Lab/dev-kohulan

feat: add rotation to CDKDepict and RDKit

app/modules/depict.py

@@ -6,7 +6,7 @@
 from jpype import JClass
 
 
-def getCDKDepiction(smiles: str, molSize=(512, 512)):
+def getCDKDepiction(smiles: str, molSize=(512, 512), rotate=0):
     """This function takes the user input SMILES and Depicts it
        using the CDK Depiction Generator.
     Args:
@@ -22,6 +22,8 @@ def getCDKDepiction(smiles: str, molSize=(512, 512)):
     DepictionGenerator = JClass(cdk_base + ".depict.DepictionGenerator")()
     Color = JClass("java.awt.Color")
     UniColor = JClass(cdk_base + ".renderer.color.UniColor")
+
+    # Generate depiction with settings
     DepictionGenerator.withSize(molSize[0], molSize[1]).withAtomValues().withParam(
         StandardGenerator.StrokeRatio.class_, 1.0
     ).withAnnotationColor(Color.BLACK).withParam(
@@ -33,6 +35,13 @@ def getCDKDepiction(smiles: str, molSize=(512, 512)):
     )
     getString = JClass("java.lang.String")
     moleculeSDG = getCDKSDG(smiles)
+
+    # Rotate molecule
+    point = JClass(cdk_base + ".geometry.GeometryTools").get2DCenter(moleculeSDG)
+    JClass(cdk_base + ".geometry.GeometryTools").rotate(
+        moleculeSDG, point, (rotate * JClass("java.lang.Math").PI / 180.0)
+    )
+
     mol_image = DepictionGenerator.depict(moleculeSDG)
     mol_imagex = mol_image.toSvgStr(getString("px")).getBytes()
 
@@ -49,7 +58,7 @@ def getCDKDepiction(smiles: str, molSize=(512, 512)):
     return rescaled_mol
 
 
-def getRDKitDepiction(smiles, molSize=(512, 512), kekulize=True):
+def getRDKitDepiction(smiles, molSize=(512, 512), rotate=0, kekulize=True):
     """This function takes the user input SMILES and Canonicalize it
        using the RDKit.
     Args:
@@ -68,6 +77,7 @@ def getRDKitDepiction(smiles, molSize=(512, 512), kekulize=True):
     if not mc.GetNumConformers():
         rdDepictor.Compute2DCoords(mc)
     drawer = rdMolDraw2D.MolDraw2DSVG(molSize[0], molSize[1])
+    drawer.drawOptions().rotate = rotate
     drawer.DrawMolecule(mc)
     drawer.FinishDrawing()
     svg = drawer.GetDrawingText()