fix: remove unused modules and imports

app/main.py

@@ -26,7 +26,7 @@
 
 @app.get("/", include_in_schema=False)
 async def docs_redirect():
-    return RedirectResponse(url='/docs')
+    return RedirectResponse(url="/docs")
 
 
 def custom_openapi():

app/modules/descriptor_calculator.py → app/modules/rdkitmodules.py

@@ -1,5 +1,5 @@
 from rdkit import Chem
-from rdkit.Chem import Descriptors, QED, Lipinski, rdMolDescriptors, rdmolops
+from rdkit.Chem import AllChem, Descriptors, QED, Lipinski, rdMolDescriptors, rdmolops
 
 
 def checkRo5Violations(mol):
@@ -20,7 +20,7 @@ def checkRo5Violations(mol):
     return num_of_violations
 
 
-def GetBasicDescriptors(smiles):
+def getBasicDescriptors(smiles):
     """Take an input SMILES and generates a selected set of molecular
     descriptors as a dictionary
     Args (str): SMILES string
@@ -62,3 +62,21 @@ def GetBasicDescriptors(smiles):
     }
 
     return AllDescriptors
+
+
+def get3Dconformers(smiles):
+    """Convert SMILES to Mol with 3D coordinates
+    Args (str): SMILES string.
+    Returns (rdkil.mol): A mol object with 3D coodinates
+    optimized with MMFF94 forcefield.
+
+    """
+    mol = Chem.MolFromSmiles(smiles)
+    if mol:
+        AllChem.Compute2DCoords(mol)
+        mol = Chem.AddHs(mol)
+        AllChem.EmbedMolecule(mol, randomSeed=0xF00D)
+        AllChem.MMFFOptimizeMolecule(mol, maxIters=200)
+        return Chem.MolToMolBlock(mol)
+    else:
+        return None

app/routers/chem.py

@@ -8,11 +8,10 @@
 from fastapi.responses import Response, HTMLResponse
 from rdkit.Chem.Scaffolds import MurckoScaffold
 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 getCDKSDGMol
 from app.modules.depict import getRDKitDepiction, getCDKDepiction
-from app.modules.depict3D import get3Dconformers
+from app.modules.rdkitmodules import getBasicDescriptors, get3Dconformers
 
 from fastapi.templating import Jinja2Templates
 
@@ -77,7 +76,7 @@ async def smiles_descriptors(smiles: str):
     - **smiles**: required (query)
     """
     if smiles:
-        return GetBasicDescriptors(smiles)
+        return getBasicDescriptors(smiles)
 
 
 @router.get("/npscore")
@@ -137,12 +136,10 @@ async def depict_molecule(
 async def depict3D_molecule(
     request: Request,
     smiles: str,
-    width: Optional[int] = 512,
-    height: Optional[int] = 512,
-    style: Optional[str] = "stick",
 ):
     if smiles:
-        return templates.TemplateResponse("mol.html", {"request": request, "molecule": Chem.MolToMolBlock(get3Dconformers(smiles))})
+        content = {"request": request, "molecule": get3Dconformers(smiles)}
+        return templates.TemplateResponse("mol.html", content)
 
 
 # @app.get("/molecules/", response_model=List[schemas.Molecule])

app/templates/mol.html

@@ -15,7 +15,7 @@
 $(document).ready(function() {
     var viewer = $3Dmol.createViewer("viewer");
     viewer.setBackgroundColor(0xffffff);
-    viewer.addModel(`{{ molecule }}`, "sdf");
+    viewer.addModel(`{{ molecule }}`, "mol");
     viewer.setStyle({stick:{}});
     viewer.zoomTo();
     viewer.render();