fix: flake8 linting issues

app/config.py

@@ -1,4 +1,4 @@
-from pydantic import BaseSettings, Field, PostgresDsn
+from pydantic import BaseSettings, Field
 
 
 class Settings(BaseSettings):

app/database.py

@@ -1,5 +1,6 @@
-from .config import settings
 import psycopg2
+import sys
+from .config import settings
 
 
 class Database:

app/modules/depict.py

@@ -72,7 +72,8 @@ def getRDKitDepiction(smiles, molSize=(512, 512), rotate=0, kekulize=True):
     if kekulize:
         try:
             Chem.Kekulize(mc)
-        except:
+        except Exception as e:
+            print(e, flush=True)
             mc = Chem.Mol(mol.ToBinary())
     if not mc.GetNumConformers():
         rdDepictor.Compute2DCoords(mc)

app/modules/descriptor_calculator.py

@@ -10,13 +10,13 @@ def checkRo5Violations(mol):
     """
     num_of_violations = 0
     if Descriptors.MolLogP(mol) > 5:
-        rule_break += 1
+        num_of_violations += 1
     if Descriptors.MolWt(mol) > 500:
-        rule_break += 1
+        num_of_violations += 1
     if Lipinski.NumHAcceptors(mol) > 10:
-        rule_break += 1
+        num_of_violations += 1
     if Lipinski.NumHDonors(mol) > 5:
-        rule_break += 1
+        num_of_violations += 1
     return num_of_violations
 
 

app/modules/npscorer.py

@@ -1,6 +1,7 @@
 # calculation of natural product-likeness as described in:
 #
-# Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries
+# Natural Product-likeness Score and Its Application for
+# Prioritization of Compound Libraries
 # Peter Ertl, Silvio Roggo, and Ansgar Schuffenhauer
 # Journal of Chemical Information and Modeling, 48, 68-74 (2008)
 # http://pubs.acs.org/doi/abs/10.1021/ci700286x
@@ -32,11 +33,6 @@
 fscore = pickle.load(gzip.open(model_path))
 
 
-def getnp_model(model_path):
-    fscore = pickle.load(gzip.open(model_path.as_posix()))
-    return fscore
-
-
 def getnp_model(model_path):
     fscore = pickle.load(gzip.open(model_path.as_posix()))
     return fscore

app/routers/chem.py

@@ -2,6 +2,7 @@
 from typing import Optional
 from rdkit import Chem
 import urllib.request
+
 # from ..database import db
 # from fastapi_pagination import Page, add_pagination, paginate
 from rdkit.Chem.EnumerateStereoisomers import (
@@ -110,7 +111,7 @@ async def smiles_iupac(smiles: Optional[str]):
 
 
 @router.post("/iupac/smiles")
-async def standardise_mol(request: Request):
+async def iupac_smiles(request: Request):
     body = await request.json()
     query = body["query"]
     if query:
@@ -163,7 +164,8 @@ async def depick_molecule(
                 content=getRDKitDepiction(smiles, [width, height], rotate),
                 media_type="image/svg+xml",
             )
-
+
+
 @router.post("/process")
 async def extract_chemicalinfo(request: Request):
     body = await request.json()
@@ -174,7 +176,10 @@ async def extract_chemicalinfo(request: Request):
         urllib.request.urlretrieve(image_path, filename)
         smiles = predict_SMILES(filename)
         os.remove(filename)
-        return JSONResponse(content={ "reference" :  reference, "smiles": smiles.split(".")})
+        return JSONResponse(
+            content={"reference": reference, "smiles": smiles.split(".")}
+        )
+
 
 # @app.get("/molecules/", response_model=List[schemas.Molecule])
 # def read_molecules(skip: int = 0, limit: int = 100, db: Session = Depends(get_db)):