feat: deployed stout package

Dockerfile

@@ -71,6 +71,14 @@ RUN apt-get update \
  && apt-get clean \
  && rm -rf /var/lib/apt/lists/*
 
+RUN apt-get update && \
+    apt-get install -y software-properties-common && \
+    apt-get update -y && \
+    apt-get install -y openjdk-11-jre
+
+ENV JAVA_HOME /usr/lib/jvm/java-11-openjdk-amd64/
+RUN export JAVA_HOME
+
 # Copy rdkit installation from rdkit-build-env
 COPY --from=rdkit-build-env /usr/lib/libRDKit* /usr/lib/
 COPY --from=rdkit-build-env /usr/lib/cmake/rdkit/* /usr/lib/cmake/rdkit/
@@ -80,11 +88,13 @@ COPY --from=rdkit-build-env /usr/lib/python3/dist-packages/rdkit /usr/lib/python
 
 WORKDIR /code
 
+RUN python3 -m pip install -U pip 
+
 COPY ./requirements.txt /code/requirements.txt
 
 RUN pip3 install --no-cache-dir --upgrade -r /code/requirements.txt
 
-RUN pip3 install chembl_structure_pipeline --no-deps
+RUN pip3 install --no-cache-dir chembl_structure_pipeline --no-deps
 
 COPY ./app /code/app
 

app/config.py

@@ -1,6 +1,5 @@
 from pydantic import BaseSettings, Field, PostgresDsn
 
-
 class Settings(BaseSettings):
     PGPASSWORD: str = Field(..., env="PGPASSWORD")
     POSTGRES_DB: str = Field(..., env="POSTGRES_DB")

app/main.py

@@ -1,5 +1,5 @@
 from fastapi import Depends, FastAPI
-from .config import settings
+# from .config import settings
 from .routers import converters, chem, compose
 from fastapi.middleware.cors import CORSMiddleware
 

app/routers/chem.py

@@ -1,14 +1,15 @@
 from fastapi import  Request, APIRouter, Depends, HTTPException
 from typing import Optional
 from rdkit import Chem
-from ..database import db
+# from ..database import db
 from fastapi_pagination import Page, add_pagination, paginate
 from rdkit.Chem.EnumerateStereoisomers import EnumerateStereoisomers, StereoEnumerationOptions
 from chembl_structure_pipeline import standardizer
 from fastapi.responses import JSONResponse
 from rdkit.Chem.Scaffolds import MurckoScaffold
 from rdkit.Chem.QED import properties
 from rdkit.Chem.rdMolDescriptors import Properties
+from STOUT import translate_forward, translate_reverse
 
 router = APIRouter(
     prefix="/chem",
@@ -84,6 +85,12 @@ async def smiles_descriptors(smiles: Optional[str]):
         m = Chem.MolFromSmiles(smiles)
         return properties(m)
 
+
+@router.get("/{smiles}/iupac")
+async def smiles_iupac(smiles: Optional[str]):
+    if smiles:
+        iupac = translate_forward(smiles)
+        return iupac
 
 # @app.get("/molecules/", response_model=List[schemas.Molecule])
 # def read_molecules(skip: int = 0, limit: int = 100, db: Session = Depends(get_db)):

app/routers/converters.py

@@ -1,6 +1,5 @@
 from fastapi import APIRouter, Depends, HTTPException
 
-
 router = APIRouter(
     prefix="/converters",
     tags=["converters"],

requirements.txt

@@ -2,4 +2,5 @@ fastapi>=0.80.0
 pydantic>=1.8.0,<2.0.0
 uvicorn>=0.15.0,<0.16.0
 psycopg2>=2.7,<2.8
-fastapi-pagination==0.10.0
+fastapi-pagination==0.10.0
+STOUT-pypi>=2.0.4