migrated the frontend file generation, changed folder structure

backend/Dockerfile

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+
+FROM ubuntu:22.04
+# Install openbabel and python
+RUN apt-get update \
+    && apt-get install --yes --quiet --no-install-recommends \
+    openbabel \
+    python3 \
+    python3-pip \
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /var/local
+
+COPY requirements.txt .
+
+# Install dependencies
+RUN /usr/bin/python3 -m pip install --no-cache-dir -r requirements.txt
+
+COPY src .
+
+CMD uvicorn app:app --host 0.0.0.0 --port ${PORT} --log-level warning

backend/docker-compose.yaml

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+services:
+  openbabel-app:
+    build:
+      context: .
+    environment:
+      PORT: 1654
+    ports:
+      - 1654:1654
+    depends_on:
+      - redis
+    restart: unless-stopped
+  redis:
+    image: "redis:alpine"
+    ports:
+      - "6379:6379"
+    restart: unless-stopped

backend/requirements.txt

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+openbabel-wheel==3.1.1.22
+fastapi[all]==0.121.3
+fastapi-cache2==0.2.2
+redis==7.1.0
+pyscf==2.11.0

backend/src/app.py

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+from collections.abc import AsyncIterator
+from contextlib import asynccontextmanager
+
+from fastapi import FastAPI
+from fastapi.exceptions import HTTPException
+from fastapi.middleware.cors import CORSMiddleware
+
+# from fastapi.requests import Request
+from fastapi.responses import JSONResponse
+from fastapi_cache import FastAPICache
+from fastapi_cache.backends.redis import RedisBackend
+from fastapi_cache.decorator import cache
+from logging_config import logger
+from openbabel import pybel
+from pyscf import gto  # pyright: ignore
+from redis import asyncio as aioredis
+from request_response_models import BasicError, ConvertRequest, MolFileModel
+
+
+@asynccontextmanager
+async def lifespan(_: FastAPI) -> AsyncIterator[None]:
+    redis = aioredis.from_url("redis://redis:6379")
+    FastAPICache.init(RedisBackend(redis), prefix="fastapi-cache")
+    pybel.ob.obErrorLog.SetOutputLevel(0)  # NOTE removes logging
+    yield
+
+
+app = FastAPI(lifespan=lifespan)
+
+
+origins = [
+    "http://localhost",
+    "http://localhost:8001",
+]
+
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=origins,
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
+
+@app.post(
+    "/convert",
+    responses={
+        200: {"description": "Coversion Successful", "model": MolFileModel},
+        400: {"description": "Item created", "model": BasicError},
+    },
+)
+def convert_molecule(req: ConvertRequest):
+    try:
+        # Rad the string and format from request
+        mol = pybel.readstring(req.format, req.text)
+
+        if req.add_hydrogen:
+            mol.addh()
+        if req.convert_3d:
+            mol.make3D()
+        if req.optimize_geometry:
+            mol.localopt()
+
+        logger.info(f"Converting from format {req.format}")
+
+        # To compute the Number of electrons and orbitals
+        atoms = [(atom.atomicnum, atom.coords) for atom in mol.atoms]
+
+        mol_pyscf = gto.Mole()
+        mol_pyscf.atom = atoms
+        mol_pyscf.basis = "sto-3g"  # simple basis
+        mol_pyscf.charge = mol.charge  # default net charge
+        mol_pyscf.spin = mol.spin - 1  # multiplicity - 1
+        mol_pyscf.build()
+
+        # Export the resulting molecule
+        mol.OBMol.SetTitle(
+            f"Charge={mol.charge} Multiplicity={mol.spin} Electrons={mol_pyscf.nelectron} Orbitals={mol_pyscf.nao_nr()}"
+        )
+
+        mol2string = mol.write("xyz")
+        return JSONResponse({"molfile": mol2string}, 200)
+    except Exception as e:
+        raise HTTPException(status_code=400, detail={"error": str(e)})
+
+
+@app.get("/informats")
+@cache()
+async def get_informats():
+    return pybel.informats
+
+
+@app.get(
+    "/health",
+    responses={
+        200: {
+            "description": "Is the service running?",
+            "content": {"application/json": {"example": {"status": "healthy"}}},
+        },
+    },
+)
+@cache()
+async def health_check():
+    return {"status": "healthy"}

backend/src/logging_config.py

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+import logging
+import logging.config
+import os
+
+ROOT_LEVEL = os.environ.get("PROD", "INFO")
+
+LOGGING_CONFIG = {
+    "version": 1,
+    "disable_existing_loggers": True,
+    "formatters": {
+        "standard": {"format": "%(asctime)s [%(levelname)s] %(name)s: %(message)s"},
+    },
+    "handlers": {
+        "default": {
+            "formatter": "standard",
+            "class": "logging.StreamHandler",
+            "stream": "ext://sys.stdout",  # Default is stderr
+        },
+    },
+    "loggers": {
+        "": {  # root logger
+            "level": ROOT_LEVEL,  # "INFO",
+            "handlers": ["default"],
+            "propagate": False,
+        },
+        "uvicorn.error": {
+            "level": "WARNING",
+            "handlers": ["default"],
+        },
+        "uvicorn.access": {
+            "level": "DEBUG",
+            "handlers": ["default"],
+        },
+    },
+}
+
+logging.config.dictConfig(LOGGING_CONFIG)
+logger = logging.getLogger(__name__)

backend/src/request_response_models.py

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+from pydantic import BaseModel
+
+
+class ConvertRequest(BaseModel):
+    text: str
+    format: str  # e.g. "mol", "smi", "sdf", "inchi", etc.
+    add_hydrogen: bool = False
+    convert_3d: bool = False
+    optimize_geometry: bool = False
+
+
+class MolFileModel(BaseModel):
+    molfile: str
+
+
+class BasicError(BaseModel):
+    error: str