added redis, added convert function

also fixed logs, split code into multiple files

.gitignore

@@ -1,3 +1,7 @@
+# postman
+.postman
+postman
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[codz]
@@ -182,9 +186,9 @@ cython_debug/
 .abstra/
 
 # Visual Studio Code
-#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#  Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
 #  that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
-#  and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#  and can be added to the global gitignore or merged into this file. However, if you prefer,
 #  you could uncomment the following to ignore the entire vscode folder
 # .vscode/
 

docker-compose.yaml

@@ -6,4 +6,11 @@ services:
       PORT: 1654
     ports:
       - 1654:1654
-    tty: true
+    depends_on:
+      - redis
+    restart: unless-stopped
+  redis:
+    image: "redis:alpine"
+    ports:
+      - "6379:6379"
+    restart: unless-stopped

dockerfile

@@ -1,12 +1,12 @@
 
 FROM ubuntu:22.04
-# Install openbabel dependencies
+# Install openbabel and python
 RUN apt-get update \
-  && apt-get install --yes --quiet --no-install-recommends \
+    && apt-get install --yes --quiet --no-install-recommends \
-  openbabel \
+    openbabel \
-  python3 \
+    python3 \
-  python3-pip \
+    python3-pip \
-  && apt-get clean && rm -rf /var/lib/apt/lists/*
+    && apt-get clean && rm -rf /var/lib/apt/lists/*
 
 WORKDIR /var/local
 
@@ -17,4 +17,4 @@ RUN /usr/bin/python3 -m pip install --no-cache-dir -r requirements.txt
 
 COPY src .
 
-CMD fastapi run app.py --port ${PORT}
+CMD uvicorn app:app --host 0.0.0.0 --port ${PORT} --log-level warning

requirements.txt

@@ -1,4 +1,5 @@
 openbabel-wheel==3.1.1.22
 fastapi[all]==0.121.3
 fastapi-cache2==0.2.2
-redis==7.1.0
+redis==7.1.0
+pyscf==2.11.0

src/app.py

@@ -2,39 +2,103 @@ from collections.abc import AsyncIterator
 from contextlib import asynccontextmanager
 
 from fastapi import FastAPI
-from starlette.requests import Request
+from fastapi.exceptions import HTTPException
-from starlette.responses import Response
+from fastapi.middleware.cors import CORSMiddleware
 
+# from fastapi.requests import Request
+from fastapi.responses import Response
 from fastapi_cache import FastAPICache
 from fastapi_cache.backends.redis import RedisBackend
 from fastapi_cache.decorator import cache
-
+from logging_config import logger
-from redis import asyncio as aioredis
 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://localhost")
+    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)
+
+        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 Response({"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("/")
+@app.get(
-@cache(expire=60)
+    "/health",
-async def index():
+    responses={
-    return dict(hello="world")
+        200: {
-
+            "description": "Is the service running?",
-
+            "content": {"application/json": {"example": {"status": "healthy"}}},
-
+        },
-
+    },
-
+)
-
+@cache()
+async def health_check():
+    return {"status": "healthy"}

src/logging_config.py

@@ -0,0 +1,38 @@
+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__)

src/request_response_models.py

@@ -0,0 +1,16 @@
+from pydantic import BaseModel
+
+
+class ConvertRequest(BaseModel):
+    text: str
+    format: str  # e.g. "mol", "smi", "sdf", "inchi", etc.
+    convert_3d: bool = False
+    optimize_geometry: bool = False
+
+
+class MolFileModel(BaseModel):
+    molfile: str
+
+
+class BasicError(BaseModel):
+    error: str