Initial commit

src/app.py

@@ -0,0 +1,101 @@
+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 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")
+    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"}