Initial commit

.gitignore

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+# postman
+.postman
+postman
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+#poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+#pdm.lock
+#pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+#pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.envrc
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Abstra
+# Abstra is an AI-powered process automation framework.
+# Ignore directories containing user credentials, local state, and settings.
+# Learn more at https://abstra.io/docs
+.abstra/
+
+# Visual Studio Code
+#  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,
+#  you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Cursor
+#  Cursor is an AI-powered code editor. `.cursorignore` specifies files/directories to
+#  exclude from AI features like autocomplete and code analysis. Recommended for sensitive data
+#  refer to https://docs.cursor.com/context/ignore-files
+.cursorignore
+.cursorindexingignore
+
+# Marimo
+marimo/_static/
+marimo/_lsp/
+__marimo__/

docker-compose.yaml

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+services:
+  qunatum-backend:
+    build:
+      context: .
+    environment:
+      PORT: 1656
+    ports:
+      - 1656:1656
+    depends_on:
+      - redis
+    restart: unless-stopped
+  redis:
+    image: "redis:alpine"
+    ports:
+      - "6379:6379"
+    restart: unless-stopped

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 \
+    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

requirements.txt

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+fastapi[all]==0.121.3
+fastapi-cache2==0.2.2
+redis==7.1.0

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 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"}

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__)

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