This repository provides a web application for displaying molecule library information. Originally developed for "kraken - Kolossal viRtual dAtabase for moleKular dEscriptors of orgaNophosphorus ligands", the platform has evolved into a flexible, multi-tenant system (one codebase serving multiple independent libraries) that can host multiple molecular databases with custom branding. You can see all available libraries at descriptor-libraries.molssi.org.
The app is built with FastAPI (a Python web framework) for the backend and React (a JavaScript UI library) for the frontend, deployed as Docker containers that connect to a PostgreSQL database with the RDKit extension for chemistry operations, containing molecule and conformer information.
- Backend: FastAPI on Uvicorn (high-performance Python web server), SQLAlchemy (automap; reflects tables at runtime), Pydantic Settings (configuration management), Alembic (database migration tool)
- Database: PostgreSQL with the RDKit extension (adds chemistry-specific functions like structure searching)
- Frontend: React + Vite (fast build tool) with MUI (Material-UI components), Plotly (interactive graphs), Ketcher (molecule editor), built to static files and served by a small Node server (
server.js) - Reverse proxy: Traefik v2 for HTTPS certificates and path-based routing (directing URLs to the right service)
- Depictions: CDK Depict service for converting SMILES notation (text representation of molecules) to images
- Containers: Docker for packaging all services; Docker Compose for local/dev orchestration
The application supports multiple molecular libraries through a namespace-based architecture:
- Each library gets its own URL path (e.g.,
/acids,/bases,/kraken) - Custom branding and content per library (logos, color schemes, text)
- Shared backend infrastructure with library-specific API endpoints (e.g.,
/api/acids) - Path-based routing through a reverse proxy (incoming requests are directed based on the URL path)
- UI path: set
VITE_BASE_URL=/<section>(e.g.,/acids). - API path: set
API_PREFIX=<section>so the backend serves/api/<section>(docs at/api/<section>/docs).
Coming soon - Docker Compose configurations for local development and testing are currently being refreshed.
Coming soon - Test suite updates for the namespace-aware architecture are in progress.
This project is a collaboration between The Molecular Sciences Software Institute and the Center for Computer Assisted Synthesis.
MolSSI is funded by the National Science Foundation OAC-1547580 and CHE-2136142. C-CAS is funded by the National Science Foundation CHE–2202693.