README.md

metadata

title: RDKit API
emoji: 🔬
colorFrom: blue
colorTo: green
sdk: gradio
sdk_version: 4.44.1
app_file: app.py
pinned: false

RDKit API

This is a Hugging Face Space providing API access to various RDKit cheminformatics functions.

Endpoints

• POST /api/name_to_smiles : Convert chemical name to SMILES
• POST /api/name_to_3d_molecule : Generate 3D molecule visualization
• POST /api/smiles_to_mol : Convert SMILES to canonical SMILES
• POST /api/molecular_weight : Calculate molecular weight
• POST /api/logp : Calculate logP (partition coefficient)
• POST /api/tpsa : Calculate TPSA (topological polar surface area)
• POST /api/chemiscope_explorer : Build a Chemiscope dataset + visualization from a batch of SMILES
• POST /api/reaction_visualizer : Generate SVG visualization of chemical reactions from reaction SMILES
• POST /api/mol_image : Generate 2D molecule image (returns PIL Image)

Usage

To deploy on Hugging Face Spaces, upload this repository.

For local testing, run:

pip install -r requirements.txt
python app.py

The API endpoints can be accessed programmatically using the Gradio client or HTTP requests.

Chemiscope-powered exploration

The new Chemiscope Explorer tab leverages the official chemiscope Python package plus the standalone Chemiscope web viewer to create rich, shareable datasets directly inside the Space:

1. Paste up to 12 SMILES (one per line or comma-separated). RDKit generates 3D ETKDG conformers, computes descriptors (MolWt, logP, TPSA, H-bond counts, rotatable bonds) and per-atom Gasteiger charges.
2. The resulting ASE frames and descriptors are converted into the Chemiscope JSON schema and embedded with the chemiscope_standalone.html viewer so you can explore structures + map plots without leaving the Space.
3. Download the .json.gz artifact and reload it later on chemiscope.org via the Load/Save menu or by hosting it and passing ?load=<url> to share interactive analyses with collaborators.

This flow keeps the Hugging Face interface lightweight while exposing the full Chemiscope feature set for interactive dataset mining.