Chemistry Tools
Software libraries and frameworks for cheminformatics and computational chemistry.
Cheminformatics Stack
| Tool | Description | Link |
|---|---|---|
| RDKit | Core cheminformatics toolkit — the foundation of most chemistry ML | rdkit.org |
| OpenBabel | Format conversion, 3D generation | openbabel.org |
| CDK | Java-based cheminformatics toolkit | cdk.github.io |
| Datamol | RDKit wrapper optimized for data science workflows | datamol.io |
Deep Learning for Molecules
| Tool | Description | Link |
|---|---|---|
| DeepChem | Comprehensive ML library for chemistry and life sciences | deepchem.io |
| PyTorch Geometric | Graph neural networks framework | pyg.org |
| DGL-LifeSci | GNN library for life science applications | github |
| Chemprop | Message passing neural networks for molecular property prediction | github |
Specialized Tools
Reaction Prediction
- RXNMapper — Atom mapping for reactions
- rxnfp — Reaction fingerprints
Molecular Generation
- REINVENT — Reinforcement learning for molecular design
- GuacaMol — Benchmarks for generative models
Visualization
- py3Dmol — 3D molecular visualization in Jupyter
- mols2grid — Interactive molecule grids
Getting Started
# Install core chemistry stack
conda create -n chem python=3.10
conda activate chem
# RDKit (via conda-forge)
conda install -c conda-forge rdkit
# Additional tools
pip install datamol deepchem