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https://github.com/hfooladi/moltoken
3D Tokenization of Molecules
https://github.com/hfooladi/moltoken
cheminformatics molecule tokenization
Last synced: 10 days ago
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3D Tokenization of Molecules
- Host: GitHub
- URL: https://github.com/hfooladi/moltoken
- Owner: HFooladi
- License: mit
- Created: 2024-10-17T21:21:26.000Z (4 months ago)
- Default Branch: main
- Last Pushed: 2025-01-28T14:05:27.000Z (11 days ago)
- Last Synced: 2025-01-28T15:22:51.040Z (11 days ago)
- Topics: cheminformatics, molecule, tokenization
- Language: Python
- Homepage:
- Size: 19.5 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
# MolToken: 3D Molecular Structure Tokenization
[](https://badge.fury.io/py/moltoken)
[](https://opensource.org/licenses/MIT)
[](https://www.python.org/downloads/release/python-380/)
MolToken is a Python library for tokenizing 3D molecular structures, enabling better representation learning and analysis of molecular geometries.
## Features
- 🧬 Tokenization of 3D molecular structures
- 🔄 Rotation and translation invariant representations
- ⚡ Fast and efficient processing
- 📊 Built-in visualization tools
- 🔌 Easy integration with deep learning frameworks
- 📁 Support for common molecular file formats (PDB, MOL, XYZ)
## Installation
### Using pip
```bash
pip install moltoken
```
### From source
```bash
# Clone the repository
git clone https://github.com/HFooladi/MolToken.git
cd MolToken
# Create and activate conda environment
conda env create -f environment.yml
conda activate tokenmol
# Install in development mode
pip install -e .
```
## Quick Start
Here's a simple example of how to use MolToken:
```python
from moltoken.tokenizer import MoleculeTokenizer
from rdkit import Chem
from rdkit.Chem import AllChem
# Initialize tokenizer
tokenizer = MoleculeTokenizer(
max_atoms=50,
spatial_resolution=0.1,
consider_bonds=True
)
# Create a simple molecule (ethanol)
mol = Chem.MolFromSmiles('CCO')
mol = Chem.AddHs(mol)
AllChem.EmbedMolecule(mol)
# Get molecular information
conf = mol.GetConformer()
coordinates = conf.GetPositions()
atom_types = [atom.GetSymbol() for atom in mol.GetAtoms()]
bonds = [(bond.GetBeginAtomIdx(), bond.GetEndAtomIdx(),
bond.GetBondTypeAsDouble()) for bond in mol.GetBonds()]
# Tokenize the molecule
tokens = tokenizer.encode_molecule(
coordinates=coordinates,
atom_types=atom_types,
bonds=bonds
)
print(f"Generated tokens: {tokens}")
```
## Documentation
For detailed documentation, visit our [documentation page]().
The documentation includes:
- Detailed API reference
- Tutorials and examples
- Advanced usage guides
- Contribution guidelines
## Development
We welcome contributions! Here's how to set up the development environment:
```bash
# Clone the repository
git clone https://github.com/hfooladi/MolToken.git
cd MolToken
# Create development environment
conda env create -f environment.yml
conda activate tokenmol
# Install development dependencies
pip install -e ".[test]"
# Run tests
pytest tests/
```
### Code Style
We use:
- Black for code formatting
- Ruff for linting
- MyPy for type checking
To format your code:
```bash
black moltoken/
ruff check moltoken/
mypy moltoken/
```
## Citation
If you use MolToken in your research, please cite:
```bibtex
@software{moltoken2024,
author = {Fooladi, Hosein},
title = {MolToken: 3D Molecular Structure Tokenization},
year = {2025},
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/hfooladi/MolToken}
}
```
## License
This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
## Contributing
We welcome contributions! Please read our [Contributing Guidelines](CONTRIBUTING.md) first.
1. Fork the repository
2. Create your feature branch (`git checkout -b feature/AmazingFeature`)
3. Commit your changes (`git commit -m 'Add some AmazingFeature'`)
4. Push to the branch (`git push origin feature/AmazingFeature`)
5. Open a Pull Request
## Acknowledgments
- Thanks to all contributors who have helped shape MolToken
- Special thanks to the RDKit and PyTorch communities
## Contact
Hosein Fooladi - [email protected]
Project Link: [https://github.com/hfooladi/MolToken](https://github.com/hfooladi/MolToken)
## Project Status
MolToken is under active development. Check our [project board](https://github.com/hfooladi/MolToken/projects) for planned features and current progress.