FractalDNA

Python routines for generating geometric models of DNA

FractalDNA is being converted to a package, it is under active developmemt

FractalDNA is a Python package to make DNA geometries that can be joined together like jigsaw puzzles. Both simple, sections of DNA and Solenoidal DNA can be built. This module was built to enable DNA-level simulations to be run in Geant4-DNA, part of the Geant4 project.

Structure models define the large scale structure of DNA, seeded from fractals. An example seeding fractal is below:

DNA Models provide straight and curved segments that can come together to make DNA for use in simulations.

Project documentation is available here alongside notebook examples

⚙️ Installation

Install FractalDNA with pip

pip install fractaldna

or install with Poetry

poetry add fractaldna

🧬 Make some DNA

from fractaldna.dna_models import dnachain as dna

# Make a DNA Chain 40 base pairs long (repeating GATC).
chain = dna.DNAChain("GTAC" * 10)

# Export it to a DataFrame for use in another program
df = chain.to_frame()

For more, check out the notebook examples in the project documentation.

🛡 License

This project is licensed under the terms of the MIT license. See LICENSE for more details.

📃 Citation

@misc{fractaldna,
  author = {Nathanael Lampe},
  title = {FractalDNA},
  year = {2021},
  publisher = {GitHub},
  journal = {GitHub repository},
  howpublished = {\url{https://github.com/natl/fractaldna}}
}

Credits

This project was generated with python-package-template