For an easy and interactive way to use Autobreak with your Cadnano designs, access the following Colab notebook. It provides a step-by-step guide to integrate Autobreak into your workflow.
We invite you to support the project by citing these references:
Design principles for accurate folding of DNA origami
Aksel et al. (2024)
https://doi.org/10.1101/2024.03.18.585609
Upon journal publication, the complete citation details will be provided here. Please check back for updates or contact the authors for the most current information.
Rapid prototyping of 3D DNA-origami shapes with caDNAno
Douglas et al. Nucleic Acids Res: 37(15):5001–6 (2009)
https://doi.org/10.1093/nar/gkp436
- Before contacting us, please read the manuscript, this README, and all documentation in the Colab notebook.
- If you encounter a technical problem, submit a New Issue. Please describe the exact steps to reproduce it. Attach or email us the Cadnano file input, as well as any file outputs that resulted from an attempted run.
We use a pyproject.toml-based build process in pip. This workflow was tested with Python 3.12 on macOS and Linux distributions in late 2023.
Setup a dev environment (Mac or Linux)
- Create a virtualenv:
python3 -m venv ~/virtualenvs/abdev - Activate virtualenv:
source ~/virtualenvs/abdev/bin/activate - Clone repo:
git clone git@github.com:douglaslab/pyOrigamiBreak.git - Change directory:
cd pyOrigamiBreak - Make desired code edits
- Build and install in editable mode:
pip install -e . - Test:
autobreak -i cadnanofile.json - Repeat previous 3 steps as needed
Build new dist and upload to PyPi
pip install build twine<- install build and twinecd /path/to/pyOrigamiBreak/python3 -m buildcreates dist/pyOrigamiBreak-x.y.z.tar.gz and pyOrigamiBreak-x.y.z-py3-none-any.whlpython3 -m twine upload dist/pyOrigamiBreak-x.y.z
This version of pyOrigamiBreak is available under the MIT License.