.. pyFuRNAce documentation master file, created by
   sphinx-quickstart on Fri Apr 25 01:31:04 2025.
   You can adapt this file completely to your liking, but it should at least
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Welcome to pyFuRNAce's documentation!
=====================================

.. image:: https://github.com/Biophysical-Engineering-Group/pyFuRNAce/blob/main/pyfurnace/app/static/logo_text.png?raw=true
   :alt: pyFuRNAce logo

**pyFuRNAce** is an open-source Python package and web-based design engine for creating complex RNA nanostructures using the co-transcriptional RNA origami approach. It streamlines the entire design pipeline — from structural motif assembly to sequence generation and primer design — into an intuitive, user-friendly platform.

|downloads_month| |downloads_total|

.. |downloads_month| image:: https://static.pepy.tech/personalized-badge/pyfurnace?period=month&units=INTERNATIONAL_SYSTEM&left_color=GREY&right_color=GREEN&left_text=Downloads/Month
   :target: https://pepy.tech/projects/pyfurnace
   :alt: Downloads per month (pepy)

.. |downloads_total| image:: https://static.pepy.tech/personalized-badge/pyfurnace?period=total&units=INTERNATIONAL_SYSTEM&left_color=GREY&right_color=RED&left_text=Downloads
   :target: https://pepy.tech/projects/pyfurnace
   :alt: Total downloads (pepy)

.. |codecov| image:: https://codecov.io/gh/Biophysical-Engineering-Group/pyFuRNAce/graph/badge.svg?token=EQX6C990WP
   :target: https://codecov.io/gh/Biophysical-Engineering-Group/pyFuRNAce
   :alt: Codecov coverage


| **WebApp:** `pyfurnace.de <http://pyfurnace.de>`_
| **GitHub:** `Biophysical-Engineering-Group/pyFuRNAce <https://github.com/Biophysical-Engineering-Group/pyFuRNAce>`_
| **PyPI:** `pyfurnace <https://pypi.org/project/pyfurnace/>`_
| **Script API examples:** `Code Examples <https://github.com/Biophysical-Engineering-Group/pyFuRNAce/tree/main/examples>`_
| **Documentation:** `Read the Docs <https://pyfurnace.readthedocs.io/en/latest/>`_

pyFuRNAce design API coverage:  |codecov|

.. image:: https://github.com/Biophysical-Engineering-Group/pyFuRNAce/blob/main/vid/demo_1min.gif?raw=true
   :alt: pyFuRNAce demo

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   about
   installation
   api
   limitations
   tutorials