Full documentation: https://viennarna.github.io/forgi
If your use of forgi results in an academic publication, please cite:
Thiel BC, Beckmann IK, Kerpedjiev P and Hofacker IL. 3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements. [version 2; peer review: 2 approved]. F1000Research 2019, 8:287 (https://doi.org/10.12688/f1000research.18458.2)
For the pseudoknot-removal code and external PDB annotation tools, see the citations therein.
pip install forgi will work in many cases. However, as forgi contains a small part of compiled code, this can fail,
especially on operating systems/ python versions for which no manylinux wheel is available.
If compilation fails, you should first try to install Cython, python development headers and a compiler. E.g. on Ubuntu
sudo apt install gcc g++ python3-dev. On other distributions/ when targeting non-default python versions, the package cpoyuld also be called python3-devel or python3.11-dev or something similar.
sphinx-build -b html doc OUTPUTFOLDER