RNAglib: Tools for learning on the structure of RNA using 2.5D geometric representations
Project description
RNA Geometric Library (rnaglib
)
RNAglib
is a Python package for studying RNA 2.5D and 3D structures. Functionality includes automated data loading, analysis,
visualization, ML model building and benchmarking.
We host RNAs annotated with molecule, base pair, and nucleotide level attributes. These include, but are not limited to:
- Secondary structure
- 3D coordinates
- Protein binding
- Small molecule binding
- Chemical modifications
- Leontis-westhof base pair geometry classification
Cite
@article{mallet2022rnaglib,
title={RNAglib: a python package for RNA 2.5 D graphs},
author={Mallet, Vincent and Oliver, Carlos and Broadbent, Jonathan and Hamilton, William L and Waldisp{\"u}hl, J{\'e}r{\^o}me},
journal={Bioinformatics},
volume={38},
number={5},
pages={1458--1459},
year={2022},
publisher={Oxford University Press}
}
Data
Data can be downloaded directrly from Zenodo or through the provided command
line utility $ rnaglib_download
.
Version | Date | Total RNAs | Total Non-Redundant | Non-redundant version | rnaglib commit |
---|---|---|---|---|---|
1.0.0 | 15-02-23 | 5759 | 1176 | 3.269 | 5446ae2c |
0.0.0 | 20-07-21 | 3739 | 899 | 3.186 | eb25dabd |
Installation
The package can be cloned and the source code used directly. We also deploy it as a pip package and recommend using this install in conda environments.
If one wants to use GPU support, one should install Pytorch and DGL with the appropriate options. Otherwise you can just skip this step and the pip installs of Pytorch and DGL will be used.
Then, one just needs to run :
pip install rnaglib
Then one can start using the packages functionalities by importing them in one's python script.
Optional Dependencies
To build 2.5D graphs from scratch locally, for the moment you need to install a fork of fr3d-python
manually.
pip install git+https://github.com/cgoliver/fr3d-python.git
``
## Associated Repositories:
[VeRNAl](https://github.com/cgoliver/vernal)
[RNAMigos](https://github.com/cgoliver/RNAmigos)
## Resources
* [Documentation](https://rnaglib.readthedocs.io/en/latest/?badge=latest)
* [Homepage](https://rnaglib.cs.mcgill.ca/)
* [Twitter](https://twitter.com/rnaglib)
* Contact: `rnaglib@cs.mcgill.ca`
## References
1. Leontis, N. B., & Zirbel, C. L. (2012). Nonredundant 3D Structure Datasets for RNA Knowledge Extraction and
Benchmarking. In RNA 3D Structure Analysis and Prediction N. Leontis & E. Westhof (Eds.), (Vol. 27, pp. 281–298).
Springer Berlin Heidelberg. doi:10.1007/978-3-642-25740-7\_13
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.