PyeMap is a Python package aimed at automatic identification of electron and hole transfer pathways in proteins. It serves as the backend for the web application eMap, and can also be used as a fully functional Python package.
- Documentation: https://readthedocs.org/projects/pyemap/
- Website: https://emap.bu.edu
- News: https://twitter.com/eMap_protein
PyeMap officially supports Python versions 3.5 and later, and has been tested for Linux and OSX platforms. Below is an abbreviated version of the instructions provided in the documentation.
The conda recipe will install all dependencies necessary for full functionality.
# create new virtual environment
$ conda create -n pyemap_env python=3.7
$ conda activate pyemap_env
# include channels for dependencies, only needs to be done once
$ conda config --add channels conda-forge --add channels salilab --add channels bioconda --add channels gayverjr
$ conda update --all
# install pyemap
$ conda install pyemap
Pip installation will only install python dependencies, and requires Graphviz in order to work. This is sufficient to run PyeMap analysis and view graph images, but some features will be missing.
pip install pyemap
For full functionality, install RDKit, MSMS, DSSP, and wget, all of which can be downloaded free of charge from their owners, and are available on most platforms.
Please see our tutorial on how to use PyeMap.
Please report any bugs and make feature requests here. For issues exclusive to the web version eMap, please send an email to emap.bu@gmail.com. We also greatly encourage users to contribute by making pull requests on GitHub!
Released under the 3-Clause BSD license (see LICENSE).
Copyright (C) 2019
James Gayvert jrg444@gmail.com
Ruslan Tazhigulov ruslan.tazhigulov@gmail.com
Ksenia Bravaya bravaya@bu.edu