msmhelper 0.6.1

Helper functions for Markov State Models.

Docs • Features • Installation • Usage

msmhelper

Warning This package is still in beta stage. Please open an issue if you encounter any bug/error.

This is a package with helper functions to work with discrete state trajectories and Markov state models. In contrast to pyemma and msmbuilder it features a very limited set of functionality. This repo is prepared to be published. In the next weeks the source code will be cleaned up, tutorials will be added and this readme will be extended.

This package will be published soon:

D. Nagel, and G. Stock, msmhelper: A Python Package for Markov State Modeling of Protein Dynamics, in preparation

We kindly ask you to cite this article in case you use this software package for published works.

Features

• Simple usage with sleek function-based API
• Supports latest Python 3.10
• Extensive documentation with many command line scripts
• ...

Installation

The package is called msmhelper and is available via PyPI or conda. To install it, simply call:

python3 -m pip install --upgrade msmhelper

or

conda install -c conda-forge msmhelper

or for the latest dev version

# via ssh key
python3 -m pip install git+ssh://[e-mail]/moldyn/msmhelper.git

# or via password-based login
python3 -m pip install git+https://github.com/moldyn/msmhelper.git

Usage

This package is mainly based on numpy and numba for all computational complex tasks.

Usage

import msmhelper as mh
...

Roadmap:

• Add unit tests for all functions
• Add examples usage scripts
• Create typing module

Development

Additional Requirements:

• wemake-python-styleguide
• flake8-spellcheck

Pytest

Running pytest with numba needs an additional flag

export NUMBA_DISABLE_JIT=1 && pytest

Credits:

• numpy
• realpython