Introduction

MD_plotting_toolkit is a Python package providing useful tools for visualizing simulation data obtained from molecular dynamics. The tools available in this package are aimed to enable easy one-line command to generate publication-quality figures. While the plotting commands are more useful for plotting output files generated by PLUMED or GROMACS (in .xvg format), the file parser in the package is able to parse any files that is readable by numpy.loadtxt or any files that only use # or @ as the delimiter. With entry points set upon the installation of this package, these commands can be executed in any directory from the terminal. These commands include plot_xy, plot_xyz, plot_hist, plot_bar, plot_violin, plot_matrix, and combine_plots. Despite different purposes of these tools, except for combine_plots, they do share some common funtionalities that could be useful. Specifically, most of the plotting commands can do the following:

  • Convert the units as needed.

  • Scale, truncate, and deduplicate the data as needed.

  • Provide simple statistics of the input data.

For more information about these commands, please refer to the tutorials.

Installation

The package has not been published to PyPI, but can be installed from our github repository using the following commands:

git clone https://github.com/wehs7661/MD_plotting_toolkit.git
cd MD_plotting_toolkit/
pip install -e .

Note that this package requries a bunch of other Python packages to be installed, including NumPy, SciPy, matplotlib, pymbar, natsort, and argparse.