PyMol_REG

Visualisation of REG results through PyMol GUI. This repository contains the Plugin 'pymol_reg.py' for PyMol (tested on version 2.5.0 Open-Source). This adds the functionality of visualising a Relative Energy Gradient (REG) analysis output from the REG.py library. This mainly works with the Interacting Quantum Atoms (IQA) topological partitioning.

Requirements

• PyMol
• numpy
• pandas

Usage

To load the pymol_reg.py script as a PyMol plugin, please follow this link. Otherwise, simply type

• run path/to/pymol_reg.py to load it in the current PyMol session.

Note that PyMol sometimes when installed has its own virtual environment, thus the above-listed dependencies need to be installed in that environment for the plugin to work.

Variables

1. selection : object/geometry of the reaction analyzed with the REG methodology uploaded in PyMol.
2. reg_file : path to the REG.xlsx file output from the REG.py library.
3. property : IQA property that is present in the REG.xlsx file. This depends on which properties have been analyzed with the REG.py library. Examples are "Vxc", "Vcl" and "Einter".
4. segment : segment number to consider for the REG values of the previously defined property. (default=1)
5. n_terms : number of REG terms to visualize, positive and negative. (default=3)
6. pos_color : color for the positive REG values. (default=red)
7. neg_color : color for the negative REG values. (default=green)
8. scale : scaling value to make visualization easier. (default=5.0)

To do

• Add a QTWidget in PyMol GUI

License

The MIT License makes this plugin available for everyone. You are more than welcome to help with the development of this repository. Please cite this github page if you use the plugin for your studies/research.