This repository contains the Plugin 'spherical_harmonics.py' for PyMol (tested on version 2.5.0 Open-Source). This adds the functionality of plotting spherical harmonics functions on any atom of a molecule loaded in PyMol. The functionality is extremely helpful for visualising Atomic Orbitals or Spherical Multipole Moments.
To load the spherical_harmonics.py script as a PyMol plugin, please follow this link.
A typical PyMol session to run the spherical harmonics plugin will look like this:
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| Figure showing an example usage of the spherical_harmonics.py plugin. The image shows a Qzz (i.e. m=2, l=0) component of the Quadrupole of benzene carbons. The 'test' molecule is the text.xyz in the test folder |
- selected_atoms : PyMol selection of atoms onto which the chosen spherical harmonic function will be plotted.
- molobj : PyMol molecule object. This can be a sub-selection of your system or your entire system as loaded.
- r : magnitude of the chosen spherical harmonic function.
- m : order of the spherical harmonic function.
- l : degree of the spherical harmonic function.
- n_points : number of points for the meshgrid.
- cmap (=viridis by default): any colormap from the matplotlib package. Examples can be found here.
- ax (=0 by default): shows global cartesian axes.
- transparency : sets the transparency of the chosen spherical harmonics function.
- mesh_type (='triangles' by default) : sets the type of mesh for the CGO object. Options are t = triangles, p = points, l = lines.
- Add a QTWidget in PyMol GUI
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.
A DOI is also available for citation at:
