chemtools.utils.output.print_vmd_script_nci

chemtools.utils.output.print_vmd_script_nci(scriptfile, densfile, rdgfile, isosurf=0.5, denscut=0.05)[source]

Generate VMD (Visual Molecular Dynamics) script for visualizing NCI isosurfaces.

Visualizes NCI (non-covalent interactions) isosurfaces subject to the constraint of density(r) < denscut, i.e. low-density, and colored based on the sign(\(\lambda_2\)) \(\rho\).

Parameters:
  • scriptfile (str) – Name of VMD script file to generate.
  • densfile (str) – Name of density cube file.
  • rdgfile (str) – Name of reduced density gradient cube file.
  • isosurf (float, default=0.5) – Reduced density gradient isosurface to visualize.
  • denscut (float, default=0.05) – Density cutoff used in creating reduced density gradient cube file. Similar to NCIPlot program, reduced density gradient of points with density > denscut will be set to 100.0 to display reduced density gradient isosurface subject to the constraint of low density.

Note

The script is the same as the one generated by NCIPlot software version 1.0.