chemtools.utils.output.print_vmd_script_multiple_cube

chemtools.utils.output.print_vmd_script_multiple_cube(scriptfile, cubes, isosurfs=None, material='Opaque', scalemin=-0.05, scalemax=0.05, colors=None)[source]

Generate VMD (Visual Molecular Dynamics) script for visualizing multiple cube files.

Visualize multiple cube files simultaneously where data from each cube file is colored differently.

Parameters:
  • scriptfile (str) – Name of VMD script file to generate.
  • cubes (list of str) – Names of cube files to plot
  • isosurfs (float, list of float) – Isovalue at which the plot (isosurface) is generated If a float is given, then this is the value of isosurface for all cube files Default value is 0.5 for all isosurfaces
  • material (str) – The material setting of the isosurface used in VMD script. One of ‘Opaque’, ‘Transparent’, ‘BrushedMetal’, ‘Diffuse’, ‘Ghost’, ‘Glass1’, ‘Glass2’, ‘Glass3’, ‘Glossy’, ‘HardPlastic’, ‘MetallicPastel’, ‘Steel’, ‘Translucent’, ‘Edgy’, ‘EdgyShiny’, ‘EdgyGlass’, ‘Goodsell’, ‘AOShiny’, ‘AOChalky’, ‘AOEdgy’, ‘BlownGlass’, ‘GlassBubble’, ‘RTChrome’. Default is ‘Opaque’
  • scalemin (float) – Smallest value to color on the isosurface used in VMD script. Default is -0.05
  • scalemax (float) – Largest value to color on the isosurface used in VMD script. Default is 0.05
  • colors (list of int) – Colors of each cube file data Each integer corresponds to a color. See VMD program or manual for details. Default selects random color for each cube file

Note

Not quite sure what happens when the number of cube files exceeds 1057 (possiblly the maximum number of ColorID’s in VMD)

Raises:
  • TypeError – If cube files are not provided as a list or tuple If colors are not provided as a list or tuple of the same length as the cube files
  • ValueError – If any of the cube files cannot be found If any of the colors are not an integer between 0 and 32