TEMP holding space

PlotCube.py

summary

PlotMesh

PlotHistogram

PlotSurace

this plots the ESP

type

python PlotCube.py PlotSurface ../test.cube

where test.cube is the cube file to be imaged

to change the colour map click on the rainbow or bwr (blue-white-red) buttons OR from the command line when you call the procedure add one of the options from this page: https://matplotlib.org/users/colormaps.html

for example python PlotCube.py PlotSurface ../test.cube colour="plasma"

options are

arguments: path for a cube file (str), factor (float, opt), alpha (float, opt), size (float, opt), axes (bool, opt), colour (str, opt), background colour (tuple/list/str, opt), minmax (bool, opt), colour bar limits (list, opt), atoms (boolean, opt), au (boolean, opt), curvature (boolean, opt), curvature upper limit (float, opt), number of curvature points (int, opt)

   calls: GetVdWPoints (from ReadCube)

   returns: -

   this function creates an interactive plot of all the points which reside within +/- half a distance from the surface defined in terms of the Van der Waals radii of the atoms in the molecule
   (half a distance represents half the distance between two diagonally adjacent points in the grid)

   it has sliders for alpha, size and zoom

   it has buttons for turning axes on/off, showing/hiding min and max, showing/hiding atoms, colour scheme, background colour

   factor = factor by which to multiply the VdW radii

   alpha = transparency of the markers

   size = size of the markers

   axes = show/hide axes

   colour = colour scheme ('rainbow' by default, change it to 'bwr' for blue-white-red) - full list here: https://matplotlib.org/users/colormaps.html

   bkg = background colour (RGB tuple/list or name - each value between 0 and 1, white by default)

   minmax = show/hide min and max

   cb_lim = limits for the colour bar (list of two floats; if not specified, the limits will be the min and max of the values; if the limits do not cover the whole range of values, a warning is printed)

   atoms = show/hide atoms

   au = if True, use atomic units (i.e. bohr for coordinates); if False, use Angstroms for coordinates

   curvature = if True, plots curvature points (either based on cv_lim if given, or cv_pts)

   cv_lim = the upper limit of the curvature for the low curvature points to be plotted (it overrides cv_pts if given)

   cv_pts = the number of low curvature points to be plotted (the points will be chosen in increasing order of their absolute curvature; this number is 5 by default)