This module has the routines and data structures necessary to allow one to generate visualizations of a atomic systems. We also include helper routines for generating colors.
- class InlineVisualizer(xsize=400, ysize=300, nrow=1, ncol=1)[source]
This class allows for a quick viewing of BigDFT systems using the py3Dmol package.
- display_system(*syslist, **kwargs)[source]
Display an animation of a sequence of systems. The colordict can be used to color each fragment. When only one system is passed it will remain still.
syslist (BigDFT.Systems.System) – the systems to visualize.
colordict (dict) – a dictionary from fragment ids to hex colors, can also be a list of dicts (one for each system) if using a grid.
field_vals (list) – values of the field to decide colors of the keys
cartoon (bool) – set to True to use the cartoon view. This only works if atom names and residues are properly defined.
gridlist (list) – if present, defines the row and column indices for visualizing multiple systems on a grid.
show (bool) – you can explicitly defer showing.
- class VMDGenerator(representation='CPK', color=16)[source]
This class contains the routines you would use for visualization of a system using the VMD program.
the vmd representation to draw with. https://www.ks.uiuc.edu/Research/vmd/allversions/repimages/#representations
- visualize_fragments(system, scriptfile, geomfile, fragcolors=None)[source]
This generates a script for visualizing the fragmentation of a system using VMD.
system (BigDFT.Systems.System) – the system to visualize.
scriptfile (str) – the name of the file to write the vmd script to (usually has extension .tcl)
geomfile (str) – the filename for where to write an xyz file of the system.
fragcolors (dict) – optionally, a dictionary from fragment ids to fragment colors. Colors are integers between 0 and 32.
- get_distinct_colors(keys, name='tab20', fuzz=True)[source]
This generates a dictionary of distinct colors based on a matplotlib colormap.
a dictionary mapping matplotlib keys to RGB colors.
- Return type
- truncate_colormap(cmap, compressed_values=None, vmin=0.0, vmax=1.0, N=- 1)[source]
Truncate a colormap from a given cmap. Taken from https://stackoverflow.com/questions/40929467/ how-to-use-and-plot-only-a-part-of-a-colorbar-in-matplotlib.
Builds a dictionary of colors for a system where each atom is its own fragment. This uses the built in colors of jmol.
sys (BigDFT.Systems.System) – a system where each atom contains a
atom. (single) –
a dictionary mapping fragment ids to colors.
- Return type
- get_colordict(keys, field_vals=None, vmin=None, vmax=None, colorcode=None)[source]
Build a dictionary of colors for each of the keys. If the field_dict is provided, order the colors of the keys in terms of the sorting of the filed values
keys (list) – keys of the color dictionary
field_vals (list) – values of the field to decide the colors of the keys
vmin (float) – minimum value of the colors. Useful to extend the range below the minimum of field_vals.
vmax (float) – maximum value of the colors. Useful to extend the range below the maximum of field_vals.
colorcode (str) – the string of the colorcode. Default is ‘rainbow’ if no field_vals are present. If field_vals have negative data, default is seismic. Otherwise Reds.
- the dictionary of the keys, and the corresponding colors.
The dictionary contains also special keys arguments to be passed to the colorbar method of matplotlib:
’__mappable__’, which is associated the reference to the matplotlib.ScalarMappable instance that is associated to the colordict. This instance can be useful to draw colorbars associated to such a colordict.
- Return type
Input a string without hash sign of RGB hex digits to compute complementary contrasting color such as for fonts. Function borrowed from https://stackoverflow.com/questions/1855884/ determine-font-color-based-on-background-color
The following is an example of module usage:
"""Visualization Example""" from BigDFT.Systems import System from BigDFT.Fragments import Fragment from BigDFT.IO import XYZReader # Read in a system. sys = System() with XYZReader("SiO") as ifile: for i, at in enumerate(ifile): sys["FRA:"+str(i)] = Fragment([at]) # Display the system. viz = InlineVisualizer(400, 300) viz.display_system(sys) # Change the colors colordict = get_distinct_colors(list(sys)) viz.display_system(sys, colordict=colordict)