CaviTracer - scanChannelParameters()

[karolamik13]

Here we have a function that will run the calcChannels() for the selected structure and check various parameters such as r2 (probe size), sparsity, and min_depth. Initially, we have r2_values=[1.2, 1.4, 1.6], sparsity_values=[1, 3, 5], min_depth_values=[3, 5, 10], but it can be changed to any values. After checking those parameters, we use calcChannelSurfaceOverlaps(), which already exists in the code, to obtain a grid of surface overlaps (similarly to MD/multi-model PDB analysis). In such a way, we can test various parameters and check which are better for a particular type of protein.

Below, analysis of two protein structures. Red region corresponds to the channels that are present in the largest number of results (various parameters), and blue regions (displayed as dots) for certain parameters.

How to use:
from prody import *
p = parsePDB('1tqn')
protein = p.select('protein')
channels_all, parameter_sets, occupancy_file = scanChannelParameters(protein, output_path='channel_parameter_grid')

@briza81 @MatthewLicht