potsim2 0.3.2
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Description:
potsim2 0.3.2
PotSim2: Simple package to segment and compare protein potential grids
Using gridDataFormats to read the grids and MDAnalysis to make pdb atom selections
Installation
pip install potsim2
Usage: Open two grids and calculate PIPSA like scores
The protein electrostatic potential grids can generated with APBS
from potsim2 import PotGrid
# read grids
grid1 = PotGrid('A__02_01.pdb', 'A__02_01.pkl')
grid2 = PotGrid('A__11_01.pdb', 'A__11_01.pkl')
# calculate skin for grid1
skin_mask1 = grid1.get_skin_mask()
grid1.apply_mask(skin_mask1)
# calculate skin for grid2
skin_mask2 = grid2.get_skin_mask()
grid2.apply_mask(skin_mask2)
# calc the Hodgkin similarity index and PIPSA like distance
hsi, dis = grid1.score(grid2)
# export the skins in uncompressed OpenDX format to be visualized in PyMol/ChimeraX
grid1.export('A__02_01.dx')
grid2.export('A__11_01.dx')
License:
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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