Simple package to segment and compare protein potential grids

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  • License: MIT License (MIT)
  • Author: Eloy Felix
  • Requires: Python >=3.9
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Project description

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')

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  • License: MIT License (MIT)
  • Author: Eloy Felix
  • Requires: Python >=3.9
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0.3.6

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