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')
2 maintainers
Metadata
2 maintainers
Release files for potsim2 0.3.6
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| potsim2-0.3.6.tar.gz | 6.9 kB | Details |
Built distributions (wheels)
Total release size: 1.3 MB
Release files / potsim2-0.3.6.tar.gz
| Download URL | potsim2-0.3.6.tar.gz |
|---|---|
| Size | 6.9 kB |
| Tags | Source |
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Release files / potsim2-0.3.6-cp313-cp313-win_amd64.whl
| Download URL | potsim2-0.3.6-cp313-cp313-win_amd64.whl |
|---|---|
| Size | 64.9 kB |
| Tags | CPython 3.13 Windows x86-64 |
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Release files / potsim2-0.3.6-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
| Download URL | potsim2-0.3.6-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl |
|---|---|
| Size | 77.6 kB |
| Tags | CPython 3.13 Linux glibc 2.24+ x86-64 Linux glibc 2.28+ x86-64 |
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Release files / potsim2-0.3.6-cp313-cp313-macosx_11_0_arm64.whl
| Download URL | potsim2-0.3.6-cp313-cp313-macosx_11_0_arm64.whl |
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| Size | 62.5 kB |
| Tags | CPython 3.13 macOS 11.0+ ARM64 |
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Release files / potsim2-0.3.6-cp313-cp313-macosx_10_13_x86_64.whl
| Download URL | potsim2-0.3.6-cp313-cp313-macosx_10_13_x86_64.whl |
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| Size | 64.1 kB |
| Tags | CPython 3.13 macOS 10.13+ x86-64 |
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Release files / potsim2-0.3.6-cp312-cp312-win_amd64.whl
| Download URL | potsim2-0.3.6-cp312-cp312-win_amd64.whl |
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| Size | 64.8 kB |
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| Download URL | potsim2-0.3.6-cp312-cp312-macosx_11_0_arm64.whl |
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| Download URL | potsim2-0.3.6-cp312-cp312-macosx_10_13_x86_64.whl |
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| Download URL | potsim2-0.3.6-cp311-cp311-win_amd64.whl |
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| Size | 64.8 kB |
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| Download URL | potsim2-0.3.6-cp311-cp311-macosx_10_9_x86_64.whl |
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| Download URL | potsim2-0.3.6-cp310-cp310-win_amd64.whl |
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