No project description provided

These details have not been verified by PyPI

Project links

Homepage

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')

Project details

These details have not been verified by PyPI

Project links

Homepage

Release history Release notifications | RSS feed

This version

0.3.2

Feb 28, 2023

0.3.1

Feb 28, 2023

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

potsim2-0.3.2.tar.gz (6.6 kB view hashes)

Uploaded Feb 28, 2023 Source

Built Distributions

potsim2-0.3.2-cp311-cp311-win_amd64.whl (60.0 kB view hashes)

Uploaded Feb 28, 2023 CPython 3.11 Windows x86-64

potsim2-0.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (93.6 kB view hashes)

Uploaded Feb 28, 2023 CPython 3.11 manylinux: glibc 2.17+ x86-64

potsim2-0.3.2-cp311-cp311-macosx_11_0_arm64.whl (58.7 kB view hashes)

Uploaded Feb 28, 2023 CPython 3.11 macOS 11.0+ ARM64

potsim2-0.3.2-cp311-cp311-macosx_10_9_x86_64.whl (60.6 kB view hashes)

Uploaded Feb 28, 2023 CPython 3.11 macOS 10.9+ x86-64

potsim2-0.3.2-cp310-cp310-win_amd64.whl (60.0 kB view hashes)

Uploaded Feb 28, 2023 CPython 3.10 Windows x86-64

potsim2-0.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (93.6 kB view hashes)

Uploaded Feb 28, 2023 CPython 3.10 manylinux: glibc 2.17+ x86-64

potsim2-0.3.2-cp310-cp310-macosx_11_0_arm64.whl (58.7 kB view hashes)

Uploaded Feb 28, 2023 CPython 3.10 macOS 11.0+ ARM64

potsim2-0.3.2-cp310-cp310-macosx_10_9_x86_64.whl (60.6 kB view hashes)

Uploaded Feb 28, 2023 CPython 3.10 macOS 10.9+ x86-64

potsim2-0.3.2-cp39-cp39-win_amd64.whl (59.7 kB view hashes)

Uploaded Feb 28, 2023 CPython 3.9 Windows x86-64

potsim2-0.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (93.5 kB view hashes)

Uploaded Feb 28, 2023 CPython 3.9 manylinux: glibc 2.17+ x86-64

potsim2-0.3.2-cp39-cp39-macosx_11_0_arm64.whl (58.8 kB view hashes)

Uploaded Feb 28, 2023 CPython 3.9 macOS 11.0+ ARM64

potsim2-0.3.2-cp39-cp39-macosx_10_9_x86_64.whl (60.7 kB view hashes)

Uploaded Feb 28, 2023 CPython 3.9 macOS 10.9+ x86-64

potsim2-0.3.2-cp38-cp38-win_amd64.whl (57.6 kB view hashes)

Uploaded Feb 28, 2023 CPython 3.8 Windows x86-64

potsim2-0.3.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (93.2 kB view hashes)

Uploaded Feb 28, 2023 CPython 3.8 manylinux: glibc 2.17+ x86-64

potsim2-0.3.2-cp38-cp38-macosx_11_0_arm64.whl (58.6 kB view hashes)

Uploaded Feb 28, 2023 CPython 3.8 macOS 11.0+ ARM64

potsim2-0.3.2-cp38-cp38-macosx_10_9_x86_64.whl (60.5 kB view hashes)

Uploaded Feb 28, 2023 CPython 3.8 macOS 10.9+ x86-64

Hashes for potsim2-0.3.2.tar.gz

Hashes for potsim2-0.3.2.tar.gz
Algorithm	Hash digest
SHA256	`9478b1fe180bd8f297e4fd37077aa87f7f1135608f18d108710f6ff70bde6901`
MD5	`a85abb4ff2cb49af94ff0e7f47c3c509`
BLAKE2b-256	`cafebf8ecf1e0b347fbe7f6e83a9194b2fe06c92d6fca1fc243e4322ff85f99e`

Hashes for potsim2-0.3.2-cp311-cp311-win_amd64.whl

Hashes for potsim2-0.3.2-cp311-cp311-win_amd64.whl
Algorithm	Hash digest
SHA256	`4f2fbb07c10d1c292752e458c570e20ea4b23b14ca789e7fc0ffd7c0382ad982`
MD5	`5a57ad1a92ad595b1e1dd639be86ae9a`
BLAKE2b-256	`69c68f1acf5ce3092075d005bb52af01ae2a9733b78378bfeec845325b3c4efb`

Hashes for potsim2-0.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Hashes for potsim2-0.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm	Hash digest
SHA256	`58b254c279e10f2d80322dc8d25fedbaebccd5942a6e001f86f7947a22134563`
MD5	`a19fde83bc64b5ad2ad106ff23ba4a53`
BLAKE2b-256	`9bd03cfe8b45ae76fb4a1d42fe4f385901cc96755729721adf994f90b72b27eb`

Hashes for potsim2-0.3.2-cp311-cp311-macosx_11_0_arm64.whl

Hashes for potsim2-0.3.2-cp311-cp311-macosx_11_0_arm64.whl
Algorithm	Hash digest
SHA256	`06d089ee20433e7cccd16abcd3f5dc96770997aca480d30bd6a12bde2f722ebd`
MD5	`10d18f3d84cb7bf8090142b36dab80a9`
BLAKE2b-256	`79ff563859afba539a708fe35f2305bd5f34dacd0eb4177072493615f9fb5acf`

Hashes for potsim2-0.3.2-cp311-cp311-macosx_10_9_x86_64.whl

Hashes for potsim2-0.3.2-cp311-cp311-macosx_10_9_x86_64.whl
Algorithm	Hash digest
SHA256	`82c8ff32cf356592e8e67f367b4990fd3e5d8197bd3a14c98dad341885dc0d23`
MD5	`e29ed9cbffddcac291aba41edfead8d7`
BLAKE2b-256	`37377092d68faa39cc0b54a15194cdd01da26d57aa1a56d9663e3e269d908c1c`

Hashes for potsim2-0.3.2-cp310-cp310-win_amd64.whl

Hashes for potsim2-0.3.2-cp310-cp310-win_amd64.whl
Algorithm	Hash digest
SHA256	`366fef8fa522afc753b02af8557875911e86ec963bc2983a18faf6acd8ee2a83`
MD5	`32149131671dbcb81285b0fa5713d78b`
BLAKE2b-256	`9a6253c439baef4a51c94e505acdd077acb2aca326bceb5b784dd888e8798ea0`

Hashes for potsim2-0.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Hashes for potsim2-0.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm	Hash digest
SHA256	`0399607945c2ef3363aeb23d59862bd31304384741a54a94f41fd7ea457c2645`
MD5	`cc1acf9cc38f197895d8b9cd53ead54e`
BLAKE2b-256	`6e45b6c513041a5d92b6eab40a0a5d7fe6b4cfabedc27af4c3e45ae9fe579696`

Hashes for potsim2-0.3.2-cp310-cp310-macosx_11_0_arm64.whl

Hashes for potsim2-0.3.2-cp310-cp310-macosx_11_0_arm64.whl
Algorithm	Hash digest
SHA256	`23b6986a3a1b36c3b1080ce5f4dd0fd19406a79b19143b6a8cc82425c08e8602`
MD5	`682ef053658234445c0784a0cbae8515`
BLAKE2b-256	`d2879a49dc07556d547ccf3c7cc3a66be89853f0a5fdf6f371b116b4e412a99b`

Hashes for potsim2-0.3.2-cp310-cp310-macosx_10_9_x86_64.whl

Hashes for potsim2-0.3.2-cp310-cp310-macosx_10_9_x86_64.whl
Algorithm	Hash digest
SHA256	`320df8bf7736648b4edc98f214c66b37b29cf9c3a065378fc8a19b264d9ee1ef`
MD5	`8674b8436f6e26ed14dfdc4099d6f373`
BLAKE2b-256	`aab201bf4d4d8739fdd06e8b6096f20873c0705508fef390e9509f0d8d059f01`

Hashes for potsim2-0.3.2-cp39-cp39-win_amd64.whl

Hashes for potsim2-0.3.2-cp39-cp39-win_amd64.whl
Algorithm	Hash digest
SHA256	`6ae1b9266e1ce55b3b940ed0682aaeb13753895dae6b53a2c8dccf48dfc9e3b3`
MD5	`5e9cdb0ffa401b0ca3ac63029342f369`
BLAKE2b-256	`448b11e13cee1a1ba874426da22081cd5e81ebf78d32f6c0d378170c45d99d5c`

Hashes for potsim2-0.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Hashes for potsim2-0.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm	Hash digest
SHA256	`50c27de1d91fa7461c86a86665b72fe2208bcaded41105ab16deae979bdb0036`
MD5	`9f77d10f327b3891924706bcbd6e872a`
BLAKE2b-256	`7a93837a376187d0de899441aca501a839a12bd542066e3ba70b07e861f14a66`

Hashes for potsim2-0.3.2-cp39-cp39-macosx_11_0_arm64.whl

Hashes for potsim2-0.3.2-cp39-cp39-macosx_11_0_arm64.whl
Algorithm	Hash digest
SHA256	`ffa481f3c23f365c83e0a231f16be4cb028304bad10eb2e1b2710b7a3888477a`
MD5	`309761c771476db85d085c2b0e522def`
BLAKE2b-256	`7833094496930bd79fd7991871b21e5b7f0377e849eddd2d70515ca3257cd784`

Hashes for potsim2-0.3.2-cp39-cp39-macosx_10_9_x86_64.whl

Hashes for potsim2-0.3.2-cp39-cp39-macosx_10_9_x86_64.whl
Algorithm	Hash digest
SHA256	`317946325de4a0cc23f6cc8088c346615f97ad459f84ac9dc0551c41a1c476ca`
MD5	`b81ba1d9ccbee9825c32639f629dd3a2`
BLAKE2b-256	`c3883a345d410c58319021da7e9f2726213dd1aac0afdd7e3ba9775979199285`

Hashes for potsim2-0.3.2-cp38-cp38-win_amd64.whl

Hashes for potsim2-0.3.2-cp38-cp38-win_amd64.whl
Algorithm	Hash digest
SHA256	`8f560c0e2e147792fcedaf4deb589abf0012ed5c986321a7b193d469aa6226a0`
MD5	`3d1a5ab5a166a0c2f5f8359bae74a160`
BLAKE2b-256	`4d6ee60808f66df140ef2a71f1febae5f4527cbea0ae0b5dc597827e031d3c2d`

Hashes for potsim2-0.3.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl

Hashes for potsim2-0.3.2-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
Algorithm	Hash digest
SHA256	`1f68843773985ad3e769de56a1230eb5ac15d68b13c3fb10506d047c147f995a`
MD5	`6134715dcc75fc8465432b60877431ba`
BLAKE2b-256	`09811e9697adf68240b450f2c5777af37f0b00374907112dfc79721d404e2eea`

Hashes for potsim2-0.3.2-cp38-cp38-macosx_11_0_arm64.whl

Hashes for potsim2-0.3.2-cp38-cp38-macosx_11_0_arm64.whl
Algorithm	Hash digest
SHA256	`b106971595c0e54135bcd3b4dd08e9a9a0a6bffa0486d3619ed9cf60778e3049`
MD5	`73e0ede26d59c203073479e2a8b12d15`
BLAKE2b-256	`ac299afb7eba85a9d589c85160dca86d7cb5cefcd3cfa750a19dfd78b51628a3`

Hashes for potsim2-0.3.2-cp38-cp38-macosx_10_9_x86_64.whl

Hashes for potsim2-0.3.2-cp38-cp38-macosx_10_9_x86_64.whl
Algorithm	Hash digest
SHA256	`82dd36204350124bb9e2fc9d8f2976638e2cdc7f7f5f75865c274585c948f829`
MD5	`38f4a6f1546fb9aa3a97553ac5969101`
BLAKE2b-256	`46cda3535647fc6e4a82de05aea550aba109393be359597d2b2fe09a86404168`