Features Based Conformational Clustering of Molecular Dynamics trajectories.
Project description
gmx_clusterByFeatures
It can be used to cluster the conformations of a molecule in a molecular dynamics trajectory using collection of features. The features could be any quantity as a function of time such as Projections of eigenvector from PCA or dihedral-PCA, distances, angles, channel radius etc.
See details at: gmx_clusterByFeatures homepage
Installation on Linux and MacOS
sudo pip3 install gmx-clusterByFeatures
No dependency on GROMACS. Install and use it.
For more details, visit download and installation section.
Usage
Command |
Function |
---|---|
Main module to perform clustering |
|
Feature vs Feature plot to check quality of clustering |
|
Distance-matrix related calculations |
|
To visulaize/plot matrix obtained from distmat |
|
To calculate cavity/channel radius using HOLE program |
|
To calculate average and plot hole output radius file |
|
To write radius as a features for clustering |
|
To plot or write radius for clusters separately |
For more details, visit usage section.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distributions
Built Distributions
Hashes for gmx_clusterByFeatures-0.1.17-cp37-cp37m-manylinux1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 82391b056cddecfa87d0869a1311ea277b029519a099d783d1af6d6715d04f60 |
|
MD5 | f2268364dae5865134a906ceb9145ac1 |
|
BLAKE2b-256 | 9fe0bf82457cae474f9a92d51d59ee2d78777aa3d7892e9ec11889f35a22cd30 |
Hashes for gmx_clusterByFeatures-0.1.17-cp37-cp37m-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 1f65f5bb0e914cb64ee261ac782af887d953d930d83b050d2269abb11d5afee8 |
|
MD5 | 61b34285969baaf452a685b4070b01b7 |
|
BLAKE2b-256 | 2b0c32e9ec1f77b5f895547aa11107c733c4018f0ec15dae34c23fb9c266ba9d |
Hashes for gmx_clusterByFeatures-0.1.17-cp37-cp37m-macosx_10_13_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | b9011b7a07525cb56602046ad72b171cf4c1013922261c70e44fdadf4d35ef04 |
|
MD5 | 050a19b9cd516c53ec31b3f9e7465d7f |
|
BLAKE2b-256 | 172737cb0d196532673e9fd2594b6f895270b8016a583ddb8466b4533e3cc56c |
Hashes for gmx_clusterByFeatures-0.1.17-cp37-cp37m-macosx_10_12_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | d1bf6a83b820008e2a04cef92658efbf21705fc68cf8009cee35bdd69c6fb98d |
|
MD5 | dda90648878ddf78bcd7a625b7fd868b |
|
BLAKE2b-256 | 2504f4dabe4cd4d2e5f98506277dc32e60a8398b26800fc682feb6dbdcc3d0c1 |
Hashes for gmx_clusterByFeatures-0.1.17-cp36-cp36m-manylinux1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 153f866a718c4eaaa35ba312f2e77d1efcd3db5170302f8d3d1168fd86a25b78 |
|
MD5 | 8e7de0a668899a4abeadfd16b9ac9f69 |
|
BLAKE2b-256 | 6d1b7d938f8b10e9d9b7b65e95336de5472fa6cf041c6e37d5e4bb4ff74d4186 |
Hashes for gmx_clusterByFeatures-0.1.17-cp36-cp36m-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 415b717edbab52f05e5b71af1baeac6fe640ffbdd7eb165c8de4ecde21198dbb |
|
MD5 | 6db56fd0bfef93d38a75cac0aba1b54a |
|
BLAKE2b-256 | 317244bf1fe15b7cc42fbbf0fb332273b08d74e9fac5d62aaf7134317d3f48e9 |
Hashes for gmx_clusterByFeatures-0.1.17-cp36-cp36m-macosx_10_13_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 512a7eca9b1c76982123fb059b98452bcc4fc3dcdb52ae125fd0430763c296f3 |
|
MD5 | 574f137390b54172453de5541d91da51 |
|
BLAKE2b-256 | 9232970f30969d36ebde5b53b04d27fd09a36c9f033acd71f6e14cfc27c4a99b |
Hashes for gmx_clusterByFeatures-0.1.17-cp36-cp36m-macosx_10_12_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | dfc8dde34eac43b46b4db91db2b19dcd24febaea0914f86656159792c8c85187 |
|
MD5 | 6e4bbcf1c5562c53fb9e89087db58cda |
|
BLAKE2b-256 | bf26ba933763e4fae907889b3b44c59edcd7261f2dde6650d6f1b12734500c2d |
Hashes for gmx_clusterByFeatures-0.1.17-cp35-cp35m-manylinux1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | b61cbb614a0f60d49834ca99ec6e7de99c818067b733c23541ca0134fef909a2 |
|
MD5 | 13ea48c1834f540cf24cd11264fab4c1 |
|
BLAKE2b-256 | 7b741339476c9908a5165975391ba964962e4b23d6dcf293e71b1ee39f2b7f5e |
Hashes for gmx_clusterByFeatures-0.1.17-cp35-cp35m-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 9caebed989d91c073cfd5001466e984930b6a8846bc077b345c30c8992722420 |
|
MD5 | e3f7285d11d0ba43faee7e0b1a0d223f |
|
BLAKE2b-256 | f60ca6242fe429080a119d437ec96915fd078cacd23d0663702a71713a421683 |
Hashes for gmx_clusterByFeatures-0.1.17-cp35-cp35m-macosx_10_13_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 408effb3158ea7a0477c8bb0e53010180ddcc6e4690c199305d8232f5b9c465f |
|
MD5 | d56bb39f5633708492db8fb3520f9477 |
|
BLAKE2b-256 | f9e42562f5760f5d43693e558d5c7fa9a3810c0357850710ea1e65ec317195c9 |
Hashes for gmx_clusterByFeatures-0.1.17-cp35-cp35m-macosx_10_12_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | ec41d9ca8e0b273c66620ef0f8b7f376e31f3392a0c55832d21a5e62c47fa925 |
|
MD5 | 85470ce83a0c69d0b893e5b11f1de0ca |
|
BLAKE2b-256 | e578f534d7b99779ad2393b5f85857842fa091bdd3853fd711770d071aa19725 |