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-0.1.16-cp37-cp37m-manylinux1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 1a9d89ed6deb750e4b812a39ae9b2a5954199b9b01fc2af7dd78f25a04d5de78 |
|
MD5 | 3e46f5564729d880c1015d6a6bf9704c |
|
BLAKE2b-256 | 3bd21d22b6940c7243e441d04120dfc713c078ef523fcdfcaae19256ce627fe8 |
Hashes for gmx_clusterByFeatures-0.1.16-cp37-cp37m-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 28a6115b8498579f9a3e76a9e0223c5497f163178a706c65b2e8b7e0c51485b0 |
|
MD5 | d79eda31e3414f758f458035d2bd9f3a |
|
BLAKE2b-256 | 5c6a9e22e4a5bfa1d39d1b033b383cbd5d96cbf8e58912c20715ab1f0ece8cf5 |
Hashes for gmx_clusterByFeatures-0.1.16-cp37-cp37m-macosx_10_13_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 3b696870e7fe1ca08757a895c3e28402e18cda2b1698940adfb5ca27178dd180 |
|
MD5 | 6ae869487ab10f828d0c088cd2045228 |
|
BLAKE2b-256 | 6ed9eb1bf5b366b50498fd2d1f17afb6ffc580b7e833040257bf6fe4b8452d2a |
Hashes for gmx_clusterByFeatures-0.1.16-cp37-cp37m-macosx_10_12_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | ccc5604ddf452ddd3d693671c4a6723977bb962ce859cea7751f77738d3c7def |
|
MD5 | f13c2a0dbc8908f74c110ae180e04389 |
|
BLAKE2b-256 | aa6780f95b122176383d17345a5f0ceaedb8d1585d60d7509cdd0180277e766f |
Hashes for gmx_clusterByFeatures-0.1.16-cp36-cp36m-manylinux1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | c34ce2f263857c314bd2a3758112334a69153403907a8a8cf277291d3cd9b9f3 |
|
MD5 | 79df67f0215527d5445362b49869ea2d |
|
BLAKE2b-256 | f25b8e996da6022fd82540bcd8cb777aff12ab55ae1f7cc320a27ea159d15e74 |
Hashes for gmx_clusterByFeatures-0.1.16-cp36-cp36m-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 68d60177a135e068d1f36c53397398706f20299735053cc96002acd6b910fdeb |
|
MD5 | 178a13feb8716d827a8ec3e588a2bf9e |
|
BLAKE2b-256 | 03bf22c64b7e8d7c0ee9d6f97dbbcbb2b4193ab6c6bb2d857c535d71f559b804 |
Hashes for gmx_clusterByFeatures-0.1.16-cp36-cp36m-macosx_10_13_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 2b4e14d7b6a45900726567012a35ae3ea39fd5d223a20b97489cdb6d4b0b468e |
|
MD5 | a177feba19cbc7ade4514ee2dcdf2b98 |
|
BLAKE2b-256 | cfbe6713f0aacd5bf45ef50218df9efc84659c5707dfd1a565f927973da77609 |
Hashes for gmx_clusterByFeatures-0.1.16-cp36-cp36m-macosx_10_12_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 1b5564b7b4b7a0d7f2b793fbcb81d1d7e3ae0dad0482b43451d6bbe99cc48228 |
|
MD5 | 2da6ac5a25bf2e2a77cb90ef772f0164 |
|
BLAKE2b-256 | 7fb833f25b8650bf7a834f47157df1a8083e97541f4fbb6bd7d881d02d1c665f |
Hashes for gmx_clusterByFeatures-0.1.16-cp35-cp35m-manylinux1_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | df82c9f0b66bf0bef0a49b82016444f7d0ee5e29a073ae571e3a76e74d87816d |
|
MD5 | ec16d5992f8daf79b8821a2dcedd8bd5 |
|
BLAKE2b-256 | 6e1a0cbaff6d7ce6e0db1b642871bae5433572cc3bab1c0dc9550d11612a9c42 |
Hashes for gmx_clusterByFeatures-0.1.16-cp35-cp35m-macosx_10_14_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 82de3b89e718d03e49b923354146f9fe211194a493a83a434047baf033211348 |
|
MD5 | da09343bf9008eb2682c38136d3ff1d5 |
|
BLAKE2b-256 | abc45060c2309784de5285c1662df96c5af56995e315a45430989d74025d0751 |
Hashes for gmx_clusterByFeatures-0.1.16-cp35-cp35m-macosx_10_13_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 5acc32ee31e7a7303412333051eb6d19b5efe93beaa58b3c842bcb1fd8f67dc0 |
|
MD5 | db9a3cd7914f53e4a4bc41c0310d8b5a |
|
BLAKE2b-256 | 547e630f7c535221bffd65bf4b81df39a8e6e67d0351e9fe61ac2a297d96872c |
Hashes for gmx_clusterByFeatures-0.1.16-cp35-cp35m-macosx_10_12_x86_64.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 31c4d46dfaeb47a366bcf8532a2987857e4d6a5e83068e3a2bfa69419ac65b6a |
|
MD5 | 9fdc75ee4506507b77e0539c0a0585c4 |
|
BLAKE2b-256 | cbffb0a064921e24c4ce27feb7ae3f07437a4d7c180d25625cfebee5a7b60221 |