https://github.com/jbarnoud/molndx

Pymol plugin to handle gromacs ndx files
https://github.com/jbarnoud/molndx

Last synced: 16 days ago
JSON representation

Pymol plugin to handle gromacs ndx files

• Host: GitHub
• URL: https://github.com/jbarnoud/molndx
• Owner: jbarnoud
• License: gpl-3.0
• Created: 2012-03-10T07:50:53.000Z (almost 13 years ago)
• Default Branch: master
• Last Pushed: 2012-08-26T08:45:22.000Z (over 12 years ago)
• Last Synced: 2024-12-24T04:41:55.501Z (18 days ago)
• Language: Python
• Homepage:
• Size: 328 KB
• Stars: 3
• Watchers: 2
• Forks: 1
• Open Issues: 1
• Metadata Files:
  • Readme: README.rst

Awesome Lists containing this project

README

        
======

Molndx

======

Molndx is a Pymol plugin to handle GROMACS index files (.ndx). It allows to save selections and to load them in Pymol.

A GROMACS index file is a succession of atom groups. Each group is described by

a header defining the group name and a list of atoms. Lines can be commented

using the ; character. Note that the atoms are numbered starting at 1 in the

index file.

An index file look like :

::

    [ group_name ]

    1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22

    23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41

    42 43 44 45

    ; This is a commented line

    [ group_name_2 ]

    1 2 3 ; The end of a line can be commented

    4 5 6

Usage

=====

To load the plugin just type :

    run molndx.py

The plugin gives access to two methods :

- ndx_save  : save all selections

- ndx_load  : load the selections

Unit tests

==========

A test suite is provided with molndx. To run it you can just execute the test_molndx.py script. However using the nosetest program is more convenient. Run

    nosetest -v test_moldnx

in the molndx directory.

The nose module can be found at https://github.com/nose-devs/nose and its documentation at http://nose.readthedocs.org/en/latest/.

Licence

=======

This program is free software: you can redistribute it and/or modify  

it under the terms of the GNU General Public License as published by   

the Free Software Foundation, either version 3 of the License, or      

(at your option) any later version.                                    

                                                                      

This program is distributed in the hope that it will be useful,        

but WITHOUT ANY WARRANTY; without even the implied warranty of         

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the          

GNU General Public License for more details.                           

                                                                          

A copy of the GNU General Public License is available at

http://www.gnu.org/licenses/gpl-3.0.html.