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
To load the plugin just type :
run molndx.py
The plugin gives access to two methods :
- ndx_save <output_file> : save all selections
- ndx_load <input_file> : load the selections
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/.
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.