DuIvyTools

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DuIvyTools (DIT) is a simple analysis and visualization tool for GROMACS result files (.xvg, .xpm, .ndx, .mdp).

This tool can perform data visualization and convertion, and may be able to cover daily simple tasks when analyzing results of molecular dynamics simulations by GROMACS.

Intro

The usage of DIT is similar to GMX, type dit and followed by commands and parameters, like:

dit xvg_show -f test.xvg
dit xpm_show -f test.xpm -ip

Type dit help for more messages.

visit https://github.com/CharlesHahn/DuIvy/tree/master/Articles/20220310-DIT for more introductions in Chinese.

Install

This tool is a python3 library which you can install it by pip.

pip install DuIvyTools

Commands

This tool contains quite a lot commands.

For XVG files:
    xvg_show, xvg_compare, xvg_ave, xvg_mvave, xvg2csv, xvg_rama
    xvg_show_distribution, xvg_show_stack, xvg_show_scatter
    xvg_energy_compute, xvg_combine, xvg_ave_bar, xvg_box
For XPM files:
    xpm_show, xpm2csv, xpm2gpl, xpm_combine
For NDX files:
    ndx_show, ndx_rm_dup, ndx_rm, ndx_preserve
    ndx_add, ndx_combine, ndx_rename
For MDP files:
    mdp_gen

Cite

still working

• python test
• one item in column_select in xvg_ave_bar
• make the calculation of moving averages faster
• the location of ticks in xpm figure procesion
• add function of prolig trjconv and center calculation
• build a GUI maybe