DuIvyTools 0.6.0

A simple tool for GROMACS results analysis and visualization

DuIvyTools

  *******           **                  **********               **
 /**////**         /**          **   **/////**///               /**
 /**    /** **   **/** **    **//** **     /**  ******   ****** /**  ******
 /**    /**/**  /**/**/**   /** //***      /** **////** **////**/** **//// 
 /**    /**/**  /**/**//** /**   /**       /**/**   /**/**   /**/**//***** 
 /**    ** /**  /**/** //****    **        /**/**   /**/**   /**/** /////**
 /*******  //******/**  //**    **         /**//****** //****** *** ****** 
 ///////    ////// //    //    //          //  //////   ////// /// //////

DuIvyTools (DIT) is a simple analysis and visualization tool for GROMACS result files, designed for fasten your analysis of molecular dynamics simulations.

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

Type dit for the commands supported. Type dit <command> -h for detailed help information of each command.

The tutorials (in Chinese) of DIT can be found at https://duivytools.readthedocs.io/

If you got any problem using DIT or suggestions, feel free to issue or contact me by 飞书 (Lark): https://applink.feishu.cn/client/chat/chatter/add_by_link?link_token=a22q9297-2060-43d5-8b28-73637c82cad6

Install

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

pip install DuIvyTools

Commands

DuIvyTools provides about 30 commands for visualization and processing of GMX result files like .xvg or .xpm.

All commands are shown below:
XVG:
    xvg_show              : easily show xvg file
    xvg_compare           : visualize xvg data
    xvg_ave               : calculate the averages of xvg data
    xvg_energy_compute    : calculate eneries between protein and ligand
    xvg_combine           : combine data of xvg files
    xvg_show_distribution : show distribution of xvg data
    xvg_show_scatter      : show xvg data by scatter plot
    xvg_show_stack        : show xvg data by stack area plot
    xvg_box_compare       : compare xvg data by violin and scatter plots
    xvg_ave_bar           : calculate and show the averages of parallelism
    xvg_rama              : draw ramachandran plot from xvg data
XPM:
    xpm_show              : visualize xpm data
    xpm2csv               : convert xpm data into csv file in form (x, y, z)
    xpm2dat               : convert xpm data into dat file in form (N*N)
    xpm_diff              : calculate the difference of xpms
    xpm_merge             : merge two xpm by half and half
Others:
    mdp_gen               : generate mdp file templates
    show_style            : show figure control style files
    find_center           : find geometric center of one group of atoms
    dccm_ascii            : convert dccm from ascii data file to xpm
    dssp                  : generate xpm and xvg from ascii file of gmx2023
    ndx_add               : new a index group to ndx file
    ndx_split             : split one index group into several groups
    ndx_show              : show the groupnames of index file

You can type `dit <command> -h` for detailed help messages about each command, like: `dit xvg_show -h`.

All possible parameters could be inspected by `dit -h` or `dit --help`.

Cite

If you used DuIvyTools in your research, cite it by doi please.

Todo

• python unittest
• better docs
• easy API for draw lines with stddev (data, stddev two columns) in xvg file
• add a command to do AND/OR set operation to hbond or sltbr existance map
• add inter-classes to ease the use of plotting xpm or xvg data

what's new in v0.6.0

• add -xp to plus or minus X or Y data, and in xpm_show cut to adjust xtick values
• set the row of legends
• to specify the figsize by commands
• add xpm.comments
• unequal number of x and y ticks in xpm like fel.xpm
• to set the tickintervals
• set the number of ticks
• speed up the xpm transforming process
• pmf xvg parsing problem
• add original xvg data to smv plot, -smv reset

new features

0. add -xp to plus or minus data
1. add --legend_ncol to set the number of columns of legends
2. add figure.figsize in DIT.mplstyle to set the size of figure
3. add --x_numticks to set the number of ticks
4. update the xvg_show and xvg_compare to support data columns without titles
5. add -smv origin to show original xvg data

bug fixed

0. cleaned the none acsii characters in dssp cmd
1. fixed the bug of calculating the confidence interval
2. fixed the bug in dssp cmd about b==0
3. fixed the bug about z_precision in 3d plot
4. fixed a bug in xvg_compare csv output with different length data
5. fixed std ste bugs in xvg_ave and xvg_ave_bar

Others

A lot of time and money have been spent for developing DuIvyTools and improve it. If possible, REWARD to help me improve it.