DuIvyTools
[](https://badge.fury.io/py/DuIvyTools)
[](https://duivytools.readthedocs.io/zh_CN/latest/?badge=latest)
[](https://github.com/CharlesHahn/DuIvyTools/compare/v0.5.0...master)
[](https://pypi.org/project/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:
```bash
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`.
```bash
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.
[](https://doi.org/10.5281/zenodo.6339993)
## 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
- [x] add -xp to plus or minus X or Y data, and in xpm_show cut to adjust xtick values
- [x] set the row of legends
- [x] to specify the figsize by commands
- [x] add xpm.comments
- [x] unequal number of x and y ticks in xpm like fel.xpm
- [x] to set the tickintervals
- [x] set the number of ticks
- [x] speed up the xpm transforming process
- [x] pmf xvg parsing problem
- [x] 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.
Raw data
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"description": "DuIvyTools\r\n\r\n[](https://badge.fury.io/py/DuIvyTools)\r\n\r\n\r\n[](https://duivytools.readthedocs.io/zh_CN/latest/?badge=latest)\r\n[](https://github.com/CharlesHahn/DuIvyTools/compare/v0.5.0...master)\r\n[](https://pypi.org/project/DuIvyTools)\r\n\r\n\r\n\r\n```\r\n ******* ** ********** **\r\n /**////** /** ** **/////**/// /**\r\n /** /** ** **/** ** **//** ** /** ****** ****** /** ******\r\n /** /**/** /**/**/** /** //*** /** **////** **////**/** **//// \r\n /** /**/** /**/**//** /** /** /**/** /**/** /**/**//***** \r\n /** ** /** /**/** //**** ** /**/** /**/** /**/** /////**\r\n /******* //******/** //** ** /**//****** //****** *** ****** \r\n /////// ////// // // // // ////// ////// /// //////\r\n```\r\n\r\nDuIvyTools (DIT) is a simple analysis and visualization tool for GROMACS result\r\nfiles, designed for fasten your analysis of molecular dynamics simulations. \r\n\r\n## Intro\r\n\r\nThe usage of DIT is similar to GMX, type `dit` and followed by commands and \r\nparameters, like:\r\n\r\n```bash\r\ndit xvg_show -f test.xvg\r\ndit xpm_show -f test.xpm\r\n```\r\n\r\nType `dit` for the commands supported. Type `dit <command> -h` for detailed help information of each command. \r\n\r\nThe tutorials (in Chinese) of DIT can be found at https://duivytools.readthedocs.io/\r\n\r\nIf you got any problem using DIT or suggestions, feel free to issue or contact me by \u98de\u4e66 (Lark): https://applink.feishu.cn/client/chat/chatter/add_by_link?link_token=a22q9297-2060-43d5-8b28-73637c82cad6\r\n\r\n\r\n\r\n## Install\r\n\r\nThis tool is a python3 library which you can install it by `pip`.\r\n\r\n```bash\r\npip install DuIvyTools\r\n```\r\n\r\n## Commands\r\n\r\nDuIvyTools provides about 30 commands for visualization and processing of GMX result files like .xvg or .xpm.\r\n\r\n```\r\nAll commands are shown below:\r\nXVG:\r\n xvg_show : easily show xvg file\r\n xvg_compare : visualize xvg data\r\n xvg_ave : calculate the averages of xvg data\r\n xvg_energy_compute : calculate eneries between protein and ligand\r\n xvg_combine : combine data of xvg files\r\n xvg_show_distribution : show distribution of xvg data\r\n xvg_show_scatter : show xvg data by scatter plot\r\n xvg_show_stack : show xvg data by stack area plot\r\n xvg_box_compare : compare xvg data by violin and scatter plots\r\n xvg_ave_bar : calculate and show the averages of parallelism\r\n xvg_rama : draw ramachandran plot from xvg data\r\nXPM:\r\n xpm_show : visualize xpm data\r\n xpm2csv : convert xpm data into csv file in form (x, y, z)\r\n xpm2dat : convert xpm data into dat file in form (N*N)\r\n xpm_diff : calculate the difference of xpms\r\n xpm_merge : merge two xpm by half and half\r\nOthers:\r\n mdp_gen : generate mdp file templates\r\n show_style : show figure control style files\r\n find_center : find geometric center of one group of atoms\r\n dccm_ascii : convert dccm from ascii data file to xpm\r\n dssp : generate xpm and xvg from ascii file of gmx2023\r\n ndx_add : new a index group to ndx file\r\n ndx_split : split one index group into several groups\r\n ndx_show : show the groupnames of index file\r\n\r\nYou can type `dit <command> -h` for detailed help messages about each command, like: `dit xvg_show -h`.\r\n\r\nAll possible parameters could be inspected by `dit -h` or `dit --help`.\r\n\r\n```\r\n\r\n## Cite\r\n\r\nIf you used DuIvyTools in your research, cite it by doi please.\r\n\r\n[](https://doi.org/10.5281/zenodo.6339993)\r\n\r\n\r\n\r\n## Todo\r\n\r\n- [ ] python unittest\r\n- [ ] better docs\r\n- [ ] easy API for draw lines with stddev (data, stddev two columns) in xvg file\r\n- [ ] add a command to do AND/OR set operation to hbond or sltbr existance map\r\n- [ ] add inter-classes to ease the use of plotting xpm or xvg data \r\n\r\n## what's new in v0.6.0\r\n\r\n- [x] add -xp to plus or minus X or Y data, and in xpm_show cut to adjust xtick values\r\n- [x] set the row of legends\r\n- [x] to specify the figsize by commands\r\n- [x] add xpm.comments\r\n- [x] unequal number of x and y ticks in xpm like fel.xpm\r\n- [x] to set the tickintervals\r\n- [x] set the number of ticks\r\n- [x] speed up the xpm transforming process\r\n- [x] pmf xvg parsing problem\r\n- [x] add original xvg data to smv plot, -smv reset\r\n\r\n#### new features\r\n\r\n0. add -xp to plus or minus data\r\n1. add --legend_ncol to set the number of columns of legends\r\n2. add figure.figsize in DIT.mplstyle to set the size of figure\r\n3. add --x_numticks to set the number of ticks\r\n4. update the xvg_show and xvg_compare to support data columns without titles\r\n5. add -smv origin to show original xvg data\r\n\r\n#### bug fixed\r\n\r\n0. cleaned the none acsii characters in dssp cmd\r\n1. fixed the bug of calculating the confidence interval\r\n2. fixed the bug in dssp cmd about b==0\r\n3. fixed the bug about z_precision in 3d plot\r\n4. fixed a bug in xvg_compare csv output with different length data\r\n5. fixed std ste bugs in xvg_ave and xvg_ave_bar\r\n\r\n\r\n## Others\r\n\r\nA lot of time and money have been spent for developing DuIvyTools and improve it. 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