A simple tool for GROMACS results analysis and visualization
Project description
DuIvyTools
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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 <comman> -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
- unequal number of x and y ticks in xpm like fel.xpm
Others
A lot of time and money have been spent for developing DuIvyTools and improve it. If possible, REWARD to help me improve it.
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