# Description
`gplt` is a very convenient python tool for plotting gromacs output file, such as `.xvg`, `.xpm` or convert `.dat` to `.xpm` for visualization. This tool is similar to [DuIvyTools](https://github.com/CharlesHahn/DuIvyTools), and these features could potentially be part of DuIvyTools. However, if time permits, I hope that it can become more powerful than DuIvyTools in the future.
# Cite
```{attention}
If `gplt` is utilized in your work, please **MUST** cite as follows in main text:
> Yujie Liu, gplt. Zenodo. [https://doi.org/10.5281/zenodo.13208831](https://doi.org/10.5281/zenodo.13208831)
```
# Installation
* Requirements
* `Python >= 3.8`
* `numpy`, `matplotlib`, `openpyxl`, etc.
* Install
The module is installed by `pip` method:
```
pip install numpy matplotlib colorama pandas openpyxl
pip install gplt -i https://test.pypi.org/simple
```
Please **ALWAYS** install Latest version.
Update this module if you have installed:
```
pip install gplt --upgrade -i https://test.pypi.org/simple
```
# Usage
## General options
Use `-h` to show available options:
```bash
gplt -h
```
## Plot xvg
```bash
gplt -f rdf.xvg
gplt -f rdf.xvg -ux angstrom
```
Of course support multi-figures:
```
gplt -f rdf1.xvg rdf2.xvg -legend lab1 lab2
```
## Plot xpm
### Free Energy Landscape
```bash
gplt -f gibbs.xpm
gplt -f gibbs.xpm -d3
```
### Protein Structure
```
gplt -f ss.xpm
```
### Hydrogen Bonds
If you provide three files: `hbond.ndx` and `hbmap.xpm` generated by `gmx hbond` and system `.gro` , the program can use `Donor-Acceptor` label (`resname+resid@atomname`) to replace yticks.
```{note}
The ndx file name must be placed before the gro/xpm file
```
```
gplt -f hbond.ndx 1EBZ.gro hbmap.xpm -yaxis 'Hbonds Pairs' -title ''
```
````{note}
You can change some plotting style by [Matplotlib style](https://matplotlib.org/stable/tutorials/introductory/customizing.html#the-matplotlibrc-file). Write a plain text file `style.mplstyle`:
```
axes.labelsize: 8
axes.linewidth: 1
xtick.labelsize: 8
ytick.labelsize: 8
ytick.left: True
ytick.direction: in
xtick.bottom: True
xtick.direction: in
lines.linewidth: 1.5
legend.fontsize: 8
legend.loc: best
font.family: Times New Roman
font.size: 8
```
Then add `-style style.mplstyle` option to gplt command line
````
## Plot dat
Some **plain text** with `.dat` file extension
1. `.dat` from `gmx densmap -od`
```
gplt -f densmap.dat && gplt -f densmap.xpm -aspect equal
```
This command will generate a `densmap.xpm` file, then you can plot it.
`-aspect equal`: Use same scaling from data to plot units for x and y
2. `dssp.dat` from `gmx dssp` (gmx >= 2023)
```
gplt -f dssp.dat && gplt -f dssp.xpm -xprec 0 -yprec 0 -o dssp.png && gplt -f scount.xvg -xprec 0 -yprec 0 -o scount.png
```
3. `.dat` with xyz columns
`gplt` also supports the file with three columns `xbin ybin zvalue`, such as:
```
1 14 0.0771830985915493
4 14 0.0771830985915493
7 14 0.0876056338028169
4 16 0.03492957746478873
6 13 0.011830985915492958
9 14 0.07887323943661971
16 14 0.08647887323943662
12 17 0.05718309859154929
13 14 0.07549295774647888
```
x and y of grid point must be integer.
```
gplt -f xyz.dat && gplt -f xyz.xpm -aspect equal
```
