https://github.com/krassowski/vmd-agr-parser
Simple script for plotting .agr (Grace) files created with VMD (Visual Molecular Dynamics). Allows export to csv/svg/png.
https://github.com/krassowski/vmd-agr-parser
agr agr-files grace matplotlib plot visual-molecular-dynamics vmd
Last synced: over 1 year ago
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Simple script for plotting .agr (Grace) files created with VMD (Visual Molecular Dynamics). Allows export to csv/svg/png.
- Host: GitHub
- URL: https://github.com/krassowski/vmd-agr-parser
- Owner: krassowski
- License: mit
- Created: 2017-02-24T01:17:47.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2020-03-08T18:03:15.000Z (over 6 years ago)
- Last Synced: 2025-01-13T18:46:13.430Z (over 1 year ago)
- Topics: agr, agr-files, grace, matplotlib, plot, visual-molecular-dynamics, vmd
- Language: Python
- Size: 130 KB
- Stars: 2
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# VMD-generated .agr files parser
[](http://choosealicense.com/licenses/mit/)
[](https://zenodo.org/badge/latestdoi/82987720)
Simple script for plotting .agr (Grace) files created with VMD (Visual Molecular Dynamics). Allows export to csv/svg/png.
VMD allows generation of .agr files which are no longer properly interpreted by xmgrace software. This small tool allows to quickly plot data from an agr file (using matplotlib underneath) or to export the data to other formats.
### Show off
```bash
./plot.py example.agr -t 'Energy of Topoisomerase I' -x 'Time (ns)' -y 'Energy (kcal/mol)' -l 1 0.6 -s 0.005 1 -e png
```
### Installation
Python 3.5 is required. You can download the code from repository, for example with:
```bash
git clone https://github.com/krassowski/vmd-agr-parser
cd vmd-agr-parser
```
If you want to create plots matplotlib will be required:
```bash
pip3 install --user matplotlib
```
If it does not work, look at [How to get pip?](#how-to-get-pip) section.
### Example usages:
Plot from file:
```bash
./plot.py example.agr
```
Export to csv (no matplotlib required):
```bash
./plot.py example.agr --export csv --do_not_plot
```
Plot and export to svg:
```bash
./plot.py example.agr --export svg
```
Restrict to only one variable and change legend position:
```bash
./plot.py example.agr --restrict_to 'Total Energy' --legend_position 1 0.12
```
Set title and axes names:
```bash
./plot.py example.agr --title 'Energy of Topoisomerase I in complex with SRSF6' -x 'Simulation frame' -y 'Energy (kcal/mol)'
```
Rescale plot axes so units can be shown:
```bash
./plot.py example.agr --scale 0.005 1 -x 'Time (ns)'
```
Use custom labels in legend:
```bash
./plot.py example.agr --restrict_to 'Total Energy' 'Bond Energies' --labels 'Total energy (includes vdW)' 'Bond energies'
```
#### Help summary:
```bash
./plot.py example.agr -h
```
```bash
usage: plot.py [-h] [--do_not_plot] [-t TITLE] [-x AXIS_X] [-y AXIS_Y]
[-r RESTRICT_TO [RESTRICT_TO ...]] [-e {csv,svg,png,jpg}]
[-s SCALE SCALE] [-l LEGEND_POSITION LEGEND_POSITION]
[--labels LABELS [LABELS ...]]
input_file
```
### How to get pip?
If you do not have `pip3`, try `python3 -m pip` or just `pip`.
Some Linux distributions have package named like `python3-pip`.
If everything fails, you can install `pip` with:
```bash
wget https://bootstrap.pypa.io/get-pip.py && python3 get-pip.py --user
```