- Notifications
You must be signed in to change notification settings - Fork0
Read, Parse and Visualize XVG/XPM Files
License
RightSZ/xvm
Folders and files
| Name | Name | Last commit message | Last commit date | |
|---|---|---|---|---|
Repository files navigation
xvm is an R package that provides tools for reading, parsing, and visualizing output files in xvg and xpm formats, which are typically generated by simulation software such as GROMACS.xvm is designed to streamline the post-processing and analysis of molecular dynamics (MD) simulation data. Withxvm, users can easily import trajectory data (e.g., RMSD, energy, temperature) and generate publication-quality plots. Targeted at researchers in computational chemistry, biophysics, and structural biology, xvm bridges the gap between raw MD outputs and actionable insights, enabling the efficient exploration of molecular stability and conformational changes.
Find out more athttps://github.com/RightSZ/xvm
install fromCRAN as follow:
# Install from CRANinstall.packages("xvm")
install the latest version fromGitHub as follow:
# Install the development version from GitHubif(!require(devtools)) install.packages("devtools")devtools::install_github("RightSZ/xvm")
# Load the xvm packagelibrary(xvm)# This example file is an xvg file containing RMSD data generated by GROMACSrmsd_file_path<- system.file("extdata/rmsd.xvg",package="xvm")# Read the xvg file using read_xvg() functionrmsd_data<- read_xvg(rmsd_file_path)# The imported xvg file is stored as a list, with the list name corresponding to the file name.names(rmsd_data)# Plot the xvg data using plot_xvg() functionplot_xvg(rmsd_data)
# This example file is an xpm file containing (free energy landscape, FEL) data generated by GROMACSgibbs_file_path<- system.file("extdata/gibbs.xpm",package="xvm")# Read the xpm file using read_xpm() functiongibbs_data<- read_xpm(gibbs_file_path)# The imported xpm file is stored as a list, with the list name corresponding to the file name.names(gibbs_data)# Plot the xpm data using plot_xpm() functionplot_xpm(gibbs_data)
About
Read, Parse and Visualize XVG/XPM Files
Resources
License
Uh oh!
There was an error while loading.Please reload this page.