GitHub - swsoyee/r3dmol: 🧬 An R package for visualizing molecular data in 3D (original) (raw)

r3dmol

This is an R package that provides support for3Dmol.js as ahtmlwidgets.

Installation

Important: This package is still very early in its development stages. Please give the repository a star on Github if you find the package is useful. In addition, we need your feedback to improve the package, feel free to create an issue if you have any question or feature requirement. You are more than welcome to submit a PR to make any feasible improvements.

You could install the released version of r3dmol fromCRAN with:

install.packages("r3dmol")

And the development version from GitHub with:

install.packages("devtools")

devtools::install_github("swsoyee/r3dmol")

Example

library(r3dmol)

r3dmol( # Set up the initial viewer viewer_spec = m_viewer_spec( cartoonQuality = 10, lowerZoomLimit = 50, upperZoomLimit = 350 ) ) %>% m_add_model( # Add model to scene data = pdb_6zsl, format = "pdb" ) %>% m_zoom_to() %>% # Zoom to encompass the whole scene m_set_style( # Set style of structures style = m_style_cartoon( color = "#00cc96" ) ) %>% m_set_style( # Set style of specific selection sel = m_sel(ss = "s"), # (selecting by secondary) style = m_style_cartoon( color = "#636efa", arrows = TRUE ) ) %>% m_set_style( # Style the alpha helix sel = m_sel(ss = "h"), # (selecting by alpha helix) style = m_style_cartoon( color = "#ff7f0e" ) ) %>% m_rotate( # Rotate the scene by given angle on given axis angle = 90, axis = "y" ) %>% m_spin() # Animate the scene by spinning it

You can find more demo athere.

About 3Dmol.js

Nicholas Rego, David Koes, 3Dmol.js: molecular visualization with WebGL, Bioinformatics, Volume 31, Issue 8, 15 April 2015, Pages 1322–1324,

Code of Conduct

Please note that the r3dmol project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.