swsoyee / r3dmol

🧬 An R package for visualizing molecular data in 3D

r3dmol

This is an R package that provides support for 3Dmol.js as a htmlwidgets.

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 from CRAN 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 at here.

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.