Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/swsoyee/r3dmol
🧬 An R package for visualizing molecular data in 3D
https://github.com/swsoyee/r3dmol
3d computational-biology computational-chemistry hacktoberfest htmlwidgets molecular-graphics molecular-modeling protein protein-structure r visualization
Last synced: 2 months ago
JSON representation
🧬 An R package for visualizing molecular data in 3D
- Host: GitHub
- URL: https://github.com/swsoyee/r3dmol
- Owner: swsoyee
- License: other
- Created: 2020-09-03T01:18:42.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2023-10-25T09:29:39.000Z (over 1 year ago)
- Last Synced: 2024-09-16T14:08:41.419Z (4 months ago)
- Topics: 3d, computational-biology, computational-chemistry, hacktoberfest, htmlwidgets, molecular-graphics, molecular-modeling, protein, protein-structure, r, visualization
- Language: JavaScript
- Homepage: https://swsoyee.github.io/r3dmol/
- Size: 31.4 MB
- Stars: 88
- Watchers: 5
- Forks: 4
- Open Issues: 7
-
Metadata Files:
- Readme: README.Rmd
- Funding: .github/FUNDING.yml
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
Awesome Lists containing this project
- awesome-shiny-extensions - r3dmol - Visualizing molecular data in 3D, based on 3Dmol.js. (Visualization / Chemical Data)
- jimsghstars - swsoyee/r3dmol - 🧬 An R package for visualizing molecular data in 3D (JavaScript)
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# r3dmol
[](https://CRAN.R-project.org/package=r3dmol)
[](https://codecov.io/gh/swsoyee/r3dmol?branch=master)
[](https://github.com/swsoyee/r3dmol/actions/workflows/R-CMD-check.yaml)
[](https://lifecycle.r-lib.org/articles/stages.html#experimental)
[](https://cran.r-project.org/package=r3dmol)
This is an R package that provides support for [`3Dmol.js`](https://3dmol.csb.pitt.edu/index.html) as a [`htmlwidgets`](https://www.htmlwidgets.org/).
## 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](https://CRAN.R-project.org) with:
``` r
install.packages("r3dmol")
```
And the development version from [GitHub](https://github.com/) with:
``` r
# install.packages("devtools")
devtools::install_github("swsoyee/r3dmol")
```
## Example
```{r, demo, eval=FALSE}
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](https://swsoyee.github.io/r3dmol/articles/r3dmol.html).
## About `3Dmol.js`
> Nicholas Rego, David Koes, [3Dmol.js: molecular visualization with WebGL](https://academic.oup.com/bioinformatics/article/31/8/1322/213186), 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](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.