https://github.com/nvelden/nglviewer

Visualize and interact with Protein Data Bank (pdb) and structural files in R and Shiny
https://github.com/nvelden/nglviewer

ngl nglviewer pdb protein-data-bank r shiny shiny-applications

Last synced: 28 days ago
JSON representation

Visualize and interact with Protein Data Bank (pdb) and structural files in R and Shiny

• Host: GitHub
• URL: https://github.com/nvelden/nglviewer
• Owner: nvelden
• License: other
• Created: 2021-02-20T09:13:16.000Z (over 3 years ago)
• Default Branch: master
• Last Pushed: 2023-07-02T13:58:42.000Z (over 1 year ago)
• Last Synced: 2024-10-10T18:40:14.769Z (28 days ago)
• Topics: ngl, nglviewer, pdb, protein-data-bank, r, shiny, shiny-applications
• Language: R
• Homepage: https://nvelden.github.io/NGLVieweR/
• Size: 24.2 MB
• Stars: 45
• Watchers: 2
• Forks: 4
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Awesome Lists containing this project

README

        


  

  


NGLVieweR - Visualize and interact with Protein Data Bank (PDB) and structural files in R and Shiny


[![R-CMD-check](https://github.com/nvelden/NGLVieweR/workflows/R-CMD-check/badge.svg)](https://github.com/nvelden/NGLVieweR/actions) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental) 

[![CRAN status](https://www.r-pkg.org/badges/version/NGLVieweR)](https://CRAN.R-project.org/package=NGLVieweR)

[![Metacran downloads](https://cranlogs.r-pkg.org/badges/grand-total/NGLVieweR)](https://cran.r-project.org/package=NGLVieweR)

### [Click here](https://niels-van-der-velden.shinyapps.io/shinyNGLVieweR/) to view a Shiny application integrating most features of **NGLVieweR**.

## Description

**NGLvieweR** provides an R interface to the [NGL.js](http://nglviewer.org/ngl/api/) JavaScript library. It can be used to visualize and interact with protein data bank (PDB) and structural files in R and Shiny applications. It includes a set of API functions to manipulate the viewer after creation and makes it possible to retrieve data from the visualization into R.

## Installation

You can install the released version of **NGLVieweR** from [CRAN](https://CRAN.R-project.org) with:

``` r

install.packages("NGLVieweR")

```

And the development version from [GitHub](https://github.com/) with:

``` {.r}

install.packages("remotes")

remotes::install_github("nvelden/NGLVieweR")

```

## Basics

You can load a PDB (or any other supported structural file) directly or use a PDB code of a structure on [RCSB.org](https://www.rcsb.org/). The below minimal example loads the PDB file and displays the structure in a "cartoon" representation.

``` {.r}

#Load local pdb file

NGLVieweR("C:/7CID.pdb") %>%

addRepresentation("cartoon")

#Load protein by PDB code

NGLVieweR("7CID") %>%

addRepresentation("cartoon")

```



## Functionality

There are functions provided to:

-   Overlay different representation styles

-   Alter the stage parameters (e.g. background, zoom- and rotation speed)

-   Zoom to specific selections

-   Add labels

-   Add contacts between residues

-   Auto rotate/rock

In Shiny apps, you can manipulate the **NGLVieweR** widget after creation using specific "API"" calls. Users can for instance add/remove representations, make snapshots, add labels or highlight specific regions. See the [Get started](https://nvelden.github.io/NGLVieweR/articles/NGLVieweR.html) section for a complete overview.