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nglviewer

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

https://github.com/nvelden/nglviewer

Science Score: 13.0%

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    Scientific vocabulary similarity
    Low similarity (16.5%) to scientific vocabulary

Keywords

ngl nglviewer pdb protein-data-bank r shiny shiny-applications
Last synced: 6 months ago · JSON representation

Repository

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

Basic Info
Statistics
  • Stars: 53
  • Watchers: 2
  • Forks: 4
  • Open Issues: 2
  • Releases: 3
Topics
ngl nglviewer pdb protein-data-bank r shiny shiny-applications
Created about 5 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License

README.md

NGLVieweR Logo

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

R-CMD-check Lifecycle: experimental CRAN status Metacran downloads <!-- badges: end -->

Click here to view a Shiny application integrating most features of NGLVieweR.

Description

NGLvieweR provides an R interface to the NGL.js 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 with:

r install.packages("NGLVieweR")

And the development version from GitHub 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. 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") ```

Cartoon representation example in NGLVieweR

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 section for a complete overview.

Owner

  • Login: nvelden
  • Kind: user

GitHub Events

Total
  • Create event: 2
  • Release event: 1
  • Issues event: 6
  • Watch event: 7
  • Issue comment event: 7
  • Push event: 20
Last Year
  • Create event: 2
  • Release event: 1
  • Issues event: 6
  • Watch event: 7
  • Issue comment event: 7
  • Push event: 20

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 82
  • Total Committers: 2
  • Avg Commits per committer: 41.0
  • Development Distribution Score (DDS): 0.159
Past Year
  • Commits: 20
  • Committers: 1
  • Avg Commits per committer: 20.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
nvelden n****n@g****m 69
Niels Van der Velden N****n@m****m 13
Committer Domains (Top 20 + Academic)
molecularpartners.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 16
  • Total pull requests: 0
  • Average time to close issues: 6 months
  • Average time to close pull requests: N/A
  • Total issue authors: 14
  • Total pull request authors: 0
  • Average comments per issue: 3.19
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 0
  • Average time to close issues: about 2 months
  • Average time to close pull requests: N/A
  • Issue authors: 4
  • Pull request authors: 0
  • Average comments per issue: 3.75
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ChristianRohde (2)
  • cwbcm (2)
  • hkarakurt8742 (1)
  • broncio123 (1)
  • evelynsq (1)
  • maximinio (1)
  • enriquead1 (1)
  • slowkow (1)
  • helder-ribeiro (1)
  • Jerry-Dong8 (1)
  • juan2089 (1)
  • carlosg-czbiohub (1)
  • lee-t (1)
  • bioboot (1)
Pull Request Authors
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 369 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 2
  • Total maintainers: 1
cran.r-project.org: NGLVieweR

Interactive 3D Visualization of Molecular Structures

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 369 Last month
Rankings
Stargazers count: 8.3%
Forks count: 17.2%
Average: 24.2%
Dependent repos count: 24.4%
Dependent packages count: 28.0%
Downloads: 43.2%
Maintainers (1)
n.s.j.vandervelden@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • htmlwidgets * imports
  • magrittr * imports
  • shiny * imports
  • tools * imports
  • knitr * suggests
  • markdown * suggests
  • rmarkdown * suggests
  • webshot * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite