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R Shiny wrapper for Mol* (/'molstar/) - A visualization toolkit of large-scale molecular data

Based onMol* (/'molstar/) and powered byshiny.react

We created a R Shiny wrapper based onshiny.react andmolstar-react(node.js library) that gives all the powerful tools of Mol* open-source toolkit for visualization and analysis of large-scale molecular data.

This package exports three new components that can be used in a Shiny application.

• Molstar creates a Molstar visualization of a protein using an URL to a valid filetype supported by Molstar or a "Protein Data Bank" id(pdbId). See more below for available databases to find a validpdbId.
• AlphaFoldMolstar similar to the Molstar component, but uses the UniProt id in the AlphaFold database to display the protein.
• AlphaFoldDetails creates a component that retrieves details of an AlphaFold protein id(title, download links and a Predict Aligned Error image)

A validpdbId can be found in public databases such as:

• EMBL-EBI database
• RSCB.org

TheuniProtId can be found in any of the AlphaFold databases:

• AlphaFold.com

To install the package, run:

remotes::install_github("Appsilon/shiny.molstar")

Take a look at basicexample app to start working with shiny.molstar.

To learn about the Mol* language, follow theViewer documentation.

A good way to learn more is to look at the examples. Once you install the library, you can run them withshiny.molstar::runExample function.

shiny.molstar::runExample("FullPage")shiny.molstar::runExample("Minimal")shiny.molstar::runExample("AlphaFold")shiny.molstar::runExample("AlphaFoldDetails")

Creating a full page viewer on a sample molecule(example also available atinst/examples/FullPage.R)

library(shiny)library(shiny.molstar)shinyApp(  ui = tagList(    tags$style(HTML("html, body { margin: 0; }")),    Molstar(      pdbId = "1LOL",      useInterface = TRUE,      showControls = TRUE,      showAxis = TRUE    )  ),  server = function(input, output) {  })

Running an example from the package(located atinst/examples/AlphaFoldDetails.R).

You can click on the button on the bottom of the example to get the minimal code to reproduce the same Shiny application(unstyled and without the footer).

shiny.molstar::runExample("AlphaFoldDetails")

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