/rkekule

Primary LanguageCSS

rkekule

rkekule is an R wrapper of the JavaScript library Kekule.js

Installation

To install the package from GitHub, you can use package remotes

# install.packages("remotes")
remotes::install_github("openanalytics/rkekule", subdir = "rkekule")

To get a package overview, run

library(rkekule)
?rkekule

chemViewer widget

Supported formats:

  • MDL MOL / moltable
  • CML
# example with CML

library(rkekule)

cml <- paste0(
    '<cml xmlns="http://www.xml-cml.org/schema">',
    '<molecule id="m1"><atomArray>',
      '<atom id="a2" elementType="C" x2="7.493264658965051" y2="35.58088907877604"/>',
      '<atom id="a3" elementType="O" x2="8.186084981992602" y2="35.18088907877604"/>',
      '<atom id="a1" elementType="C" x2="6.800444335937501" y2="35.18088907877604"/>',
    '</atomArray><bondArray>',
      '<bond id="b2" order="S" atomRefs2="a2 a3"/>',
      '<bond id="b1" order="S" atomRefs2="a2 a1"/>',
    '</bondArray></molecule></cml>')

widget <- chemViewer(cml, width = 400, height = 200, chemicalFormat = "cml", renderType = "2D")

widget

Shiny integration

To render chemical structures in a Shiny app, you can use

  • renderRkekule in your server code
  • rkekuleOutput in your ui code

See examples/exampleShiny.R for an example.

DT integration

See examples/exampleDT.R for an example.

Roadmap

  • simplify DT integration boilerplate
  • optional support for other formats such as SMILES and InCHI via ChemmineOB
  • RMarkdown support
  • plotly hover support
  • support for other Kekule.js widgets:
    • Kekule.ChemWidget.PeriodicTable
    • Kekule.Editor.Composer