Molstar shiny element
Molstar.Rd
Shiny.react component to show Molstar molecular visualizations.
It can use a "Protein Data Bank" id, an URL to a valid .pdb
/.cif
file
in the internet.
Usage
Molstar(
class = NULL,
url = NULL,
pdbId = NULL,
dimensions = NULL,
useInterface = FALSE,
showControls = FALSE,
showAxes = FALSE,
...
)
Arguments
- class
character string for the class name to apply to the outer parent element.
- url
Load a structure by passing in the URL of the file. This file type needs to be supported by Molstar (
.pdb
,.cif
).- pdbId
Load an official PDB structure by supplying its 4 letter ID. See the details for example databses.
- dimensions
an integer vector indicating the dimensions of the visualization in pixels (
c(width, height)
). By default the molstar plugin will take up the full screen.- useInterface
a logical value indicating if the full Molstar interface will be used around the core canvas.
- showControls
a logical value indicating if the controls will be shown around the sides of the interface. It needs the
useInterface
parameter to be alsoTRUE
. Only recommended for large sizes.- showAxes
a logical value indicating if axes will appear in the bottom left corner.
- ...
Component other props and children.
Details
A pdbId
can be found in public databases such as:
https://www.ebi.ac.uk/pdbe/entry/search/index/
https://www.rcsb.org/
The file
parameter is supported by the react library, but it should not
be used in Shiny.
Examples
Molstar(pdbId = "1LOL", dimensions = c(300, 300))
#> <div class="react-container" data-react-id="vhoipeyoohljamkajowk">
#> <script class="react-data" type="application/json">{"type":"element","module":"molstar-react","name":"Molstar","props":{"type":"raw","value":{"className":null,"url":null,"pdbId":"1LOL","dimensions":[300,300],"useInterface":false,"showControls":false,"showAxes":false}}}</script>
#> <script>jsmodule['@/shiny.react'].findAndRenderReactData('vhoipeyoohljamkajowk')</script>
#> </div>
Molstar(pdbId = "1y98", dimensions = c(300, 300))
#> <div class="react-container" data-react-id="npghmxkfrbzdnvsgovam">
#> <script class="react-data" type="application/json">{"type":"element","module":"molstar-react","name":"Molstar","props":{"type":"raw","value":{"className":null,"url":null,"pdbId":"1y98","dimensions":[300,300],"useInterface":false,"showControls":false,"showAxes":false}}}</script>
#> <script>jsmodule['@/shiny.react'].findAndRenderReactData('npghmxkfrbzdnvsgovam')</script>
#> </div>
url <- "https://alphafold.ebi.ac.uk/files/AF-A0A1U8FD60-F1-model_v4.pdb"
Molstar(url = url, dimensions = c(300, 300))
#> <div class="react-container" data-react-id="uvkfkrnrnvswaxznjupq">
#> <script class="react-data" type="application/json">{"type":"element","module":"molstar-react","name":"Molstar","props":{"type":"raw","value":{"className":null,"url":"https://alphafold.ebi.ac.uk/files/AF-A0A1U8FD60-F1-model_v4.pdb","pdbId":null,"dimensions":[300,300],"useInterface":false,"showControls":false,"showAxes":false}}}</script>
#> <script>jsmodule['@/shiny.react'].findAndRenderReactData('uvkfkrnrnvswaxznjupq')</script>
#> </div>
url2 <- "https://alphafold.ebi.ac.uk/files/AF-A0A1U8FD60-F1-model_v4.cif"
Molstar(url = url2, dimensions = c(300, 300))
#> <div class="react-container" data-react-id="wogxwgkudferwyoprgbx">
#> <script class="react-data" type="application/json">{"type":"element","module":"molstar-react","name":"Molstar","props":{"type":"raw","value":{"className":null,"url":"https://alphafold.ebi.ac.uk/files/AF-A0A1U8FD60-F1-model_v4.cif","pdbId":null,"dimensions":[300,300],"useInterface":false,"showControls":false,"showAxes":false}}}</script>
#> <script>jsmodule['@/shiny.react'].findAndRenderReactData('wogxwgkudferwyoprgbx')</script>
#> </div>