inst/doc/NGLVieweR.R

In NGLVieweR: Interactive 3D Visualization of Molecular Structures

## ----setup, echo = FALSE, message = FALSE-------------------------------------
knitr::opts_chunk$set(tidy = FALSE, comment = "#>")

## ----eval=FALSE---------------------------------------------------------------
#  install.packages("remotes")
#  remotes::install_github("nvelden/NGLVieweR")

## ----eval=FALSE---------------------------------------------------------------
#  #Load local pdb file
#  NGLVieweR("C:/7CID.pdb") %>%
#  addRepresentation("cartoon")
#  #Load protein by PDB code
#  NGLVieweR("7CID") %>%
#  addRepresentation("cartoon")

## ----Loading, echo=FALSE, screenshot.force=FALSE------------------------------
library(NGLVieweR)
#Load local pdb file
NGLVieweR("7CID") %>%
addRepresentation("cartoon")

## ----eval=FALSE---------------------------------------------------------------
#  library(NGLVieweR)
#  library(shiny)
#  NGLVieweR_example("basic")

## ----fileformat, screenshot.force=FALSE---------------------------------------

#Note that line formatting needs to be exact when reading from console!
benz <- "
702
  -OEChem-02271511112D
  9  8  0     0  0  0  0  0  0999 V2000
    0.5369    0.9749    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4030    0.4749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2690    0.9749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8015    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0044    0.0000    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9590    1.5118    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8059    1.2849    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5790    0.4380    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.6649    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  9  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  3  7  1  0  0  0  0
  3  8  1  0  0  0  0
M  END
> <ID>
00001
> <DESCRIPTION>
Solvent produced by yeast-based fermentation of sugars.
$$$$
"
NGLVieweR(benz, format="sdf") %>%
  addRepresentation("ball+stick")

## ----eval=FALSE---------------------------------------------------------------
#  NGLVieweR("7CID") %>%
#  addRepresentation("cartoon") %>%
#  addRepresentation("ball+stick")

## ----representations, screenshot.force=FALSE----------------------------------
NGLVieweR("7CID") %>%
  addRepresentation("cartoon",
    param = list(colorScheme = "residueindex")
  ) %>%
  addRepresentation("ball+stick",
    param = list(
      sele = "233-248",
      colorValue = "red",
      colorScheme = "element"
    )
  ) %>%
  addRepresentation("surface",
    param = list(
      colorValue = "white",
      opacity = 0.1
    )
  )

## ----stage, screenshot.force=FALSE--------------------------------------------
NGLVieweR("7CID") %>%
  stageParameters(backgroundColor = "white", zoomSpeed = 1) %>%
  addRepresentation("cartoon",
    param = list(name = "cartoon", colorScheme = "residueindex")
  ) %>%
  setSpin()

## ----labels, screenshot.force=FALSE-------------------------------------------
NGLVieweR("7CID") %>%
  addRepresentation("cartoon") %>%
  addRepresentation("ball+stick", param = list(
    colorScheme = "element",
    colorValue = "yellow",
    sele = "20"
  )) %>%
  addRepresentation("label",
    param = list(
      sele = "20",
      labelType = "format",
      labelFormat = "[%(resname)s]%(resno)s", # or enter custom text
      labelGrouping = "residue", # or "atom" (eg. sele = "20:A.CB")
      color = "white",
      fontFamiliy = "sans-serif",
      xOffset = 1,
      yOffset = 0,
      zOffset = 0,
      fixedSize = TRUE,
      radiusType = 1,
      radiusSize = 1.5, # Label size
      showBackground = FALSE
      # backgroundColor="black",
      # backgroundOpacity=0.5
    )
  )

## ----zoom, screenshot.force=FALSE---------------------------------------------
NGLVieweR("7CID") %>%
  addRepresentation("cartoon") %>%
  addRepresentation("ball+stick",
    param = list(
      colorScheme = "element",
      colorValue = "yellow",
      sele = "20"
    )
  ) %>%
  addRepresentation("label",
    param = list(
      sele = "20",
      labelType = "format",
      labelFormat = "[%(resname)s]%(resno)s", # or enter custom text
      labelGrouping = "residue", # or "atom" (eg. sele = "20:A.CB")
      color = "white",
      xOffset = 1,
      fixedSize = TRUE,
      radiusType = 1,
      radiusSize = 1.5
    ) # Label size
  ) %>%
  zoomMove(
    center = "20",
    zoom = "20",
    duration = 0, # animation time in ms
    z_offSet = -20
  )

## ----contact, screenshot.force=FALSE------------------------------------------
NGLVieweR("3RY2") %>%
  addRepresentation("cartoon") %>%
  addRepresentation("ball+stick",
    param = list(
      name = "biotin",
      colorvalue = "grey",
      colorScheme = "element",
      sele = "5001"
    )
  ) %>%
  addRepresentation("ball+stick",
    param = list(
      name = "interacting",
      colorScheme = "element",
      colorValue = "green",
      sele = "23 or 27 or 43 or 45 or 128"
    )
  ) %>%
  zoomMove(
    center = "27:B",
    zoom = "27:B",
    z_offSet = -20
  ) %>%
  addRepresentation("contact",
    param = list(
      name = "contact",
      sele = "5001 or 23 or 27 or 43 or 45 or 128",
      filterSele = list("23 or 27 or 45 or 128", "5001"),
      labelVisible = TRUE,
      labelFixedSize = FALSE,
      labelUnit = "angstrom", # "", "angstrom", "nm"
      labelSize = 2
      # hydrogenBond=TRUE,
      # weakHydrogenBond=FALSE,
      # waterHydrogenBond=FALSE,
      # backboneHydrogenBond=TRUE,
      # hydrophobic=FALSE,
      # halogenBond=TRUE,
      # ionicInteraction=TRUE,
      # metalCoordination=TRUE,
      # cationPi=TRUE,
      # piStacking=TRUE,
      # maxHydrophobicDist= 4.0,
      # maxHbondDist= 3.5,
      # maxHbondSulfurDist= 4.1,
      # maxHbondAccAngle= 45,
      # maxHbondDonAngle= 45,
      # maxHbondAccPlaneAngle= 90,
      # maxHbondDonPlaneAngle= 30,
      # maxPiStackingDist= 5.5,
      # maxPiStackingOffset= 2.0,
      # maxPiStackingAngle= 30,
      # maxCationPiDist= 6.0,
      # maxCationPiOffset= 2.0,
      # maxIonicDist= 5.0,
      # maxHalogenBondDist= 3.5,
      # maxHalogenBondAngle= 30,
      # maxMetalDist= 3.0,
      # refineSaltBridges= TRUE,
      # masterModelIndex= -1,
      # lineOfSightDistFactor= 1
    )
  )

## ----eval=FALSE---------------------------------------------------------------
#  library(shiny)
#  library(NGLVieweR)
#  ui <- fluidPage(NGLVieweROutput("structure"))
#  server <- function(input, output) {
#    output$structure <- renderNGLVieweR({
#      NGLVieweR("7CID") %>%
#        addRepresentation("cartoon",
#          param = list(
#            name = "cartoon", color =
#              "residueindex"
#          )
#        ) %>%
#        addRepresentation("ball+stick",
#          param = list(
#            name = "cartoon",
#            sele = "1-20",
#            colorScheme = "element"
#          )
#        ) %>%
#        stageParameters(backgroundColor = "black") %>%
#        setQuality("high") %>%
#        setFocus(0) %>%
#        setSpin(TRUE)
#    })
#  }
#  shinyApp(ui, server)

## ---- echo=FALSE--------------------------------------------------------------
knitr::include_graphics("../man/figures/basic_shiny.PNG")

## ----eval=FALSE---------------------------------------------------------------
#  library(shiny)
#  library(NGLVieweR)
#  ui <- fluidPage(
#    titlePanel("Viewer with API inputs"),
#    sidebarLayout(
#      sidebarPanel(
#        textInput("selection", "Selection", "1-20"),
#        selectInput("type", "Type", c("ball+stick", "cartoon", "backbone")),
#        selectInput("color", "Color", c("orange", "grey", "white")),
#        actionButton("add", "Add"),
#        actionButton("remove", "Remove")
#      ),
#      mainPanel(
#        NGLVieweROutput("structure")
#      )
#    )
#  )
#  server <- function(input, output) {
#    output$structure <- renderNGLVieweR({
#      NGLVieweR("7CID") %>%
#        addRepresentation("cartoon",
#          param = list(name = "cartoon", colorScheme = "residueindex")
#        ) %>%
#        stageParameters(backgroundColor = input$backgroundColor) %>%
#        setQuality("high") %>%
#        setFocus(0) %>%
#        setSpin(TRUE)
#    })
#    observeEvent(input$add, {
#      NGLVieweR_proxy("structure") %>%
#        addSelection(isolate(input$type),
#          param =
#            list(
#              name = "sel1",
#              sele = isolate(input$selection),
#              colorValue = isolate(input$color)
#            )
#        )
#    })
#    observeEvent(input$remove, {
#      NGLVieweR_proxy("structure") %>%
#        removeSelection("sel1")
#    })
#  }
#  shinyApp(ui, server)

## ---- echo=FALSE--------------------------------------------------------------
knitr::include_graphics("../man/figures/API_shiny.PNG")