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")

## ----structures, 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
    )
  )

## ----representations, screenshot.force=FALSE----------------------------------
NGLVieweR("1CRN") %>%
  addRepresentation("cartoon", param = list(color = "blue")) %>%
  addStructure("1CRN") %>%
  addRepresentation("cartoon", param = list(color = "orange")) %>%
  setPosition(x = 20, y = 0, z = 0) %>%
  setRotation(x = 2, y = 0, z = 0, degrees = FALSE) %>% 
  setScale(0.5)

## ----superpose, screenshot.force=FALSE----------------------------------------
NGLVieweR("1GZM") %>%
   addRepresentation("cartoon", param = list(color = "blue")) %>%
   addStructure("1U19") %>%
   addRepresentation("cartoon", param = list(color = "orange")) %>%
   setSuperpose(
     reference = 1, 
     sele_reference = ":A", 
     sele_target = ":A", 
     superpose = TRUE
     )

## ----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, fig.cap="A basic NGLVieweR Shiny app"------------------------
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$add, {
#     if (isolate(input$type) == "cartoon") {
#       # For cartoon, use the color parameter
#       NGLVieweR_proxy("structure") %>%
#         addSelection(isolate(input$type),
#                      param = list(
#                        name = "sel1",
#                        sele = isolate(input$selection),
#                        color = isolate(input$color)
#                      )
#         )
#     } else {
#       # For other types, use colorValue
#       NGLVieweR_proxy("structure") %>%
#         addSelection(isolate(input$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, fig.cap="NGLVieweR API in Shiny"-----------------------------
knitr::include_graphics("../man/figures/API_shiny.PNG")

## ----eval=FALSE---------------------------------------------------------------
# library(shiny)
# library(NGLVieweR)
# library(stringr)
# 
# ui <- fluidPage(
#   titlePanel("Viewer with click interaction"),
#   sidebarLayout(
#     sidebarPanel(verbatimTextOutput('selection')),
#     mainPanel(NGLVieweROutput("structure"))
#   )
# )
# 
# server <- function(input, output) {
#   output$structure <- renderNGLVieweR({
#     NGLVieweR("3RY2") %>%
#       addRepresentation("cartoon") %>%
#       addRepresentation(
#         "ball+stick",
#         param = list(
#           name = "biotin",
#           colorvalue = "grey",
#           colorScheme = "element",
#           sele = "5001"
#         )
#       ) %>%
#       zoomMove(center = "27:B",
#                zoom = "27:B",
#                z_offSet = -20) %>%
#       selectionParameters(3, "residue") #"atom"
#   })
# 
#   #Save click selections
#   sele <- reactiveValues()
# 
#   observe({
#     sele$aa <-
#       str_extract(input$structure_selection, "(?<=[\\[])(.*?)(?=\\])")
#     sele$aa_bond <-
#       str_extract(input$structure_selection, "(?<=[\\]])(.*?)(?=[:space:])")
#     sele$resiChain <-
#       str_extract(input$structure_selection, "(?<=[]])(.*?)(?=[.])")
#     sele$resi <-
#       str_extract(input$structure_selection, "(?<=[]])(.*?)(?=[:])")
#     sele$fileName <-
#       str_extract(input$structure_selection, "(?<=[(])(.*?)(?=[.])")
#   })
# 
#   output$selection = renderPrint({
#     #Full selection
#     print(input$structure_selection)
#     #Amino Acid
#     print(sele$aa)
#     #Bond
#     print(sele$aa_bond)
#     #Residue number + ChainNAme
#     print(sele$resiChain)
#     #Residue number
#     print(sele$resi)
#     #PDB name
#     print(sele$fileName)
#     #SelAround
#     print(input$structure_selAround)
#   })
# 
#   observeEvent(input$structure_selAround, {
#     NGLVieweR_proxy("structure") %>% removeSelection("selAround")
# 
#     NGLVieweR_proxy("structure") %>%
#       addSelection(
#         "ball+stick",
#         param =
#           list(
#             name = "selAround",
#             sele = input$structure_selAround,
#             colorValue = "grey"
#           )
#       )
# 
#   })
# 
#   observeEvent(sele$resiChain, {
#     #Remove any selections
#     NGLVieweR_proxy("structure") %>% removeSelection("label")
#     NGLVieweR_proxy("structure") %>% removeSelection("contact")
# 
#     #Add label and contacts
#     NGLVieweR_proxy("structure") %>%
# 
#       addSelection(
#         "label",
#         param = list(
#           name = "label",
#           sele = sele$resiChain,
#           labelType = "format",
#           labelFormat = "[%(resname)s]%(resno)s",
#           # or enter custom text
#           labelGrouping = "residue",
#           # or "atom" (eg. sele = "20:A.CB")
#           color = "white",
#           xOffset = 1,
#           fixedSize = TRUE,
#           radiusType = 1,
#           radiusSize = 1.5
#         )
#       ) %>%
#       addSelection(
#         "contact",
#         param = list(
#           name = "contact",
#           sele = "*",
#           #Select all residues
#           filterSele =
#             list(sele$resiChain, # Show bonds between selected residue
#                  "*"),
#           # and all other residues
#           labelVisible = TRUE,
#           labelFixedSize = FALSE,
#           labelUnit = "angstrom",
#           # "", "angstrom", "nm"
#           labelSize = 2
#         )
#       )
#   })
# 
# }
# shinyApp(ui, server)

## ----echo=FALSE, fig.cap="Click interaction example in NGLVieweR"-------------
knitr::include_graphics("../man/figures/click_interaction.PNG")