NGLVieweR (original) (raw)
Installation
NGLVieweR is available through GitHub
Loading PDB files
You can load a PDB (or and other supported format) directly or use a PDB code of a structure on RCSB.org. The below minimal example loads the PDB file and displays the structure in a “cartoon” representation.
Note: Use mouse for selection (left-click), rotate/move (left/right-click hold) and zooming (scroll wheel).
You can view a “basic” NGLVieweR Shiny application by running the below code. Use “API” for an example using API calls or any of the function names (e.g “addSelection”“) for function specific examples.
Loading other structural files
This package has been developed and tested using PDB files but supports loading of any of the following structural files: .mmcif, .cif, .mcif, .ent, .pqr, .gro, .sdf, .sd, .mol2 and .mmtf.
By default NGLVieweR guesses the file format from the file extension. Use the format parameter in case no or the wrong file extension is provided.
#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. <span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow></mrow><annotation encoding="application/x-tex"></annotation></semantics></math></span><span class="katex-html" aria-hidden="true"></span></span>$$
"
NGLVieweR(benz, format="sdf") %>%
addRepresentation("ball+stick")Representations
You can load the structure as a “cartoon”, “ball+stick”, “line”, “surface”, “ribbon”, or any other representation listed in the NGL.js manual under “StructureRepresentation”. Multiple representations of the same structure can be overlaid by chaining the [addSelection()](../reference/addSelection.html)function. Also see the “structure” tab in the demoapp for a list of possible representations.
You can alter the appearance of select residues using theparam argument. For a full list of options see the NGL.js“RepresentationParameters” and the “Selection language” section.
Structures
Using [addStructure()](../reference/addStructure.html), you can load multiple structures into the same stage. In this example, the first structure is represented in blue, while the second representation of the structure is represented in orange. Transformations such as [setPosition()](../reference/setPosition.html),[setRotation()](../reference/setRotation.html), and [setScale()](../reference/setScale.html) apply to the second (most recently added) structure.
Superpose
Structures can be superposed onto each other using the[setSuperpose()](../reference/setSuperpose.html) function. It aligns the structures by specifying a reference structure (defaulting to the first one loaded) and defining the selections within each structure to be used for alignment.
Stage
You can alter the background color or set the zoom or rotation speed using the [stageParameters()](../reference/stageParameters.html) function. For a full list of options, see the “StageParameters” method in the official NGL.js manual. In additions there are specific functions to set:
- Animation:
[setRock()](../reference/setRock.html)or[setSpin()](../reference/setSpin.html) - Focus:
[setFocus()](../reference/setFocus.html) - Quality:
[setQuality()](../reference/setQuality.html)
Note: Changes in background color are not visible in the RStudio viewer.
Labels
Labels can be added by setting the [addRepresentation()](../reference/addRepresentation.html)type parameter to “label”. For a full list of of options, see the LabelRepresentationParameters section in the NGL.js manual. Also see the “label” tab in the demoapp for possible label settings.
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
)
)Transformation functions
The package provides a set of transformation functions that allow for adjusting the scale, rotation, and position of the visualized structures.
Zoom
You can zoom into specific residues using the ZoomMove()function.
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
)Contacts between residues can be added by setting the[addRepresentation()](../reference/addRepresentation.html) type parameter to “contact”. Using thesele parameter contacts for specific residues can be selected. The filterSele parameter can be used to only show contacts between two selections. In the below example Biotin and residues 23, 27, 43, 45, and 128 are selectedsele="5001 or 23 or 27 or 43 or 45 or 128" and contacts are only shown between the residues and biotinfilterSele=list("23 or 27 or 43 or 45 or 128", "5001"). This prevents the display of contacts between residues or water molecules.
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
)
)Shiny
The [NGLVieweROutput()](../reference/NGLVieweR-shiny.html) and [renderNGLVieweR()](../reference/NGLVieweR-shiny.html)functions enable you to visualize PDB files within Shiny applications. See the NGLVieweR_example("basic") and “API” for live examples.
A basic NGLVieweR Shiny app
API
In Shiny apps, you can manipulate the NGLVieweRwidget after creation using specific “API” calls. You can for instance add or remove representations by referring to their name using the[addSelection()](../reference/addSelection.html) or [removeSelection()](../reference/removeSelection.html)functions.
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$remove, {
NGLVieweR_proxy("structure") %>%
removeSelection("sel1")
})
}
shinyApp(ui, server)
NGLVieweR API in Shiny
In a Shiny application one can retrieve information from the widget as inputs based on the NGLVieweR outputID. Suppose theoutputID is “structure”, then the following information can be retrieved:
- input$structure_selection - Get details on the clicked residue.
- input$structure_sequence - will return the sequence of the PDB file as a character vector.
- input$structure_resno - will return all the sequence numbers as a numeric vector.
- input$structure_chainname - will return the chainname of each amino acid as a character vector,
- input$structure_rendering - will return
TRUEif the widget is loading orFALSEwhen completed. - input$structure_PDB - will return the PDB file as a text string.
- input$structure_selAround - will return a list of atoms surrounding a clicked residue.
In the below example a label, all contacts and residues in proximity of the clicked residue are displayed.
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)
Click interaction example in NGLVieweR