Rpdb (version 2.3.4)

addLabels: Add Labels to the ‘rgl’ Scene

Description

Add Labels to the current ‘rgl’ scene.

Usage

addResLab(x, ...)
# S3 method for atoms
addResLab(x, at.centre = TRUE, col = "black", ...)
# S3 method for pdb
addResLab(x, at.centre = TRUE, col = "black", ...)
addEleLab(x, ...)
# S3 method for atoms
addEleLab(x, eleid = FALSE, col = "black", ...)
# S3 method for pdb
addEleLab(x, eleid = FALSE, col = "black", ...)
info3d(...)
# S3 method for atoms
info3d(x, id = rgl::rgl.ids(), col = "black", verbose = TRUE, adj = 0, ...)
# S3 method for pdb
info3d(x, id = rgl::rgl.ids(), col = "black", verbose = TRUE, adj = 0, ...)

Value

addResLab and addEleLab return (using invisible) a two-column data.frame containing the IDs and type indicators of the objects added to the scene.

Arguments

x

an R object containing atomic coordinates.

...

further arguments passed to or from other methods.

at.centre

a single element logical vector indicating if residue labels have to be added only at the position of the residue's centre-of-mass instead of at each atomic position.

col

the colors used to display the labels.

eleid

a single element logical vector indicating if the element ids have to be concatenated with the element names to prepare the labels.

id

vector of ID numbers of ‘rgl’ items, as returned by rgl.ids. The vertexes of these items are used to display the labels.

verbose

a logical value specifying if information have to be printed to the terminal.

adj

one value specifying the horizontal adjustment, or two, specifying horizontal and vertical adjustment respectively. See text3d

Details

addResLab add residue labels to the scene. If at.centre==TRUE only one label per residue is added at the centre of the residue. Otherwise, residue labels are added at each atomic positions. addEleLab add element labels to the scene at each atomic positions. info3d activate an interactive mode to add labels by selecting atoms by right-clicking on the current ‘rgl’ scene. To escape the interactive mode press the ESC key. The labels are as follow: "ResidResname:EleidElename"

See Also

pdb, visualize, measure

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
visualize(x, type = "l", mode = NULL)
addResLab(x)
x <- read.pdb(system.file("examples/Pentacene.pdb", package="Rpdb"))
visualize(x, type = "l", mode = NULL)
addEleLab(x)