Visualize a Molecular Structure
Use the rgl library to visualize in 3D a molecular structure.
visualize(...) ## S3 method for class 'coords' visualize(x, elename = NULL, cryst1 = NULL, conect = NULL, mode = NULL, type = "l", xyz = NULL, abc = NULL, pbc.box = NULL, lwd = 2, lwd.xyz = lwd, lwd.abc = lwd, lwd.pbc.box = lwd, cex.xyz = 2, cex.abc = 2, col = NULL, bg = "#FAFAD2", radii = "rvdw", add = FALSE, windowRect = c(0, 0, 800, 600), FOV = 0, userMatrix = diag(4), ...) ## S3 method for class 'data.frame' visualize(x, elename = NULL, cryst1 = NULL, conect = NULL, mode = NULL, type = "l", xyz = NULL, abc = NULL, pbc.box = NULL, lwd = 2, lwd.xyz = lwd, lwd.abc = lwd, lwd.pbc.box = lwd, cex.xyz = 2, cex.abc = 2, col = NULL, bg = "#FAFAD2", radii = "rvdw", add = FALSE, windowRect = c(0, 0, 800, 600), FOV = 0, userMatrix = diag(4), ...) ## S3 method for class 'matrix' visualize(x, elename = NULL, cryst1 = NULL, conect = NULL, mode = NULL, type = "l", xyz = NULL, abc = NULL, pbc.box = NULL, lwd = 2, lwd.xyz = lwd, lwd.abc = lwd, lwd.pbc.box = lwd, cex.xyz = 2, cex.abc = 2, col = NULL, bg = "#FAFAD2", radii = "rvdw", add = FALSE, windowRect = c(0, 0, 800, 600), FOV = 0, userMatrix = diag(4), ...) ## S3 method for class 'atoms' visualize(x, cryst1 = NULL, conect = NULL, mode = NULL, type = "l", xyz = NULL, abc = NULL, pbc.box = NULL, lwd = 2, lwd.xyz = lwd, lwd.abc = lwd, lwd.pbc.box = lwd, cex.xyz = 2, cex.abc = 2, col = NULL, bg = "#FAFAD2", radii = "rvdw", add = FALSE, windowRect = c(0, 0, 800, 600), FOV = 0, userMatrix = diag(4), ...) ## S3 method for class 'pdb' visualize(x, mode = NULL, type = "l", xyz = NULL, abc = NULL, pbc.box = NULL, lwd = 2, lwd.xyz = lwd, lwd.abc = lwd, lwd.pbc.box = lwd, cex.xyz = 2, cex.abc = 2, col = NULL, bg = "#FAFAD2", radii = "rvdw", add = FALSE, windowRect = c(0, 0, 800, 600), FOV = 0, userMatrix = diag(4), ...) ## S3 method for class 'character' visualize(x, mode = NULL, type = "l", xyz = NULL, abc = NULL, pbc.box = NULL, lwd = 2, lwd.xyz = lwd, lwd.abc = lwd, lwd.pbc.box = lwd, cex.xyz = 2, cex.abc = 2, col = NULL, bg = "#FAFAD2", radii = "rvdw", add = FALSE, windowRect = c(0, 0, 800, 600), FOV = 0, userMatrix = diag(4), ...)
x |
an object or the name of a PDB file containing the molecular structure to visualize. |
elename |
a character vector containing the atomic names used to chose atom colors and radii. |
cryst1 |
an object of class ‘cryst1’. See |
conect |
an object of class ‘conect’. See |
mode |
a single element character vector indicating the visualization mode (See details). |
type |
a character string indicating the visualization style (See details). |
xyz |
a logical value indicating whether the x, y and z axes have to be added to the scene. See details |
abc |
a logical value indicating whether the a, b and c axes have to be added to the scene. See details |
pbc.box |
a logical value indicating whether the pbc box has to be added to the scene. See details |
lwd |
a numeric value indication the line width used to plot the axes, the pbc box and atomic bonds when |
lwd.xyz |
a numeric value indicating the line width used to plot the x, y and z axes. |
lwd.abc |
a numeric value indicating the line width used to plot the a, b and c axes. |
lwd.pbc.box |
a numeric value indicating the line width used to plot the pbc box. |
cex.xyz |
a numeric value indicating the magnification used to plot the labels of the x, y and z axes. |
cex.abc |
a numeric value indicating the magnification used to plot the labels of the a, b and c axes. |
col |
a vector indicating the colors to use to plot each atom. |
bg |
the color of the background |
radii |
either a character string indicating the type of radii or a numeric vector specifying the radii of each atom to use to plot atoms as spheres (see details). |
add |
a logical value indicating whether the plot has be to added to a existing scene (see |
windowRect |
a vector of four integers indicating the left, top, right and bottom of the displayed window in pixels (see |
FOV |
the field of view. This controls the degree of parallax in the perspective view (see par3d). |
userMatrix |
a 4 by 4 matrix describing user actions to display the scene (see |
... |
further arguments passed to or from other methods. |
Three different visualization styles are allowed.
When type="p": Points are drawn at each atomic positions (very light visualization mode).
When type="l": Lines are drawn between bonded atoms. The connectivity of the system has to be specifyed.
When type="s": Spheres are drawn at each atomic positions (heavy visualization mode).
The radii of the spheres are given by radii.
When radii="rcov": Covalent radii, taken from the elements data set, are used.
When radii="rvdw": Van der Waals radii, taken from the elements data set, are used.
When radii is a numeric vector: The numeric values are used to assign to each atom a radius. If length(radii) != natom(pdb) radii is recycled.
When xyz, abc or pbc.box are NULL, the axis or pbc box are are added depending if a ‘cryst1’ object can be found.
Two different interactive visualization modes are avalable:
When mode="measure": bond lengths, angles and dihedrals can be measured by right-clicing on the atoms.
When mode="info": atomic labels can be added to the scene by right-clicing on the atoms. The labels are as follow: "ResidResname:EleidElename"
When mode=NULL the interactive mode is disabled. To escape the interactive mode press the ESC key.
Return (using invisible) a two-column data.frame containing the IDs and type indicators of the objects added to the scene.
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb",package="Rpdb"))
visualize(x, type = "l", mode = NULL)
visualize(x, type = "s", radii = "rcov", mode = NULL)
visualize(x, type = "s", radii = "rvdw", mode = NULL)
visualize(x, type = "p", mode = NULL)
visualize(subset(x, resid != 1), type = "l", mode = NULL)
visualize(subset(x, resid == 1), type = "s", add = TRUE, mode = NULL)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.