bond-angle-dihedral: Atomic Bond Lengths, Angles and Dihedrals

Description

Compute bond lengths, angles and dihedral from atomic coordinates.

Usage

bond(...)
# S3 method for coords
bond(x, sel1, sel2, ...)
# S3 method for pdb
bond(x, sel1, sel2, ...)
angle(...)
# S3 method for coords
angle(x, sel1, sel2, sel3, ...)
# S3 method for pdb
angle(x, sel1, sel2, sel3, ...)
dihedral(...)
# S3 method for coords
dihedral(x, sel1, sel2, sel3, sel4, ...)
# S3 method for pdb
dihedral(x, sel1, sel2, sel3, sel4, ...)
measure(...)
# S3 method for default
measure(id = rgl::rgl.ids(), verbose = TRUE, ...)
# S3 method for coords
measure(x, id = rgl::rgl.ids(), verbose = TRUE, ...)
# S3 method for pdb
measure(x, id = rgl::rgl.ids(), verbose = TRUE, ...)

Value

A numeric vector containing atomic bond lengths (in Angstrom), angles or dihedrals (in degrees)

Arguments

...: further arguments passed to or from other methods.
x: an R object containing atomic coordinates.
sel1, sel2, sel3, sel4: an integer or logical vector used to select atoms defining bonds, angles or dihedrals. See details.
id: vector of ID numbers of ‘rgl’ items, as returned by rgl.ids. The vertexes of these items are used to compute the bond lengths, angles or dihedrals.
verbose: a logical value specifying if the information have to be printed to the terminal.

Details

The number of selected atoms with sel1, sel2, sel3 and sel4 must be the same. sel1, sel2, sel3 and sel4 respectively select the first, second, third and fouth atoms defining bonds, angles or dihedrals.

measure activate an interactive mode to compute bond lengths, angles and dihedrals by selecting atoms by right-clicing on the current ‘rgl’ scene. To escape the active mode press the ESC key.

Examples

Run this code

Pen <- read.pdb(system.file("examples/Pentacene.pdb", package="Rpdb"))
visualize(Pen, mode = NULL)
text3d(coords(Pen), texts = Pen$atoms$eleid)
bond(Pen, 3:4, 1:2)
angle(Pen, 3:4, 1:2, 5:6)
dihedral(Pen, 3:4, 1:2, 5:6, 6:5)