Atomic Bond Lengths, Angles and Dihedrals
Compute bond lengths, angles and dihedral from atomic coordinates.
bond(...) ## S3 method for class 'coords' bond(x, sel1, sel2, ...) ## S3 method for class 'pdb' bond(x, sel1, sel2, ...) angle(...) ## S3 method for class 'coords' angle(x, sel1, sel2, sel3, ...) ## S3 method for class 'pdb' angle(x, sel1, sel2, sel3, ...) dihedral(...) ## S3 method for class 'coords' dihedral(x, sel1, sel2, sel3, sel4, ...) ## S3 method for class 'pdb' dihedral(x, sel1, sel2, sel3, sel4, ...) measure(...) ## Default S3 method: measure(id = rgl::rgl.ids(), verbose = TRUE, ...) ## S3 method for class 'coords' measure(x, id = rgl::rgl.ids(), verbose = TRUE, ...) ## S3 method for class 'pdb' measure(x, id = rgl::rgl.ids(), verbose = TRUE, ...)
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
|
verbose |
a logical value specifying if the information have to be printed to the terminal. |
... |
further arguments passed to or from other methods. |
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.
A numeric vector containing atomic bond lengths (in Angstrom), angles or dihedrals (in degrees)
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.