Calculate the Angle Between Three Atoms
A function for basic bond angle determination.
angle.xyz(xyz, atm.inc = 3)
xyz |
a numeric vector of Cartisean coordinates. |
atm.inc |
a numeric value indicating the number of atoms to increment by between successive angle evaluations (see below). |
Returns a numeric vector of angles.
With atm.inc=1, angles are calculated for each set of
three successive atoms contained in xyz (i.e. moving along one
atom, or three elements of xyz, between sucessive
evaluations). With atm.inc=3, angles are calculated for each set
of three successive non-overlapping atoms contained in xyz
(i.e. moving along three atoms, or nine elements of xyz, between
sucessive evaluations).
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
## Read a PDB file
pdb <- read.pdb( system.file("examples/1hel.pdb", package="bio3d") )
## Angle between N-CA-C atoms of residue four
inds <- atom.select(pdb, resno=4, elety=c("N","CA","C"))
angle.xyz(pdb$xyz[inds$xyz])
## Basic stats of all N-CA-C bound angles
inds <- atom.select(pdb, elety=c("N","CA","C"))
summary( angle.xyz(pdb$xyz[inds$xyz]) )
#hist( angle.xyz(pdb$xyz[inds$xyz]), xlab="Angle" )Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.