angle.xyz {bio3d}

Calculate the Angle Between Three Atoms

Description

A function for basic bond angle determination.

Usage

angle.xyz(xyz, atm.inc = 3)

Arguments

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).

Value

Returns a numeric vector of angles.

Note

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).

Author(s)

Barry Grant

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.

See Also

torsion.pdb, torsion.xyz, read.pdb, read.dcd.

Examples

## 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" )