angle.xyz. bio3d 2.3-0

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).

Description

A function for basic bond angle determination.

Value

Returns a numeric vector of angles.

References

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

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).

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])

[1] 106.7501


## 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]) )

   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  105.9   109.9   112.0   112.1   113.8   122.2 

#hist( angle.xyz(pdb$xyz[inds$xyz]), xlab="Angle" )

Author

Barry Grant

Calculate the Angle Between Three Atoms