Defined from the Cartesian coordinates of four successive atoms (A-B-C-D) the torsion or dihedral angle is calculated about an axis defined by the middle pair of atoms (B-C).
torsion.xyz(xyz, atm.inc =4)
Arguments
xyz: a numeric vector of Cartisean coordinates.
atm.inc: a numeric value indicating the number of atoms to increment by between successive torsion evaluations (see below).
Details
The conformation of a polypeptide or nucleotide chain can be usefully described in terms of angles of internal rotation around its constituent bonds.
If a system of four atoms A-B-C-D is projected onto a plane normal to bond B-C, the angle between the projection of A-B and the projection of C-D is described as the torsion angle of A and D about bond B-C.
By convention angles are measured in the range -180 to +180, rather than from 0 to 360, with positive values defined to be in the clockwise direction.
With atm.inc=1, torsion angles are calculated for each set of four successive atoms contained in xyz (i.e. moving along one atom, or three elements of xyz, between sucessive evaluations). With atm.inc=4, torsion angles are calculated for each set of four successive non-overlapping atoms contained in xyz (i.e. moving along four atoms, or twelve elements of xyz, between sucessive evaluations).
Returns
A numeric vector of torsion angles.
References
Grant, B.J. et al. (2006) Bioinformatics 22 , 2695--2696.