ZMatrixToCartesian Class Reference

Provides a method that transforms Z-matrix coordinates into Cartesian system. More...

List of all members.

Static Public Member Functions

static final Vector3D transform (Vector3D v1, Vector3D v2, Vector3D v3, double r, double planar, double torsion)
 Transforms a point specified by Z-matrix coordinates into Cartesian coordinates.


Detailed Description

Provides a method that transforms Z-matrix coordinates into Cartesian system.

Z matrix hold internal coordinates for all atoms in a system: bond length, bond angle, and dihedral angle. The information content is identical: Z-matrices can be converted to Cartesian coordinates and back.

This class implements Natural Extension Reference Frame (NERF) algorithm: Parsons, J., Holmes, J. B., Rojas, J. M., Tsai, J., Strauss, C. E., "Practical conversion from torsion space to cartesian space for in silico protein synthesis." J Comput Chem 26 (2005), 1063-1068.


Member Function Documentation

static final Vector3D transform ( Vector3D  v1,
Vector3D  v2,
Vector3D  v3,
double  r,
double  planar,
double  torsion 
) [static]

Transforms a point specified by Z-matrix coordinates into Cartesian coordinates.

To convert a point, three previous points must be given in order to define torsion angle. Thus the three first arguments of this method: v1, v2 and v3 defines a reference frame. The remaining three arguments are the Z-matrix coordinates to be transformed.

As a result a point (say, p) in 3D Cartesian space is returned. The planar angle formed by v2, v3 and p is equal to planar value given to this method; dihedral angle formed by v1, v2, v3 and p is equal to torsion value given to this method

Parameters:
v1 - the first reference point
v2 - the second reference point
v3 - the third reference point
r - bond length (first of three Z-matrix coordinates)
planar - bond angle (second Z-coordinate)
torsion - torsion angle (third Z-coordinate)
Returns:
a new vector holding resulting position

References Vector3D.getX(), Vector3D.getY(), Vector3D.getZ(), Vector3D.x, Vector3D.y, and Vector3D.z.


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