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