Class ZMatrixTools

  • public class ZMatrixTools
    extends Object
    A set of static utility classes for dealing with Z matrices.
    Source code:
    Belongs to CDK module:
    Created on:
    • Constructor Detail

      • ZMatrixTools

        public ZMatrixTools()
    • Method Detail

      • zmatrixToCartesian

        public static javax.vecmath.Point3d[] zmatrixToCartesian​(double[] distances,
                                                                 int[] first_atoms,
                                                                 double[] angles,
                                                                 int[] second_atoms,
                                                                 double[] dihedrals,
                                                                 int[] third_atoms)
        Takes the given Z Matrix coordinates and converts them to cartesian coordinates. The first Atom end up in the origin, the second on on the x axis, and the third one in the XY plane. The rest is added by applying the Zmatrix distances, angles and dihedrals. Angles are in degrees.
        distances - Array of distance variables of the Z matrix
        angles - Array of angle variables of the Z matrix
        dihedrals - Array of distance variables of the Z matrix
        first_atoms - Array of atom ids of the first invoked atom in distance, angle and dihedral
        second_atoms - Array of atom ids of the second invoked atom in angle and dihedral
        third_atoms - Array of atom ids of the third invoked atom in dihedral
        Dictionary pointer(s):
        zmatrixCoordinatesIntoCartesianCoordinates in the Blue Obelisk Chemoinformatics Dictionary [blue-obelisk:zmatrixCoordinatesIntoCartesianCoordinates]