Class ZMatrixTools

java.lang.Object
org.openscience.cdk.geometry.ZMatrixTools

public class ZMatrixTools extends Object
A set of static utility classes for dealing with Z matrices.
Source code:
main
Belongs to CDK module:
io
Keywords:
Z-matrix
Created on:
2004-02-09
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Modifier and Type
    Method
    Description
    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.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
  • Constructor Details

    • ZMatrixTools

      public ZMatrixTools()
  • Method Details

    • 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.
      Parameters:
      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]