org.openscience.cdk.geometry

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:

master

Belongs to CDK module:

io

Keywords:

Z-matrix

Created on:

2004-02-09

Constructor Summary

Constructors

Constructor and Description
ZMatrixTools()

Method Summary

Modifier and Type	Method and 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 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.

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]