org.openscience.cdk.hash.stereo.Tetrahedral3DParity Maven / Gradle / Ivy
/*
* Copyright (c) 2013 John May
*
* Contact: [email protected]
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
* All we ask is that proper credit is given for our work, which includes
* - but is not limited to - adding the above copyright notice to the beginning
* of your source code files, and to any copyright notice that you may distribute
* with programs based on this work.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 U
*/
package org.openscience.cdk.hash.stereo;
import javax.vecmath.Point3d;
/**
* Geometric parity for 3D tetrahedral geometry. This class requires four 3D
* coordinates. The 3D coordinates correspond to the four ligands of a
* tetrahedral atom. If a tetrahedral atom has an implicit hydrogen (only 3
* ligands) the forth coordinate should be that of the atom at the centre
* {@cdk.cite Cieplak2001}.
*
* @author John May
* @cdk.module hash
* @see Cieplak,
* T and Wisniewski, J.L. 2001
* @cdk.githash
*/
final class Tetrahedral3DParity extends GeometricParity {
/* array of four 3D coordinates */
private final Point3d[] coordinates;
/**
* Create a new geometric parity for 3D tetrahedral geometry by specifying
* the coordinates.
*
* @param coordinates non-null, 4 3D coordinates
* @throws IllegalArgumentException if the number of coordinates was not 4
*/
public Tetrahedral3DParity(Point3d[] coordinates) {
if (coordinates.length != 4) throw new IllegalArgumentException("4 coordinates expected");
this.coordinates = coordinates;
}
/**
* @inheritDoc
*/
@Override
public int parity() {
double x1 = coordinates[0].x;
double x2 = coordinates[1].x;
double x3 = coordinates[2].x;
double x4 = coordinates[3].x;
double y1 = coordinates[0].y;
double y2 = coordinates[1].y;
double y3 = coordinates[2].y;
double y4 = coordinates[3].y;
double z1 = coordinates[0].z;
double z2 = coordinates[1].z;
double z3 = coordinates[2].z;
double z4 = coordinates[3].z;
double det = (z1 * det(x2, y2, x3, y3, x4, y4)) - (z2 * det(x1, y1, x3, y3, x4, y4))
+ (z3 * det(x1, y1, x2, y2, x4, y4)) - (z4 * det(x1, y1, x2, y2, x3, y3));
return (int) Math.signum(det);
}
// 3x3 determinant helper for a constant third column
private static double det(double xa, double ya, double xb, double yb, double xc, double yc) {
return (xa - xc) * (yb - yc) - (ya - yc) * (xb - xc);
}
}
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