//  $Id: AtomStats.java,v 1.1 2006/05/20 17:02:03 Sasha Buzko Exp $
//
//  Copyright (c) 2000-2002  San Diego Supercomputer Center (SDSC),
//  a facility operated jointly by the University of California,
//  San Diego (UCSD) and General Atomics, San Diego, California, USA.
//
//  Users and possessors of this source code are hereby granted a
//  nonexclusive, royalty-free copyright and design patent license to
//  use this code in individual software.  License is not granted for
//  commercial resale, in whole or in part, without prior written
//  permission from SDSC.  This source is provided "AS IS" without express
//  or implied warranty of any kind.
//
//  For further information, please see:  http://mbt.sdsc.edu
//
//  History:
//  $Log: AtomStats.java,v $
//  Revision 1.1  2006/05/20 17:02:03  Sasha Buzko
//  Updated version
//
//  Revision 1.1  2006/04/30 20:13:59  Sasha Buzko
//  New version of the app
//
//  Revision 1.1  2006/04/15 19:42:27  Sasha Buzko
//  Initial commit
//
//  Revision 1.1  2005/11/13 04:35:04  Administrator
//  *** empty log message ***
//
//  Revision 1.1  2003/04/23 22:52:06  moreland
//  Created utility methods for computing coordinate bounds and averages.
//
//  Revision 1.1.1.1  2002/07/16 18:00:21  moreland
//  Initial revision.
//


package edu.sdsc.mbt.util;

import edu.sdsc.mbt.*;


/**
 *  The AtomStats class provides a number of static methods for computing
 *  useful information about a collection of Atom objects.
 *  <P>
 *  @see edu.sdsc.mbt.Atom
 *  <P>
 *  @author John L. Moreland
 */
public class AtomStats
{
	/**
	 * Return the coordinate bounds for given a Structure.
	 * <P>
	 * double[0][0] = min x<BR>
	 * double[0][1] = min y<BR>
	 * double[0][2] = min z<BR>
	 * double[1][0] = max x<BR>
	 * double[1][1] = max y<BR>
	 * double[1][2] = max z<BR>
	 * <P>
	 */
	public static double[][] getAtomCoordinateBounds( Structure structure )
	{
		if ( structure == null )
			throw new IllegalArgumentException( "null structure" );

		int atomCount = structure.getStructureComponentCount(
			StructureComponentRegistry.TYPE_ATOM );

		double coordinateBounds[][] = new double[2][3];
		if ( atomCount <= 0 ) return coordinateBounds;

		Atom atom = (Atom) structure.getStructureComponentByIndex(
			StructureComponentRegistry.TYPE_ATOM, 0 );

		coordinateBounds[0][0] = atom.coordinate[0];  // min x
		coordinateBounds[0][1] = atom.coordinate[1];  // min y
		coordinateBounds[0][2] = atom.coordinate[2];  // min z
		coordinateBounds[1][0] = atom.coordinate[0];  // max x
		coordinateBounds[1][1] = atom.coordinate[1];  // max y
		coordinateBounds[1][2] = atom.coordinate[2];  // max z

		for ( int i=1; i<atomCount; i++ )
		{
			atom = (Atom) structure.getStructureComponentByIndex(
				StructureComponentRegistry.TYPE_ATOM, i );

			if ( atom.coordinate[0] < coordinateBounds[0][0] )
				coordinateBounds[0][0] = atom.coordinate[0];  // min x

			if ( atom.coordinate[1] < coordinateBounds[0][1] )
				coordinateBounds[0][1] = atom.coordinate[1];  // min y

			if ( atom.coordinate[2] < coordinateBounds[0][2] )
				coordinateBounds[0][2] = atom.coordinate[2];  // min z

			if ( atom.coordinate[0] > coordinateBounds[1][0] )
				coordinateBounds[1][0] = atom.coordinate[0];  // max x

			if ( atom.coordinate[1] > coordinateBounds[1][1] )
				coordinateBounds[1][1] = atom.coordinate[1];  // max y

			if ( atom.coordinate[2] > coordinateBounds[1][2] )
				coordinateBounds[1][2] = atom.coordinate[2];  // max z
		}

		return coordinateBounds;
	}

	/**
	 * Return the coordinate average for a Structure's atom coordinates.
	 * <P>
	 * double[0] = x<BR>
	 * double[1] = y<BR>
	 * double[2] = z<BR>
	 * <P>
	 */
	public static double[] getAtomCoordinateAverage( Structure structure )
		throws IllegalArgumentException
	{
		if ( structure == null )
			throw new IllegalArgumentException( "null structure" );

		int atomCount = structure.getStructureComponentCount(
			StructureComponentRegistry.TYPE_ATOM );

		double coordinateAverage[] = new double[3];
		if ( atomCount <= 0 ) return coordinateAverage;

		Atom atom = (Atom) structure.getStructureComponentByIndex(
				StructureComponentRegistry.TYPE_ATOM, 0 );

		for ( int i=1; i<atomCount; i++ )
		{
			atom = (Atom) structure.getStructureComponentByIndex(
				StructureComponentRegistry.TYPE_ATOM, i );

			coordinateAverage[0] += atom.coordinate[0];
			coordinateAverage[1] += atom.coordinate[1];
			coordinateAverage[2] += atom.coordinate[2];
		}

		coordinateAverage[0] /= (double) atomCount;
		coordinateAverage[1] /= (double) atomCount;
		coordinateAverage[2] /= (double) atomCount;

		return coordinateAverage;
	}
}