//  $Id: BondSearch.java,v 1.6 2004/04/08 23:55:06 moreland Exp $
//
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//  Molecular Biology Toolkit (MBT)
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//  FAX: (858) 534-7345, E-MAIL:invent@ucsd.edu.
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//  DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING
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//  History:
//  $Log: BondSearch.java,v $
//  Revision 1.6  2004/04/08 23:55:06  moreland
//  Updated copyright to new UCSD wording.
//
//  Revision 1.5  2004/01/30 02:07:35  moreland
//  Updated copyright and class block comments.
//
//  Revision 1.4  2003/09/17 16:23:58  moreland
//  Added print of bondIndex value.
//
//  Revision 1.3  2003/04/24 00:28:28  moreland
//  Modified to use the new Bond StructureComponent.
//
//  Revision 1.2  2003/02/21 23:03:09  moreland
//  Changed example URL load -u command line option to point to beta repository:
//  ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF.gz/all/5ebx.cif.gz
//
//  Revision 1.1  2003/02/21 22:17:32  moreland
//  Added example program that demonstrates how to obtain derived bonds.
//
//  Revision 1.1  2003/01/27 22:32:51  moreland
//  Added statistics generation example.
//
//  Revision 1.0  2003/01/27 20:45:18  moreland
//  First revision.
//


// Core
import java.io.File;
import java.net.*;
import java.util.*;

// MBT
import edu.sdsc.mbt.*;
import edu.sdsc.mbt.io.*;
import edu.sdsc.mbt.util.*;


/**
 *  An example program which demonsrates how to obtain derived bond pairs.
 *  <P>
 *  @author	John L. Moreland
 */
public class BondSearch
{
	/**
	 *  This the main application entry point for the example program.
	 */
	public static void main( String args[] )
	{
		//
		// Load a sample data set.
		//

		Structure structure = null;
		for ( int i=0; i<args.length; i++ )
		{
			if ( args[i].equals( "-f" ) )
			{
				structure = StructureFactory.load( new File( args[++i] ) );
			}
			else if ( args[i].equals( "-u" ) )
			{
				try
				{
					structure = StructureFactory.load( new URL( args[++i] ) );
				}
				catch ( MalformedURLException e )
				{
					System.err.println( e );
				}
			}
			else if ( args[i].equals( "-p" ) )
			{
				structure = StructureFactory.load( args[++i] );
			}
			else
			{
				System.err.println( "You must specify a structure data set:" );
				System.err.println( "   -f ../data/5ebx.cif" );
				System.err.println( "   -u  ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF.gz/all/5ebx.cif.gz" );
				System.err.println( "   -p 5ebx" );
			}
		}

		if ( structure == null )
		{
			System.err.println( "Sorry, the Structure load failed." );
			System.exit( 1 );
		}
		else
		{
			System.err.println( "dataset = " + structure.getUrlString() );
		}

		//
		// Get the StructureMap since it knows how to derive bond pairs.
		//

		StructureMap structureMap = structure.getStructureMap( );

		//
		// Use the BondFactory class to generate some Bonds,
		// then add them to the StructureMap.
		//

		Vector bonds = BondFactory.generateBonds( structure );
		structureMap.addBonds( bonds );

		//
		// Ask the StructureMap to generate bond pairs for the Structure.
		//

		int bondCount = structureMap.getBondCount( );

		//
		// Print out the bond information.
		//

		System.err.println( "BondSearch: bondCount = " + bondCount );
		for ( int i=0; i<bondCount; i++ )
		{
			Bond bond = structureMap.getBond( i );
			int bondIndex = structureMap.getBondIndex( bond );
			Atom atom0 = bond.getAtom( 0 );
			Atom atom1 = bond.getAtom( 1 );
			int atom0Index = structureMap.getAtomIndex( atom0 );
			int atom1Index = structureMap.getAtomIndex( atom1 );
			System.err.println( "BondSearch: bondIndex = " + bondIndex + ", atoms = " + atom0Index + " - " + atom1Index );
		}
	}
}