HydrogenPlacer.java

/* $RCSfile$    
 * $Author$    
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 * Copyright (C) 2003-2007  The Chemistry Development Kit (CDK) project
 * 
 * Contact: cdk-devel@lists.sourceforge.net
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 * 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
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 * - 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.
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 * This program is distributed in the hope that it will be useful,
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 * GNU Lesser General Public License for more details.
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package org.openscience.cdk.layout;

import java.util.List;

import javax.vecmath.Point2d;

import org.openscience.cdk.geometry.GeometryTools;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;

/**
 * This is a wrapper class for some existing methods in AtomPlacer. It helps
 * you to layout 2D and 3D coordinates for hydrogen atoms added to a molecule
 * which already has coordinates for the rest of the atoms.
 *
 * @author       Christop Steinbeck
 * @cdk.created  2003-08-06
 * @cdk.module   sdg
 * @cdk.githash
 */
public class HydrogenPlacer {
    
	public final static boolean debug = false;
	public final static boolean debug1 = false;
	
	public  void placeHydrogens2D(IAtomContainer atomContainer, double bondLength){
	    ILoggingTool logger =
	        LoggingToolFactory.createLoggingTool(HydrogenPlacer.class);
	    logger.debug("Entering Hydrogen Placement...");
	    IAtom atom = null; 
	    for (int f = 0; f < atomContainer.getAtomCount();f++)
	    {
	        atom = atomContainer.getAtom(f);
//	        if (!atom.getSymbol().equals("H"))
//	        {
	            if (debug1) System.out.println("Now placing hydrogens at atom " + f);
	            logger.debug("Now placing hydrogens at atom " + f);
	            placeHydrogens2D(atomContainer, atom, bondLength);
//	        }
	    }
	    logger.debug("Hydrogen Placement finished");
	}
	
	
	public  void placeHydrogens2D(IAtomContainer atomContainer, IAtom atom)
	{
		double bondLength = GeometryTools.getBondLengthAverage(atomContainer);
		placeHydrogens2D(atomContainer, atom, bondLength);
		
	
	}
	
	public  void placeHydrogens2D(IAtomContainer atomContainer, IAtom atom, double bondLength){
		ILoggingTool logger =
		    LoggingToolFactory.createLoggingTool(HydrogenPlacer.class);
		
		//double startAngle = 0.0;
		//double addAngle = 0.0; 
		AtomPlacer atomPlacer = new AtomPlacer();
		atomPlacer.setMolecule(atomContainer);
		//Vector atomVector = new Vector();
		logger.debug("bondLength ", bondLength);
		List<IAtom> connectedAtoms = atomContainer.getConnectedAtomsList(atom);
		IAtomContainer placedAtoms = atomContainer.getBuilder().newAtomContainer();
		IAtomContainer unplacedAtoms = atomContainer.getBuilder().newAtomContainer();
		
		for (int f = 0; f < connectedAtoms.size(); f++) {
			IAtom conAtom = (IAtom)connectedAtoms.get(f);
			if (conAtom.getSymbol().equals("H") && conAtom.getPoint2d()==null) {
				unplacedAtoms.addAtom(conAtom);
			} else {
				placedAtoms.addAtom(conAtom);
			}
		}
		logger.debug("Atom placement before procedure:");
		logger.debug("Center atom ", atom.getSymbol(), ": ", atom.getPoint2d());
		for (int f = 0; f < unplacedAtoms.getAtomCount(); f++)
		{
			logger.debug("H-" + f, ": ", unplacedAtoms.getAtom(f).getPoint2d());
		}
        Point2d centerPlacedAtoms = GeometryTools.get2DCenter(placedAtoms);
        atomPlacer.distributePartners(atom, placedAtoms, centerPlacedAtoms, unplacedAtoms, bondLength);
		logger.debug("Atom placement after procedure:");
		logger.debug("Center atom ", atom.getSymbol(), ": ", atom.getPoint2d());
		for (int f = 0; f < unplacedAtoms.getAtomCount(); f++)
		{
			logger.debug("H-" + f, ": ", unplacedAtoms.getAtom(f).getPoint2d());
		}				
	}
}