AtomTypeTools.java

/*  $RCSfile$
 *  $Author$
 *  $Date$
 *  $Revision$
 *
 *  Copyright (C) 2005-2007  Christian Hoppe <chhoppe@users.sf.net>
 *
 *  Contact: cdk-devel@lists.sourceforge.net
 *
 *  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.
 *
 *  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 USA.
 *
 */
package org.openscience.cdk.tools;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IRing;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.ringsearch.SSSRFinder;
import org.openscience.cdk.smiles.SmilesGenerator;
import org.openscience.cdk.tools.manipulator.RingSetManipulator;


/**
* AtomTypeTools is a helper class for assigning atom types to an atom.
*
* @author         cho
* @cdk.created    2005-18-07
* @cdk.module     extra
 * @cdk.githash
*/

public class AtomTypeTools {
	
	private static ILoggingTool logger =
	    LoggingToolFactory.createLoggingTool(AtomTypeTools.class);
	HOSECodeGenerator hcg=null;
	SmilesGenerator sg=null;
	
	/**
	 * Constructor for the MMFF94AtomTypeMatcher object.
	 */
	public AtomTypeTools() {
		hcg = new HOSECodeGenerator();
	}
	
	public IRingSet assignAtomTypePropertiesToAtom(IMolecule molecule) throws Exception{
		return assignAtomTypePropertiesToAtom(molecule, true);
	}
	
		
	/**
	 *  Method assigns certain properties to an atom. Necessary for the atom type matching 
	 *  Properties:
	 *  <ul>
	 *   <li>aromaticity)
	 *   <li>ChemicalGroup (CDKChemicalRingGroupConstant)
	 *	 <li>SSSR
	 *	 <li>Ring/Group, ringSize, aromaticity
	 *	 <li>SphericalMatcher (HoSe Code)
	 *  </ul>
	 *  
	 *@param aromaticity booelan true/false true if aromaticity should be calculated
	 *@return                sssrf ringSetofTheMolecule
	 *@exception  Exception  Description of the Exception
	 */
	public IRingSet assignAtomTypePropertiesToAtom(IMolecule molecule, boolean aromaticity) throws Exception{
        SmilesGenerator sg = new SmilesGenerator();

		//logger.debug("assignAtomTypePropertiesToAtom Start ...");
		logger.debug("assignAtomTypePropertiesToAtom Start ...");
		String hoseCode = "";
		IRingSet ringSetA = null;
		IRingSet ringSetMolecule = new SSSRFinder(molecule).findSSSR();
		logger.debug(ringSetMolecule);
		
		if (aromaticity){
			try {
				CDKHueckelAromaticityDetector.detectAromaticity(molecule);
			} catch (Exception cdk1) {
				//logger.debug("AROMATICITYError: Cannot determine aromaticity due to: " + cdk1.toString());
				logger.error("AROMATICITYError: Cannot determine aromaticity due to: " + cdk1.toString());
			}
		}

		for (int i = 0; i < molecule.getAtomCount(); i++) {
			// FIXME: remove casting
			org.openscience.cdk.Atom atom2 = (org.openscience.cdk.Atom)molecule.getAtom(i);
			//Atom aromatic is set by HueckelAromaticityDetector
			//Atom in ring?
			if (ringSetMolecule.contains((org.openscience.cdk.interfaces.IAtom)atom2)) {
				ringSetA = ringSetMolecule.getRings(atom2);
				RingSetManipulator.sort(ringSetA);
				IRing sring = (IRing) ringSetA.getAtomContainer(ringSetA.getAtomContainerCount()-1);
				atom2.setProperty(CDKConstants.PART_OF_RING_OF_SIZE, Integer.valueOf(sring.getRingSize()));
				atom2.setProperty(CDKConstants.CHEMICAL_GROUP_CONSTANT, Integer.valueOf(ringSystemClassifier(
						sring, sg.createSMILES(atom2.getBuilder().newMolecule(sring)))
				));
				atom2.setFlag(CDKConstants.ISINRING, true);
				atom2.setFlag(CDKConstants.ISALIPHATIC, false);
			}else{
				atom2.setProperty(CDKConstants.CHEMICAL_GROUP_CONSTANT, 
					Integer.valueOf(CDKConstants.ISNOTINRING)
				);
				atom2.setFlag(CDKConstants.ISINRING, false);
				atom2.setFlag(CDKConstants.ISALIPHATIC,true);
			}
			try {
				hoseCode = hcg.getHOSECode(molecule, atom2, 3);
				hoseCode=removeAromaticityFlagsFromHoseCode(hoseCode);
				atom2.setProperty(CDKConstants.SPHERICAL_MATCHER, hoseCode);
			} catch (CDKException ex1) {
				throw new CDKException("Could not build HOSECode from atom "+ i + " due to " + ex1.toString(), ex1);
			}
		}
		return ringSetMolecule;
	}
	

	/**
	 *  Identifies ringSystem and returns a number which corresponds to 
	 *  CDKChemicalRingConstant
	 *
	 *@param  ring	Ring class with the ring system  
	 *@param  smile  smile of the ring system
	 *@return     chemicalRingConstant
	 */
	private int ringSystemClassifier(IRing ring, String smile) {
		/*System.out.println("IN AtomTypeTools Smile:"+smile);*/
		logger.debug("Comparing ring systems: SMILES=", smile);
		
		if (smile.equals("c1ccnc1"))return 4;
		else if (smile.equals("c1ccoc1"))return 6;
		else if (smile.equals("c1ccsc1"))return 8;
		else if (smile.equals("c1ccncc1"))return 10;
		else if (smile.equals("c1cncnc1"))return 12;
		else if (smile.equals("c1ccccc1"))return 5;
		
		int ncount=0;
		for (int i=0; i<ring.getAtomCount();i++){
			if (ring.getAtom(i).getSymbol().equals("N")){
				ncount=ncount+1;
			}
		}
			
		if (ring.getAtomCount()==6 & ncount==1){
			return 10;
		}else if (ring.getAtomCount()==5 & ncount==1){
			return 4;
		}
		
		if (ncount==0){
			return 3;
		}else{
			return 0;
		}
	}
	
	private String removeAromaticityFlagsFromHoseCode(String hoseCode){
		String hosecode="";
		for (int i=0;i<hoseCode.length();i++){
			if (hoseCode.charAt(i)!= '*'){
				hosecode=hosecode+hoseCode.charAt(i);
			}
		}
		return hosecode;
	}
}