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LongestAliphaticChainDescriptor.java

/*
 *  $RCSfile$
 *  $Author: rajarshi $
 *  $Date: 2007-02-01 20:46:29 +0100 (Thu, 01 Feb 2007) $
 *  $Revision: 7844 $
 *
 *  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.qsar.descriptors.molecular;

import org.openscience.cdk.AtomContainer;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.PathTools;
import org.openscience.cdk.graph.matrix.ConnectionMatrix;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IMolecularDescriptor;
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.qsar.result.IntegerResult;
import org.openscience.cdk.ringsearch.SSSRFinder;

import java.util.Vector;

/**
 *  Class that returns the number of atoms in the longest aliphatic chain.
 *
 * <p>This descriptor uses these parameters:
 * <table border="1">
 *   <tr>
 *     <td>Name</td>
 *     <td>Default</td>
 *     <td>Description</td>
 *   </tr>
 *   <tr>
 *     <td>checkRingSystem</td>
 *     <td>false</td>
 *     <td>True is the CDKConstant.ISINRING has to be set</td>
 *   </tr>
 * </table>
 *
 * Returns a single value named <i>nAtomLAC</i>
 * @author      chhoppe from EUROSCREEN
 * @cdk.created 2006-1-03
 * @cdk.module  qsar
 * @cdk.set     qsar-descriptors
 * @cdk.dictref qsar-descriptors:largestAliphaticChain
 */

00070 public class LongestAliphaticChainDescriptor implements IMolecularDescriptor {
      private boolean checkRingSystem = false;


    /**
     *  Constructor for the LongestAliphaticChainDescriptor object.
     */
00077     public LongestAliphaticChainDescriptor() { }

    /**
     * Returns a <code>Map</code> which specifies which descriptor
     * is implemented by this class. 
     *
     * These fields are used in the map:
     * <ul>
     * <li>Specification-Reference: refers to an entry in a unique dictionary
     * <li>Implementation-Title: anything
     * <li>Implementation-Identifier: a unique identifier for this version of
     *  this class
     * <li>Implementation-Vendor: CDK, JOELib, or anything else
     * </ul>
     *
     * @return An object containing the descriptor specification
     */
00094     public DescriptorSpecification getSpecification() {
        return new DescriptorSpecification(
                "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#longestAliphaticChain",
                this.getClass().getName(),
                "$Id: LongestAliphaticChainDescriptor.java 7844 2007-02-01 19:46:29Z rajarshi $",
                "The Chemistry Development Kit");
    }


    /**
     *  Sets the parameters attribute of the LongestAliphaticChainDescriptor object.
     *
     * This descriptor takes one parameter, which should be Boolean to indicate whether
     * aromaticity has been checked (TRUE) or not (FALSE).
     * 
     * @param  params            The new parameters value
     * @exception  CDKException if more than one parameter or a non-Boolean parameter is specified
     * @see #getParameters
     */
00113     public void setParameters(Object[] params) throws CDKException {
        if (params.length > 1) {
            throw new CDKException("LongestAliphaticChainDescriptor only expects one parameter");
        }
        if (!(params[0] instanceof Boolean)) {
            throw new CDKException("Both parameters must be of type Boolean");
        }
        // ok, all should be fine
        checkRingSystem = ((Boolean) params[0]).booleanValue();
    }


    /**
     *  Gets the parameters attribute of the LongestAliphaticChainDescriptor object.
     *
     * @return    The parameters value
     * @see #setParameters
     */
00131     public Object[] getParameters() {
        // return the parameters as used for the descriptor calculation
        Object[] params = new Object[1];
        params[0] = new Boolean(checkRingSystem);
        return params;
    }


    /**
     * Calculate the count of atoms of the longest aliphatic chain in the supplied {@link AtomContainer}.
     * 
     *  The method require one parameter:
     *  if checkRingSyste is true the CDKConstant.ISINRING will be set
     *
     *@param  container  The {@link AtomContainer} for which this descriptor is to be calculated
     *@return                   the number of atoms in the longest aliphatic chain of this AtomContainer
     *@throws CDKException if there is a problem in aromaticity detection
     *@see #setParameters
     */
00150     public DescriptorValue calculate(IAtomContainer container) throws CDKException {
      
      //logger.debug("LongestAliphaticChainDescriptor");
      IRingSet rs = null;
      if (checkRingSystem) {
            rs = new SSSRFinder(container).findSSSR();
            for (int i=0;i<container.getAtomCount();i++){
                  if (rs.contains(container.getAtom(i))){
                        container.getAtom(i).setFlag(CDKConstants.ISINRING,true);
                  }
            }
        }
            
      int longestChainAtomsCount=0;
        int tmpLongestChainAtomCount=0;
      //IAtom[] atoms = container.getAtoms();
      Vector startSphere = null;
      Vector path = null;
      //Set all VisitedFlags to False
      for (int i =0;i<container.getAtomCount();i++){
            container.getAtom(i).setFlag(CDKConstants.VISITED, false);
            }
      //logger.debug("Set all atoms to Visited False");
      for (int i =0;i<container.getAtomCount();i++){
            IAtom atomi = container.getAtom(i);
            //logger.debug("atom:"+i+" maxBondOrder:"+container.getMaximumBondOrder(atoms[i])+" Aromatic:"+atoms[i].getFlag(CDKConstants.ISAROMATIC)+" Ring:"+atoms[i].getFlag(CDKConstants.ISINRING)+" FormalCharge:"+atoms[i].getFormalCharge()+" Charge:"+atoms[i].getCharge()+" Flag:"+atoms[i].getFlag(CDKConstants.VISITED));
            if ((!atomi.getFlag(CDKConstants.ISAROMATIC) && !atomi.getFlag(CDKConstants.ISINRING) & atomi.getSymbol().equals("C")) & !atomi.getFlag(CDKConstants.VISITED)){
                  //logger.debug("...... -> Accepted");
                  startSphere = new Vector();
                  path = new Vector();
                  startSphere.addElement(atomi);
                  breadthFirstSearch(container, startSphere, path);
                  //create Atomcontainer
                  //logger.debug("Create new Atom Container");
                  AtomContainer aliphaticChain =createAtomContainerFromPath(container,path);
                  if (aliphaticChain.getAtomCount()>1){
                        double[][] conMat = ConnectionMatrix.getMatrix(aliphaticChain);
                        //logger.debug("Computing all-pairs-shortest-pathes ");
                        int[][] apsp = PathTools.computeFloydAPSP(conMat);
                        tmpLongestChainAtomCount=getLongestChainPath(apsp);
                        //logger.debug(" lengthPath:"+tmpLongestChainAtomCount+" allLength:"+longestChainAtomsCount);
                        if (tmpLongestChainAtomCount>longestChainAtomsCount){
                              longestChainAtomsCount=tmpLongestChainAtomCount;
                        }
                  }
            }           
      }
  
        return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
                new IntegerResult(longestChainAtomsCount), new String[] {"nAtomLAC"});
    }

    /**
     * Returns the specific type of the DescriptorResult object.
     * <p/>
     * The return value from this method really indicates what type of result will
     * be obtained from the {@link org.openscience.cdk.qsar.DescriptorValue} object. Note that the same result
     * can be achieved by interrogating the {@link org.openscience.cdk.qsar.DescriptorValue} object; this method
     * allows you to do the same thing, without actually calculating the descriptor.
     *
     * @return an object that implements the {@link org.openscience.cdk.qsar.result.IDescriptorResult} interface indicating
     *         the actual type of values returned by the descriptor in the {@link org.openscience.cdk.qsar.DescriptorValue} object
     */
00213     public IDescriptorResult getDescriptorResultType() {
        return new IntegerResult(1);
    }

    private int getLongestChainPath(int[][] apsp){
        int longestPath=0;
        for (int i = 0; i < apsp.length; i++){
            for (int j = 0; j < apsp.length; j++){
                    if (apsp[i][j]+1 > longestPath){
                        longestPath = apsp[i][j]+1;
                    }
            }
        }
        return longestPath;
    }
    
    
    
    private AtomContainer createAtomContainerFromPath(IAtomContainer container, Vector path){
      AtomContainer aliphaticChain = new org.openscience.cdk.AtomContainer();
      for (int i=0;i<path.size()-1;i++){
            if (!aliphaticChain.contains((IAtom)path.get(i))){
                  aliphaticChain.addAtom((IAtom)path.get(i));
            }
            for (int j=1;j<path.size();j++){
                  if (container.getBond((IAtom)path.get(i),(IAtom)path.get(j))!=null){
                        if (!aliphaticChain.contains((IAtom)path.get(j))){
                        aliphaticChain.addAtom((IAtom)path.get(j));
                  }
                        aliphaticChain.addBond(container.getBond((IAtom)path.get(i),(IAtom)path.get(j)));
                  }
            }
      }
      
      //for (int i=0;i<aliphaticChain.getAtomCount();i++){
      //    logger.debug("container-->atom:"+i+" Nr: "+container.getAtomNumber(aliphaticChain.getAtomAt(i))+" maxBondOrder:"+aliphaticChain.getMaximumBondOrder(aliphaticChain.getAtomAt(i))+" Aromatic:"+aliphaticChain.getAtomAt(i).getFlag(CDKConstants.ISAROMATIC)+" Ring:"+aliphaticChain.getAtomAt(i).getFlag(CDKConstants.ISINRING)+" FormalCharge:"+aliphaticChain.getAtomAt(i).getFormalCharge()+" Charge:"+aliphaticChain.getAtomAt(i).getCharge()+" Flag:"+aliphaticChain.getAtomAt(i).getFlag(CDKConstants.VISITED));
      //}
      //logger.debug("BondCount:"+aliphaticChain.getBondCount());
      if (aliphaticChain.getBondCount()==0){
            aliphaticChain.removeAllElements();
      }
      return aliphaticChain;
    }
    
      /**
       *  Performs a breadthFirstSearch in an AtomContainer starting with a
       *  particular sphere, which usually consists of one start atom, and searches
       *  for a pi system. 
       *
       *@param  container                                              The AtomContainer to
       *      be searched
       *@param  sphere                                          A sphere of atoms to
       *      start the search with
       *@param  path                                          A vector which stores the atoms belonging to the pi system
       *@exception  org.openscience.cdk.exception.CDKException  Description of the
       *      Exception
       */
00270       public  void breadthFirstSearch(IAtomContainer container, Vector sphere, Vector path) throws org.openscience.cdk.exception.CDKException{
            IAtom atom = null;
            IAtom nextAtom = null;
            Vector newSphere = new Vector();
            for (int i = 0; i < sphere.size(); i++){
                  atom = (IAtom) sphere.elementAt(i);
                  java.util.List bonds = container.getConnectedBondsList(atom);
                  for (int j = 0; j < bonds.size(); j++){
                        nextAtom = ((IBond)bonds.get(j)).getConnectedAtom(atom);
                        if ((!nextAtom.getFlag(CDKConstants.ISAROMATIC)&& !nextAtom.getFlag(CDKConstants.ISINRING)& nextAtom.getSymbol().equals("C")) & !nextAtom.getFlag(CDKConstants.VISITED)){
                        path.addElement(nextAtom);
                        nextAtom.setFlag(CDKConstants.VISITED, true);
                        if (container.getConnectedBondsCount(nextAtom) > 1){
                                    newSphere.addElement(nextAtom);
                              }
                        }else{
                              nextAtom.setFlag(CDKConstants.VISITED, true);
                        }
                  }
            }
            if (newSphere.size() > 0){
                  breadthFirstSearch(container, newSphere, path);
            }
      }

    
    /**
     *  Gets the parameterNames attribute of the LongestAliphaticChainDescriptor object.
     *
     *@return    The parameterNames value
     */
00301     public String[] getParameterNames() {
        String[] params = new String[1];
        params[0] = "checkRingSystem";
        return params;
    }



    /**
     *  Gets the parameterType attribute of the LongestAliphaticChainDescriptor object.
     *
     *@param  name  Description of the Parameter
     *@return       An Object of class equal to that of the parameter being requested
     */
00315     public Object getParameterType(String name) {
        Object[] paramTypes = new Object[1];
       paramTypes[0] = new Boolean(true);
        return paramTypes;
    }
}

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