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ExtendedFingerprinter.java

/* $Revision$ $Author$ $Date$
 *
 * Copyright (C) 2002-2007  Stefan Kuhn <shk3@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.
 * All we ask is that proper credit is given for our work, which includes
 * - 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.
 *
 * 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.fingerprint;

import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.ringsearch.RingPartitioner;
import org.openscience.cdk.ringsearch.SSSRFinder;
import org.openscience.cdk.tools.manipulator.MolecularFormulaManipulator;

import java.util.BitSet;
import java.util.List;

/**
 * Generates an extended fingerprint for a given {@link IAtomContainer}, that
 * extends the {@link Fingerprinter} with additional bits describing ring
 * features.
 *  
 * @author         shk3
 * @cdk.created    2006-01-13
 * @cdk.keyword    fingerprint
 * @cdk.keyword    similarity
 * @cdk.module     fingerprint
 * @cdk.githash
 * 
 * @see            org.openscience.cdk.fingerprint.Fingerprinter
 */
@TestClass("org.openscience.cdk.fingerprint.ExtendedFingerprinterTest")
00054 public class ExtendedFingerprinter implements IFingerprinter {

      private final int RESERVED_BITS = 25;
      
      private Fingerprinter fingerprinter = null;

      /**
       * Creates a fingerprint generator of length <code>DEFAULT_SIZE</code>
       * and with a search depth of <code>DEFAULT_SEARCH_DEPTH</code>.
       */
00064       public ExtendedFingerprinter() {
            this(Fingerprinter.DEFAULT_SIZE, 
                   Fingerprinter.DEFAULT_SEARCH_DEPTH);
      }
      
      public ExtendedFingerprinter(int size) {
            this(size, Fingerprinter.DEFAULT_SEARCH_DEPTH);
      }
      
      /**
       * Constructs a fingerprint generator that creates fingerprints of
       * the given size, using a generation algorithm with the given search
       * depth.
       *
       * @param  size        The desired size of the fingerprint
       * @param  searchDepth The desired depth of search
       */
00081       public ExtendedFingerprinter(int size, int searchDepth) {
      this.fingerprinter = new Fingerprinter(size-RESERVED_BITS, searchDepth);
      }
      
      /**
       * Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics
       * It contains the informations from getFingerprint() and bits which tell if the structure has 0 rings, 1 or less rings,
       * 2 or less rings ... 10 or less rings (referring to smallest set of smallest rings) and bits which tell if 
       * there is a fused ring system with 1,2...8 or more rings in it
       *
       *@param     container         The AtomContainer for which a Fingerprint is generated
       */
    @TestMethod("testGetFingerprint_IAtomContainer")
00094     public BitSet getFingerprint(IAtomContainer container) throws CDKException {
            return this.getFingerprint(container,null,null);
      }
            
      /**
       * Generates a fingerprint of the default size for the given AtomContainer, using path and ring metrics
       * It contains the informations from getFingerprint() and bits which tell if the structure has 0 rings, 1 or less rings,
       * 2 or less rings ... 10 or less rings and bits which tell if there is a fused ring system with 1,2...8 or more rings in it
       * The RingSet used is passed via rs parameter. This must be a smallesSetOfSmallestRings.
       * The List must be a list of all ring systems in the molecule.
       *
       *@param     atomContainer         The AtomContainer for which a Fingerprint is generated
       *@param     ringSet         An SSSR RingSet of ac (if not available, use  getExtendedFingerprint(AtomContainer ac), which does the calculation)
       *@param     rslist           A list of all ring systems in ac
       *@exception CDKException  Description of the Exception
     * @return a BitSet representing the fingerprint
       */
    @TestMethod("testGetFingerprint_IAtomContainer_IRingSet_List")
00112     public BitSet getFingerprint(IAtomContainer atomContainer, IRingSet ringSet, List<IRingSet> rslist) throws CDKException {
        IAtomContainer container;
        try {
            container = (IAtomContainer) atomContainer.clone();
        } catch (CloneNotSupportedException e) {
            throw new CDKException("Could not clone input");
        }
        
        BitSet bitSet = fingerprinter.getFingerprint(container);
            int size = this.getSize();
            double weight = MolecularFormulaManipulator.getTotalNaturalAbundance(MolecularFormulaManipulator.getMolecularFormula(container));
            for(int i=1;i<11;i++){
                  if(weight>(100*i))
                        bitSet.set(size-26+i); // 26 := RESERVED_BITS+1
            }
            if(ringSet==null){
                  ringSet=new SSSRFinder(container).findSSSR();
                  rslist=RingPartitioner.partitionRings(ringSet);
            }
            for(int i=0;i<7;i++){
                  if(ringSet.getAtomContainerCount()>i)
                        bitSet.set(size-15+i); // 15 := RESERVED_BITS+1+10 mass bits
            }
            int maximumringsystemsize=0;
            for(int i=0;i<rslist.size();i++){
                  if(((IRingSet)rslist.get(i)).getAtomContainerCount()>maximumringsystemsize)
                        maximumringsystemsize=((IRingSet)rslist.get(i)).getAtomContainerCount();
            }
            for(int i=0;i<maximumringsystemsize && i<9;i++){
                  bitSet.set(size-8+i-3);
            }
            return bitSet;
      }

    @TestMethod("testGetSize")
00147     public int getSize() {
            return fingerprinter.getSize()+RESERVED_BITS;
      }

}

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