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RotatableBondsCountDescriptor.java

/*
 *  $RCSfile$
 *  $Author: rajarshi $
 *  $Date: 2007-02-01 20:46:29 +0100 (Thu, 01 Feb 2007) $
 *  $Revision: 7844 $
 *
 *  Copyright (C) 2004-2007  The Chemistry Development Kit (CDK) project
 *
 *  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.CDKConstants;
import org.openscience.cdk.exception.CDKException;
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.AllRingsFinder;

import java.util.Iterator;
import java.util.List;

/**
 *  The number of rotatable bonds is given by the SMARTS specified by Daylight on
 *  <a href="http://www.daylight.com/dayhtml_tutorials/languages/smarts/smarts_examples.html#EXMPL">SMARTS tutorial</a><p>
 *
 * <p>This descriptor uses these parameters:
 * <table border="1">
 *   <tr>
 *     <td>Name</td>
 *     <td>Default</td>
 *     <td>Description</td>
 *   </tr>
 *   <tr>
 *     <td>includeTerminals</td>
 *     <td>false</td>
 *     <td>True if terminal bonds are included</td>
 *   </tr>
 * </table>
 *
 * Returns a single value named <i>nRotB</i>
 *
 * @author      mfe4
 * @cdk.created 2004-11-03
 * @cdk.module  qsar
 * @cdk.set     qsar-descriptors
 * @cdk.dictref qsar-descriptors:rotatableBondsCount
 * 
 * @cdk.keyword bond count, rotatable
 * @cdk.keyword descriptor
 */
00072 public class RotatableBondsCountDescriptor implements IMolecularDescriptor {
      private boolean includeTerminals = false;


      /**
       *  Constructor for the RotatableBondsCountDescriptor object
       */
00079       public RotatableBondsCountDescriptor() { }


      /**
       *  Gets the specification attribute of the RotatableBondsCountDescriptor
       *  object
       *
       *@return    The specification value
       */
00088       public DescriptorSpecification getSpecification() {
        return new DescriptorSpecification(
            "http://www.blueobelisk.org/ontologies/chemoinformatics-algorithms/#rotatableBondsCount",
                this.getClass().getName(),
                "$Id: RotatableBondsCountDescriptor.java 7844 2007-02-01 19:46:29Z rajarshi $",
            "The Chemistry Development Kit");
      }


      /**
       *  Sets the parameters attribute of the RotatableBondsCountDescriptor object
       *
       *@param  params            a boolean true means that terminal atoms must be included in the count
       *@exception  CDKException  Description of the Exception
       */
00103       public void setParameters(Object[] params) throws CDKException {
            if (params.length != 1) {
                  throw new CDKException("RotatableBondsCount expects one parameter");
            }
            if (!(params[0] instanceof Boolean)) {
                  throw new CDKException("The parameter must be of type Boolean");
            }
            // ok, all should be fine
            includeTerminals = ((Boolean) params[0]).booleanValue();
      }


      /**
       *  Gets the parameters attribute of the RotatableBondsCountDescriptor object
       *
       *@return    The parameters value
       */
00120       public Object[] getParameters() {
            // return the parameters as used for the descriptor calculation
            Object[] params = new Object[1];
            params[0] = new Boolean(includeTerminals);
            return params;
      }


      /**
       *  The method calculates the number of rotatable bonds of an atom container.
       *  If the boolean parameter is set to true, terminal bonds are included.
       *
       *@param  ac                AtomContainer
       *@return                   number of rotatable bonds
       *@exception  CDKException  Possible Exceptions
       */
00136       public DescriptorValue calculate(IAtomContainer ac) throws CDKException {
            int rotatableBondsCount = 0;
            Iterator bonds = ac.bonds();
            int degree0 = 0;
            int degree1 = 0;
            IRingSet ringSet = null;
            AllRingsFinder arf = new AllRingsFinder();
            ringSet = arf.findAllRings(ac);
            List ringsWithThisBond = null;
            while (bonds.hasNext()) {
                  IBond bond = (IBond)bonds.next();
                  ringsWithThisBond = ringSet.getRings(bond);
                  if (ringsWithThisBond.size() > 0) {
                        bond.setFlag(CDKConstants.ISINRING, true);
                  }
            }
            bonds = ac.bonds();
            while (bonds.hasNext()) {
                  IBond bond = (IBond)bonds.next();
                  IAtom atom0 = bond.getAtom(0);
                  IAtom atom1 = bond.getAtom(1);
                  if (bond.getOrder() == CDKConstants.BONDORDER_SINGLE) {
                        if ((ac.getMaximumBondOrder(atom0) < 3.0) && (ac.getMaximumBondOrder(atom1) < 3.0)) {
                              if (bond.getFlag(CDKConstants.ISINRING) == false) {
                                    degree0 = ac.getConnectedBondsCount(atom0);
                                    degree1 = ac.getConnectedBondsCount(atom1);
                                    if ((degree0 == 1) || (degree1 == 1)) {
                                          if (includeTerminals == true) {
                                                rotatableBondsCount += 1;
                                          }
                                          if (includeTerminals == false) {
                                                rotatableBondsCount += 0;
                                          }
                                    } else {
                                          rotatableBondsCount += 1;
                                    }
                              }
                        }
                  }
            }
            return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(), new IntegerResult(rotatableBondsCount),
                new String[] { includeTerminals ? "nRotBt" : "nRotB"});
      }

    /**
     * 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
     */
00191     public IDescriptorResult getDescriptorResultType() {
        return new IntegerResult(1);
    }


    /**
     *  Gets the parameterNames attribute of the RotatableBondsCountDescriptor
     *  object
     *
     *@return    The parameterNames value
     */
00202     public String[] getParameterNames() {
        String[] params = new String[1];
        params[0] = "includeTerminals";
        return params;
    }



      /**
       *  Gets the parameterType attribute of the RotatableBondsCountDescriptor
       *  object
       *
       *@param  name  Description of the Parameter
       *@return       The parameterType value
       */
00217       public Object getParameterType(String name) {
            return new Boolean(true);
      }
}


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