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AromaticityCalculator.java

/* $RCSfile$
 * $Author: egonw $
 * $Date: 2007-01-11 22:24:17 +0100 (Thu, 11 Jan 2007) $
 * $Revision: 7707 $
 *
 *  Copyright (C) 2001-2007  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.
 *  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.aromaticity;

import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.interfaces.IRing;

/**
 * @cdk.module standard
 *
 * @author     Oliver Horlacher <oliver.horlacher@therastrat.com>
 * @cdk.created    2002-03-14
 *
 * @cdk.keyword aromaticity detector
 */
00045 public class AromaticityCalculator
{

      /**
       *  Tests the <code>ring</code> in the <code>molecule</code> for aromaticity. Uses the 
     *  H&uuml;ckle rule (4n + 2) pie electrons. sp<sup>2</sup> hybridized C contibute 1 electron non 
     *  sp<sup>2</sup> hybridized heteroatoms contribute 2 electrons (N and O should never be sp in 
     *  or anything else in a ring and d electron elements get to complicated) 
     *  sp<sup>2</sup> hybridized heteroatoms contribute 1 electron hybridization is worked out by
     *  counting the number of bonds with order 2. Therefore sp<sup>2</sup> hybridization is assumed 
     *  if there is one bond of order 2. Otherwise sp<sup>3</sup> hybridization is assumed.
       *
       * @param  ring      the ring to test
       * @param  atomContainer  the AtomContainer the ring is in
       * @return           true if the ring is aromatic false otherwise.
       */
00061       public static boolean isAromatic(IRing ring, IAtomContainer atomContainer)
      {
            
            java.util.Iterator ringAtoms = ring.atoms();
            int eCount = 0;
            java.util.List conectedBonds;
            int numDoubleBond = 0;
            boolean allConnectedBondsSingle;
            
            while (ringAtoms.hasNext())
            {
                  IAtom atom = (IAtom)ringAtoms.next();
                  numDoubleBond = 0;
                  allConnectedBondsSingle = true;
                  conectedBonds = atomContainer.getConnectedBondsList(atom);
                  for (int j = 0; j < conectedBonds.size(); j++)
                  {
                        IBond bond = (IBond)conectedBonds.get(j);
                        if (bond.getOrder() == 2 && ring.contains(bond))
                        {
                              numDoubleBond++;
                        }
                        
                        // Count the Electron if bond order = 1.5
                        else if (bond.getOrder() == 1.5 && ring.contains(bond))
                        {
                              numDoubleBond = 1;
                        }
                        
                        if (bond.getOrder() != 1) {
                              allConnectedBondsSingle = false;
                        }
                  }
                  if (numDoubleBond == 1)
                  {
                        //C or heteroatoms both contibute 1 electron in sp2 hybridized form
                        eCount++;
                  }
                  else if (!atom.getSymbol().equals("C"))
                  {
                        //Heteroatom probably in sp3 hybrid therefore 2 electrons contributed.
                        eCount = eCount + 2;
                  }
                  else if (atom.getFlag(CDKConstants.ISAROMATIC))
                  {
                        eCount++;
                  }
                  else if (allConnectedBondsSingle 
                              && atom.getSymbol().equals("C") 
                              && atom.getFormalCharge() == 1.0)
                  {
                        // This is for tropylium and kinds. 
                        // Dependence on hybridisation would be better:
                        // empty p-orbital is needed
                        continue;
                  }
                  else
                  {
                        return false;     
                  }
            }
            if (eCount - 2 != 0 && (eCount - 2) % 4 == 0)
            {
                  return true;
            }
            return false;
      }
}


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