/*
* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* Copyright (C) 2007 Andreas Schueller <archvile18@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.tools.manipulator;
import java.io.IOException;
import java.util.Comparator;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* <p>Compares two IAtomContainers for order with the following criteria with decreasing priority:</p>
* <ul>
* <li>Compare atom count
* <li>Compare molecular weight (heavy atoms only)
* <li>Compare bond count
* <li>Compare sum of bond orders (heavy atoms only)
* </ul>
* <p>If no difference can be found with the above criteria, the IAtomContainers are
* considered equal.</p>
*
* @author Andreas Schueller
* @cdk.created 2007-09-05
* @cdk.module standard
* @cdk.githash
*/
@TestClass("org.openscience.cdk.tools.manipulator.AtomContainerComparatorTest")
public class AtomContainerComparator implements Comparator {
/** Configure LoggingTool */
private ILoggingTool logger =
LoggingToolFactory.createLoggingTool(AtomContainerComparator.class);
/** Creates a new instance of AtomContainerComparator */
public AtomContainerComparator() {
}
/*
* <p>Compares two IAtomContainers for order with the following criteria with decreasing priority:</p>
* <ul>
* <li>Compare atom count
* <li>Compare molecular weight (heavy atoms only)
* <li>Compare bond count
* <li>Compare sum of bond orders (heavy atoms only)
* </ul>
* <p>If no difference can be found with the above criteria, the IAtomContainers are
* considered equal.</p>
* <p>Returns a negative integer, zero, or a positive integer as the first argument is less than,
* equal to, or greater than the second.</p>
* <p>This method is null safe.</p>
*
* @param o1 the first IAtomContainer
* @param o2 the second IAtomContainer
* @return a negative integer, zero, or a positive integer as the first argument is less than, equal
* to, or greater than the second.
*/
@TestMethod("testCompare_Object_Object")
public int compare(Object o1, Object o2) {
// Check for nulls
if (o1 == null && o2 == null)
return 0;
if (o1 == null)
return -1;
if (o2 == null)
return 1;
// Check for correct instances
if (!(o1 instanceof IAtomContainer) && !(o2 instanceof IAtomContainer))
return 0;
if (!(o1 instanceof IAtomContainer))
return -1;
if (!(o2 instanceof IAtomContainer))
return 1;
IAtomContainer atomContainer1 = (IAtomContainer) o1;
IAtomContainer atomContainer2 = (IAtomContainer) o2;
// 1. Compare atom count
if (atomContainer1.getAtomCount() > atomContainer2.getAtomCount())
return 1;
else if (atomContainer1.getAtomCount() < atomContainer2.getAtomCount())
return -1;
else {
// 2. Atom count equal, compare molecular weight (heavy atoms only)
double mw1 = 0;
double mw2 = 0;
try {
mw1 = getMolecularWeight(atomContainer1);
mw2 = getMolecularWeight(atomContainer2);
} catch (CDKException e) {
logger.warn("Exception in molecular mass calculation.");
return 0;
}
if (mw1 > mw2)
return 1;
else if (mw1 < mw2)
return -1;
else {
// 3. Molecular weight equal, compare bond count
if (atomContainer1.getBondCount() > atomContainer2.getBondCount())
return 1;
else if (atomContainer1.getBondCount() < atomContainer2.getBondCount())
return -1;
else {
// 4. Bond count equal, compare sum of bond orders (heavy atoms only)
double bondOrderSum1 = AtomContainerManipulator.getSingleBondEquivalentSum(atomContainer1);
double bondOrderSum2 = AtomContainerManipulator.getSingleBondEquivalentSum(atomContainer2);
if (bondOrderSum1 > bondOrderSum2)
return 1;
else if (bondOrderSum1 < bondOrderSum2)
return -1;
}
}
}
// AtomContainers are equal in terms of this comparator
return 0;
}
/**
* Returns the molecular weight (exact mass) of the major isotopes
* of all heavy atoms of the given IAtomContainer.
* @param atomContainer an IAtomContainer to calculate the mocular weight for
* @throws org.openscience.cdk.exception.CDKException if an error occurs with the IsotopeFactory
* @return the molecularweight (exact mass) of the major isotopes
* of all heavy atoms of the given IAtomContainer
*/
private double getMolecularWeight(IAtomContainer atomContainer) throws CDKException {
double mw = 0.0;
try {
for (IAtom atom : atomContainer.atoms()) {
if (!atom.getSymbol().equals("H"))
mw += IsotopeFactory.getInstance(atomContainer.getBuilder()).getMajorIsotope(atom.getSymbol()).getExactMass();
}
} catch (IOException e) {
throw new CDKException(e.getMessage(), e);
}
return mw;
}
}