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DefaultMatcher.java
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DefaultMatcher.java
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/* Copyright (C) 2009-2010 Syed Asad Rahman <asad@ebi.ac.uk>
*
* 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.
*
* MX Cheminformatics Tools for Java
*
* Copyright (c) 2007-2009 Metamolecular, LLC
*
* http://metamolecular.com
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.openscience.cdk.smsd.algorithm.matchers;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
/**
* Checks if atom is matching between query and target molecules.
* @cdk.module smsd
* @cdk.githash
* @author Syed Asad Rahman <asad@ebi.ac.uk>
*/
public class DefaultMatcher {
public static boolean isBondMatch(BondMatcher bondMatcher, IAtomContainer ac2, IBond bondA2,
boolean shouldMatchBonds) {
// ok, bonds match
if (bondMatcher.matches(ac2, bondA2)) {
// System.out.println("Bond Matched");
return true;
}
return false;
}
public static boolean isAtomMatch(AtomMatcher atomMatcher1, AtomMatcher atomMatcher2, IAtomContainer ac2,
IBond bondA2, boolean shouldMatchBonds) {
// ok, atoms match
if (atomMatcher1.matches(ac2, bondA2.getAtom(0)) && atomMatcher2.matches(ac2, bondA2.getAtom(1))) {
// System.out.println("Atom Matched");
return true;
}
// ok, atoms match
if (atomMatcher1.matches(ac2, bondA2.getAtom(1)) && atomMatcher2.matches(ac2, bondA2.getAtom(0))) {
// System.out.println("Atom Matched");
return true;
}
return false;
}
}