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HanserRingFinder.java
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HanserRingFinder.java
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/*
* 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.
*
* 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.
*
*/
package org.openscience.cdk.smsd.ring;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
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.IRing;
import org.openscience.cdk.interfaces.IRingSet;
/**
* Finds the Set of all Rings. This is an implementation of the algorithm
* published in {@cdk.cite HAN96}. Some of the comments refer to pseudo code
* fragments listed in this article. The concept is that a regular molecular
* graph is first converted into a path graph (refer PathGraph.java),
* i.e. a graph where the edges are actually paths. This can list several
* nodes that are implicitly connecting the two nodes between the path
* is formed (refer PathEdge.java).
*
* The paths that join source and sink node are step by step fused and the joined
* nodes are deleted from the path graph (collapsed path). What remains is a graph
* of paths that have the same start and endpoint and are thus rings (source=sink=ring).
*
* @cdk.module smsd
* @cdk.githash
* @author Syed Asad Rahman <asad@ebi.ac.uk> 2009-2010
*
*/
public class HanserRingFinder implements RingFinder {
private List<List<IAtom>> rings;
public HanserRingFinder() {
rings = new ArrayList<List<IAtom>>();
}
/**
* Returns a collection of rings.
*
* @param molecule
* @return a {@link Collection} of {@link List}s containing one ring each
* @see org.openscience.cdk.smsd.ring.RingFinder#findRings(org.openscience.cdk.interfaces.IAtomContainer)
*/
@Override
public Collection<List<IAtom>> findRings(IAtomContainer molecule) {
if (molecule == null) return null;
rings.clear();
PathGraph graph = new PathGraph(molecule);
for (int i = 0; i < molecule.getAtomCount(); i++) {
List<PathEdge> edges = graph.remove(molecule.getAtom(i));
for (PathEdge edge : edges) {
List<IAtom> ring = edge.getAtoms();
rings.add(ring);
}
}
return rings;
}
/**
* Returns Ring set based on Hanser Ring Finding method
* @param molecule
* @return report collected the rings
* @see org.openscience.cdk.smsd.ring.RingFinder#getRingSet(org.openscience.cdk.interfaces.IAtomContainer)
*/
@Override
public IRingSet getRingSet(IAtomContainer molecule) throws CDKException {
Collection<List<IAtom>> cycles = findRings(molecule);
IRingSet ringSet = molecule.getBuilder().newInstance(IRingSet.class);
for (List<IAtom> ringAtoms : cycles) {
IRing ring = molecule.getBuilder().newInstance(IRing.class);
for (IAtom atom : ringAtoms) {
atom.setFlag(CDKConstants.ISINRING, true);
ring.addAtom(atom);
for (IAtom atomNext : ringAtoms) {
if (!atom.equals(atomNext)) {
IBond bond = molecule.getBond(atom, atomNext);
if (bond != null) {
bond.setFlag(CDKConstants.ISINRING, true);
ring.addElectronContainer(bond);
}
}
}
}
ringSet.addAtomContainer(ring);
}
return ringSet;
}
}