/* $RCSfile$
* $Author$
* $Date$
* $Revision$
*
* 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.isomorphism.matchers.smarts;
import java.util.BitSet;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
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.isomorphism.UniversalIsomorphismTester;
import org.openscience.cdk.isomorphism.matchers.IQueryAtom;
import org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer;
import org.openscience.cdk.isomorphism.mcss.RMap;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* This matches recursive smarts atoms.
*
* @cdk.module smarts
* @cdk.githash
* @cdk.keyword SMARTS
*/
public class RecursiveSmartsAtom extends SMARTSAtom {
private static final long serialVersionUID = 1L;
private final static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(
RecursiveSmartsAtom.class);
/**
* AtomContainer of the target molecule to which this recursive smarts query trying to match
*/
private IAtomContainer atomContainer = null;
/**
* The IQueryAtomContainer created by parsing the recursive smarts
*/
private IQueryAtomContainer recursiveQuery = null;
/**
* BitSet that records which atom in the target molecule matches the
* recursive smarts
*/
private BitSet bitSet = null;
/**
* Creates a new instance
*
* @param query
*/
public RecursiveSmartsAtom(IQueryAtomContainer query) {
super();
this.recursiveQuery = query;
}
/* (non-Javadoc)
* @see org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom#matches(org.openscience.cdk.interfaces.IAtom)
*/
public boolean matches(IAtom atom) {
if (recursiveQuery.getAtomCount() == 1) { // only one atom. Then just match that atom
return ((IQueryAtom)recursiveQuery.getAtom(0)).matches(atom);
}
// Check wither atomContainer has been set
if (atomContainer == null) {
logger.error("In RecursiveSmartsAtom, atomContainer can't be null! You must set it before matching");
return false;
}
// initialize bitsets
if (bitSet == null) {
try {
initilizeBitSets();
} catch (CDKException cex) {
logger.error("Error found when matching recursive smarts: " + cex.getMessage());
return false;
}
}
int atomNumber = atomContainer.getAtomNumber(atom);
return bitSet.get(atomNumber);
}
/**
* This method calculates all possible matches of this recursive smarts
* to the AtomContainer. It set the index of the first atom of each match
* in the bitset to be true.
*
* @throws CDKException
*/
private void initilizeBitSets() throws CDKException {
List<List<RMap>> bondMappings = null;
bondMappings = UniversalIsomorphismTester.getSubgraphMaps(atomContainer, recursiveQuery);
bitSet = new BitSet(atomContainer.getAtomCount());
for (List<RMap> bondMapping : bondMappings) {
Collections.sort(bondMapping, new Comparator<RMap>() {
public int compare(RMap r1, RMap r2) {
if (r1.getId2() > r2.getId2()) return 1;
else if (r1.getId2() == r2.getId2()) return 0;
else return -1;
}
});
RMap rmap0 = bondMapping.get(0);
IBond bond0 = atomContainer.getBond(rmap0.getId1());
IAtom atom0 = bond0.getAtom(0);
IAtom atom1 = bond0.getAtom(1);
IBond qbond0 = recursiveQuery.getBond(rmap0.getId2());
IQueryAtom qatom0 = (IQueryAtom)qbond0.getAtom(0);
IQueryAtom qatom1 = (IQueryAtom)qbond0.getAtom(1);
if ( (qatom0.matches(atom0) && qatom1.matches(atom1))
&& (qatom0.matches(atom1) && qatom1.matches(atom0)) ) { // they match each other no matter what order
if (bondMapping.size() > 1) { // look for the second bond
IBond bond1 = atomContainer.getBond(bondMapping.get(1).getId1());
IBond qbond1 = recursiveQuery.getBond(bondMapping.get(1).getId2());
if (recursiveQuery.getAtomNumber(qatom0) == 0) {
if (qbond1.contains(qatom0) && bond1.contains(atom0)) { // atom0 <-> qatom0
bitSet.set(atomContainer.getAtomNumber(atom0), true);
} else if (qbond1.contains(qatom0) && bond1.contains(atom1)) { // atom1 <-> qatom0
bitSet.set(atomContainer.getAtomNumber(atom1), true);
} else if (!qbond1.contains(qatom0) && bond1.contains(atom0)) { // ! (qatom0 <-> atom0)
bitSet.set(atomContainer.getAtomNumber(atom1), true);
} else { // (!qbond1.contains(qatom0) && bond1.contains(atom1) // ! (qatom0 <-> atom1 )
bitSet.set(atomContainer.getAtomNumber(atom0), true);
}
} else {
if (qbond1.contains(qatom1) && bond1.contains(atom0)) {
bitSet.set(atomContainer.getAtomNumber(atom0), true);
} else if (qbond1.contains(qatom1) && bond1.contains(atom1)) {
bitSet.set(atomContainer.getAtomNumber(atom1), true);
} else if (!qbond1.contains(qatom1) && bond1.contains(atom1)) {
bitSet.set(atomContainer.getAtomNumber(atom0), true);
} else {
bitSet.set(atomContainer.getAtomNumber(atom1), true);
}
}
} else {
// both matches
bitSet.set(atomContainer.getAtomNumber(atom1), true);
bitSet.set(atomContainer.getAtomNumber(atom0), true);
}
} else {
if (recursiveQuery.getAtomNumber(qatom0) == 0) { // starts from qatom1
if (qatom0.matches(atom0) && qatom1.matches(atom1)) {
bitSet.set(atomContainer.getAtomNumber(atom0), true);
} else {
bitSet.set(atomContainer.getAtomNumber(atom1), true);
}
} else { // qatom1 is the first atom
if (qatom0.matches(atom1) && qatom1.matches(atom0)) {
bitSet.set(atomContainer.getAtomNumber(atom0), true);
} else {
bitSet.set(atomContainer.getAtomNumber(atom1), true);
}
}
}
}
}
public IQueryAtomContainer getRecursiveQuery() {
return recursiveQuery;
}
public void setRecursiveQuery(IQueryAtomContainer query) {
this.recursiveQuery = query;
}
public IAtomContainer getAtomContainer() {
return atomContainer;
}
public void setAtomContainer(IAtomContainer atomContainer) {
this.atomContainer = atomContainer;
this.bitSet = null; // new atom container, reset matching bitset.
}
}