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[Cdk-commits] SF.net SVN: cdk: [9128] trunk/cdk/src/org/openscience/cdk/aromaticity/ CDKHueckelAromaticityDetector.java
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From: <eg...@us...> - 2007-10-16 20:05:53
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Revision: 9128
http://cdk.svn.sourceforge.net/cdk/?rev=9128&view=rev
Author: egonw
Date: 2007-10-16 13:05:50 -0700 (Tue, 16 Oct 2007)
Log Message:
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Added a new Hueckel-based aromaticity detector, using the new atom types
Added Paths:
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trunk/cdk/src/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector.java
Added: trunk/cdk/src/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector.java (rev 0)
+++ trunk/cdk/src/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector.java 2007-10-16 20:05:50 UTC (rev 9128)
@@ -0,0 +1,166 @@
+/* $Revision: 8373 $ $Author: rajarshi $ $Date: 2007-06-22 21:29:09 +0200 (Fri, 22 Jun 2007) $
+ *
+ * Copyright (C) 2007 Egon Willighagen <eg...@us...>
+ *
+ * Contact: cdk...@li...
+ *
+ * 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 java.util.Iterator;
+
+import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.exception.CDKException;
+import org.openscience.cdk.graph.ConnectivityChecker;
+import org.openscience.cdk.graph.SpanningTree;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.ringsearch.SSSRFinder;
+import org.openscience.cdk.tools.LoggingTool;
+
+/**
+ * This aromaticity detector detects the aromaticity based on the Hückel
+ * 4n+2 pi-electrons rule applied to isolated ring systems. It assumes
+ * CDK atom types to be perceived.
+ *
+ * @author egonw
+ * @cdk.module experimental
+ * @cdk.created 2007-10-05
+ *
+ * @see org.openscience.cdk.CDKConstants
+ */
+public class CDKHueckelAromaticityDetector {
+
+ static LoggingTool logger = new LoggingTool(CDKHueckelAromaticityDetector.class);
+
+ public static boolean detectAromaticity(IAtomContainer atomContainer) throws CDKException {
+ IAtomContainer ringSystems = getRingSystemsOnly(atomContainer);
+ if (ringSystems.getAtomCount() == 0) {
+ // If there are no rings, then there cannot be any aromaticity
+ return false;
+ }
+
+ boolean foundSomeAromaticity = false;
+ Iterator<IAtomContainer> isolatedRingSystems = ConnectivityChecker.partitionIntoMolecules(ringSystems).atomContainers();
+ while (isolatedRingSystems.hasNext()) {
+ IAtomContainer isolatedSystem = isolatedRingSystems.next();
+ Iterator<IAtomContainer> singleRings = new SSSRFinder(isolatedSystem).findSSSR().atomContainers();
+ while (singleRings.hasNext()) {
+ IAtomContainer singleRing = singleRings.next();
+ if (isRingSystemSproutedWithNonRingDoubleBonds(atomContainer, singleRing)) {
+// OK, this ring is not aromatic
+ } else {
+ // FIXME: ring might be aromatic -> check that
+ // OK, all atoms must be sp2, or sp3 with a lone pair
+ Iterator<IAtom> ringAtoms = singleRing.atoms();
+ boolean allAtomsSuitable = true;
+ while (ringAtoms.hasNext()) {
+ IAtom ringAtom = ringAtoms.next();
+ if (ringAtom.getHybridization() == CDKConstants.HYBRIDIZATION_SP2) {
+ // for example, a carbon
+ // note: the double bond is in the ring, that has been tested earlier
+ // FIXME: this does assume bond orders to be resolved too, when detecting
+ // sprouting double bonds
+ } else if (ringAtom.getHybridization() == CDKConstants.HYBRIDIZATION_SP3 &&
+ getLonePairCount(ringAtom) > 0) {
+ // for example, a nitrogen or oxygen
+ } else {
+ // OK, not aromatic, need to break the while loop now
+ allAtomsSuitable = false;
+ }
+ }
+ if (allAtomsSuitable) {
+ foundSomeAromaticity = true;
+ markRingAtomsAndBondsAromatic(singleRing);
+ }
+ }
+ }
+ }
+
+ return foundSomeAromaticity;
+ }
+
+ /**
+ * Determines if the isolatedRingSystem has attached double bonds, which are not part of the ring system itself,
+ * and not part of any other ring system.
+ */
+ private static boolean isRingSystemSproutedWithNonRingDoubleBonds(IAtomContainer fullContainer, IAtomContainer isolatedRingSystem) {
+ Iterator<IAtom> atoms = isolatedRingSystem.atoms();
+ while (atoms.hasNext()) {
+ Iterator<IBond> neighborBonds = fullContainer.getConnectedBondsList(atoms.next()).iterator();
+ while (neighborBonds.hasNext()) {
+ IBond neighborBond = neighborBonds.next();
+ if (!neighborBond.getFlag(CDKConstants.ISINRING) &&
+ neighborBond.getOrder() == CDKConstants.BONDORDER_DOUBLE ||
+ neighborBond.getOrder() == CDKConstants.BONDORDER_TRIPLE) {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Returns a new IAtomContainer which contains only atoms and bonds that
+ * participate in a ring system.
+ */
+ private static IAtomContainer getRingSystemsOnly(IAtomContainer container) {
+ IAtomContainer ringSystem = container.getBuilder().newAtomContainer();
+
+ new SpanningTree(container);
+ // atoms and bonds are now marked with the flag ISINRING
+
+ // add all ring atoms and ring bonds to the ring system container
+ Iterator<IAtom> atoms = container.atoms();
+ while (atoms.hasNext()) {
+ IAtom atom = atoms.next();
+ if (atom.getFlag(CDKConstants.ISINRING)) {
+ ringSystem.addAtom(atom);
+ }
+ }
+ Iterator<IBond> bonds = container.bonds();
+ while (bonds.hasNext()) {
+ IBond bond = bonds.next();
+ if (bond.getFlag(CDKConstants.ISINRING)) {
+ ringSystem.addBond(bond);
+ }
+ }
+
+ return ringSystem;
+ }
+
+ private static int getLonePairCount(IAtom atom) {
+ Integer count = (Integer)atom.getProperty(CDKConstants.LONE_PAIR_COUNT);
+ if (count == null) {
+ return 0;
+ } else {
+ return count.intValue();
+ }
+ }
+
+ private static void markRingAtomsAndBondsAromatic(IAtomContainer container) {
+ Iterator<IAtom> atoms = container.atoms();
+ while (atoms.hasNext()) atoms.next().setFlag(CDKConstants.ISAROMATIC, true);
+ Iterator<IBond> bonds = container.bonds();
+ while (bonds.hasNext()) bonds.next().setFlag(CDKConstants.ISAROMATIC, true);
+ }
+}
+
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