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[Cdk-commits] SF.net SVN: cdk: [9480] branches/egonw/ibondorder
|
From: <eg...@us...> - 2007-11-23 10:32:07
|
Revision: 9480
http://cdk.svn.sourceforge.net/cdk/?rev=9480&view=rev
Author: egonw
Date: 2007-11-23 02:31:00 -0800 (Fri, 23 Nov 2007)
Log Message:
-----------
Synchronized with trunk rev 9479
Revision Links:
--------------
http://cdk.svn.sourceforge.net/cdk/?rev=9479&view=rev
Modified Paths:
--------------
branches/egonw/ibondorder/.classpath
branches/egonw/ibondorder/src/META-INF/qsar.datafiles
branches/egonw/ibondorder/src/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector.java
branches/egonw/ibondorder/src/org/openscience/cdk/atomtype/EStateAtomTypeMatcher.java
branches/egonw/ibondorder/src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
branches/egonw/ibondorder/src/org/openscience/cdk/fingerprint/Fingerprinter.java
branches/egonw/ibondorder/src/org/openscience/cdk/iupac/parser/MoleculeBuilder.java
branches/egonw/ibondorder/src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/bond/IPBondDescriptor.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/ALOGP.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/AromaticAtomsCountDescriptor.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/AromaticBondsCountDescriptor.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptor.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/TPSADescriptor.java
branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java
branches/egonw/ibondorder/src/org/openscience/cdk/reaction/type/HydrogenRearrangementDeltaReaction.java
branches/egonw/ibondorder/src/org/openscience/cdk/reaction/type/HydrogenRearrangementGammaReaction.java
branches/egonw/ibondorder/src/org/openscience/cdk/smiles/DeduceBondSystemTool.java
branches/egonw/ibondorder/src/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java
branches/egonw/ibondorder/src/org/openscience/cdk/test/aromaticity/CDKHueckelAromaticityDetectorTest.java
branches/egonw/ibondorder/src/org/openscience/cdk/test/graph/invariant/ConjugatedPiSystemsDetectorTest.java
branches/egonw/ibondorder/src/org/openscience/cdk/test/io/cml/CML2WriterTest.java
branches/egonw/ibondorder/src/org/openscience/cdk/test/isomorphism/UniversalIsomorphismTesterTest.java
branches/egonw/ibondorder/src/org/openscience/cdk/test/layout/StructureDiagramGeneratorTest.java
branches/egonw/ibondorder/src/org/openscience/cdk/test/modulesuites/MexperimentalTests.java
branches/egonw/ibondorder/src/org/openscience/cdk/test/modulesuites/MqsarMolecularTests.java
branches/egonw/ibondorder/src/org/openscience/cdk/test/modulesuites/MstandardTests.java
branches/egonw/ibondorder/src/org/openscience/cdk/test/pharmacophore/PharmacophoreMatcherTest.java
branches/egonw/ibondorder/src/org/openscience/cdk/test/ringsearch/AllRingsFinderTest.java
branches/egonw/ibondorder/src/org/openscience/cdk/test/smiles/SmilesParserTest.java
branches/egonw/ibondorder/src/org/openscience/cdk/test/smiles/smarts/parser/RecursiveTest.java
branches/egonw/ibondorder/src/org/openscience/cdk/test/tools/HOSECodeGeneratorTest.java
branches/egonw/ibondorder/src/org/openscience/cdk/tools/AtomTypeTools.java
branches/egonw/ibondorder/src/org/openscience/cdk/tools/AtomicProperties.java
branches/egonw/ibondorder/src/org/openscience/cdk/tools/CDKUtilities.java
Added Paths:
-----------
branches/egonw/ibondorder/src/org/openscience/cdk/test/qsar/descriptors/molecular/ALOGPDescriptorTest.java
Removed Paths:
-------------
branches/egonw/ibondorder/src/org/openscience/cdk/aromaticity/HueckelAromaticityDetector.java
branches/egonw/ibondorder/src/org/openscience/cdk/test/aromaticity/HueckelAromaticityDetectorTest.java
branches/egonw/ibondorder/src/org/openscience/cdk/test/tools/MassToFormulaToolTest.java
Modified: branches/egonw/ibondorder/.classpath
===================================================================
--- branches/egonw/ibondorder/.classpath 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/.classpath 2007-11-23 10:31:00 UTC (rev 9480)
@@ -1,7 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry excluding="org/openscience/cdk/libio/joelib/Convertor.java|org/openscience/cdk/test/libio/joelib/JOELibIOTest.java" kind="src" path="src"/>
- <classpathentry kind="src" path="perf"/>
<classpathentry kind="lib" path="develjar/ant_doxygen.jar"/>
<classpathentry kind="lib" path="develjar/dbdoclet.jar"/>
<classpathentry kind="lib" path="doc/jar/jabref.jar"/>
Modified: branches/egonw/ibondorder/src/META-INF/qsar.datafiles
===================================================================
--- branches/egonw/ibondorder/src/META-INF/qsar.datafiles 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/META-INF/qsar.datafiles 2007-11-23 10:31:00 UTC (rev 9480)
@@ -1,5 +1,6 @@
org/openscience/cdk/qsar/model/data/*.R
org/openscience/cdk/qsar/descriptors/data/*.txt
data/arff/*.arff
+org/openscience/cdk/config/data/whim*
qsar-descriptors.set
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -51,7 +51,6 @@
public class CDKHueckelAromaticityDetector {
private static AtomTypeFactory factory = null;
- private static AllRingsFinder ringFinder = new AllRingsFinder();
public static boolean detectAromaticity(IAtomContainer atomContainer) throws CDKException {
SpanningTree spanningTree = new SpanningTree(atomContainer);
@@ -90,7 +89,7 @@
if (!foundSomeAromaticity && !atLeastOneRingIsSprouted &&
singleRings.getAtomContainerCount() == 2) {
// every ring system consisting of more than two rings is too difficult
- Iterator<IAtomContainer> allRingsIterator = ringFinder.findAllRingsInIsolatedRingSystem(isolatedSystem).atomContainers();
+ Iterator<IAtomContainer> allRingsIterator = new AllRingsFinder().findAllRingsInIsolatedRingSystem(isolatedSystem).atomContainers();
while (allRingsIterator.hasNext()) {
// there should be exactly three rings, of which only one has a size larger
// than the two previous ones
Deleted: branches/egonw/ibondorder/src/org/openscience/cdk/aromaticity/HueckelAromaticityDetector.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/aromaticity/HueckelAromaticityDetector.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/aromaticity/HueckelAromaticityDetector.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -1,313 +0,0 @@
-/* $RCSfile: $
- * $Author$
- * $Date$
- * $Revision$
- *
- * Copyright (C) 2002-2007 The Chemistry Development Kit (CDK) project
- *
- * 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 org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IRing;
-import org.openscience.cdk.interfaces.IRingSet;
-import org.openscience.cdk.ringsearch.AllRingsFinder;
-import org.openscience.cdk.tools.LoggingTool;
-
-/**
- * The HueckelAromaticityDetector detects the aromaticity based on the Hueckel
- * 4n+2 pi-electrons Rule. This is done by one of the detectAromaticity
- * methods. They set the aromaticity flags of appropriate Atoms, Bonds and
- * Rings. After the detection, you can use getFlag(CDKConstants.ISAROMATIC) on
- * these ChemObjects.
- *
- * @author steinbeck
- * @author kaihartmann
- * @cdk.module standard
- * @cdk.svnrev $Revision$
- * @cdk.created 2001-09-04
- *
- * @see org.openscience.cdk.CDKConstants
- */
-public class HueckelAromaticityDetector
-{
-
- static LoggingTool logger = new LoggingTool(HueckelAromaticityDetector.class);
- AllRingsFinder ringFinder = null;
- static IRingSet ringSet=null;
- static long timeout=5000;
-
-
- public static IRingSet getRingSet() {
- return ringSet;
- }
-
- /**
- * Retrieves the set of all rings and performs an aromaticity detection based
- * on Hueckels 4n+2 rule.
- *
- * @param atomContainer AtomContainer to detect rings in
- * @return True if the molecule has aromatic features
- * @exception CDKException Thrown if something goes wrong or in
- * case of a AllRingsFinder timeout
- */
- public static boolean detectAromaticity(IAtomContainer atomContainer) throws CDKException
- {
- return (detectAromaticity(atomContainer, true));
- }
-
-
- /**
- * Uses precomputed set of ALL rings and performs an aromaticity detection
- * based on Hueckels 4n+2 rule.
- *
- * @param ringSet set of ALL rings
- * @param atomContainer The AtomContainer to detect rings in
- * @return True if molecule has aromatic features
- * @exception org.openscience.cdk.exception.CDKException Thrown in case of errors or an
- * AllRingsFinder timeout
- */
- public static boolean detectAromaticity(IAtomContainer atomContainer, IRingSet ringSet) throws org.openscience.cdk.exception.CDKException
- {
- return (detectAromaticity(atomContainer, ringSet, true));
- }
-
-
- /**
- * Retrieves the set of all rings and performs an aromaticity detection based
- * on Hueckels 4n + 2 rule.
- *
- *@param removeAromatictyFlags When true, we leaves ChemObjects that
- * are already marked as aromatic as they are
- *@param atomContainer AtomContainer to be searched for
- * rings
- *@return True, if molecule has aromatic features
- *@exception CDKException Thrown in case of errors or an
- * AllRingsFinder timeout
- */
- public static boolean detectAromaticity(IAtomContainer atomContainer, boolean removeAromatictyFlags) throws org.openscience.cdk.exception.CDKException
- {
- return detectAromaticity(atomContainer, removeAromatictyFlags, null);
- }
-
-
- /**
- * Retrieves the set of all rings and performs an aromaticity detection based
- * on Hueckels 4n + 2 rule. An AllRingsFinder with customized timeout may be
- * assigned to this method.
- *@param removeAromatictyFlags When true, we leaves ChemObjects that
- * are already marked as aromatic as they are
- *@param atomContainer AtomContainer to be searched for
- *@param arf AllRingsFinder to be employed for the
- * ringsearch. Use this to customize the
- * AllRingsFinder timeout feature
- * rings
- *@return True, if molecule has aromatic features
- *@exception CDKException Thrown in case of errors or an
- * AllRingsFinder timeout
- */
- public static boolean detectAromaticity(IAtomContainer atomContainer, boolean removeAromatictyFlags, AllRingsFinder arf) throws org.openscience.cdk.exception.CDKException
- {
- logger.debug("Entered Aromaticity Detection");
- logger.debug("Starting AllRingsFinder");
- long before = System.currentTimeMillis();
- if (arf == null)
- {
- arf = new AllRingsFinder();
- arf.setTimeout(timeout);
- }
- ringSet = arf.findAllRings(atomContainer);
- long after = System.currentTimeMillis();
- logger.debug("time for finding all rings: " + (after - before) + " milliseconds");
- logger.debug("Finished AllRingsFinder");
- return ringSet.getAtomContainerCount() > 0 && detectAromaticity(atomContainer, ringSet, removeAromatictyFlags);
- }
-
-
- /**
- * Uses precomputed set of ALL rings and performs an aromaticity detection
- * based on Hueckels 4n + 2 rule.
- *
- *@param ringSet set of ALL rings
- *@param removeAromaticityFlags Leaves ChemObjects that are already marked as
- * aromatic as they are
- *@param atomContainer AtomContainer to be searched for rings
- *@return True, if molecules contains an
- * aromatic feature
- */
- public static boolean detectAromaticity(IAtomContainer atomContainer, IRingSet ringSet, boolean removeAromaticityFlags)
- {
- boolean foundSomething = false;
- if (removeAromaticityFlags)
- {
- for (int f = 0; f < atomContainer.getAtomCount(); f++)
- {
- atomContainer.getAtom(f).setFlag(CDKConstants.ISAROMATIC, false);
- }
- for (int f = 0; f < atomContainer.getBondCount(); f++)
- {
- atomContainer.getBond(f).setFlag(CDKConstants.ISAROMATIC, false);
- }
- for (int f = 0; f < ringSet.getAtomContainerCount(); f++)
- {
- ringSet.getAtomContainer(f).setFlag(CDKConstants.ISAROMATIC, false);
- }
- }
-
- IRing ring;
- //RingSetManipulator.sort(ringSet);
- for (int f = 0; f < ringSet.getAtomContainerCount(); f++)
- {
- ring = (IRing) ringSet.getAtomContainer(f);
- logger.debug("Testing for aromaticity in ring no ", f);
- if (AromaticityCalculator.isAromatic(ring, atomContainer))
- {
- ring.setFlag(CDKConstants.ISAROMATIC, true);
-
- for (int g = 0; g < ring.getAtomCount(); g++)
- {
- ring.getAtom(g).setFlag(CDKConstants.ISAROMATIC, true);
- }
-
- for (int g = 0; g < ring.getBondCount(); g++)
- {
- ring.getBond(g).setFlag(CDKConstants.ISAROMATIC, true);
- }
-
- foundSomething = true;
- logger.debug("This ring is aromatic: ", f);
- } else
- {
- logger.debug("This ring is *not* aromatic: ", f);
- }
- }
- return foundSomething;
- }
-
-
- /**
- * This method sets the aromaticity flags for a RingSet from the Atom flags.
- * It can be used after the aromaticity detection to set the appropriate flags
- * for a RingSet from the SSSR search.
- *
- *@param ringset the RingSet to set the flags for
- */
- public static void setRingFlags(IRingSet ringset)
- {
- for (int i = 0; i < ringset.getAtomContainerCount(); i++)
- {
- boolean aromatic = true;
- IRing ring = (IRing) ringset.getAtomContainer(i);
- for (int j = 0; j < ring.getAtomCount(); j++)
- {
- if (!ring.getAtom(j).getFlag(CDKConstants.ISAROMATIC))
- {
- aromatic = false;
- break;
- }
- }
- if (aromatic)
- {
- ring.setFlag(CDKConstants.ISAROMATIC, true);
- } else
- {
- ring.setFlag(CDKConstants.ISAROMATIC, false);
- }
- }
- }
-
-
- /*
- * Sets the current AllRingsFinder instance Use this if you want to customize
- * the timeout for the AllRingsFinder. AllRingsFinder is stopping its quest to
- * find all rings after a default of 5 seconds.
- *
- *@param ringFinder The value to assign ringFinder.
- *@see org.openscience.cdk.ringsearch.AllRingsFinder
- */
-// public void setRingFinder(AllRingsFinder ringFinder)
-// {
-// this.ringFinder = ringFinder;
-// }
-
- /**
- * Sets the timeout for the AllRingsFinder. The default is 5000ms.
- *
- * @param timeout The timeout for the AllRingsFinder.
- */
- public static void setTimeout(long timeout) {
- HueckelAromaticityDetector.timeout = timeout;
- }
-
- /*
- * public static boolean isAromatic(AtomContainer ac, Ring ring)
- * {
- * return AromaticityCalculator.isAromatic(ring, ac);
- * }
- * * public static boolean isAromatic(AtomContainer ac, Ring ring)
- * {
- * int piElectronCount = 0;
- * int freeElectronPairCount = 0;
- * Atom atom = null;
- * Bond bond = null;
- * int aromaCounter = 0;
- * logger.debug("isAromatic() -> ring.size(): " + ring.getAtomCount());
- * for (int g = 0; g < ring.getAtomCount(); g++)
- * {
- * atom = ring.getAtomAt(g);
- * if ("O-N-S-P".indexOf(atom.getSymbol()) > -1)
- * {
- * freeElectronPairCount += 1;
- * }
- * if (atom.getFlag(CDKConstants.ISAROMATIC))
- * {
- * aromaCounter ++;
- * }
- * }
- * for (int g = 0; g < ring.getElectronContainerCount(); g++) {
- * ElectronContainer ec = ring.getElectronContainerAt(g);
- * if (ec instanceof org.openscience.cdk.interfaces.Bond) {
- * bond = (Bond)ec;
- * if (bond.getOrder() > 1) {
- * piElectronCount += 2*(bond.getOrder()-1);
- * }
- * }
- * }
- * for (int f = 0; f < ((ring.getAtomCount() - 2)/4) + 2; f ++)
- * {
- * logger.debug("isAromatic() -> freeElectronPairCount: " + freeElectronPairCount);
- * logger.debug("isAromatic() -> piElectronCount: " + piElectronCount);
- * logger.debug("isAromatic() -> f: " + f);
- * logger.debug("isAromatic() -> (4 * f) + 2: " + ((4 * f) + 2));
- * logger.debug("isAromatic() -> ring.size(): " + ring.getAtomCount());
- * logger.debug("isAromatic() -> aromaCounter: " + aromaCounter);
- * if (aromaCounter == ring.getAtomCount()) return true;
- * else if ((piElectronCount == ring.getAtomCount())&&((4 * f) + 2 == piElectronCount)) return true;
- * else if ((4 * f) + 2 == piElectronCount + (freeElectronPairCount * 2) && ring.getAtomCount() < piElectronCount + (freeElectronPairCount * 2)) return true;
- * }
- * return false;
- * }
- */
-}
-
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/atomtype/EStateAtomTypeMatcher.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/atomtype/EStateAtomTypeMatcher.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/atomtype/EStateAtomTypeMatcher.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -25,47 +25,56 @@
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.interfaces.*;
-import org.openscience.cdk.ringsearch.AllRingsFinder;
/**
* Determines the EState atom types.
- *
- * @author Todd Martin
+ *
+ * @author Todd Martin
+ * @author nick
* @cdk.module standard
- * @cdk.svnrev $Revision: 9162 $
+ * @cdk.svnrev $Revision: 9162 $
*/
+
+
+
public class EStateAtomTypeMatcher implements IAtomTypeMatcher {
- public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom) {
+ IRingSet ringSet = null;
+
+ public void setRingSet(IRingSet rs)
+ {
+ ringSet = rs;
+ }
+
+ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
+ {
+
IAtomType atomType = null;
-
try {
- String fragment;
-
- AllRingsFinder arf = new AllRingsFinder();
- IRingSet rs = arf.findAllRings(atomContainer);
-
+ String fragment = "";
+ int NumHAtoms = 0;
int NumSingleBonds2 = 0;
int NumDoubleBonds2 = 0;
int NumTripleBonds2 = 0;
int NumAromaticBonds2 = 0;
int NumAromaticBondsTotal2 = 0;
-
+
String element = atom.getSymbol();
-
- java.util.List<IAtom> attachedAtoms = atomContainer.getConnectedAtomsList(atom);
-
+
+ java.util.List attachedAtoms = atomContainer.getConnectedAtomsList(atom);
+
for (int j = 0; j <= attachedAtoms.size() - 1; j++) {
- IAtom attached = attachedAtoms.get(j);
+ IAtom attached = (IAtom)attachedAtoms.get(j);
IBond b = atomContainer.getBond(atom, attached);
-
+ if(attached.getSymbol().equals("H"))
+ NumHAtoms++;
+
if (atom.getFlag(CDKConstants.ISAROMATIC)
- && attached
- .getFlag(CDKConstants.ISAROMATIC)) {
-
+ && attached.getFlag(CDKConstants.ISAROMATIC)) {
+
boolean SameRing = inSameAromaticRing(atomContainer, atom,
- attached, rs);
-
+ attached, ringSet);
+
if (SameRing) {
NumAromaticBonds2++;
if (element.equals("N")) {
@@ -82,9 +91,9 @@
if (b.getOrder() == IBond.Order.TRIPLE)
NumTripleBonds2++;
}
-
+
} else {
-
+
if (b.getOrder() == IBond.Order.SINGLE)
NumSingleBonds2++;
if (b.getOrder() == IBond.Order.DOUBLE)
@@ -93,81 +102,78 @@
NumTripleBonds2++;
}
}
-
+ NumSingleBonds2 = NumSingleBonds2 - NumHAtoms;
+
// assign frag here
fragment = "S";
-
+
for (int j = 0; j <= NumTripleBonds2 - 1; j++) {
fragment += "t";
}
-
+
for (int j = 0; j <= NumDoubleBonds2 - 1; j++) {
fragment += "d";
}
-
+
for (int j = 0; j <= NumSingleBonds2 - 1; j++) {
fragment += "s";
}
-
+
for (int j = 0; j <= NumAromaticBonds2 - 1; j++) {
fragment += "a";
}
-
+
fragment += element;
-
+
if (atom.getFormalCharge() == 1) {
fragment += "p";
} else if (atom.getFormalCharge() == -1) {
fragment += "m";
}
-
- fragment += "*";// flag it as unassigned fragment
-
- // for now set #H = 0 TODO- add routine to figure out #Hs for
- // possible valence states
- atom.setHydrogenCount(0);
+ if (NumHAtoms == 1)
+ fragment += "H";
+ else
+ if (NumHAtoms > 1)
+ fragment += ("H" + NumHAtoms);
+
+ //atom.setHydrogenCount(0);
+
atomType = atom.getBuilder().newAtomType(fragment, atom.getSymbol());
atomType.setFormalCharge(atom.getFormalCharge());
if (atom.getFlag(CDKConstants.ISAROMATIC))
atomType.setFlag(CDKConstants.ISAROMATIC, true);
-
+
} catch (Exception e) {
e.printStackTrace();
}
-
+
return atomType;
}
public static boolean inSameAromaticRing(IAtomContainer m, IAtom atom1,
- IAtom atom2, IRingSet rs) {
-
- for (int i = 0; i <= rs.getAtomContainerCount() - 1; i++) {
+ IAtom atom2, IRingSet rs)
+ {
+ for (int i = 0; i <= rs.getAtomContainerCount() - 1; i++)
+ {
IRing r = (IRing) rs.getAtomContainer(i);
-
- if (!r.getFlag(CDKConstants.ISAROMATIC))
- continue;
-
- // ArrayList al=new ArrayList();
-
- boolean HaveOne = false;
- boolean HaveTwo = false;
-
- for (int j = 0; j <= r.getAtomCount() - 1; j++) {
- if (m.getAtomNumber(r.getAtom(j)) == m.getAtomNumber(atom1))
- HaveOne = true;
- if (m.getAtomNumber(r.getAtom(j)) == m.getAtomNumber(atom2))
- HaveTwo = true;
+ if (r.contains(atom1) && r.contains(atom2))
+ {
+ if (isAromaticRing(r))
+ return(true);
}
-
- if (HaveOne && HaveTwo) {
- return true;
- }
-
- } // end ring for loop
-
+ }
return false;
}
-
-
+
+
+ static boolean isAromaticRing(IRing ring)
+ {
+ for (int i = 0; i < ring.getAtomCount(); i++)
+ if(!ring.getAtom(i).getFlag(CDKConstants.ISAROMATIC))
+ return(false);
+
+ return(true);
+ }
+
}
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -23,11 +23,20 @@
*/
package org.openscience.cdk.charges;
+import java.io.IOException;
+
import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.config.AtomTypeFactory;
import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.interfaces.*;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomContainerSet;
+import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.interfaces.IMoleculeSet;
+import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.type.BreakingBondReaction;
import org.openscience.cdk.reaction.type.HyperconjugationReaction;
@@ -35,8 +44,6 @@
import org.openscience.cdk.tools.StructureResonanceGenerator;
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import java.io.IOException;
-
/**
* <p>The calculation of the Gasteiger (PEPE) partial charges is based on
* {@cdk.cite Saller85}. This class doesn't implement the original method of the Marsili but the
@@ -437,8 +444,8 @@
/*aromatic*/
double fA = 1.0;
try {
- if(HueckelAromaticityDetector.detectAromaticity(ac))
- if(!HueckelAromaticityDetector.detectAromaticity(atomContainer))
+ if(CDKHueckelAromaticityDetector.detectAromaticity(ac))
+ if(!CDKHueckelAromaticityDetector.detectAromaticity(atomContainer))
fA = 0.3;
} catch (CDKException e) {
e.printStackTrace();
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/fingerprint/Fingerprinter.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/fingerprint/Fingerprinter.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/fingerprint/Fingerprinter.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -32,12 +32,13 @@
import java.util.Map;
import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.ringsearch.AllRingsFinder;
import org.openscience.cdk.tools.LoggingTool;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
/**
* Generates a Fingerprint for a given AtomContainer. Fingerprints are
@@ -127,7 +128,8 @@
logger.debug("Entering Fingerprinter");
logger.debug("Starting Aromaticity Detection");
long before = System.currentTimeMillis();
- HueckelAromaticityDetector.detectAromaticity(ac, false, ringFinder);
+ AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(ac);
+ CDKHueckelAromaticityDetector.detectAromaticity(ac);
long after = System.currentTimeMillis();
logger.debug("time for aromaticity calculation: " + (after - before) + " milliseconds");
logger.debug("Finished Aromaticity Detection");
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/iupac/parser/MoleculeBuilder.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/iupac/parser/MoleculeBuilder.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/iupac/parser/MoleculeBuilder.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -31,7 +31,7 @@
import org.openscience.cdk.Bond;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.Ring;
-import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
@@ -40,6 +40,7 @@
import org.openscience.cdk.interfaces.IBond.Order;
import org.openscience.cdk.templates.MoleculeFactory;
import org.openscience.cdk.tools.CDKHydrogenAdder;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
/**
@@ -296,7 +297,8 @@
//Detect Aromacity in the benzene ring.
try
{
- HueckelAromaticityDetector.detectAromaticity(benzene);
+ AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(benzene);
+ CDKHueckelAromaticityDetector.detectAromaticity(benzene);
}
catch (Exception exc)
{
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -24,22 +24,28 @@
*/
package org.openscience.cdk.modeling.builder3d;
+import java.io.InputStream;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.Vector;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.exception.NoSuchAtomTypeException;
-import org.openscience.cdk.interfaces.*;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomType;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.interfaces.IPseudoAtom;
+import org.openscience.cdk.interfaces.IRing;
+import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.ringsearch.SSSRFinder;
import org.openscience.cdk.tools.HOSECodeGenerator;
import org.openscience.cdk.tools.manipulator.RingSetManipulator;
-import java.io.InputStream;
-import java.util.Hashtable;
-import java.util.Iterator;
-import java.util.Vector;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
/**
* Reads in a force field configuration file, set the atom types into a vector, and the data into a hashtable
* Therfore it uses the class MM2BasedParamterSetReader
@@ -243,7 +249,7 @@
IRingSet ringSetMolecule = new SSSRFinder(molecule).findSSSR();
boolean isInHeteroRing = false;
try {
- HueckelAromaticityDetector.detectAromaticity(molecule);
+ CDKHueckelAromaticityDetector.detectAromaticity(molecule);
} catch (Exception cdk1) {
System.out.println("AROMATICITYError: Cannot determine aromaticity due to: " + cdk1.toString());
}
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -20,12 +20,21 @@
*/
package org.openscience.cdk.qsar.descriptors.atomic;
+import java.util.Iterator;
+import java.util.List;
+
import org.openscience.cdk.AtomContainerSet;
import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector;
-import org.openscience.cdk.interfaces.*;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.interfaces.IMoleculeSet;
+import org.openscience.cdk.interfaces.IReaction;
+import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IAtomicDescriptor;
@@ -35,10 +44,8 @@
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.type.ElectronImpactNBEReaction;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import java.util.Iterator;
-import java.util.List;
-
/**
* This class returns the ionization potential of an atom containg lone
* pair electrons. It is
@@ -131,7 +138,8 @@
double[] resultsH;
/*control if it is into an aromatic or conjugated system*/
- HueckelAromaticityDetector.detectAromaticity(localClone,true);
+ AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(localClone);
+ CDKHueckelAromaticityDetector.detectAromaticity(localClone);
AtomContainerSet conjugatedPi = ConjugatedPiSystemsDetector.detect(localClone);
Iterator acI = conjugatedPi.atomContainers();
while(acI.hasNext()){
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -25,18 +25,17 @@
package org.openscience.cdk.qsar.descriptors.atomic;
import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IMolecule;
-import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.nonotify.NNMolecule;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IAtomicDescriptor;
import org.openscience.cdk.qsar.result.IntegerResult;
-import org.openscience.cdk.ringsearch.AllRingsFinder;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
/**
* This descriptor returns 1 if the protons is directly bonded to an aromatic system,
@@ -144,8 +143,8 @@
int isProtonInAromaticSystem = 0;
IMolecule mol = new NNMolecule(clonedAtomContainer);
if (checkAromaticity) {
- IRingSet rs = (new AllRingsFinder()).findAllRings(mol);
- HueckelAromaticityDetector.detectAromaticity(mol, rs, true);
+ AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(mol);
+ CDKHueckelAromaticityDetector.detectAromaticity(mol);
}
java.util.List neighboor = mol.getConnectedAtomsList(clonedAtom);
IAtom neighbour0 = (IAtom)neighboor.get(0);
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -26,7 +26,7 @@
import org.openscience.cdk.AtomContainerSet;
import org.openscience.cdk.Molecule;
-import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector;
import org.openscience.cdk.interfaces.IAtom;
@@ -35,6 +35,7 @@
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IAtomicDescriptor;
import org.openscience.cdk.qsar.result.BooleanResult;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
/**
* This class evaluates if a proton is joined to a conjugated system.
@@ -140,7 +141,8 @@
boolean isProtonInPiSystem = false;
Molecule mol = new Molecule(clonedAtomContainer);
if (checkAromaticity) {
- HueckelAromaticityDetector.detectAromaticity(mol);
+ AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(mol);
+ CDKHueckelAromaticityDetector.detectAromaticity(mol);
}
if(atom.getSymbol().equals("H")) {
if(acold!=clonedAtomContainer){
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -21,28 +21,34 @@
*/
package org.openscience.cdk.qsar.descriptors.atomic;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.vecmath.Point3d;
+import javax.vecmath.Vector3d;
+
import org.openscience.cdk.AtomContainerSet;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.Ring;
-import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector;
-import org.openscience.cdk.interfaces.*;
+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;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IAtomicDescriptor;
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.ringsearch.AllRingsFinder;
import org.openscience.cdk.tools.LoggingTool;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import javax.vecmath.Point3d;
-import javax.vecmath.Vector3d;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-
/**
* This class calculates G3R proton descriptors used in neural networks for H1
* NMR shift.
@@ -189,8 +195,8 @@
}
}
if (checkAromaticity) {
- HueckelAromaticityDetector.detectAromaticity(varAtomContainer,
- varRingSet, true);
+ AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(varAtomContainer);
+ CDKHueckelAromaticityDetector.detectAromaticity(varAtomContainer);
}
List<IRing> rsAtom;
Ring ring;
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -21,28 +21,34 @@
*/
package org.openscience.cdk.qsar.descriptors.atomic;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.vecmath.Point3d;
+import javax.vecmath.Vector3d;
+
import org.openscience.cdk.AtomContainerSet;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.Ring;
-import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector;
-import org.openscience.cdk.interfaces.*;
+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;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IAtomicDescriptor;
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.ringsearch.AllRingsFinder;
import org.openscience.cdk.tools.LoggingTool;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import javax.vecmath.Point3d;
-import javax.vecmath.Vector3d;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-
/**
* This class calculates GDR proton descriptors used in neural networks for H1 NMR shift.
* <p/>
@@ -176,7 +182,8 @@
}
}
if (checkAromaticity) {
- HueckelAromaticityDetector.detectAromaticity(varAtomContainer, varRingSet, true);
+ AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(varAtomContainer);
+ CDKHueckelAromaticityDetector.detectAromaticity(varAtomContainer);
}
List rsAtom;
Ring ring;
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -21,29 +21,35 @@
*/
package org.openscience.cdk.qsar.descriptors.atomic;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.vecmath.Point3d;
+import javax.vecmath.Vector3d;
+
import org.openscience.cdk.AtomContainerSet;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.Ring;
-import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector;
-import org.openscience.cdk.interfaces.*;
+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;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IAtomicDescriptor;
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.ringsearch.AllRingsFinder;
import org.openscience.cdk.tools.LoggingTool;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import javax.vecmath.Point3d;
-import javax.vecmath.Vector3d;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-
/**
* This class calculates GHR proton descriptors used in neural networks for H1 NMR shift.
* <p/>
@@ -180,7 +186,8 @@
}
}
if (checkAromaticity) {
- HueckelAromaticityDetector.detectAromaticity(varAtomContainer, varRingSet, true);
+ AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(varAtomContainer);
+ CDKHueckelAromaticityDetector.detectAromaticity(varAtomContainer);
}
List rsAtom;
Ring ring;
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -33,7 +33,7 @@
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.Ring;
-import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.MoleculeGraphs;
@@ -49,6 +49,7 @@
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.ringsearch.AllRingsFinder;
import org.openscience.cdk.tools.LoggingTool;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
/**
* This class calculates GHR topological proton descriptors used in neural networks for H1 NMR shift.
@@ -182,7 +183,8 @@
}
}
if (checkAromaticity) {
- HueckelAromaticityDetector.detectAromaticity(varAtomContainer, varRingSet, true);
+ AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(varAtomContainer);
+ CDKHueckelAromaticityDetector.detectAromaticity(varAtomContainer);
}
List<IRing> rsAtom;
Ring ring;
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -21,28 +21,34 @@
*/
package org.openscience.cdk.qsar.descriptors.atomic;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.vecmath.Point3d;
+import javax.vecmath.Vector3d;
+
import org.openscience.cdk.AtomContainerSet;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.Molecule;
import org.openscience.cdk.Ring;
-import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector;
-import org.openscience.cdk.interfaces.*;
+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;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IAtomicDescriptor;
import org.openscience.cdk.qsar.result.DoubleArrayResult;
import org.openscience.cdk.ringsearch.AllRingsFinder;
import org.openscience.cdk.tools.LoggingTool;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import javax.vecmath.Point3d;
-import javax.vecmath.Vector3d;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-
/**
* This class calculates GDR proton descriptors used in neural networks for H1 NMR shift.
* <p/>
@@ -175,7 +181,8 @@
}
}
if (checkAromaticity) {
- HueckelAromaticityDetector.detectAromaticity(varAtomContainer, varRingSet, true);
+ AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(varAtomContainer);
+ CDKHueckelAromaticityDetector.detectAromaticity(varAtomContainer);
}
List rsAtom;
Ring ring;
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -22,7 +22,7 @@
import org.openscience.cdk.AtomContainerSet;
import org.openscience.cdk.Molecule;
-import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector;
import org.openscience.cdk.interfaces.IAtom;
@@ -31,6 +31,7 @@
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IAtomPairDescriptor;
import org.openscience.cdk.qsar.result.BooleanResult;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
/**
* This class checks if two atoms have pi-contact (this is true when there is
@@ -143,7 +144,8 @@
Molecule mol = new Molecule(ac);
if (checkAromaticity) {
- HueckelAromaticityDetector.detectAromaticity(mol);
+ AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(mol);
+ CDKHueckelAromaticityDetector.detectAromaticity(mol);
}
boolean piContact = false;
int counter = 0;
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/bond/IPBondDescriptor.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/bond/IPBondDescriptor.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/bond/IPBondDescriptor.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -20,12 +20,20 @@
*/
package org.openscience.cdk.qsar.descriptors.bond;
+import java.util.Iterator;
+
import org.openscience.cdk.AtomContainerSet;
import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector;
-import org.openscience.cdk.interfaces.*;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.interfaces.IMoleculeSet;
+import org.openscience.cdk.interfaces.IReaction;
+import org.openscience.cdk.interfaces.IReactionSet;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IBondDescriptor;
@@ -36,9 +44,8 @@
import org.openscience.cdk.qsar.result.DoubleResult;
import org.openscience.cdk.reaction.IReactionProcess;
import org.openscience.cdk.reaction.type.ElectronImpactPDBReaction;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import java.util.Iterator;
-
/**
*
* This class returns the ionization potential of a Bond. It is
@@ -130,7 +137,8 @@
double[] resultsH = null;
try{
- HueckelAromaticityDetector.detectAromaticity(localClone,true);
+ AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(localClone);
+ CDKHueckelAromaticityDetector.detectAromaticity(localClone);
} catch (Exception exc){
exc.printStackTrace();
}
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -24,11 +24,21 @@
*/
package org.openscience.cdk.qsar.descriptors.bond;
+import java.util.ArrayList;
+
import org.openscience.cdk.CDKConstants;
-import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
+import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.charges.GasteigerPEPEPartialCharges;
import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.interfaces.*;
+import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IAtomContainerSet;
+import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IMapping;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.interfaces.IMoleculeSet;
+import org.openscience.cdk.interfaces.IReactionSet;
+import org.openscience.cdk.interfaces.IRingSet;
import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer;
import org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator;
@@ -43,9 +53,8 @@
import org.openscience.cdk.reaction.type.BreakingBondReaction;
import org.openscience.cdk.ringsearch.SSSRFinder;
import org.openscience.cdk.tools.StructureResonanceGenerator;
+import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
-import java.util.ArrayList;
-
/**
* <p>The calculation of Resonance stabilization of a positive charge of an heavy
* atom is based on Gasteiger H.Saller.</p>
@@ -135,6 +144,7 @@
throw new CDKException("Error during clone");
}
IBond clonedBond = localClone.getBond(atomContainer.getBondNumber(bond));
+ AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(localClone);
cleanFlagReactiveCenter((IMolecule) localClone);
@@ -208,7 +218,7 @@
int maxNumbStruc = 50;
boolean isAromatic = false;
- if(HueckelAromaticityDetector.detectAromaticity(localClone)){
+ if(CDKHueckelAromaticityDetector.detectAromaticity(localClone)){
isAromatic = true;
IRingSet ringSet = new SSSRFinder(product).findSSSR();
if( ringSet.getAtomContainerCount() > 4)
Modified: branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/ALOGP.java
===================================================================
--- branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/ALOGP.java 2007-11-23 10:06:53 UTC (rev 9479)
+++ branches/egonw/ibondorder/src/org/openscience/cdk/qsar/descriptors/molecular/ALOGP.java 2007-11-23 10:31:00 UTC (rev 9480)
@@ -23,18 +23,10 @@
*/
package org.openscience.cdk.qsar.descriptors.molecular;
-import java.lang.reflect.Method;
-
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.atomtype.EStateAtomTypeMatcher;
-import org.openscience.cdk.atomtype.IAtomTypeMatcher;
import org.openscience.cdk.exception.CDKException;
-import org.openscience.cdk.interfaces.IAtom;
-import org.openscience.cdk.interfaces.IAtomContainer;
-import org.openscience.cdk.interfaces.IAtomType;
-import org.openscience.cdk.interfaces.IBond;
-import org.openscience.cdk.interfaces.IRing;
-import org.openscience.cdk.interfaces.IRingSet;
+import org.openscience.cdk.interfaces.*;
import org.openscience.cdk.qsar.DescriptorSpecification;
import org.openscience.cdk.qsar.DescriptorValue;
import org.openscience.cdk.qsar.IMolecularDescriptor;
@@ -42,10 +34,22 @@
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.ringsearch.AllRingsFinder;
import org.openscience.cdk.tools.AtomicProperties;
+import org.openscience.cdk.tools.LoggingTool;
+import org.openscience.cdk.tools.manipulator.BondManipulator;
+import java.lang.reflect.Method;
+
/**
* This class calculates ALOGP (Ghose-Crippen LogKow) and the
* Ghose-Crippen molar refractivity.
+ *
+ * <b>Note</b> The code assumes that aromaticity has been detected before
+ * evaluating this descriptor. The code also expects that the molecule
+ * will have hydrogens explicitly set. For SD files, this is usually not
+ * a problem since hydrogens are explicit. But for the case of molecules
+ * obtained from SMILES, hydrogens must be made explicit.
+ *
+
*
* <p>TODO: what should sub return if have missing fragment?
* Just report sum for other fragments? Or report as -9999 and
@@ -74,1908 +78,1936 @@
* </ol>
*
* @author Todd Martin
- * @cdk.module nocompile
- * @cdk.svnrev $Revision: 9162 $
+ * @cdk.module qsar
+ * @cdk.svnrev $Revision: 9162 $
* @cdk.set qsar-descriptors
+ * @cdk.keyword logP
+ * @cdk.keyword lipophilicity
+ * @cdk.keyword refractivity
+ * @see org.openscience.cdk.tools.HydrogenAdder
+ * @see org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector
*/
public class ALOGP implements IMolecularDescriptor {
+ private LoggingTool logger;
- IAtomContainer atomContainer;
- IRingSet rs;
- String[] fragment; // estate fragments for each atom
+ private boolean printDebugInfo = false;
+ IAtomContainer atomContainer;
+ IRingSet rs;
+ String[] fragment; // estate fragments for each atom
- AtomicProperties ap; // needed to retrieve electronegativities
-
- int[] frags = new int[121]; // counts of each type of fragment in the molecule
- public int[] alogpfrag; // alogp fragments for each atom (used to see which atoms have missing fragments)
- double[] fragval = new double[121];// coefficients for alogp model
- double[] refracval = new double[121]; // coefficients for refractivity model
- public String UnassignedAtoms="";
+ AtomicProperties ap; // needed to retrieve electronegativities
- ...
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