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[Cdk-commits] SF.net SVN: cdk: [9477] branches/egonw/remove-non-cdkatomtype-code.patch
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From: <eg...@us...> - 2007-11-23 09:46:12
|
Revision: 9477
http://cdk.svn.sourceforge.net/cdk/?rev=9477&view=rev
Author: egonw
Date: 2007-11-23 01:46:09 -0800 (Fri, 23 Nov 2007)
Log Message:
-----------
Updated patch: zero regressions now, and because I did not receive any comments I will apply it to trunk now...
Modified Paths:
--------------
branches/egonw/remove-non-cdkatomtype-code.patch
Modified: branches/egonw/remove-non-cdkatomtype-code.patch
===================================================================
--- branches/egonw/remove-non-cdkatomtype-code.patch 2007-11-23 09:38:46 UTC (rev 9476)
+++ branches/egonw/remove-non-cdkatomtype-code.patch 2007-11-23 09:46:09 UTC (rev 9477)
@@ -1,7 +1,7 @@
Index: .project
===================================================================
---- .project (.../trunk/cdk) (revision 9446)
-+++ .project (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- .project (.../trunk/cdk) (revision 9476)
++++ .project (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -1,6 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
@@ -12,8 +12,8 @@
</projects>
Index: src/org/openscience/cdk/tools/AtomTypeTools.java
===================================================================
---- src/org/openscience/cdk/tools/AtomTypeTools.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/tools/AtomTypeTools.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/tools/AtomTypeTools.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/tools/AtomTypeTools.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -25,11 +25,11 @@
package org.openscience.cdk.tools;
@@ -39,8 +39,8 @@
logger.error("AROMATICITYError: Cannot determine aromaticity due to: " + cdk1.toString());
Index: src/org/openscience/cdk/tools/CDKUtilities.java
===================================================================
---- src/org/openscience/cdk/tools/CDKUtilities.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/tools/CDKUtilities.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/tools/CDKUtilities.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/tools/CDKUtilities.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -26,13 +26,15 @@
import java.util.List;
@@ -73,8 +73,8 @@
} catch (Exception e) {
Index: src/org/openscience/cdk/iupac/parser/MoleculeBuilder.java
===================================================================
---- src/org/openscience/cdk/iupac/parser/MoleculeBuilder.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/iupac/parser/MoleculeBuilder.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/iupac/parser/MoleculeBuilder.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/iupac/parser/MoleculeBuilder.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -31,13 +31,14 @@
import org.openscience.cdk.Bond;
import org.openscience.cdk.Molecule;
@@ -103,8 +103,8 @@
{
Index: src/org/openscience/cdk/reaction/type/HydrogenRearrangementGammaReaction.java
===================================================================
---- src/org/openscience/cdk/reaction/type/HydrogenRearrangementGammaReaction.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/reaction/type/HydrogenRearrangementGammaReaction.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/reaction/type/HydrogenRearrangementGammaReaction.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/reaction/type/HydrogenRearrangementGammaReaction.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -33,7 +33,7 @@
import org.openscience.cdk.Molecule;
import org.openscience.cdk.Ring;
@@ -134,8 +134,8 @@
ringSet = arf.findAllRings((Molecule) reactant);
Index: src/org/openscience/cdk/reaction/type/HydrogenRearrangementDeltaReaction.java
===================================================================
---- src/org/openscience/cdk/reaction/type/HydrogenRearrangementDeltaReaction.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/reaction/type/HydrogenRearrangementDeltaReaction.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/reaction/type/HydrogenRearrangementDeltaReaction.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/reaction/type/HydrogenRearrangementDeltaReaction.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -33,7 +33,7 @@
import org.openscience.cdk.Molecule;
import org.openscience.cdk.Ring;
@@ -165,8 +165,8 @@
/* no rearrangement if H belongs to ring*/
Index: src/org/openscience/cdk/aromaticity/HueckelAromaticityDetector.java
===================================================================
---- src/org/openscience/cdk/aromaticity/HueckelAromaticityDetector.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/aromaticity/HueckelAromaticityDetector.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/aromaticity/HueckelAromaticityDetector.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/aromaticity/HueckelAromaticityDetector.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -1,313 +0,0 @@
-/* $RCSfile: $
- * $Author$
@@ -483,8 +483,8 @@
-
Index: src/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector.java
===================================================================
---- src/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/aromaticity/CDKHueckelAromaticityDetector.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -51,7 +51,6 @@
public class CDKHueckelAromaticityDetector {
@@ -504,8 +504,8 @@
// than the two previous ones
Index: src/org/openscience/cdk/fingerprint/Fingerprinter.java
===================================================================
---- src/org/openscience/cdk/fingerprint/Fingerprinter.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/fingerprint/Fingerprinter.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/fingerprint/Fingerprinter.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/fingerprint/Fingerprinter.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -32,12 +32,13 @@
import java.util.Map;
@@ -533,8 +533,8 @@
logger.debug("Finished Aromaticity Detection");
Index: src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
===================================================================
---- src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -23,11 +23,20 @@
*/
package org.openscience.cdk.charges;
@@ -580,8 +580,8 @@
e.printStackTrace();
Index: src/org/openscience/cdk/test/ringsearch/AllRingsFinderTest.java
===================================================================
---- src/org/openscience/cdk/test/ringsearch/AllRingsFinderTest.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/test/ringsearch/AllRingsFinderTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/test/ringsearch/AllRingsFinderTest.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/test/ringsearch/AllRingsFinderTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -20,16 +20,27 @@
*/
package org.openscience.cdk.test.ringsearch;
@@ -636,8 +636,8 @@
}
Index: src/org/openscience/cdk/test/tools/HOSECodeGeneratorTest.java
===================================================================
---- src/org/openscience/cdk/test/tools/HOSECodeGeneratorTest.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/test/tools/HOSECodeGeneratorTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/test/tools/HOSECodeGeneratorTest.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/test/tools/HOSECodeGeneratorTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -34,7 +34,7 @@
import junit.framework.TestSuite;
@@ -732,8 +732,8 @@
hcg.getSpheres((Molecule) molecule, molecule.getAtom(0), 3, true);
Index: src/org/openscience/cdk/test/graph/invariant/ConjugatedPiSystemsDetectorTest.java
===================================================================
---- src/org/openscience/cdk/test/graph/invariant/ConjugatedPiSystemsDetectorTest.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/test/graph/invariant/ConjugatedPiSystemsDetectorTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/test/graph/invariant/ConjugatedPiSystemsDetectorTest.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/test/graph/invariant/ConjugatedPiSystemsDetectorTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -32,7 +32,7 @@
import org.openscience.cdk.AtomContainerSet;
import org.openscience.cdk.ChemFile;
@@ -864,8 +864,8 @@
Index: src/org/openscience/cdk/test/aromaticity/HueckelAromaticityDetectorTest.java
===================================================================
---- src/org/openscience/cdk/test/aromaticity/HueckelAromaticityDetectorTest.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/test/aromaticity/HueckelAromaticityDetectorTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/test/aromaticity/HueckelAromaticityDetectorTest.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/test/aromaticity/HueckelAromaticityDetectorTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -1,783 +0,0 @@
-/* $RCSfile$
- * $Author$
@@ -1652,8 +1652,8 @@
-
Index: src/org/openscience/cdk/test/aromaticity/CDKHueckelAromaticityDetectorTest.java
===================================================================
---- src/org/openscience/cdk/test/aromaticity/CDKHueckelAromaticityDetectorTest.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/test/aromaticity/CDKHueckelAromaticityDetectorTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/test/aromaticity/CDKHueckelAromaticityDetectorTest.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/test/aromaticity/CDKHueckelAromaticityDetectorTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -496,7 +496,6 @@
public void testBenzene() throws Exception {
Molecule molecule = MoleculeFactory.makeBenzene();
@@ -1664,8 +1664,8 @@
assertTrue(molecule.getAtom(f).getFlag(CDKConstants.ISAROMATIC));
Index: src/org/openscience/cdk/test/isomorphism/UniversalIsomorphismTesterTest.java
===================================================================
---- src/org/openscience/cdk/test/isomorphism/UniversalIsomorphismTesterTest.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/test/isomorphism/UniversalIsomorphismTesterTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/test/isomorphism/UniversalIsomorphismTesterTest.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/test/isomorphism/UniversalIsomorphismTesterTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -29,6 +29,7 @@
package org.openscience.cdk.test.isomorphism;
@@ -1711,8 +1711,8 @@
list = UniversalIsomorphismTester.getOverlaps(mol2, mol1);
Index: src/org/openscience/cdk/test/layout/StructureDiagramGeneratorTest.java
===================================================================
---- src/org/openscience/cdk/test/layout/StructureDiagramGeneratorTest.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/test/layout/StructureDiagramGeneratorTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/test/layout/StructureDiagramGeneratorTest.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/test/layout/StructureDiagramGeneratorTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -25,12 +25,10 @@
import java.io.InputStream;
@@ -1769,8 +1769,8 @@
Index: src/org/openscience/cdk/test/modulesuites/MstandardTests.java
===================================================================
---- src/org/openscience/cdk/test/modulesuites/MstandardTests.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/test/modulesuites/MstandardTests.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/test/modulesuites/MstandardTests.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/test/modulesuites/MstandardTests.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -29,7 +29,6 @@
import org.openscience.cdk.test.StandardCoverageTest;
@@ -1789,8 +1789,8 @@
suite.addTest(GeometryToolsTest.suite());
Index: src/org/openscience/cdk/test/pharmacophore/PharmacophoreMatcherTest.java
===================================================================
---- src/org/openscience/cdk/test/pharmacophore/PharmacophoreMatcherTest.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/test/pharmacophore/PharmacophoreMatcherTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/test/pharmacophore/PharmacophoreMatcherTest.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/test/pharmacophore/PharmacophoreMatcherTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -1,9 +1,17 @@
package org.openscience.cdk.test.pharmacophore;
@@ -1833,8 +1833,8 @@
boolean status = matcher.matches(mol);
Index: src/org/openscience/cdk/test/smiles/SmilesParserTest.java
===================================================================
---- src/org/openscience/cdk/test/smiles/SmilesParserTest.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/test/smiles/SmilesParserTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/test/smiles/SmilesParserTest.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/test/smiles/SmilesParserTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -1002,7 +1002,7 @@
for (int i=0; i<7; i++) {
IBond bond = mol.getBond(i);
@@ -1846,8 +1846,8 @@
Assert.assertTrue(bond.getFlag(CDKConstants.ISAROMATIC));
Index: src/org/openscience/cdk/test/smiles/smarts/parser/RecursiveTest.java
===================================================================
---- src/org/openscience/cdk/test/smiles/smarts/parser/RecursiveTest.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/test/smiles/smarts/parser/RecursiveTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/test/smiles/smarts/parser/RecursiveTest.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/test/smiles/smarts/parser/RecursiveTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -20,8 +20,12 @@
*/
package org.openscience.cdk.test.smiles.smarts.parser;
@@ -1883,8 +1883,8 @@
nmatch++;
Index: src/org/openscience/cdk/test/io/cml/CML2WriterTest.java
===================================================================
---- src/org/openscience/cdk/test/io/cml/CML2WriterTest.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/test/io/cml/CML2WriterTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/test/io/cml/CML2WriterTest.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/test/io/cml/CML2WriterTest.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -40,7 +40,7 @@
import org.openscience.cdk.Crystal;
import org.openscience.cdk.Molecule;
@@ -1905,8 +1905,8 @@
cmlWriter.write(molecule);
Index: src/org/openscience/cdk/smiles/DeduceBondSystemTool.java
===================================================================
---- src/org/openscience/cdk/smiles/DeduceBondSystemTool.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/smiles/DeduceBondSystemTool.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/smiles/DeduceBondSystemTool.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/smiles/DeduceBondSystemTool.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -35,7 +35,7 @@
import org.openscience.cdk.Molecule;
import org.openscience.cdk.Ring;
@@ -1936,8 +1936,8 @@
// Figure out which rings we want to make sure are aromatic:
Index: src/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java
===================================================================
---- src/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/smiles/smarts/SMARTSQueryTool.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -20,6 +20,13 @@
*/
package org.openscience.cdk.smiles.smarts;
@@ -1973,8 +1973,8 @@
logger.debug(e.toString());
Index: src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java
===================================================================
---- src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -24,22 +24,28 @@
*/
package org.openscience.cdk.modeling.builder3d;
@@ -2024,8 +2024,8 @@
}
Index: src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/bond/ResonancePositiveChargeDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -24,11 +24,21 @@
*/
package org.openscience.cdk.qsar.descriptors.bond;
@@ -2080,8 +2080,8 @@
if( ringSet.getAtomContainerCount() > 4)
Index: src/org/openscience/cdk/qsar/descriptors/bond/IPBondDescriptor.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/bond/IPBondDescriptor.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/bond/IPBondDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/bond/IPBondDescriptor.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/bond/IPBondDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -20,12 +20,20 @@
*/
package org.openscience.cdk.qsar.descriptors.bond;
@@ -2128,8 +2128,8 @@
}
Index: src/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/molecular/BCUTDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -29,7 +29,7 @@
import org.openscience.cdk.CDKConstants;
@@ -2151,8 +2151,8 @@
// find number of heavy atoms
Index: src/org/openscience/cdk/qsar/descriptors/molecular/AromaticBondsCountDescriptor.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/molecular/AromaticBondsCountDescriptor.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/molecular/AromaticBondsCountDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/molecular/AromaticBondsCountDescriptor.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/molecular/AromaticBondsCountDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -24,6 +24,8 @@
*/
package org.openscience.cdk.qsar.descriptors.molecular;
@@ -2183,8 +2183,8 @@
Iterator bonds = ac.bonds();
Index: src/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -24,23 +24,22 @@
*/
package org.openscience.cdk.qsar.descriptors.molecular;
@@ -2226,8 +2226,8 @@
Vector startSphere = null;
Index: src/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -24,9 +24,11 @@
*/
package org.openscience.cdk.qsar.descriptors.molecular;
@@ -2252,30 +2252,49 @@
/**
* Class that returns the number of atoms in the largest chain.
* <p/>
-@@ -165,14 +166,14 @@
+@@ -165,26 +166,18 @@
*/
public DescriptorValue calculate(IAtomContainer container) throws CDKException {
//logger.debug("LargestChainDescriptor");
- IRingSet rs = null;
-+ IRingSet rs = (IRingSet) (new AllRingsFinder()).findAllRings(container);
-
- if (checkAromaticity && !checkRingSystem) {
+-
+- if (checkAromaticity && !checkRingSystem) {
- rs = (IRingSet) (new AllRingsFinder()).findAllRings(container);
- HueckelAromaticityDetector.detectAromaticity(container, rs, true);
-+ AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(container);
-+ CDKHueckelAromaticityDetector.detectAromaticity(container);
- } else if (checkAromaticity && checkRingSystem) {
+- } else if (checkAromaticity && checkRingSystem) {
- rs = (IRingSet) (new AllRingsFinder()).findAllRings(container);
- HueckelAromaticityDetector.detectAromaticity(container, rs, true);
+- for (int i = 0; i < container.getAtomCount(); i++) {
+- if (rs.contains(container.getAtom(i))) {
+- container.getAtom(i).setFlag(CDKConstants.ISINRING, true);
+- }
+- }
+- } else if (!checkAromaticity && checkRingSystem) {
+- rs = (IRingSet) new SSSRFinder(container).findSSSR();
+- for (int i = 0; i < container.getAtomCount(); i++) {
+- if (rs.contains(container.getAtom(i))) {
+- container.getAtom(i).setFlag(CDKConstants.ISINRING, true);
+- }
+- }
++ if (checkRingSystem) {
++ IRingSet rs = (IRingSet) new SSSRFinder(container).findSSSR();
++ for (int i = 0; i < container.getAtomCount(); i++) {
++ if (rs.contains(container.getAtom(i))) {
++ container.getAtom(i).setFlag(CDKConstants.ISINRING, true);
++ }
++ }
++ }
++
++ if (checkAromaticity) {
+ AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(container);
+ CDKHueckelAromaticityDetector.detectAromaticity(container);
- for (int i = 0; i < container.getAtomCount(); i++) {
- if (rs.contains(container.getAtom(i))) {
- container.getAtom(i).setFlag(CDKConstants.ISINRING, true);
+ }
+
+
Index: src/org/openscience/cdk/qsar/descriptors/molecular/TPSADescriptor.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/molecular/TPSADescriptor.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/molecular/TPSADescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/molecular/TPSADescriptor.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/molecular/TPSADescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -41,6 +41,22 @@
import java.util.HashMap;
import java.util.Vector;
@@ -2313,8 +2332,8 @@
java.util.Iterator atoms = ac.atoms();
Index: src/org/openscience/cdk/qsar/descriptors/molecular/AromaticAtomsCountDescriptor.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/molecular/AromaticAtomsCountDescriptor.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/molecular/AromaticAtomsCountDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/molecular/AromaticAtomsCountDescriptor.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/molecular/AromaticAtomsCountDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -28,13 +28,12 @@
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.exception.CDKException;
@@ -2339,10 +2358,39 @@
CDKHueckelAromaticityDetector.detectAromaticity(ac);
}
for (int i = 0; i < ac.getAtomCount(); i++) {
+Index: src/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptor.java
+===================================================================
+--- src/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptor.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/molecular/RotatableBondsCountDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
+@@ -36,6 +36,7 @@
+ import org.openscience.cdk.qsar.result.IDescriptorResult;
+ import org.openscience.cdk.qsar.result.IntegerResult;
+ import org.openscience.cdk.ringsearch.AllRingsFinder;
++import org.openscience.cdk.ringsearch.SSSRFinder;
+
+ import java.util.Iterator;
+ import java.util.List;
+@@ -139,14 +140,10 @@
+ Iterator bonds = ac.bonds();
+ int degree0 = 0;
+ int degree1 = 0;
+- IRingSet ringSet = null;
+- AllRingsFinder arf = new AllRingsFinder();
+- ringSet = arf.findAllRings(ac);
+- List ringsWithThisBond = null;
++ IRingSet ringSet = (IRingSet) new SSSRFinder(ac).findSSSR();
+ while (bonds.hasNext()) {
+ IBond bond = (IBond)bonds.next();
+- ringsWithThisBond = ringSet.getRings(bond);
+- if (ringsWithThisBond.size() > 0) {
++ if (ringSet.getRings(bond).size() > 0) {
+ bond.setFlag(CDKConstants.ISINRING, true);
+ }
+ }
Index: src/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/molecular/HBondAcceptorCountDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -25,7 +25,7 @@
package org.openscience.cdk.qsar.descriptors.molecular;
@@ -2375,8 +2423,8 @@
// labelled for loop to allow for labelled continue statements within the loop
Index: src/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/molecular/XLogPDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -41,6 +41,7 @@
import org.openscience.cdk.qsar.result.IDescriptorResult;
import org.openscience.cdk.ringsearch.AllRingsFinder;
@@ -2385,8 +2433,12 @@
import org.openscience.cdk.tools.manipulator.RingSetManipulator;
import java.util.ArrayList;
-@@ -198,6 +199,7 @@
- IRingSet rs = (IRingSet) (new AllRingsFinder()).findAllRings(ac);
+@@ -195,9 +196,10 @@
+ throw new CDKException("Error during clone");
+ }
+
+- IRingSet rs = (IRingSet) (new AllRingsFinder()).findAllRings(ac);
++ IRingSet rs = (IRingSet) new SSSRFinder(ac).findSSSR();
IRingSet atomRingSet=null;
if (checkAromaticity) {
+ AtomContainerManipulator.percieveAtomTypesAndConfigerAtoms(ac);
@@ -2395,8 +2447,8 @@
double xlogP = 0;
Index: src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/atomic/IPAtomicDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -20,12 +20,21 @@
*/
package org.openscience.cdk.qsar.descriptors.atomic;
@@ -2445,8 +2497,8 @@
while(acI.hasNext()){
Index: src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInConjugatedPiSystemDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -26,7 +26,7 @@
import org.openscience.cdk.AtomContainerSet;
@@ -2476,8 +2528,8 @@
if(acold!=clonedAtomContainer){
Index: src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -21,28 +21,34 @@
*/
package org.openscience.cdk.qsar.descriptors.atomic;
@@ -2533,8 +2585,8 @@
Ring ring;
Index: src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -21,29 +21,35 @@
*/
package org.openscience.cdk.qsar.descriptors.atomic;
@@ -2591,8 +2643,8 @@
Ring ring;
Index: src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -21,28 +21,34 @@
*/
package org.openscience.cdk.qsar.descriptors.atomic;
@@ -2649,8 +2701,8 @@
Ring ring;
Index: src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -21,28 +21,34 @@
*/
package org.openscience.cdk.qsar.descriptors.atomic;
@@ -2706,8 +2758,8 @@
Ring ring;
Index: src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -25,18 +25,17 @@
package org.openscience.cdk.qsar.descriptors.atomic;
@@ -2742,8 +2794,8 @@
IAtom neighbour0 = (IAtom)neighboor.get(0);
Index: src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -21,30 +21,36 @@
*/
package org.openscience.cdk.qsar.descriptors.atomic;
@@ -2801,8 +2853,8 @@
Ring ring;
Index: src/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java
===================================================================
---- src/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java (.../trunk/cdk) (revision 9446)
-+++ src/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9446)
+--- src/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java (.../trunk/cdk) (revision 9476)
++++ src/org/openscience/cdk/qsar/descriptors/atompair/PiContactDetectionDescriptor.java (.../branches/egonw/remove-non-cdkatomtype-code) (revision 9476)
@@ -22,7 +22,7 @@
import org.openscience.cdk.AtomContainerSet;
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