From: <eg...@us...> - 2008-07-26 20:36:15
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Revision: 11772 http://cdk.svn.sourceforge.net/cdk/?rev=11772&view=rev Author: egonw Date: 2008-07-26 20:36:12 +0000 (Sat, 26 Jul 2008) Log Message: ----------- Removed dependency on nonotify Modified Paths: -------------- cdk/trunk/src/META-INF/qsaratomic.cdkdepends cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationDescriptor.java cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/PartialSigmaChargeDescriptor.java Modified: cdk/trunk/src/META-INF/qsaratomic.cdkdepends =================================================================== --- cdk/trunk/src/META-INF/qsaratomic.cdkdepends 2008-07-26 20:28:45 UTC (rev 11771) +++ cdk/trunk/src/META-INF/qsaratomic.cdkdepends 2008-07-26 20:36:12 UTC (rev 11772) @@ -1,6 +1,5 @@ cdk-interfaces.jar cdk-data.jar -cdk-nonotify.jar cdk-core.jar cdk-standard.jar cdk-valencycheck.jar Modified: cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationDescriptor.java =================================================================== --- cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationDescriptor.java 2008-07-26 20:28:45 UTC (rev 11771) +++ cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/AtomHybridizationDescriptor.java 2008-07-26 20:36:12 UTC (rev 11772) @@ -1,9 +1,5 @@ -/* - * $RCSfile$ - * $Author$ - * $Date$ - * $Revision$ - * +/* $Revision$ $Author$ $Date$ + * * Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project * * Contact: cdk...@li... @@ -32,7 +28,6 @@ import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IAtomType; import org.openscience.cdk.interfaces.IAtomType.Hybridization; -import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; @@ -68,19 +63,10 @@ public class AtomHybridizationDescriptor implements IAtomicDescriptor { AtomTypeManipulator atman = null; - CDKAtomTypeMatcher atm = null; IAtom atom = null; IAtomType matched = null; /** - * Constructor for the AtomHybridizationDescriptor object - */ - public AtomHybridizationDescriptor() { - atm = CDKAtomTypeMatcher.getInstance(NoNotificationChemObjectBuilder.getInstance()); - } - - - /** * Gets the specification attribute of the AtomHybridizationDescriptor object * *@return The specification value @@ -135,7 +121,7 @@ @TestMethod(value="testCalculate_IAtomContainer") public DescriptorValue calculate(IAtom atom, IAtomContainer container) { try { - matched = atm.findMatchingAtomType(container, atom); + matched = CDKAtomTypeMatcher.getInstance(atom.getBuilder()).findMatchingAtomType(container, atom); } catch (CDKException e) { return getDummyDescriptorValue(e); } Modified: cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java =================================================================== --- cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java 2008-07-26 20:28:45 UTC (rev 11771) +++ cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/IsProtonInAromaticSystemDescriptor.java 2008-07-26 20:36:12 UTC (rev 11772) @@ -1,9 +1,5 @@ -/* - * $RCSfile$ - * $Author$ - * $Date$ - * $Revision$ - * +/* $Revision$ $Author$ $Date$ + * * Copyright (C) 2004-2007 The Chemistry Development Kit (CDK) project * * Contact: cdk...@li... @@ -32,7 +28,6 @@ import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.nonotify.NNMolecule; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; import org.openscience.cdk.qsar.IAtomicDescriptor; @@ -156,7 +151,7 @@ IAtom clonedAtom = clonedAtomContainer.getAtom(atomContainer.getAtomNumber(atom)); int isProtonInAromaticSystem = 0; - IMolecule mol = new NNMolecule(clonedAtomContainer); + IMolecule mol = atom.getBuilder().newMolecule(clonedAtomContainer); if (checkAromaticity) { try { AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol); Modified: cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/PartialSigmaChargeDescriptor.java =================================================================== --- cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/PartialSigmaChargeDescriptor.java 2008-07-26 20:28:45 UTC (rev 11771) +++ cdk/trunk/src/main/org/openscience/cdk/qsar/descriptors/atomic/PartialSigmaChargeDescriptor.java 2008-07-26 20:36:12 UTC (rev 11772) @@ -1,8 +1,4 @@ -/* - * $RCSfile$ - * $Author$ - * $Date$ - * $Revision$ +/* $Revision$ $Author$ $Date$ * * Copyright (C) 2004-2007 Miguel Rojas <mig...@un...> * @@ -31,7 +27,6 @@ import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.nonotify.NNMolecule; import org.openscience.cdk.qsar.AbstractAtomicDescriptor; import org.openscience.cdk.qsar.DescriptorSpecification; import org.openscience.cdk.qsar.DescriptorValue; @@ -147,7 +142,7 @@ @TestMethod(value="testCalculate_IAtomContainer") public DescriptorValue calculate(IAtom atom, IAtomContainer ac) { if (!isCachedAtomContainer(ac)) { - IMolecule mol = new NNMolecule(ac); + IMolecule mol = atom.getBuilder().newMolecule(ac); if (maxIterations != 0) peoe.setMaxGasteigerIters(maxIterations); try { peoe.assignGasteigerMarsiliSigmaPartialCharges(mol, true); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |