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[Cdk-commits] CVS: cdk/src/org/openscience/cdk/qsar APolDescriptor.java,1.9,1.10 AromaticAtomsCountDescriptor.java,1.12,1.13 AromaticBondsCountDescriptor.java,1.12,1.13 AtomCountDescriptor.java,1.23,1.24 AtomDegreeDescriptor.java,1.6,1.7 AtomHybridizationDescriptor.java,1.4,1.5 AtomHybridizationVSEPRDescriptor.java,1.3,1.4 AtomValenceDescriptor.java,1.7,1.8 BCUTDescriptor.java,1.17,1.18 BPolDescriptor.java,1.7,1.8 BondCountDescriptor.java,1.14,1.15 BondsToAtomDescriptor.java,1.6,1.7 CPSADescriptor.java,1.2,1.3 CarbonConnectivityOrderOneDescriptor.java,1.2,1.3 CarbonConnectivityOrderZeroDescriptor.java,1.2,1.3 ConnectivityOrderOneDescriptor.java,1.11,1.12 ConnectivityOrderZeroDescriptor.java,1.10,1.11 Descriptor.java,1.13,1.14 DistanceToAtomDescriptor.java,1.6,1.7 EccentricConnectivityIndexDescriptor.java,1.2,1.3 EffectivePolarizabilityDescriptor.java,1.14,1.15 GravitationalIndexDescriptor.java,1.15,1.16 HBondAcceptorCountDescriptor.java,1.11,1.12 HBondDonorCountDescriptor.java,1.11,1.12 InductiveAtomicHardnessDescriptor.java,1.4,1.5 InductiveAtomicSoftnessDescriptor.java,1.4,1.5 IsProtonInAromaticSystemDescriptor.java,1.15,1.16 IsProtonInConjugatedPiSystemDescriptor.java,1.13,1.14 KappaShapeIndicesDescriptor.java,1.9,1.10 MomentOfInertiaDescriptor.java,1.7,1.8 PeriodicTablePositionDescriptor.java,1.5,1.6 PetitjeanNumberDescriptor.java,1.9,1.10 PiContactDetectionDescriptor.java,1.5,1.6 ProtonTotalPartialChargeDescriptor.java,1.13,1.14 RDFProtonDescriptor.java,1.9,1.10 RotatableBondsCountDescriptor.java,1.15,1.16 RuleOfFiveDescriptor.java,1.9,1.10 SigmaElectronegativityDescriptor.java,1.13,1.14 TPSADescriptor.java,1.12,1.13 VAdjMaDescriptor.java,1.12,1.13 ValenceCarbonConnectivityOrderOneDescriptor.java,1.2,1.3 ValenceCarbonConnectivityOrderZeroDescriptor.java,1.2,1.3 ValenceConnectivityOrderOneDescriptor.java,1.15,1.16 ValenceConnectivityOrderZeroDescriptor.java,1.15,1.16 VdWRadiusDescriptor.java,1.10,1.11 WHIMDescriptor.java,1.16,1.17 WeightDescriptor.java,1.15,1.16 WienerNumbersDescriptor.java,1.12,1.13 XLogPDescriptor.java,1.13,1.14 ZagrebIndexDescriptor.java,1.13,1.14
Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv25886/src/org/openscience/cdk/qsar Modified Files: APolDescriptor.java AromaticAtomsCountDescriptor.java AromaticBondsCountDescriptor.java AtomCountDescriptor.java AtomDegreeDescriptor.java AtomHybridizationDescriptor.java AtomHybridizationVSEPRDescriptor.java AtomValenceDescriptor.java BCUTDescriptor.java BPolDescriptor.java BondCountDescriptor.java BondsToAtomDescriptor.java CPSADescriptor.java CarbonConnectivityOrderOneDescriptor.java CarbonConnectivityOrderZeroDescriptor.java ConnectivityOrderOneDescriptor.java ConnectivityOrderZeroDescriptor.java Descriptor.java DistanceToAtomDescriptor.java EccentricConnectivityIndexDescriptor.java EffectivePolarizabilityDescriptor.java GravitationalIndexDescriptor.java HBondAcceptorCountDescriptor.java HBondDonorCountDescriptor.java InductiveAtomicHardnessDescriptor.java InductiveAtomicSoftnessDescriptor.java IsProtonInAromaticSystemDescriptor.java IsProtonInConjugatedPiSystemDescriptor.java KappaShapeIndicesDescriptor.java MomentOfInertiaDescriptor.java PeriodicTablePositionDescriptor.java PetitjeanNumberDescriptor.java PiContactDetectionDescriptor.java ProtonTotalPartialChargeDescriptor.java RDFProtonDescriptor.java RotatableBondsCountDescriptor.java RuleOfFiveDescriptor.java SigmaElectronegativityDescriptor.java TPSADescriptor.java VAdjMaDescriptor.java ValenceCarbonConnectivityOrderOneDescriptor.java ValenceCarbonConnectivityOrderZeroDescriptor.java ValenceConnectivityOrderOneDescriptor.java ValenceConnectivityOrderZeroDescriptor.java VdWRadiusDescriptor.java WHIMDescriptor.java WeightDescriptor.java WienerNumbersDescriptor.java XLogPDescriptor.java ZagrebIndexDescriptor.java Log Message: Removed a large number of unused imports Index: APolDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/APolDescriptor.java,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- APolDescriptor.java 2 Jul 2005 18:38:25 -0000 1.9 +++ APolDescriptor.java 4 Aug 2005 14:36:32 -0000 1.10 @@ -25,11 +25,11 @@ package org.openscience.cdk.qsar; import org.openscience.cdk.Atom; -import org.openscience.cdk.Element; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.Element; import org.openscience.cdk.config.IsotopeFactory; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.tools.LoggingTool; /** Index: AromaticAtomsCountDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/AromaticAtomsCountDescriptor.java,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- AromaticAtomsCountDescriptor.java 2 Jul 2005 18:38:25 -0000 1.12 +++ AromaticAtomsCountDescriptor.java 4 Aug 2005 14:36:32 -0000 1.13 @@ -27,13 +27,11 @@ import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.RingSet; -import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; -import org.openscience.cdk.qsar.result.*; -import java.util.Map; -import java.util.Hashtable; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.IntegerResult; +import org.openscience.cdk.ringsearch.AllRingsFinder; /** * Class that returns the number of aromatic atoms in an atom container. Index: AromaticBondsCountDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/AromaticBondsCountDescriptor.java,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- AromaticBondsCountDescriptor.java 2 Jul 2005 18:38:25 -0000 1.12 +++ AromaticBondsCountDescriptor.java 4 Aug 2005 14:36:32 -0000 1.13 @@ -27,13 +27,11 @@ import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Bond; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.RingSet; -import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; -import org.openscience.cdk.qsar.result.*; -import java.util.Map; -import java.util.Hashtable; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.IntegerResult; +import org.openscience.cdk.ringsearch.AllRingsFinder; /** * This Class contains a method that returns the number of aromatic atoms in an AtomContainer. Index: AtomCountDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/AtomCountDescriptor.java,v retrieving revision 1.23 retrieving revision 1.24 diff -u -r1.23 -r1.24 --- AtomCountDescriptor.java 12 Jul 2005 21:39:44 -0000 1.23 +++ AtomCountDescriptor.java 4 Aug 2005 14:36:32 -0000 1.24 @@ -25,16 +25,9 @@ package org.openscience.cdk.qsar; import org.openscience.cdk.Atom; -import org.openscience.cdk.AtomType; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.Bond; -import org.openscience.cdk.ChemObject; -import org.openscience.cdk.Molecule; -import org.openscience.cdk.CDKConstants; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; -import java.util.Map; -import java.util.Hashtable; +import org.openscience.cdk.qsar.result.IntegerResult; /** * Descriptor based on the number of atoms of a certain element type. Index: AtomDegreeDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/AtomDegreeDescriptor.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- AtomDegreeDescriptor.java 2 Jul 2005 18:38:25 -0000 1.6 +++ AtomDegreeDescriptor.java 4 Aug 2005 14:36:32 -0000 1.7 @@ -25,15 +25,10 @@ package org.openscience.cdk.qsar; import org.openscience.cdk.Atom; -import org.openscience.cdk.AtomType; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.Molecule; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; -import org.openscience.cdk.config.AtomTypeFactory; +import org.openscience.cdk.qsar.result.IntegerResult; import org.openscience.cdk.tools.LoggingTool; -import org.openscience.cdk.graph.*; -import org.openscience.cdk.graph.matrix.*; /** * This class returns the number of not-Hs substituents of an atom, also defined as "atom degree". Index: AtomHybridizationDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/AtomHybridizationDescriptor.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- AtomHybridizationDescriptor.java 12 Jul 2005 20:42:33 -0000 1.4 +++ AtomHybridizationDescriptor.java 4 Aug 2005 14:36:32 -0000 1.5 @@ -25,17 +25,13 @@ package org.openscience.cdk.qsar; import org.openscience.cdk.Atom; -import org.openscience.cdk.tools.manipulator.*; -import org.openscience.cdk.atomtype.HybridizationStateATMatcher; -import org.openscience.cdk.AtomType; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.Molecule; +import org.openscience.cdk.AtomType; +import org.openscience.cdk.atomtype.HybridizationStateATMatcher; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; -import org.openscience.cdk.config.AtomTypeFactory; +import org.openscience.cdk.qsar.result.IntegerResult; import org.openscience.cdk.tools.LoggingTool; -import org.openscience.cdk.graph.*; -import org.openscience.cdk.graph.matrix.*; +import org.openscience.cdk.tools.manipulator.AtomTypeManipulator; /** * This class returns the hybridization of an atom. Index: AtomHybridizationVSEPRDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/AtomHybridizationVSEPRDescriptor.java,v retrieving revision 1.3 retrieving revision 1.4 diff -u -r1.3 -r1.4 --- AtomHybridizationVSEPRDescriptor.java 28 Apr 2005 08:20:40 -0000 1.3 +++ AtomHybridizationVSEPRDescriptor.java 4 Aug 2005 14:36:32 -0000 1.4 @@ -25,15 +25,13 @@ package org.openscience.cdk.qsar; import org.openscience.cdk.Atom; -import org.openscience.cdk.AtomType; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.Molecule; +import org.openscience.cdk.AtomType; +import org.openscience.cdk.CDKConstants; import org.openscience.cdk.config.AtomTypeFactory; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; -import org.openscience.cdk.config.AtomTypeFactory; +import org.openscience.cdk.qsar.result.IntegerResult; import org.openscience.cdk.tools.LoggingTool; -import org.openscience.cdk.CDKConstants; /** * This class returns the hybridization of an atom. Index: AtomValenceDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/AtomValenceDescriptor.java,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- AtomValenceDescriptor.java 28 Apr 2005 08:20:40 -0000 1.7 +++ AtomValenceDescriptor.java 4 Aug 2005 14:36:32 -0000 1.8 @@ -24,17 +24,12 @@ */ package org.openscience.cdk.qsar; -import org.openscience.cdk.Atom; -import org.openscience.cdk.AtomType; +import java.util.Hashtable; + import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.Molecule; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; -import org.openscience.cdk.config.AtomTypeFactory; +import org.openscience.cdk.qsar.result.IntegerResult; import org.openscience.cdk.tools.LoggingTool; -import org.openscience.cdk.graph.*; -import org.openscience.cdk.graph.matrix.*; -import java.util.Hashtable; /** * This class returns the valence of an atom. Index: BCUTDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/BCUTDescriptor.java,v retrieving revision 1.17 retrieving revision 1.18 diff -u -r1.17 -r1.18 --- BCUTDescriptor.java 14 Jul 2005 23:49:08 -0000 1.17 +++ BCUTDescriptor.java 4 Aug 2005 14:36:32 -0000 1.18 @@ -23,27 +23,21 @@ */ package org.openscience.cdk.qsar; -import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Bond; -import org.openscience.cdk.Molecule; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import org.openscience.cdk.tools.HydrogenAdder; -import org.openscience.cdk.config.IsotopeFactory; +import org.openscience.cdk.Molecule; +import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges; import org.openscience.cdk.charges.Polarizability; -import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; -import org.openscience.cdk.qsar.result.*; - -import java.util.Vector; -import java.util.ArrayList; -import java.util.Map; -import java.util.Hashtable; +import org.openscience.cdk.config.IsotopeFactory; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.DoubleArrayResult; +import org.openscience.cdk.tools.HydrogenAdder; +import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import Jama.Matrix; import Jama.EigenvalueDecomposition; +import Jama.Matrix; /** * Eigenvalue based descriptor noted for its utility in chemical diversity. Index: BPolDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/BPolDescriptor.java,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- BPolDescriptor.java 28 Apr 2005 08:20:44 -0000 1.7 +++ BPolDescriptor.java 4 Aug 2005 14:36:32 -0000 1.8 @@ -25,12 +25,12 @@ package org.openscience.cdk.qsar; import org.openscience.cdk.Atom; +import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Bond; import org.openscience.cdk.Element; -import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; import org.openscience.cdk.config.IsotopeFactory; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.tools.LoggingTool; /** Index: BondCountDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/BondCountDescriptor.java,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- BondCountDescriptor.java 28 Apr 2005 08:20:44 -0000 1.14 +++ BondCountDescriptor.java 4 Aug 2005 14:36:32 -0000 1.15 @@ -27,9 +27,7 @@ import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Bond; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; -import java.util.Map; -import java.util.Hashtable; +import org.openscience.cdk.qsar.result.IntegerResult; /** * Descriptor based on the number of bonds of a certain bond order. Index: BondsToAtomDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/BondsToAtomDescriptor.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- BondsToAtomDescriptor.java 28 Apr 2005 08:20:44 -0000 1.6 +++ BondsToAtomDescriptor.java 4 Aug 2005 14:36:32 -0000 1.7 @@ -24,15 +24,12 @@ package org.openscience.cdk.qsar; import org.openscience.cdk.Atom; -import org.openscience.cdk.AtomType; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Molecule; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; -import org.openscience.cdk.config.AtomTypeFactory; +import org.openscience.cdk.graph.MoleculeGraphs; +import org.openscience.cdk.qsar.result.IntegerResult; import org.openscience.cdk.tools.LoggingTool; -import org.openscience.cdk.graph.*; -import org.openscience.cdk.graph.matrix.*; /** * This class returns the number of bonds on the shortest path between two atoms. Index: CPSADescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/CPSADescriptor.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- CPSADescriptor.java 26 Jun 2005 23:16:41 -0000 1.2 +++ CPSADescriptor.java 4 Aug 2005 14:36:32 -0000 1.3 @@ -20,21 +20,13 @@ package org.openscience.cdk.qsar; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.config.IsotopeFactory; -import org.openscience.cdk.geometry.GeometryTools; -import org.openscience.cdk.tools.MFAnalyser; import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges; +import org.openscience.cdk.config.IsotopeFactory; +import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.geometry.surface.NumericalSurface; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.tools.LoggingTool; -import org.openscience.cdk.exception.CDKException; -import javax.vecmath.*; -import java.lang.Math; - - -import Jama.Matrix; -import Jama.EigenvalueDecomposition; +import org.openscience.cdk.tools.MFAnalyser; /** * Calculates 29 Charged Partial Surface Area (CPSA) descriptors. Index: CarbonConnectivityOrderOneDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/CarbonConnectivityOrderOneDescriptor.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- CarbonConnectivityOrderOneDescriptor.java 28 Apr 2005 08:20:44 -0000 1.2 +++ CarbonConnectivityOrderOneDescriptor.java 4 Aug 2005 14:36:32 -0000 1.3 @@ -24,12 +24,13 @@ */ package org.openscience.cdk.qsar; +import java.util.ArrayList; + import org.openscience.cdk.Atom; -import org.openscience.cdk.Bond; import org.openscience.cdk.AtomContainer; +import org.openscience.cdk.Bond; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; -import java.util.ArrayList; +import org.openscience.cdk.qsar.result.DoubleResult; /** * CarbonConnectivity index (order 1): Index: CarbonConnectivityOrderZeroDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/CarbonConnectivityOrderZeroDescriptor.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- CarbonConnectivityOrderZeroDescriptor.java 28 Apr 2005 08:20:44 -0000 1.2 +++ CarbonConnectivityOrderZeroDescriptor.java 4 Aug 2005 14:36:32 -0000 1.3 @@ -27,7 +27,7 @@ import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.qsar.result.DoubleResult; /** * Carbon Connectivity index (order 0): Index: ConnectivityOrderOneDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/ConnectivityOrderOneDescriptor.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- ConnectivityOrderOneDescriptor.java 28 Apr 2005 08:20:44 -0000 1.11 +++ ConnectivityOrderOneDescriptor.java 4 Aug 2005 14:36:32 -0000 1.12 @@ -24,12 +24,13 @@ */ package org.openscience.cdk.qsar; +import java.util.ArrayList; + import org.openscience.cdk.Atom; -import org.openscience.cdk.Bond; import org.openscience.cdk.AtomContainer; +import org.openscience.cdk.Bond; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; -import java.util.ArrayList; +import org.openscience.cdk.qsar.result.DoubleResult; /** * Connectivity index (order 1): Index: ConnectivityOrderZeroDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/ConnectivityOrderZeroDescriptor.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- ConnectivityOrderZeroDescriptor.java 28 Apr 2005 08:20:44 -0000 1.10 +++ ConnectivityOrderZeroDescriptor.java 4 Aug 2005 14:36:32 -0000 1.11 @@ -27,7 +27,7 @@ import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.qsar.result.DoubleResult; /** * Connectivity index (order 0): Index: Descriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/Descriptor.java,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- Descriptor.java 1 Jul 2005 15:43:25 -0000 1.13 +++ Descriptor.java 4 Aug 2005 14:36:32 -0000 1.14 @@ -25,7 +25,6 @@ import org.openscience.cdk.AtomContainer; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; /** * Classes that implement this interface are QSAR descriptor calculators. Index: DistanceToAtomDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/DistanceToAtomDescriptor.java,v retrieving revision 1.6 retrieving revision 1.7 diff -u -r1.6 -r1.7 --- DistanceToAtomDescriptor.java 12 Jul 2005 19:33:13 -0000 1.6 +++ DistanceToAtomDescriptor.java 4 Aug 2005 14:36:32 -0000 1.7 @@ -24,17 +24,13 @@ */ package org.openscience.cdk.qsar; +import javax.vecmath.Point3d; + import org.openscience.cdk.Atom; -import org.openscience.cdk.AtomType; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.Molecule; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; -import org.openscience.cdk.config.AtomTypeFactory; +import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.tools.LoggingTool; -import org.openscience.cdk.graph.*; -import org.openscience.cdk.graph.matrix.*; -import javax.vecmath.*; /** * This class returns the 3D distance between two atoms. Index: EccentricConnectivityIndexDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/EccentricConnectivityIndexDescriptor.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- EccentricConnectivityIndexDescriptor.java 28 Apr 2005 08:20:44 -0000 1.2 +++ EccentricConnectivityIndexDescriptor.java 4 Aug 2005 14:36:53 -0000 1.3 @@ -19,17 +19,13 @@ */ package org.openscience.cdk.qsar; -import org.openscience.cdk.Bond; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.config.IsotopeFactory; -import org.openscience.cdk.qsar.result.*; -import org.openscience.cdk.tools.LoggingTool; -import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; import org.openscience.cdk.graph.PathTools; import org.openscience.cdk.graph.matrix.AdjacencyMatrix; -import java.lang.Math; -import java.util.Vector; +import org.openscience.cdk.qsar.result.IntegerResult; +import org.openscience.cdk.tools.LoggingTool; +import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; /** Index: EffectivePolarizabilityDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/EffectivePolarizabilityDescriptor.java,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- EffectivePolarizabilityDescriptor.java 23 Jun 2005 11:01:31 -0000 1.14 +++ EffectivePolarizabilityDescriptor.java 4 Aug 2005 14:36:53 -0000 1.15 @@ -27,10 +27,9 @@ import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Molecule; -import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.charges.Polarizability; -import org.openscience.cdk.qsar.result.*; -import java.util.Hashtable; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.DoubleResult; /** * Effective polarizability of an heavy atom and its protons Index: GravitationalIndexDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/GravitationalIndexDescriptor.java,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- GravitationalIndexDescriptor.java 26 Jun 2005 23:16:41 -0000 1.15 +++ GravitationalIndexDescriptor.java 4 Aug 2005 14:36:53 -0000 1.16 @@ -24,16 +24,15 @@ */ package org.openscience.cdk.qsar; -import org.openscience.cdk.Bond; +import java.util.Vector; + import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.Bond; import org.openscience.cdk.config.IsotopeFactory; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.tools.LoggingTool; -import java.lang.Math; -import java.util.Vector; - /** * Descriptor characterizing the mass distribution of the molecule. Index: HBondAcceptorCountDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/HBondAcceptorCountDescriptor.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- HBondAcceptorCountDescriptor.java 26 Jul 2005 08:58:16 -0000 1.11 +++ HBondAcceptorCountDescriptor.java 4 Aug 2005 14:36:53 -0000 1.12 @@ -26,13 +26,10 @@ import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.Molecule; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; -import org.openscience.cdk.qsar.result.*; -import java.util.Map; -import java.util.Hashtable; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.IntegerResult; /** * This descriptor calculates the number of hydrogen bond acceptors using a slightly simplified version of the Index: HBondDonorCountDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/HBondDonorCountDescriptor.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- HBondDonorCountDescriptor.java 26 Jul 2005 08:58:16 -0000 1.11 +++ HBondDonorCountDescriptor.java 4 Aug 2005 14:36:53 -0000 1.12 @@ -25,15 +25,9 @@ package org.openscience.cdk.qsar; import org.openscience.cdk.Atom; -import org.openscience.cdk.Element; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.Molecule; -import org.openscience.cdk.CDKConstants; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; -import org.openscience.cdk.qsar.result.*; -import java.util.Map; -import java.util.Hashtable; +import org.openscience.cdk.qsar.result.IntegerResult; /** * This descriptor calculates the number of hydrogen bond donors using a slightly simplified version of the Index: InductiveAtomicHardnessDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/InductiveAtomicHardnessDescriptor.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- InductiveAtomicHardnessDescriptor.java 12 Jul 2005 19:33:13 -0000 1.4 +++ InductiveAtomicHardnessDescriptor.java 4 Aug 2005 14:36:54 -0000 1.5 @@ -24,15 +24,17 @@ */ package org.openscience.cdk.qsar; +import java.io.IOException; + +import javax.vecmath.Point3d; + import org.openscience.cdk.Atom; -import org.openscience.cdk.AtomType; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.AtomType; import org.openscience.cdk.config.AtomTypeFactory; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.tools.LoggingTool; -import javax.vecmath.*; -import java.io.*; /** * Inductive atomic hardness of an atom in a polyatomic system can be defined * as the "resistance" to a change of the atomic charge. <p> Index: InductiveAtomicSoftnessDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/InductiveAtomicSoftnessDescriptor.java,v retrieving revision 1.4 retrieving revision 1.5 diff -u -r1.4 -r1.5 --- InductiveAtomicSoftnessDescriptor.java 12 Jul 2005 19:33:13 -0000 1.4 +++ InductiveAtomicSoftnessDescriptor.java 4 Aug 2005 14:36:54 -0000 1.5 @@ -24,15 +24,17 @@ */ package org.openscience.cdk.qsar; +import java.io.IOException; + +import javax.vecmath.Point3d; + import org.openscience.cdk.Atom; -import org.openscience.cdk.AtomType; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.AtomType; import org.openscience.cdk.config.AtomTypeFactory; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.tools.LoggingTool; -import javax.vecmath.*; -import java.io.*; /** * Inductive atomic softness of an atom in a polyatomic system can be defined * as charge delocalizing ability. <p> Index: IsProtonInAromaticSystemDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/IsProtonInAromaticSystemDescriptor.java,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- IsProtonInAromaticSystemDescriptor.java 7 Jun 2005 09:39:26 -0000 1.15 +++ IsProtonInAromaticSystemDescriptor.java 4 Aug 2005 14:36:54 -0000 1.16 @@ -27,12 +27,12 @@ import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.Molecule; import org.openscience.cdk.RingSet; -import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; -import org.openscience.cdk.Molecule; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.IntegerResult; +import org.openscience.cdk.ringsearch.AllRingsFinder; /** * This descriptor returns 1 if the protons is directly bonded to an aromatic system, Index: IsProtonInConjugatedPiSystemDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/IsProtonInConjugatedPiSystemDescriptor.java,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- IsProtonInConjugatedPiSystemDescriptor.java 23 Jun 2005 11:01:31 -0000 1.13 +++ IsProtonInConjugatedPiSystemDescriptor.java 4 Aug 2005 14:36:54 -0000 1.14 @@ -26,15 +26,12 @@ import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.tools.HydrogenAdder; +import org.openscience.cdk.Molecule; +import org.openscience.cdk.SetOfAtomContainers; +import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector; -import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; -import org.openscience.cdk.SetOfAtomContainers; -import java.util.Map; -import java.util.Hashtable; -import org.openscience.cdk.Molecule; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.qsar.result.BooleanResult; /** * This class evaluates if a proton is joined to a conjugated system. Index: KappaShapeIndicesDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/KappaShapeIndicesDescriptor.java,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- KappaShapeIndicesDescriptor.java 28 Apr 2005 08:20:44 -0000 1.9 +++ KappaShapeIndicesDescriptor.java 4 Aug 2005 14:36:54 -0000 1.10 @@ -24,12 +24,12 @@ */ package org.openscience.cdk.qsar; +import java.util.ArrayList; + import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.tools.*; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; -import java.util.ArrayList; +import org.openscience.cdk.qsar.result.DoubleArrayResult; /** * Kier and Hall kappa molecular shape indices compare the molecular graph with minimal and maximal molecular graphs; Index: MomentOfInertiaDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/MomentOfInertiaDescriptor.java,v retrieving revision 1.7 retrieving revision 1.8 diff -u -r1.7 -r1.8 --- MomentOfInertiaDescriptor.java 12 Jul 2005 19:33:13 -0000 1.7 +++ MomentOfInertiaDescriptor.java 4 Aug 2005 14:36:54 -0000 1.8 @@ -19,20 +19,19 @@ */ package org.openscience.cdk.qsar; -import org.openscience.cdk.AtomContainer; +import javax.vecmath.Point3d; + import org.openscience.cdk.Atom; -import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.AtomContainer; import org.openscience.cdk.config.IsotopeFactory; +import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.geometry.GeometryTools; -import org.openscience.cdk.tools.MFAnalyser; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.tools.LoggingTool; -import javax.vecmath.*; -import java.lang.Math; - +import org.openscience.cdk.tools.MFAnalyser; -import Jama.Matrix; import Jama.EigenvalueDecomposition; +import Jama.Matrix; /** * A descriptor that calculates the moment of inertia and radius of gyration. Index: PeriodicTablePositionDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/PeriodicTablePositionDescriptor.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- PeriodicTablePositionDescriptor.java 28 Apr 2005 08:20:44 -0000 1.5 +++ PeriodicTablePositionDescriptor.java 4 Aug 2005 14:36:54 -0000 1.6 @@ -24,17 +24,12 @@ */ package org.openscience.cdk.qsar; -import org.openscience.cdk.Atom; -import org.openscience.cdk.AtomType; +import java.util.Hashtable; + import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.Molecule; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; -import org.openscience.cdk.config.AtomTypeFactory; +import org.openscience.cdk.qsar.result.IntegerResult; import org.openscience.cdk.tools.LoggingTool; -import org.openscience.cdk.graph.*; -import org.openscience.cdk.graph.matrix.*; -import java.util.Hashtable; /** * This class returns the period in the periodic table of an atom belonging to an atom container Index: PetitjeanNumberDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/PetitjeanNumberDescriptor.java,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- PetitjeanNumberDescriptor.java 28 Apr 2005 08:20:44 -0000 1.9 +++ PetitjeanNumberDescriptor.java 4 Aug 2005 14:36:54 -0000 1.10 @@ -26,9 +26,9 @@ import org.openscience.cdk.AtomContainer; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; -import org.openscience.cdk.graph.*; -import org.openscience.cdk.graph.matrix.*; +import org.openscience.cdk.graph.PathTools; +import org.openscience.cdk.graph.matrix.ConnectionMatrix; +import org.openscience.cdk.qsar.result.DoubleResult; /** Index: PiContactDetectionDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/PiContactDetectionDescriptor.java,v retrieving revision 1.5 retrieving revision 1.6 diff -u -r1.5 -r1.6 --- PiContactDetectionDescriptor.java 28 Apr 2005 08:20:44 -0000 1.5 +++ PiContactDetectionDescriptor.java 4 Aug 2005 14:36:54 -0000 1.6 @@ -26,15 +26,12 @@ import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.tools.HydrogenAdder; +import org.openscience.cdk.Molecule; +import org.openscience.cdk.SetOfAtomContainers; +import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector; -import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; -import org.openscience.cdk.SetOfAtomContainers; -import java.util.Map; -import java.util.Hashtable; -import org.openscience.cdk.Molecule; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.qsar.result.BooleanResult; /** * This class checks if two atoms have pi-contact (this is true when there is Index: ProtonTotalPartialChargeDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/ProtonTotalPartialChargeDescriptor.java,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- ProtonTotalPartialChargeDescriptor.java 28 Apr 2005 08:20:44 -0000 1.13 +++ ProtonTotalPartialChargeDescriptor.java 4 Aug 2005 14:36:54 -0000 1.14 @@ -27,13 +27,9 @@ import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Molecule; -import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges; -import org.openscience.cdk.qsar.result.*; - -import java.util.Map; -import java.util.Hashtable; -import java.util.ArrayList; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.DoubleArrayResult; /** * The calculation of partial charges of an heavy atom and its protons is based on Gasteiger Marsili (PEOE) Index: RDFProtonDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/RDFProtonDescriptor.java,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- RDFProtonDescriptor.java 23 Jun 2005 11:01:31 -0000 1.9 +++ RDFProtonDescriptor.java 4 Aug 2005 14:36:54 -0000 1.10 @@ -24,27 +24,27 @@ */ package org.openscience.cdk.qsar; +import java.util.ArrayList; +import java.util.Vector; + +import javax.vecmath.Point3d; +import javax.vecmath.Vector3d; + import org.openscience.cdk.Atom; -import org.openscience.cdk.Bond; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.Molecule; +import org.openscience.cdk.Bond; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.SetOfAtomContainers; -import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.RingSet; +import org.openscience.cdk.Molecule; import org.openscience.cdk.Ring; -import org.openscience.cdk.ringsearch.AllRingsFinder; +import org.openscience.cdk.RingSet; +import org.openscience.cdk.SetOfAtomContainers; import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; -import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector; -import org.openscience.cdk.graph.*; -import org.openscience.cdk.graph.matrix.*; -// import org.openscience.cdk.modeling.forcefield.*; -// import org.openscience.cdk.modeling.builder3d.*; import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges; -import javax.vecmath.*; -import java.util.Vector; -import java.util.ArrayList; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.graph.MoleculeGraphs; +import org.openscience.cdk.graph.invariant.ConjugatedPiSystemsDetector; +import org.openscience.cdk.qsar.result.IntegerArrayResult; +import org.openscience.cdk.ringsearch.AllRingsFinder; /** * This class calculates 5 RDF proton descriptors used in neural networks for H1 NMR shift. Index: RotatableBondsCountDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/RotatableBondsCountDescriptor.java,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- RotatableBondsCountDescriptor.java 28 Apr 2005 08:20:44 -0000 1.15 +++ RotatableBondsCountDescriptor.java 4 Aug 2005 14:36:54 -0000 1.16 @@ -24,17 +24,16 @@ */ package org.openscience.cdk.qsar; +import java.util.Vector; + import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Bond; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.RingSet; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.IntegerResult; import org.openscience.cdk.ringsearch.AllRingsFinder; -import org.openscience.cdk.qsar.result.*; -import java.util.Vector; -import java.util.Map; -import java.util.Hashtable; /** * The number of rotatable bonds is given by the SMARTS specified by Daylight on Index: RuleOfFiveDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/RuleOfFiveDescriptor.java,v retrieving revision 1.9 retrieving revision 1.10 diff -u -r1.9 -r1.10 --- RuleOfFiveDescriptor.java 1 Jul 2005 15:43:25 -0000 1.9 +++ RuleOfFiveDescriptor.java 4 Aug 2005 14:36:54 -0000 1.10 @@ -24,16 +24,9 @@ package org.openscience.cdk.qsar; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.Bond; -import org.openscience.cdk.Molecule; -import org.openscience.cdk.CDKConstants; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.RingSet; -import org.openscience.cdk.ringsearch.AllRingsFinder; -import org.openscience.cdk.qsar.result.*; -import java.util.Map; -import java.util.Hashtable; -import org.openscience.cdk.tools.HydrogenAdder; +import org.openscience.cdk.qsar.result.DoubleResult; +import org.openscience.cdk.qsar.result.IntegerResult; /** * This Class contains a method that returns the number failures of the Index: SigmaElectronegativityDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/SigmaElectronegativityDescriptor.java,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- SigmaElectronegativityDescriptor.java 28 Apr 2005 08:20:44 -0000 1.13 +++ SigmaElectronegativityDescriptor.java 4 Aug 2005 14:36:54 -0000 1.14 @@ -26,11 +26,9 @@ import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Molecule; -import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges; -import org.openscience.cdk.qsar.result.*; -import java.util.Map; -import java.util.Hashtable; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.DoubleResult; /** * Sigma electronegativity is given by X = a + bq + c(q*q) Index: TPSADescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/TPSADescriptor.java,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- TPSADescriptor.java 27 Jun 2005 23:39:52 -0000 1.12 +++ TPSADescriptor.java 4 Aug 2005 14:36:54 -0000 1.13 @@ -23,19 +23,19 @@ */ package org.openscience.cdk.qsar; +import java.util.HashMap; +import java.util.Vector; + import org.openscience.cdk.Atom; +import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Bond; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Ring; -import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.tools.*; -import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; -import java.util.Vector; -import java.util.HashMap; import org.openscience.cdk.RingSet; +import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.ringsearch.AllRingsFinder; -import org.openscience.cdk.qsar.result.*; import org.openscience.cdk.tools.manipulator.RingSetManipulator; /** Index: VAdjMaDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/VAdjMaDescriptor.java,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- VAdjMaDescriptor.java 28 Apr 2005 08:20:44 -0000 1.12 +++ VAdjMaDescriptor.java 4 Aug 2005 14:36:54 -0000 1.13 @@ -25,10 +25,9 @@ package org.openscience.cdk.qsar; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.tools.*; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; -import java.lang.Math; +import org.openscience.cdk.qsar.result.DoubleResult; +import org.openscience.cdk.tools.MFAnalyser; /** * Vertex adjacency information (magnitude): Index: ValenceCarbonConnectivityOrderOneDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/ValenceCarbonConnectivityOrderOneDescriptor.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- ValenceCarbonConnectivityOrderOneDescriptor.java 28 Apr 2005 08:20:45 -0000 1.2 +++ ValenceCarbonConnectivityOrderOneDescriptor.java 4 Aug 2005 14:36:54 -0000 1.3 @@ -23,16 +23,17 @@ */ package org.openscience.cdk.qsar; +import java.util.ArrayList; +import java.util.Hashtable; + import org.openscience.cdk.Atom; +import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Bond; import org.openscience.cdk.Element; -import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.config.IsotopeFactory; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.tools.LoggingTool; -import java.util.Hashtable; -import java.util.ArrayList; /** Index: ValenceCarbonConnectivityOrderZeroDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/ValenceCarbonConnectivityOrderZeroDescriptor.java,v retrieving revision 1.2 retrieving revision 1.3 diff -u -r1.2 -r1.3 --- ValenceCarbonConnectivityOrderZeroDescriptor.java 28 Apr 2005 08:20:45 -0000 1.2 +++ ValenceCarbonConnectivityOrderZeroDescriptor.java 4 Aug 2005 14:36:54 -0000 1.3 @@ -23,14 +23,15 @@ */ package org.openscience.cdk.qsar; +import java.util.Hashtable; + import org.openscience.cdk.Atom; -import org.openscience.cdk.Element; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.Element; import org.openscience.cdk.config.IsotopeFactory; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.tools.LoggingTool; -import java.util.Hashtable; /** Index: ValenceConnectivityOrderOneDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/ValenceConnectivityOrderOneDescriptor.java,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- ValenceConnectivityOrderOneDescriptor.java 28 Apr 2005 08:20:45 -0000 1.15 +++ ValenceConnectivityOrderOneDescriptor.java 4 Aug 2005 14:36:54 -0000 1.16 @@ -23,16 +23,17 @@ */ package org.openscience.cdk.qsar; +import java.util.ArrayList; +import java.util.Hashtable; + import org.openscience.cdk.Atom; +import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Bond; import org.openscience.cdk.Element; -import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.config.IsotopeFactory; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.tools.LoggingTool; -import java.util.Hashtable; -import java.util.ArrayList; /** Index: ValenceConnectivityOrderZeroDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/ValenceConnectivityOrderZeroDescriptor.java,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- ValenceConnectivityOrderZeroDescriptor.java 28 Apr 2005 08:20:45 -0000 1.15 +++ ValenceConnectivityOrderZeroDescriptor.java 4 Aug 2005 14:36:54 -0000 1.16 @@ -23,14 +23,15 @@ */ package org.openscience.cdk.qsar; +import java.util.Hashtable; + import org.openscience.cdk.Atom; -import org.openscience.cdk.Element; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.Element; import org.openscience.cdk.config.IsotopeFactory; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.tools.LoggingTool; -import java.util.Hashtable; /** Index: VdWRadiusDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/VdWRadiusDescriptor.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- VdWRadiusDescriptor.java 2 Jul 2005 18:19:00 -0000 1.10 +++ VdWRadiusDescriptor.java 4 Aug 2005 14:36:54 -0000 1.11 @@ -24,16 +24,15 @@ */ package org.openscience.cdk.qsar; -import org.openscience.cdk.Atom; -import org.openscience.cdk.AtomType; +import java.io.IOException; + import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.AtomType; import org.openscience.cdk.config.AtomTypeFactory; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.DoubleResult; import org.openscience.cdk.tools.LoggingTool; -import java.io.*; - /** * This class return the VdW radius of a given atom. * Index: WHIMDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/WHIMDescriptor.java,v retrieving revision 1.16 retrieving revision 1.17 diff -u -r1.16 -r1.17 --- WHIMDescriptor.java 14 Jul 2005 23:51:06 -0000 1.16 +++ WHIMDescriptor.java 4 Aug 2005 14:36:54 -0000 1.17 @@ -23,29 +23,16 @@ */ package org.openscience.cdk.qsar; -import org.openscience.cdk.Atom; +import java.util.Hashtable; + import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.Bond; import org.openscience.cdk.Molecule; -import org.openscience.cdk.CDKConstants; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import org.openscience.cdk.tools.HydrogenAdder; -import org.openscience.cdk.config.IsotopeFactory; -import org.openscience.cdk.charges.GasteigerMarsiliPartialCharges; -import org.openscience.cdk.charges.Polarizability; -import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.tools.LoggingTool; -import java.lang.Math; -import java.util.Vector; -import java.util.ArrayList; -import java.util.Map; -import java.util.Hashtable; - -import Jama.Matrix; import Jama.EigenvalueDecomposition; +import Jama.Matrix; Index: WeightDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/WeightDescriptor.java,v retrieving revision 1.15 retrieving revision 1.16 diff -u -r1.15 -r1.16 --- WeightDescriptor.java 1 Jul 2005 15:52:32 -0000 1.15 +++ WeightDescriptor.java 4 Aug 2005 14:36:54 -0000 1.16 @@ -25,18 +25,10 @@ package org.openscience.cdk.qsar; import org.openscience.cdk.Atom; -import org.openscience.cdk.AtomType; import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.Bond; -import org.openscience.cdk.ChemObject; -import org.openscience.cdk.Molecule; -import org.openscience.cdk.tools.MFAnalyser; -import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; import org.openscience.cdk.config.IsotopeFactory; -import java.util.Map; -import java.util.Hashtable; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.qsar.result.DoubleResult; /** * Descriptor based on the weight of atoms of a certain element type. Index: WienerNumbersDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/WienerNumbersDescriptor.java,v retrieving revision 1.12 retrieving revision 1.13 diff -u -r1.12 -r1.13 --- WienerNumbersDescriptor.java 2 Jul 2005 18:19:00 -0000 1.12 +++ WienerNumbersDescriptor.java 4 Aug 2005 14:36:54 -0000 1.13 @@ -25,10 +25,10 @@ import org.openscience.cdk.AtomContainer; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; -import org.openscience.cdk.graph.*; +import org.openscience.cdk.graph.PathTools; +import org.openscience.cdk.graph.matrix.ConnectionMatrix; +import org.openscience.cdk.qsar.result.DoubleArrayResult; import org.openscience.cdk.tools.manipulator.AtomContainerManipulator; -import org.openscience.cdk.graph.matrix.*; /** Index: XLogPDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/XLogPDescriptor.java,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- XLogPDescriptor.java 26 Jun 2005 23:16:41 -0000 1.13 +++ XLogPDescriptor.java 4 Aug 2005 14:36:54 -0000 1.14 @@ -24,19 +24,18 @@ package org.openscience.cdk.qsar; import org.openscience.cdk.Atom; +import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Bond; import org.openscience.cdk.CDKConstants; -import org.openscience.cdk.AtomContainer; -import org.openscience.cdk.tools.*; -import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; import org.openscience.cdk.RingSet; -import org.openscience.cdk.ringsearch.AllRingsFinder; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.aromaticity.HueckelAromaticityDetector; +import org.openscience.cdk.exception.CDKException; +import org.openscience.cdk.isomorphism.UniversalIsomorphismTester; import org.openscience.cdk.isomorphism.matchers.QueryAtomContainer; import org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator; -import org.openscience.cdk.isomorphism.UniversalIsomorphismTester; -import org.openscience.cdk.isomorphism.mcss.*; +import org.openscience.cdk.qsar.result.DoubleResult; +import org.openscience.cdk.qsar.result.IntegerResult; +import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.smiles.SmilesParser; /** Index: ZagrebIndexDescriptor.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/qsar/ZagrebIndexDescriptor.java,v retrieving revision 1.13 retrieving revision 1.14 diff -u -r1.13 -r1.14 --- ZagrebIndexDescriptor.java 26 Jun 2005 23:16:41 -0000 1.13 +++ ZagrebIndexDescriptor.java 4 Aug 2005 14:36:54 -0000 1.14 @@ -27,7 +27,7 @@ import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.exception.CDKException; -import org.openscience.cdk.qsar.result.*; +import org.openscience.cdk.qsar.result.DoubleResult; /** * Zagreb index: the sum of the squares of atom degree over all heavy atoms i. |