Binary compatibility report for the CDK library between 1.5.0 and 1.5.1 versions

Test Info

Library Name	CDK
Version #1	1.5.0
Version #2	1.5.1

Test Results

Total Java ARchives	1
Total Methods / Classes	36953 / 3491
Verdict	Incompatible (0.9%)

Problem Summary

	Severity	Count
Added Methods	-	5262
Removed Methods	High	58
Problems with Data Types	High	10
	Medium	17
	Low	37
Problems with Methods	High	16
	Medium	0
	Low	0
Other Changes in Data Types	-	17

Added Methods (5262)

cdk-1.5.1.jar, Abs.class
package org.apache.commons.math3.analysis.function
Abs.Abs ( )
Abs.value ( double x ) :  double

cdk-1.5.1.jar, AbstractConvergenceChecker.class
package org.apache.commons.math3.optimization
AbstractConvergenceChecker.AbstractConvergenceChecker ( )
AbstractConvergenceChecker.AbstractConvergenceChecker ( double relativeThreshold, double absoluteThreshold )
AbstractConvergenceChecker.converged ( int p1, Object p2, Object p3 ) [abstract] :  boolean
AbstractConvergenceChecker.getAbsoluteThreshold ( ) :  double
AbstractConvergenceChecker.getRelativeThreshold ( ) :  double

cdk-1.5.1.jar, AbstractDifferentiableUnivariateSolver.class
package org.apache.commons.math3.analysis.solvers
AbstractDifferentiableUnivariateSolver.AbstractDifferentiableUnivariateSolver ( double absoluteAccuracy )
AbstractDifferentiableUnivariateSolver.AbstractDifferentiableUnivariateSolver ( double relativeAccuracy, double absoluteAccuracy, double functionValueAccuracy )
AbstractDifferentiableUnivariateSolver.computeDerivativeObjectiveValue ( double point ) :  double
AbstractDifferentiableUnivariateSolver.setup ( int maxEval, DifferentiableUnivariateFunction f, double min, double max, double startValue ) :  void
AbstractDifferentiableUnivariateSolver.setup ( int x0, UnivariateFunction x1, double x2, double x3, double x4 ) :  void

cdk-1.5.1.jar, AbstractFieldMatrix.class
package org.apache.commons.math3.linear
AbstractFieldMatrix.AbstractFieldMatrix ( )
AbstractFieldMatrix.AbstractFieldMatrix ( Field field )
AbstractFieldMatrix.AbstractFieldMatrix ( Field field, int rowDimension, int columnDimension )
AbstractFieldMatrix.add ( FieldMatrix m ) :  FieldMatrix
AbstractFieldMatrix.addToEntry ( int p1, int p2, FieldElement p3 ) [abstract] :  void
AbstractFieldMatrix.buildArray ( Field field, int length ) [static] :  FieldElement[ ]
AbstractFieldMatrix.buildArray ( Field field, int rows, int columns ) [static] :  FieldElement[ ][ ]
AbstractFieldMatrix.checkAdditionCompatible ( FieldMatrix m ) :  void
AbstractFieldMatrix.checkColumnIndex ( int column ) :  void
AbstractFieldMatrix.checkMultiplicationCompatible ( FieldMatrix m ) :  void
AbstractFieldMatrix.checkRowIndex ( int row ) :  void
AbstractFieldMatrix.checkSubMatrixIndex ( int startRow, int endRow, int startColumn, int endColumn ) :  void
AbstractFieldMatrix.checkSubMatrixIndex ( int[ ] selectedRows, int[ ] selectedColumns ) :  void
AbstractFieldMatrix.checkSubtractionCompatible ( FieldMatrix m ) :  void
AbstractFieldMatrix.copy ( ) [abstract] :  FieldMatrix
AbstractFieldMatrix.copySubMatrix ( int startRow, int endRow, int startColumn, int endColumn, FieldElement[ ][ ] destination ) :  void
AbstractFieldMatrix.copySubMatrix ( int[ ] selectedRows, int[ ] selectedColumns, FieldElement[ ][ ] destination ) :  void
AbstractFieldMatrix.createMatrix ( int p1, int p2 ) [abstract] :  FieldMatrix
AbstractFieldMatrix.equals ( Object object ) :  boolean
AbstractFieldMatrix.extractField ( FieldElement[ ] d ) [static] :  Field
AbstractFieldMatrix.extractField ( FieldElement[ ][ ] d ) [static] :  Field
AbstractFieldMatrix.getColumn ( int column ) :  FieldElement[ ]
AbstractFieldMatrix.getColumnDimension ( ) [abstract] :  int
AbstractFieldMatrix.getColumnMatrix ( int column ) :  FieldMatrix
AbstractFieldMatrix.getColumnVector ( int column ) :  FieldVector
AbstractFieldMatrix.getData ( ) :  FieldElement[ ][ ]
AbstractFieldMatrix.getEntry ( int p1, int p2 ) [abstract] :  FieldElement
AbstractFieldMatrix.getField ( ) :  Field
AbstractFieldMatrix.getRow ( int row ) :  FieldElement[ ]
AbstractFieldMatrix.getRowDimension ( ) [abstract] :  int
AbstractFieldMatrix.getRowMatrix ( int row ) :  FieldMatrix
AbstractFieldMatrix.getRowVector ( int row ) :  FieldVector
AbstractFieldMatrix.getSubMatrix ( int startRow, int endRow, int startColumn, int endColumn ) :  FieldMatrix
AbstractFieldMatrix.getSubMatrix ( int[ ] selectedRows, int[ ] selectedColumns ) :  FieldMatrix
AbstractFieldMatrix.getTrace ( ) :  FieldElement
AbstractFieldMatrix.hashCode ( ) :  int
AbstractFieldMatrix.isSquare ( ) :  boolean
AbstractFieldMatrix.multiply ( FieldMatrix m ) :  FieldMatrix
AbstractFieldMatrix.multiplyEntry ( int p1, int p2, FieldElement p3 ) [abstract] :  void
AbstractFieldMatrix.operate ( FieldElement[ ] v ) :  FieldElement[ ]
AbstractFieldMatrix.operate ( FieldVector v ) :  FieldVector
AbstractFieldMatrix.power ( int p ) :  FieldMatrix
AbstractFieldMatrix.preMultiply ( FieldElement[ ] v ) :  FieldElement[ ]
AbstractFieldMatrix.preMultiply ( FieldMatrix m ) :  FieldMatrix
AbstractFieldMatrix.preMultiply ( FieldVector v ) :  FieldVector
AbstractFieldMatrix.scalarAdd ( FieldElement d ) :  FieldMatrix
AbstractFieldMatrix.scalarMultiply ( FieldElement d ) :  FieldMatrix
AbstractFieldMatrix.setColumn ( int column, FieldElement[ ] array ) :  void
AbstractFieldMatrix.setColumnMatrix ( int column, FieldMatrix matrix ) :  void
AbstractFieldMatrix.setColumnVector ( int column, FieldVector vector ) :  void
AbstractFieldMatrix.setEntry ( int p1, int p2, FieldElement p3 ) [abstract] :  void
AbstractFieldMatrix.setRow ( int row, FieldElement[ ] array ) :  void
AbstractFieldMatrix.setRowMatrix ( int row, FieldMatrix matrix ) :  void
AbstractFieldMatrix.setRowVector ( int row, FieldVector vector ) :  void
AbstractFieldMatrix.setSubMatrix ( FieldElement[ ][ ] subMatrix, int row, int column ) :  void
AbstractFieldMatrix.subtract ( FieldMatrix m ) :  FieldMatrix
AbstractFieldMatrix.toString ( ) :  String
AbstractFieldMatrix.transpose ( ) :  FieldMatrix
AbstractFieldMatrix.walkInColumnOrder ( FieldMatrixChangingVisitor visitor ) :  FieldElement
AbstractFieldMatrix.walkInColumnOrder ( FieldMatrixChangingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  FieldElement
AbstractFieldMatrix.walkInColumnOrder ( FieldMatrixPreservingVisitor visitor ) :  FieldElement
AbstractFieldMatrix.walkInColumnOrder ( FieldMatrixPreservingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  FieldElement
AbstractFieldMatrix.walkInOptimizedOrder ( FieldMatrixChangingVisitor visitor ) :  FieldElement
AbstractFieldMatrix.walkInOptimizedOrder ( FieldMatrixChangingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  FieldElement
AbstractFieldMatrix.walkInOptimizedOrder ( FieldMatrixPreservingVisitor visitor ) :  FieldElement
AbstractFieldMatrix.walkInOptimizedOrder ( FieldMatrixPreservingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  FieldElement
AbstractFieldMatrix.walkInRowOrder ( FieldMatrixChangingVisitor visitor ) :  FieldElement
AbstractFieldMatrix.walkInRowOrder ( FieldMatrixChangingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  FieldElement
AbstractFieldMatrix.walkInRowOrder ( FieldMatrixPreservingVisitor visitor ) :  FieldElement
AbstractFieldMatrix.walkInRowOrder ( FieldMatrixPreservingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  FieldElement

cdk-1.5.1.jar, AbstractFormat.class
package org.apache.commons.math3.fraction
AbstractFormat.AbstractFormat ( )
AbstractFormat.AbstractFormat ( NumberFormat format )
AbstractFormat.AbstractFormat ( NumberFormat numeratorFormat, NumberFormat denominatorFormat )
AbstractFormat.format ( double value, StringBuffer buffer, FieldPosition position ) :  StringBuffer
AbstractFormat.format ( long value, StringBuffer buffer, FieldPosition position ) :  StringBuffer
AbstractFormat.getDefaultNumberFormat ( ) [static] :  NumberFormat
AbstractFormat.getDefaultNumberFormat ( Locale locale ) [static] :  NumberFormat
AbstractFormat.getDenominatorFormat ( ) :  NumberFormat
AbstractFormat.getNumeratorFormat ( ) :  NumberFormat
AbstractFormat.parseAndIgnoreWhitespace ( String source, ParsePosition pos ) [static] :  void
AbstractFormat.parseNextCharacter ( String source, ParsePosition pos ) [static] :  char
AbstractFormat.setDenominatorFormat ( NumberFormat format ) :  void
AbstractFormat.setNumeratorFormat ( NumberFormat format ) :  void

cdk-1.5.1.jar, AbstractIntegerDistribution.class
package org.apache.commons.math3.distribution
AbstractIntegerDistribution.AbstractIntegerDistribution ( )
AbstractIntegerDistribution.cumulativeProbability ( int x0, int x1 ) :  double
AbstractIntegerDistribution.inverseCumulativeProbability ( double p ) :  int
AbstractIntegerDistribution.reseedRandomGenerator ( long seed ) :  void
AbstractIntegerDistribution.sample ( ) :  int
AbstractIntegerDistribution.sample ( int sampleSize ) :  int[ ]
AbstractIntegerDistribution.solveInverseCumulativeProbability ( double p, int lower, int upper ) :  int

cdk-1.5.1.jar, AbstractIntegrator.class
package org.apache.commons.math3.ode
AbstractIntegrator.AbstractIntegrator ( )
AbstractIntegrator.AbstractIntegrator ( String name )
AbstractIntegrator.acceptStep ( AbstractStepInterpolator interpolator, double[ ] y, double[ ] yDot, double tEnd ) :  double
AbstractIntegrator.addEventHandler ( EventHandler handler, double maxCheckInterval, double convergence, int maxIterationCount ) :  void
AbstractIntegrator.addEventHandler ( EventHandler handler, double maxCheckInterval, double convergence, int maxIterationCount, UnivariateSolver solver ) :  void
AbstractIntegrator.addStepHandler ( StepHandler handler ) :  void
AbstractIntegrator.clearEventHandlers ( ) :  void
AbstractIntegrator.clearStepHandlers ( ) :  void
AbstractIntegrator.computeDerivatives ( double t, double[ ] y, double[ ] yDot ) :  void
AbstractIntegrator.getCurrentSignedStepsize ( ) :  double
AbstractIntegrator.getCurrentStepStart ( ) :  double
AbstractIntegrator.getEvaluations ( ) :  int
AbstractIntegrator.getEventHandlers ( ) :  Collection
AbstractIntegrator.getMaxEvaluations ( ) :  int
AbstractIntegrator.getName ( ) :  String
AbstractIntegrator.getStepHandlers ( ) :  Collection
AbstractIntegrator.initIntegration ( double t0, double[ ] y0, double t ) :  void
AbstractIntegrator.integrate ( ExpandableStatefulODE p1, double p2 ) [abstract] :  void
AbstractIntegrator.integrate ( FirstOrderDifferentialEquations equations, double t0, double[ ] y0, double t, double[ ] y ) :  double
AbstractIntegrator.sanityChecks ( ExpandableStatefulODE equations, double t ) :  void
AbstractIntegrator.setEquations ( ExpandableStatefulODE equations ) :  void
AbstractIntegrator.setMaxEvaluations ( int maxEvaluations ) :  void
AbstractIntegrator.setStateInitialized ( boolean stateInitialized ) :  void

cdk-1.5.1.jar, AbstractLeastSquaresOptimizer.class
package org.apache.commons.math3.optimization.general
AbstractLeastSquaresOptimizer.AbstractLeastSquaresOptimizer ( )
AbstractLeastSquaresOptimizer.AbstractLeastSquaresOptimizer ( ConvergenceChecker checker )
AbstractLeastSquaresOptimizer.getChiSquare ( ) :  double
AbstractLeastSquaresOptimizer.getCovariances ( ) :  double[ ][ ]
AbstractLeastSquaresOptimizer.getCovariances ( double threshold ) :  double[ ][ ]
AbstractLeastSquaresOptimizer.getJacobianEvaluations ( ) :  int
AbstractLeastSquaresOptimizer.getRMS ( ) :  double
AbstractLeastSquaresOptimizer.guessParametersErrors ( ) :  double[ ]
AbstractLeastSquaresOptimizer.optimize ( int maxEval, DifferentiableMultivariateVectorFunction f, double[ ] target, double[ ] weights, double[ ] startPoint ) :  PointVectorValuePair
AbstractLeastSquaresOptimizer.optimize ( int x0, MultivariateVectorFunction x1, double[ ] x2, double[ ] x3, double[ ] x4 ) :  PointVectorValuePair
AbstractLeastSquaresOptimizer.updateJacobian ( ) :  void
AbstractLeastSquaresOptimizer.updateResidualsAndCost ( ) :  void

cdk-1.5.1.jar, AbstractLinearOptimizer.class
package org.apache.commons.math3.optimization.linear
AbstractLinearOptimizer.AbstractLinearOptimizer ( )
AbstractLinearOptimizer.doOptimize ( ) [abstract] :  PointValuePair
AbstractLinearOptimizer.getConstraints ( ) :  Collection
AbstractLinearOptimizer.getFunction ( ) :  LinearObjectiveFunction
AbstractLinearOptimizer.getGoalType ( ) :  GoalType
AbstractLinearOptimizer.getIterations ( ) :  int
AbstractLinearOptimizer.getMaxIterations ( ) :  int
AbstractLinearOptimizer.incrementIterationsCounter ( ) :  void
AbstractLinearOptimizer.optimize ( LinearObjectiveFunction f, Collection constraints, GoalType goalType, boolean restrictToNonNegative ) :  PointValuePair
AbstractLinearOptimizer.restrictToNonNegative ( ) :  boolean
AbstractLinearOptimizer.setMaxIterations ( int maxIterations ) :  void

cdk-1.5.1.jar, AbstractListChromosome.class
package org.apache.commons.math3.genetics
AbstractListChromosome.AbstractListChromosome ( List representation )
AbstractListChromosome.AbstractListChromosome ( Object[ ] representation )
AbstractListChromosome.checkValidity ( List p1 ) [abstract] :  void
AbstractListChromosome.getLength ( ) :  int
AbstractListChromosome.getRepresentation ( ) :  List
AbstractListChromosome.newFixedLengthChromosome ( List p1 ) [abstract] :  AbstractListChromosome
AbstractListChromosome.toString ( ) :  String

cdk-1.5.1.jar, AbstractMultipleLinearRegression.class
package org.apache.commons.math3.stat.regression
AbstractMultipleLinearRegression.AbstractMultipleLinearRegression ( )
AbstractMultipleLinearRegression.calculateBeta ( ) [abstract] :  RealVector
AbstractMultipleLinearRegression.calculateBetaVariance ( ) [abstract] :  RealMatrix
AbstractMultipleLinearRegression.calculateErrorVariance ( ) :  double
AbstractMultipleLinearRegression.calculateResiduals ( ) :  RealVector
AbstractMultipleLinearRegression.calculateYVariance ( ) :  double
AbstractMultipleLinearRegression.estimateErrorVariance ( ) :  double
AbstractMultipleLinearRegression.estimateRegressandVariance ( ) :  double
AbstractMultipleLinearRegression.estimateRegressionParameters ( ) :  double[ ]
AbstractMultipleLinearRegression.estimateRegressionParametersStandardErrors ( ) :  double[ ]
AbstractMultipleLinearRegression.estimateRegressionParametersVariance ( ) :  double[ ][ ]
AbstractMultipleLinearRegression.estimateRegressionStandardError ( ) :  double
AbstractMultipleLinearRegression.estimateResiduals ( ) :  double[ ]
AbstractMultipleLinearRegression.getX ( ) :  RealMatrix
AbstractMultipleLinearRegression.getY ( ) :  RealVector
AbstractMultipleLinearRegression.isNoIntercept ( ) :  boolean
AbstractMultipleLinearRegression.newSampleData ( double[ ] data, int nobs, int nvars ) :  void
AbstractMultipleLinearRegression.newXSampleData ( double[ ][ ] x ) :  void
AbstractMultipleLinearRegression.newYSampleData ( double[ ] y ) :  void
AbstractMultipleLinearRegression.setNoIntercept ( boolean noIntercept ) :  void
AbstractMultipleLinearRegression.validateCovarianceData ( double[ ][ ] x, double[ ][ ] covariance ) :  void
AbstractMultipleLinearRegression.validateSampleData ( double[ ][ ] x, double[ ] y ) :  void

cdk-1.5.1.jar, AbstractParameterizable.class
package org.apache.commons.math3.ode
AbstractParameterizable.AbstractParameterizable ( Collection names )
AbstractParameterizable.AbstractParameterizable ( String[ ] names )
AbstractParameterizable.complainIfNotSupported ( String name ) :  void
AbstractParameterizable.getParametersNames ( ) :  Collection
AbstractParameterizable.isSupported ( String name ) :  boolean

cdk-1.5.1.jar, AbstractPolynomialSolver.class
package org.apache.commons.math3.analysis.solvers
AbstractPolynomialSolver.AbstractPolynomialSolver ( double absoluteAccuracy )
AbstractPolynomialSolver.AbstractPolynomialSolver ( double relativeAccuracy, double absoluteAccuracy )
AbstractPolynomialSolver.AbstractPolynomialSolver ( double relativeAccuracy, double absoluteAccuracy, double functionValueAccuracy )
AbstractPolynomialSolver.getCoefficients ( ) :  double[ ]
AbstractPolynomialSolver.setup ( int maxEval, PolynomialFunction f, double min, double max, double startValue ) :  void
AbstractPolynomialSolver.setup ( int x0, UnivariateFunction x1, double x2, double x3, double x4 ) :  void

cdk-1.5.1.jar, AbstractRandomGenerator.class
package org.apache.commons.math3.random
AbstractRandomGenerator.AbstractRandomGenerator ( )
AbstractRandomGenerator.clear ( ) :  void
AbstractRandomGenerator.nextBoolean ( ) :  boolean
AbstractRandomGenerator.nextBytes ( byte[ ] bytes ) :  void
AbstractRandomGenerator.nextDouble ( ) [abstract] :  double
AbstractRandomGenerator.nextFloat ( ) :  float
AbstractRandomGenerator.nextGaussian ( ) :  double
AbstractRandomGenerator.nextInt ( ) :  int
AbstractRandomGenerator.nextInt ( int n ) :  int
AbstractRandomGenerator.nextLong ( ) :  long
AbstractRandomGenerator.setSeed ( int seed ) :  void
AbstractRandomGenerator.setSeed ( int[ ] seed ) :  void
AbstractRandomGenerator.setSeed ( long p1 ) [abstract] :  void

cdk-1.5.1.jar, AbstractRealDistribution.class
package org.apache.commons.math3.distribution
AbstractRealDistribution.AbstractRealDistribution ( )
AbstractRealDistribution.cumulativeProbability ( double x0, double x1 ) :  double
AbstractRealDistribution.getSolverAbsoluteAccuracy ( ) :  double
AbstractRealDistribution.inverseCumulativeProbability ( double p ) :  double
AbstractRealDistribution.reseedRandomGenerator ( long seed ) :  void
AbstractRealDistribution.sample ( ) :  double
AbstractRealDistribution.sample ( int sampleSize ) :  double[ ]

cdk-1.5.1.jar, AbstractRealMatrix.class
package org.apache.commons.math3.linear
AbstractRealMatrix.AbstractRealMatrix ( )
AbstractRealMatrix.AbstractRealMatrix ( int rowDimension, int columnDimension )
AbstractRealMatrix.add ( RealMatrix m ) :  RealMatrix
AbstractRealMatrix.addToEntry ( int row, int column, double increment ) :  void
AbstractRealMatrix.copy ( ) [abstract] :  RealMatrix
AbstractRealMatrix.copySubMatrix ( int startRow, int endRow, int startColumn, int endColumn, double[ ][ ] destination ) :  void
AbstractRealMatrix.copySubMatrix ( int[ ] selectedRows, int[ ] selectedColumns, double[ ][ ] destination ) :  void
AbstractRealMatrix.createMatrix ( int p1, int p2 ) [abstract] :  RealMatrix
AbstractRealMatrix.equals ( Object object ) :  boolean
AbstractRealMatrix.getColumn ( int column ) :  double[ ]
AbstractRealMatrix.getColumnDimension ( ) [abstract] :  int
AbstractRealMatrix.getColumnMatrix ( int column ) :  RealMatrix
AbstractRealMatrix.getColumnVector ( int column ) :  RealVector
AbstractRealMatrix.getData ( ) :  double[ ][ ]
AbstractRealMatrix.getEntry ( int p1, int p2 ) [abstract] :  double
AbstractRealMatrix.getFrobeniusNorm ( ) :  double
AbstractRealMatrix.getNorm ( ) :  double
AbstractRealMatrix.getRow ( int row ) :  double[ ]
AbstractRealMatrix.getRowDimension ( ) [abstract] :  int
AbstractRealMatrix.getRowMatrix ( int row ) :  RealMatrix
AbstractRealMatrix.getRowVector ( int row ) :  RealVector
AbstractRealMatrix.getSubMatrix ( int startRow, int endRow, int startColumn, int endColumn ) :  RealMatrix
AbstractRealMatrix.getSubMatrix ( int[ ] selectedRows, int[ ] selectedColumns ) :  RealMatrix
AbstractRealMatrix.getTrace ( ) :  double
AbstractRealMatrix.hashCode ( ) :  int
AbstractRealMatrix.isSquare ( ) :  boolean
AbstractRealMatrix.multiply ( RealMatrix m ) :  RealMatrix
AbstractRealMatrix.multiplyEntry ( int row, int column, double factor ) :  void
AbstractRealMatrix.operate ( double[ ] v ) :  double[ ]
AbstractRealMatrix.operate ( RealVector v ) :  RealVector
AbstractRealMatrix.power ( int p ) :  RealMatrix
AbstractRealMatrix.preMultiply ( double[ ] v ) :  double[ ]
AbstractRealMatrix.preMultiply ( RealMatrix m ) :  RealMatrix
AbstractRealMatrix.preMultiply ( RealVector v ) :  RealVector
AbstractRealMatrix.scalarAdd ( double d ) :  RealMatrix
AbstractRealMatrix.scalarMultiply ( double d ) :  RealMatrix
AbstractRealMatrix.setColumn ( int column, double[ ] array ) :  void
AbstractRealMatrix.setColumnMatrix ( int column, RealMatrix matrix ) :  void
AbstractRealMatrix.setColumnVector ( int column, RealVector vector ) :  void
AbstractRealMatrix.setEntry ( int p1, int p2, double p3 ) [abstract] :  void
AbstractRealMatrix.setRow ( int row, double[ ] array ) :  void
AbstractRealMatrix.setRowMatrix ( int row, RealMatrix matrix ) :  void
AbstractRealMatrix.setRowVector ( int row, RealVector vector ) :  void
AbstractRealMatrix.setSubMatrix ( double[ ][ ] subMatrix, int row, int column ) :  void
AbstractRealMatrix.subtract ( RealMatrix m ) :  RealMatrix
AbstractRealMatrix.toString ( ) :  String
AbstractRealMatrix.transpose ( ) :  RealMatrix
AbstractRealMatrix.walkInColumnOrder ( RealMatrixChangingVisitor visitor ) :  double
AbstractRealMatrix.walkInColumnOrder ( RealMatrixChangingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  double
AbstractRealMatrix.walkInColumnOrder ( RealMatrixPreservingVisitor visitor ) :  double
AbstractRealMatrix.walkInColumnOrder ( RealMatrixPreservingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  double
AbstractRealMatrix.walkInOptimizedOrder ( RealMatrixChangingVisitor visitor ) :  double
AbstractRealMatrix.walkInOptimizedOrder ( RealMatrixChangingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  double
AbstractRealMatrix.walkInOptimizedOrder ( RealMatrixPreservingVisitor visitor ) :  double
AbstractRealMatrix.walkInOptimizedOrder ( RealMatrixPreservingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  double
AbstractRealMatrix.walkInRowOrder ( RealMatrixChangingVisitor visitor ) :  double
AbstractRealMatrix.walkInRowOrder ( RealMatrixChangingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  double
AbstractRealMatrix.walkInRowOrder ( RealMatrixPreservingVisitor visitor ) :  double
AbstractRealMatrix.walkInRowOrder ( RealMatrixPreservingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  double

cdk-1.5.1.jar, AbstractRegion.class
package org.apache.commons.math3.geometry.partitioning
AbstractRegion.AbstractRegion ( )
AbstractRegion.AbstractRegion ( BSPTree tree )
AbstractRegion.AbstractRegion ( Collection boundary )
AbstractRegion.AbstractRegion ( Hyperplane[ ] hyperplanes )
AbstractRegion.applyTransform ( Transform transform ) :  AbstractRegion
AbstractRegion.buildNew ( BSPTree p1 ) [abstract] :  AbstractRegion
AbstractRegion.buildNew ( BSPTree x0 ) :  Region
AbstractRegion.checkPoint ( BSPTree node, Vector point ) :  Region.Location
AbstractRegion.checkPoint ( Vector point ) :  Region.Location
AbstractRegion.computeGeometricalProperties ( ) [abstract] :  void
AbstractRegion.contains ( Region region ) :  boolean
AbstractRegion.copySelf ( ) :  AbstractRegion
AbstractRegion.copySelf ( ) :  Region
AbstractRegion.getBarycenter ( ) :  Vector
AbstractRegion.getBoundarySize ( ) :  double
AbstractRegion.getSize ( ) :  double
AbstractRegion.getTree ( boolean includeBoundaryAttributes ) :  BSPTree
AbstractRegion.intersection ( SubHyperplane sub ) :  SubHyperplane
AbstractRegion.isEmpty ( ) :  boolean
AbstractRegion.isEmpty ( BSPTree node ) :  boolean
AbstractRegion.setBarycenter ( Vector barycenter ) :  void
AbstractRegion.setSize ( double size ) :  void
AbstractRegion.side ( Hyperplane hyperplane ) :  Side

cdk-1.5.1.jar, AbstractRenderer.class
package org.openscience.cdk.renderer
AbstractRenderer.AbstractRenderer ( RendererModel rendererModel )

cdk-1.5.1.jar, AbstractScalarDifferentiableOptimizer.class
package org.apache.commons.math3.optimization.general
AbstractScalarDifferentiableOptimizer.AbstractScalarDifferentiableOptimizer ( )
AbstractScalarDifferentiableOptimizer.AbstractScalarDifferentiableOptimizer ( ConvergenceChecker checker )
AbstractScalarDifferentiableOptimizer.computeObjectiveGradient ( double[ ] evaluationPoint ) :  double[ ]
AbstractScalarDifferentiableOptimizer.optimize ( int maxEval, DifferentiableMultivariateFunction f, GoalType goalType, double[ ] startPoint ) :  PointValuePair
AbstractScalarDifferentiableOptimizer.optimize ( int x0, MultivariateFunction x1, GoalType x2, double[ ] x3 ) :  PointValuePair

cdk-1.5.1.jar, AbstractSimplex.class
package org.apache.commons.math3.optimization.direct
AbstractSimplex.AbstractSimplex ( double[ ] steps )
AbstractSimplex.AbstractSimplex ( double[ ][ ] referenceSimplex )
AbstractSimplex.AbstractSimplex ( int n )
AbstractSimplex.AbstractSimplex ( int n, double sideLength )
AbstractSimplex.build ( double[ ] startPoint ) :  void
AbstractSimplex.evaluate ( MultivariateFunction evaluationFunction, Comparator comparator ) :  void
AbstractSimplex.getDimension ( ) :  int
AbstractSimplex.getPoint ( int index ) :  PointValuePair
AbstractSimplex.getPoints ( ) :  PointValuePair[ ]
AbstractSimplex.getSize ( ) :  int
AbstractSimplex.iterate ( MultivariateFunction p1, Comparator p2 ) [abstract] :  void
AbstractSimplex.replaceWorstPoint ( PointValuePair pointValuePair, Comparator comparator ) :  void
AbstractSimplex.setPoint ( int index, PointValuePair point ) :  void
AbstractSimplex.setPoints ( PointValuePair[ ] points ) :  void

cdk-1.5.1.jar, AbstractStepInterpolator.class
package org.apache.commons.math3.ode.sampling
AbstractStepInterpolator.AbstractStepInterpolator ( )
AbstractStepInterpolator.AbstractStepInterpolator ( AbstractStepInterpolator interpolator )
AbstractStepInterpolator.AbstractStepInterpolator ( double[ ] y, boolean forward, EquationsMapper primaryMapper, EquationsMapper[ ] secondaryMappers )
AbstractStepInterpolator.computeInterpolatedStateAndDerivatives ( double p1, double p2 ) [abstract] :  void
AbstractStepInterpolator.copy ( ) :  StepInterpolator
AbstractStepInterpolator.doCopy ( ) [abstract] :  StepInterpolator
AbstractStepInterpolator.doFinalize ( ) :  void
AbstractStepInterpolator.finalizeStep ( ) :  void
AbstractStepInterpolator.getCurrentTime ( ) :  double
AbstractStepInterpolator.getGlobalCurrentTime ( ) :  double
AbstractStepInterpolator.getGlobalPreviousTime ( ) :  double
AbstractStepInterpolator.getInterpolatedDerivatives ( ) :  double[ ]
AbstractStepInterpolator.getInterpolatedSecondaryDerivatives ( int index ) :  double[ ]
AbstractStepInterpolator.getInterpolatedSecondaryState ( int index ) :  double[ ]
AbstractStepInterpolator.getInterpolatedState ( ) :  double[ ]
AbstractStepInterpolator.getInterpolatedTime ( ) :  double
AbstractStepInterpolator.getPreviousTime ( ) :  double
AbstractStepInterpolator.isForward ( ) :  boolean
AbstractStepInterpolator.readBaseExternal ( ObjectInput in ) :  double
AbstractStepInterpolator.readExternal ( ObjectInput p1 ) [abstract] :  void
AbstractStepInterpolator.reinitialize ( double[ ] y, boolean isForward, EquationsMapper primary, EquationsMapper[ ] secondary ) :  void
AbstractStepInterpolator.setInterpolatedTime ( double time ) :  void
AbstractStepInterpolator.setSoftCurrentTime ( double softCurrentTime ) :  void
AbstractStepInterpolator.setSoftPreviousTime ( double softPreviousTime ) :  void
AbstractStepInterpolator.shift ( ) :  void
AbstractStepInterpolator.storeTime ( double t ) :  void
AbstractStepInterpolator.writeBaseExternal ( ObjectOutput out ) :  void
AbstractStepInterpolator.writeExternal ( ObjectOutput p1 ) [abstract] :  void

cdk-1.5.1.jar, AbstractStorelessUnivariateStatistic.class
package org.apache.commons.math3.stat.descriptive
AbstractStorelessUnivariateStatistic.AbstractStorelessUnivariateStatistic ( )
AbstractStorelessUnivariateStatistic.clear ( ) [abstract] :  void
AbstractStorelessUnivariateStatistic.copy ( ) :  UnivariateStatistic
AbstractStorelessUnivariateStatistic.copy ( ) [abstract] :  StorelessUnivariateStatistic
AbstractStorelessUnivariateStatistic.equals ( Object object ) :  boolean
AbstractStorelessUnivariateStatistic.evaluate ( double[ ] values ) :  double
AbstractStorelessUnivariateStatistic.evaluate ( double[ ] values, int begin, int length ) :  double
AbstractStorelessUnivariateStatistic.getResult ( ) [abstract] :  double
AbstractStorelessUnivariateStatistic.hashCode ( ) :  int
AbstractStorelessUnivariateStatistic.increment ( double p1 ) [abstract] :  void
AbstractStorelessUnivariateStatistic.incrementAll ( double[ ] values ) :  void
AbstractStorelessUnivariateStatistic.incrementAll ( double[ ] values, int begin, int length ) :  void

cdk-1.5.1.jar, AbstractSubHyperplane.class
package org.apache.commons.math3.geometry.partitioning
AbstractSubHyperplane.AbstractSubHyperplane ( Hyperplane hyperplane, Region remainingRegion )
AbstractSubHyperplane.applyTransform ( Transform transform ) :  AbstractSubHyperplane
AbstractSubHyperplane.buildNew ( Hyperplane p1, Region p2 ) [abstract] :  AbstractSubHyperplane
AbstractSubHyperplane.copySelf ( ) :  AbstractSubHyperplane
AbstractSubHyperplane.copySelf ( ) :  SubHyperplane
AbstractSubHyperplane.getHyperplane ( ) :  Hyperplane
AbstractSubHyperplane.getRemainingRegion ( ) :  Region
AbstractSubHyperplane.getSize ( ) :  double
AbstractSubHyperplane.isEmpty ( ) :  boolean
AbstractSubHyperplane.reunite ( SubHyperplane other ) :  AbstractSubHyperplane
AbstractSubHyperplane.reunite ( SubHyperplane x0 ) :  SubHyperplane
AbstractSubHyperplane.side ( Hyperplane p1 ) [abstract] :  Side
AbstractSubHyperplane.split ( Hyperplane p1 ) [abstract] :  SubHyperplane.SplitSubHyperplane

cdk-1.5.1.jar, AbstractUnivariateSolver.class
package org.apache.commons.math3.analysis.solvers
AbstractUnivariateSolver.AbstractUnivariateSolver ( double absoluteAccuracy )
AbstractUnivariateSolver.AbstractUnivariateSolver ( double relativeAccuracy, double absoluteAccuracy )
AbstractUnivariateSolver.AbstractUnivariateSolver ( double relativeAccuracy, double absoluteAccuracy, double functionValueAccuracy )

cdk-1.5.1.jar, AbstractUnivariateStatistic.class
package org.apache.commons.math3.stat.descriptive
AbstractUnivariateStatistic.AbstractUnivariateStatistic ( )
AbstractUnivariateStatistic.copy ( ) [abstract] :  UnivariateStatistic
AbstractUnivariateStatistic.evaluate ( ) :  double
AbstractUnivariateStatistic.evaluate ( double[ ] p1, int p2, int p3 ) [abstract] :  double
AbstractUnivariateStatistic.evaluate ( double[ ] values ) :  double
AbstractUnivariateStatistic.getData ( ) :  double[ ]
AbstractUnivariateStatistic.getDataRef ( ) :  double[ ]
AbstractUnivariateStatistic.setData ( double[ ] values ) :  void
AbstractUnivariateStatistic.setData ( double[ ] values, int begin, int length ) :  void
AbstractUnivariateStatistic.test ( double[ ] values, double[ ] weights, int begin, int length ) :  boolean
AbstractUnivariateStatistic.test ( double[ ] values, double[ ] weights, int begin, int length, boolean allowEmpty ) :  boolean
AbstractUnivariateStatistic.test ( double[ ] values, int begin, int length ) :  boolean
AbstractUnivariateStatistic.test ( double[ ] values, int begin, int length, boolean allowEmpty ) :  boolean

cdk-1.5.1.jar, AbstractWell.class
package org.apache.commons.math3.random
AbstractWell.AbstractWell ( int k, int m1, int m2, int m3 )
AbstractWell.AbstractWell ( int k, int m1, int m2, int m3, int seed )
AbstractWell.AbstractWell ( int k, int m1, int m2, int m3, int[ ] seed )
AbstractWell.AbstractWell ( int k, int m1, int m2, int m3, long seed )
AbstractWell.next ( int p1 ) [abstract] :  int
AbstractWell.setSeed ( int seed ) :  void
AbstractWell.setSeed ( int[ ] seed ) :  void
AbstractWell.setSeed ( long seed ) :  void

cdk-1.5.1.jar, AcidicGroupCountDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
AcidicGroupCountDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, Acos.class
package org.apache.commons.math3.analysis.function
Acos.Acos ( )
Acos.derivative ( ) :  UnivariateFunction
Acos.value ( double x ) :  double

cdk-1.5.1.jar, Acosh.class
package org.apache.commons.math3.analysis.function
Acosh.Acosh ( )
Acosh.derivative ( ) :  UnivariateFunction
Acosh.value ( double x ) :  double

cdk-1.5.1.jar, Action.class
package org.apache.commons.math3.ode.events
EventHandler.Action.valueOf ( String name ) [static] :  EventHandler.Action
EventHandler.Action.values ( ) [static] :  EventHandler.Action[ ]

cdk-1.5.1.jar, AdamsBashforthIntegrator.class
package org.apache.commons.math3.ode.nonstiff
AdamsBashforthIntegrator.AdamsBashforthIntegrator ( int nSteps, double minStep, double maxStep, double scalAbsoluteTolerance, double scalRelativeTolerance )
AdamsBashforthIntegrator.AdamsBashforthIntegrator ( int nSteps, double minStep, double maxStep, double[ ] vecAbsoluteTolerance, double[ ] vecRelativeTolerance )
AdamsBashforthIntegrator.integrate ( ExpandableStatefulODE equations, double t ) :  void

cdk-1.5.1.jar, AdamsIntegrator.class
package org.apache.commons.math3.ode.nonstiff
AdamsIntegrator.AdamsIntegrator ( String name, int nSteps, int order, double minStep, double maxStep, double scalAbsoluteTolerance, double scalRelativeTolerance )
AdamsIntegrator.AdamsIntegrator ( String name, int nSteps, int order, double minStep, double maxStep, double[ ] vecAbsoluteTolerance, double[ ] vecRelativeTolerance )
AdamsIntegrator.initializeHighOrderDerivatives ( double h, double[ ] t, double[ ][ ] y, double[ ][ ] yDot ) :  Array2DRowRealMatrix
AdamsIntegrator.integrate ( ExpandableStatefulODE p1, double p2 ) [abstract] :  void
AdamsIntegrator.updateHighOrderDerivativesPhase1 ( Array2DRowRealMatrix highOrder ) :  Array2DRowRealMatrix
AdamsIntegrator.updateHighOrderDerivativesPhase2 ( double[ ] start, double[ ] end, Array2DRowRealMatrix highOrder ) :  void

cdk-1.5.1.jar, AdamsMoultonIntegrator.class
package org.apache.commons.math3.ode.nonstiff
AdamsMoultonIntegrator.AdamsMoultonIntegrator ( int nSteps, double minStep, double maxStep, double scalAbsoluteTolerance, double scalRelativeTolerance )
AdamsMoultonIntegrator.AdamsMoultonIntegrator ( int nSteps, double minStep, double maxStep, double[ ] vecAbsoluteTolerance, double[ ] vecRelativeTolerance )
AdamsMoultonIntegrator.integrate ( ExpandableStatefulODE equations, double t ) :  void

cdk-1.5.1.jar, AdamsNordsieckTransformer.class
package org.apache.commons.math3.ode.nonstiff
AdamsNordsieckTransformer.getInstance ( int nSteps ) [static] :  AdamsNordsieckTransformer
AdamsNordsieckTransformer.getNSteps ( ) :  int
AdamsNordsieckTransformer.initializeHighOrderDerivatives ( double h, double[ ] t, double[ ][ ] y, double[ ][ ] yDot ) :  Array2DRowRealMatrix
AdamsNordsieckTransformer.updateHighOrderDerivativesPhase1 ( Array2DRowRealMatrix highOrder ) :  Array2DRowRealMatrix
AdamsNordsieckTransformer.updateHighOrderDerivativesPhase2 ( double[ ] start, double[ ] end, Array2DRowRealMatrix highOrder ) :  void

cdk-1.5.1.jar, AdaptiveStepsizeIntegrator.class
package org.apache.commons.math3.ode.nonstiff
AdaptiveStepsizeIntegrator.AdaptiveStepsizeIntegrator ( String name, double minStep, double maxStep, double scalAbsoluteTolerance, double scalRelativeTolerance )
AdaptiveStepsizeIntegrator.AdaptiveStepsizeIntegrator ( String name, double minStep, double maxStep, double[ ] vecAbsoluteTolerance, double[ ] vecRelativeTolerance )
AdaptiveStepsizeIntegrator.filterStep ( double h, boolean forward, boolean acceptSmall ) :  double
AdaptiveStepsizeIntegrator.getCurrentStepStart ( ) :  double
AdaptiveStepsizeIntegrator.getMaxStep ( ) :  double
AdaptiveStepsizeIntegrator.getMinStep ( ) :  double
AdaptiveStepsizeIntegrator.initializeStep ( boolean forward, int order, double[ ] scale, double t0, double[ ] y0, double[ ] yDot0, double[ ] y1, double[ ] yDot1 ) :  double
AdaptiveStepsizeIntegrator.integrate ( ExpandableStatefulODE p1, double p2 ) [abstract] :  void
AdaptiveStepsizeIntegrator.resetInternalState ( ) :  void
AdaptiveStepsizeIntegrator.sanityChecks ( ExpandableStatefulODE equations, double t ) :  void
AdaptiveStepsizeIntegrator.setInitialStepSize ( double initialStepSize ) :  void
AdaptiveStepsizeIntegrator.setStepSizeControl ( double minimalStep, double maximalStep, double absoluteTolerance, double relativeTolerance ) :  void
AdaptiveStepsizeIntegrator.setStepSizeControl ( double minimalStep, double maximalStep, double[ ] absoluteTolerance, double[ ] relativeTolerance ) :  void

cdk-1.5.1.jar, Add.class
package org.apache.commons.math3.analysis.function
Add.Add ( )
Add.value ( double x, double y ) :  double

cdk-1.5.1.jar, AggregateSummaryStatistics.class
package org.apache.commons.math3.stat.descriptive
AggregateSummaryStatistics.aggregate ( Collection statistics ) [static] :  StatisticalSummaryValues
AggregateSummaryStatistics.AggregateSummaryStatistics ( )
AggregateSummaryStatistics.AggregateSummaryStatistics ( SummaryStatistics prototypeStatistics )
AggregateSummaryStatistics.AggregateSummaryStatistics ( SummaryStatistics prototypeStatistics, SummaryStatistics initialStatistics )
AggregateSummaryStatistics.createContributingStatistics ( ) :  SummaryStatistics
AggregateSummaryStatistics.getGeometricMean ( ) :  double
AggregateSummaryStatistics.getMax ( ) :  double
AggregateSummaryStatistics.getMean ( ) :  double
AggregateSummaryStatistics.getMin ( ) :  double
AggregateSummaryStatistics.getN ( ) :  long
AggregateSummaryStatistics.getSecondMoment ( ) :  double
AggregateSummaryStatistics.getStandardDeviation ( ) :  double
AggregateSummaryStatistics.getSum ( ) :  double
AggregateSummaryStatistics.getSummary ( ) :  StatisticalSummary
AggregateSummaryStatistics.getSumOfLogs ( ) :  double
AggregateSummaryStatistics.getSumsq ( ) :  double
AggregateSummaryStatistics.getVariance ( ) :  double

cdk-1.5.1.jar, AllowedSolution.class
package org.apache.commons.math3.analysis.solvers
AllowedSolution.valueOf ( String name ) [static] :  AllowedSolution
AllowedSolution.values ( ) [static] :  AllowedSolution[ ]

cdk-1.5.1.jar, ALOGPDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
ALOGPDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, AminoAcidCountDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
AminoAcidCountDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, AnyMatrix.class
package org.apache.commons.math3.linear
AnyMatrix.getColumnDimension ( ) [abstract] :  int
AnyMatrix.getRowDimension ( ) [abstract] :  int
AnyMatrix.isSquare ( ) [abstract] :  boolean

cdk-1.5.1.jar, APolDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
APolDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, ArgUtils.class
package org.apache.commons.math3.exception.util
ArgUtils.flatten ( Object[ ] array ) [static] :  Object[ ]

cdk-1.5.1.jar, ArithmeticUtils.class
package org.apache.commons.math3.util
ArithmeticUtils.addAndCheck ( int x, int y ) [static] :  int
ArithmeticUtils.addAndCheck ( long a, long b ) [static] :  long
ArithmeticUtils.binomialCoefficient ( int n, int k ) [static] :  long
ArithmeticUtils.binomialCoefficientDouble ( int n, int k ) [static] :  double
ArithmeticUtils.binomialCoefficientLog ( int n, int k ) [static] :  double
ArithmeticUtils.factorial ( int n ) [static] :  long
ArithmeticUtils.factorialDouble ( int n ) [static] :  double
ArithmeticUtils.factorialLog ( int n ) [static] :  double
ArithmeticUtils.gcd ( int p, int q ) [static] :  int
ArithmeticUtils.gcd ( long p, long q ) [static] :  long
ArithmeticUtils.isPowerOfTwo ( long n ) [static] :  boolean
ArithmeticUtils.lcm ( int a, int b ) [static] :  int
ArithmeticUtils.lcm ( long a, long b ) [static] :  long
ArithmeticUtils.mulAndCheck ( int x, int y ) [static] :  int
ArithmeticUtils.mulAndCheck ( long a, long b ) [static] :  long
ArithmeticUtils.pow ( BigInteger k, BigInteger e ) [static] :  BigInteger
ArithmeticUtils.pow ( BigInteger k, int e ) [static] :  BigInteger
ArithmeticUtils.pow ( BigInteger k, long e ) [static] :  BigInteger
ArithmeticUtils.pow ( int k, int e ) [static] :  int
ArithmeticUtils.pow ( int k, long e ) [static] :  int
ArithmeticUtils.pow ( long k, int e ) [static] :  long
ArithmeticUtils.pow ( long k, long e ) [static] :  long
ArithmeticUtils.subAndCheck ( int x, int y ) [static] :  int
ArithmeticUtils.subAndCheck ( long a, long b ) [static] :  long

cdk-1.5.1.jar, AromaticAtomsCountDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
AromaticAtomsCountDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, AromaticBondsCountDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
AromaticBondsCountDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, Array2DRowFieldMatrix.class
package org.apache.commons.math3.linear
Array2DRowFieldMatrix.add ( Array2DRowFieldMatrix m ) :  Array2DRowFieldMatrix
Array2DRowFieldMatrix.addToEntry ( int row, int column, FieldElement increment ) :  void
Array2DRowFieldMatrix.Array2DRowFieldMatrix ( Field field )
Array2DRowFieldMatrix.Array2DRowFieldMatrix ( Field field, FieldElement[ ] v )
Array2DRowFieldMatrix.Array2DRowFieldMatrix ( Field field, FieldElement[ ][ ] d )
Array2DRowFieldMatrix.Array2DRowFieldMatrix ( Field field, FieldElement[ ][ ] d, boolean copyArray )
Array2DRowFieldMatrix.Array2DRowFieldMatrix ( Field field, int rowDimension, int columnDimension )
Array2DRowFieldMatrix.Array2DRowFieldMatrix ( FieldElement[ ] v )
Array2DRowFieldMatrix.Array2DRowFieldMatrix ( FieldElement[ ][ ] d )
Array2DRowFieldMatrix.Array2DRowFieldMatrix ( FieldElement[ ][ ] d, boolean copyArray )
Array2DRowFieldMatrix.copy ( ) :  FieldMatrix
Array2DRowFieldMatrix.createMatrix ( int rowDimension, int columnDimension ) :  FieldMatrix
Array2DRowFieldMatrix.getColumnDimension ( ) :  int
Array2DRowFieldMatrix.getData ( ) :  FieldElement[ ][ ]
Array2DRowFieldMatrix.getDataRef ( ) :  FieldElement[ ][ ]
Array2DRowFieldMatrix.getEntry ( int row, int column ) :  FieldElement
Array2DRowFieldMatrix.getRowDimension ( ) :  int
Array2DRowFieldMatrix.multiply ( Array2DRowFieldMatrix m ) :  Array2DRowFieldMatrix
Array2DRowFieldMatrix.multiplyEntry ( int row, int column, FieldElement factor ) :  void
Array2DRowFieldMatrix.operate ( FieldElement[ ] v ) :  FieldElement[ ]
Array2DRowFieldMatrix.preMultiply ( FieldElement[ ] v ) :  FieldElement[ ]
Array2DRowFieldMatrix.setEntry ( int row, int column, FieldElement value ) :  void
Array2DRowFieldMatrix.setSubMatrix ( FieldElement[ ][ ] subMatrix, int row, int column ) :  void
Array2DRowFieldMatrix.subtract ( Array2DRowFieldMatrix m ) :  Array2DRowFieldMatrix
Array2DRowFieldMatrix.walkInColumnOrder ( FieldMatrixChangingVisitor visitor ) :  FieldElement
Array2DRowFieldMatrix.walkInColumnOrder ( FieldMatrixChangingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  FieldElement
Array2DRowFieldMatrix.walkInColumnOrder ( FieldMatrixPreservingVisitor visitor ) :  FieldElement
Array2DRowFieldMatrix.walkInColumnOrder ( FieldMatrixPreservingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  FieldElement
Array2DRowFieldMatrix.walkInRowOrder ( FieldMatrixChangingVisitor visitor ) :  FieldElement
Array2DRowFieldMatrix.walkInRowOrder ( FieldMatrixChangingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  FieldElement
Array2DRowFieldMatrix.walkInRowOrder ( FieldMatrixPreservingVisitor visitor ) :  FieldElement
Array2DRowFieldMatrix.walkInRowOrder ( FieldMatrixPreservingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  FieldElement

cdk-1.5.1.jar, Array2DRowRealMatrix.class
package org.apache.commons.math3.linear
Array2DRowRealMatrix.add ( Array2DRowRealMatrix m ) :  Array2DRowRealMatrix
Array2DRowRealMatrix.addToEntry ( int row, int column, double increment ) :  void
Array2DRowRealMatrix.Array2DRowRealMatrix ( )
Array2DRowRealMatrix.Array2DRowRealMatrix ( double[ ] v )
Array2DRowRealMatrix.Array2DRowRealMatrix ( double[ ][ ] d )
Array2DRowRealMatrix.Array2DRowRealMatrix ( double[ ][ ] d, boolean copyArray )
Array2DRowRealMatrix.Array2DRowRealMatrix ( int rowDimension, int columnDimension )
Array2DRowRealMatrix.copy ( ) :  RealMatrix
Array2DRowRealMatrix.createMatrix ( int rowDimension, int columnDimension ) :  RealMatrix
Array2DRowRealMatrix.getColumnDimension ( ) :  int
Array2DRowRealMatrix.getData ( ) :  double[ ][ ]
Array2DRowRealMatrix.getDataRef ( ) :  double[ ][ ]
Array2DRowRealMatrix.getEntry ( int row, int column ) :  double
Array2DRowRealMatrix.getRowDimension ( ) :  int
Array2DRowRealMatrix.multiply ( Array2DRowRealMatrix m ) :  Array2DRowRealMatrix
Array2DRowRealMatrix.multiplyEntry ( int row, int column, double factor ) :  void
Array2DRowRealMatrix.operate ( double[ ] v ) :  double[ ]
Array2DRowRealMatrix.preMultiply ( double[ ] v ) :  double[ ]
Array2DRowRealMatrix.setEntry ( int row, int column, double value ) :  void
Array2DRowRealMatrix.setSubMatrix ( double[ ][ ] subMatrix, int row, int column ) :  void
Array2DRowRealMatrix.subtract ( Array2DRowRealMatrix m ) :  Array2DRowRealMatrix
Array2DRowRealMatrix.walkInColumnOrder ( RealMatrixChangingVisitor visitor ) :  double
Array2DRowRealMatrix.walkInColumnOrder ( RealMatrixChangingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  double
Array2DRowRealMatrix.walkInColumnOrder ( RealMatrixPreservingVisitor visitor ) :  double
Array2DRowRealMatrix.walkInColumnOrder ( RealMatrixPreservingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  double
Array2DRowRealMatrix.walkInRowOrder ( RealMatrixChangingVisitor visitor ) :  double
Array2DRowRealMatrix.walkInRowOrder ( RealMatrixChangingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  double
Array2DRowRealMatrix.walkInRowOrder ( RealMatrixPreservingVisitor visitor ) :  double
Array2DRowRealMatrix.walkInRowOrder ( RealMatrixPreservingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  double

cdk-1.5.1.jar, ArrayFieldVector.class
package org.apache.commons.math3.linear
ArrayFieldVector.add ( ArrayFieldVector v ) :  ArrayFieldVector
ArrayFieldVector.add ( FieldVector v ) :  FieldVector
ArrayFieldVector.append ( ArrayFieldVector v ) :  ArrayFieldVector
ArrayFieldVector.append ( FieldElement in ) :  FieldVector
ArrayFieldVector.append ( FieldVector v ) :  FieldVector
ArrayFieldVector.ArrayFieldVector ( ArrayFieldVector v )
ArrayFieldVector.ArrayFieldVector ( ArrayFieldVector v, boolean deep )
ArrayFieldVector.ArrayFieldVector ( ArrayFieldVector v1, ArrayFieldVector v2 )
ArrayFieldVector.ArrayFieldVector ( ArrayFieldVector v1, FieldElement[ ] v2 )
ArrayFieldVector.ArrayFieldVector ( Field field )
ArrayFieldVector.ArrayFieldVector ( Field field, FieldElement[ ] d )
ArrayFieldVector.ArrayFieldVector ( Field field, FieldElement[ ] d, boolean copyArray )
ArrayFieldVector.ArrayFieldVector ( Field field, FieldElement[ ] d, int pos, int size )
ArrayFieldVector.ArrayFieldVector ( Field field, FieldElement[ ] v1, FieldElement[ ] v2 )
ArrayFieldVector.ArrayFieldVector ( Field field, int size )
ArrayFieldVector.ArrayFieldVector ( FieldElement[ ] d )
ArrayFieldVector.ArrayFieldVector ( FieldElement[ ] d, boolean copyArray )
ArrayFieldVector.ArrayFieldVector ( FieldElement[ ] d, int pos, int size )
ArrayFieldVector.ArrayFieldVector ( FieldElement[ ] v1, ArrayFieldVector v2 )
ArrayFieldVector.ArrayFieldVector ( FieldElement[ ] v1, FieldElement[ ] v2 )
ArrayFieldVector.ArrayFieldVector ( FieldVector v )
ArrayFieldVector.ArrayFieldVector ( int size, FieldElement preset )
ArrayFieldVector.checkVectorDimensions ( FieldVector v ) :  void
ArrayFieldVector.checkVectorDimensions ( int n ) :  void
ArrayFieldVector.copy ( ) :  FieldVector
ArrayFieldVector.dotProduct ( ArrayFieldVector v ) :  FieldElement
ArrayFieldVector.dotProduct ( FieldVector v ) :  FieldElement
ArrayFieldVector.ebeDivide ( ArrayFieldVector v ) :  ArrayFieldVector
ArrayFieldVector.ebeDivide ( FieldVector v ) :  FieldVector
ArrayFieldVector.ebeMultiply ( ArrayFieldVector v ) :  ArrayFieldVector
ArrayFieldVector.ebeMultiply ( FieldVector v ) :  FieldVector
ArrayFieldVector.equals ( Object other ) :  boolean
ArrayFieldVector.getData ( ) :  FieldElement[ ]
ArrayFieldVector.getDataRef ( ) :  FieldElement[ ]
ArrayFieldVector.getDimension ( ) :  int
ArrayFieldVector.getEntry ( int index ) :  FieldElement
ArrayFieldVector.getField ( ) :  Field
ArrayFieldVector.getSubVector ( int index, int n ) :  FieldVector
ArrayFieldVector.hashCode ( ) :  int
ArrayFieldVector.mapAdd ( FieldElement d ) :  FieldVector
ArrayFieldVector.mapAddToSelf ( FieldElement d ) :  FieldVector
ArrayFieldVector.mapDivide ( FieldElement d ) :  FieldVector
ArrayFieldVector.mapDivideToSelf ( FieldElement d ) :  FieldVector
ArrayFieldVector.mapInv ( ) :  FieldVector
ArrayFieldVector.mapInvToSelf ( ) :  FieldVector
ArrayFieldVector.mapMultiply ( FieldElement d ) :  FieldVector
ArrayFieldVector.mapMultiplyToSelf ( FieldElement d ) :  FieldVector
ArrayFieldVector.mapSubtract ( FieldElement d ) :  FieldVector
ArrayFieldVector.mapSubtractToSelf ( FieldElement d ) :  FieldVector
ArrayFieldVector.outerProduct ( ArrayFieldVector v ) :  FieldMatrix
ArrayFieldVector.outerProduct ( FieldVector v ) :  FieldMatrix
ArrayFieldVector.projection ( ArrayFieldVector v ) :  ArrayFieldVector
ArrayFieldVector.projection ( FieldVector v ) :  FieldVector
ArrayFieldVector.set ( FieldElement value ) :  void
ArrayFieldVector.set ( int index, ArrayFieldVector v ) :  void
ArrayFieldVector.setEntry ( int index, FieldElement value ) :  void
ArrayFieldVector.setSubVector ( int index, FieldVector v ) :  void
ArrayFieldVector.subtract ( ArrayFieldVector v ) :  ArrayFieldVector
ArrayFieldVector.subtract ( FieldVector v ) :  FieldVector
ArrayFieldVector.toArray ( ) :  FieldElement[ ]

cdk-1.5.1.jar, ArrayRealVector.class
package org.apache.commons.math3.linear
ArrayRealVector.add ( RealVector v ) :  ArrayRealVector
ArrayRealVector.add ( RealVector x0 ) :  RealVector
ArrayRealVector.addToEntry ( int index, double increment ) :  void
ArrayRealVector.append ( ArrayRealVector v ) :  ArrayRealVector
ArrayRealVector.append ( double in ) :  RealVector
ArrayRealVector.append ( RealVector v ) :  RealVector
ArrayRealVector.ArrayRealVector ( )
ArrayRealVector.ArrayRealVector ( ArrayRealVector v )
ArrayRealVector.ArrayRealVector ( ArrayRealVector v, boolean deep )
ArrayRealVector.ArrayRealVector ( ArrayRealVector v1, ArrayRealVector v2 )
ArrayRealVector.ArrayRealVector ( ArrayRealVector v1, double[ ] v2 )
ArrayRealVector.ArrayRealVector ( ArrayRealVector v1, RealVector v2 )
ArrayRealVector.ArrayRealVector ( double[ ] d )
ArrayRealVector.ArrayRealVector ( Double[ ] d )
ArrayRealVector.ArrayRealVector ( double[ ] d, boolean copyArray )
ArrayRealVector.ArrayRealVector ( double[ ] d, int pos, int size )
ArrayRealVector.ArrayRealVector ( Double[ ] d, int pos, int size )
ArrayRealVector.ArrayRealVector ( double[ ] v1, ArrayRealVector v2 )
ArrayRealVector.ArrayRealVector ( double[ ] v1, double[ ] v2 )
ArrayRealVector.ArrayRealVector ( int size )
ArrayRealVector.ArrayRealVector ( int size, double preset )
ArrayRealVector.ArrayRealVector ( RealVector v )
ArrayRealVector.ArrayRealVector ( RealVector v1, ArrayRealVector v2 )
ArrayRealVector.checkVectorDimensions ( int n ) :  void
ArrayRealVector.checkVectorDimensions ( RealVector v ) :  void
ArrayRealVector.combine ( double a, double b, RealVector y ) :  ArrayRealVector
ArrayRealVector.combine ( double x0, double x1, RealVector x2 ) :  RealVector
ArrayRealVector.combineToSelf ( double a, double b, RealVector y ) :  ArrayRealVector
ArrayRealVector.combineToSelf ( double x0, double x1, RealVector x2 ) :  RealVector
ArrayRealVector.copy ( ) :  ArrayRealVector
ArrayRealVector.copy ( ) :  RealVector
ArrayRealVector.dotProduct ( RealVector v ) :  double
ArrayRealVector.ebeDivide ( RealVector v ) :  ArrayRealVector
ArrayRealVector.ebeDivide ( RealVector x0 ) :  RealVector
ArrayRealVector.ebeMultiply ( RealVector v ) :  ArrayRealVector
ArrayRealVector.ebeMultiply ( RealVector x0 ) :  RealVector
ArrayRealVector.equals ( Object other ) :  boolean
ArrayRealVector.getDataRef ( ) :  double[ ]
ArrayRealVector.getDimension ( ) :  int
ArrayRealVector.getDistance ( RealVector v ) :  double
ArrayRealVector.getEntry ( int index ) :  double
ArrayRealVector.getL1Distance ( RealVector v ) :  double
ArrayRealVector.getL1Norm ( ) :  double
ArrayRealVector.getLInfDistance ( RealVector v ) :  double
ArrayRealVector.getLInfNorm ( ) :  double
ArrayRealVector.getNorm ( ) :  double
ArrayRealVector.getSubVector ( int index, int n ) :  RealVector
ArrayRealVector.hashCode ( ) :  int
ArrayRealVector.isInfinite ( ) :  boolean
ArrayRealVector.isNaN ( ) :  boolean
ArrayRealVector.map ( UnivariateFunction function ) :  ArrayRealVector
ArrayRealVector.map ( UnivariateFunction x0 ) :  RealVector
ArrayRealVector.mapAddToSelf ( double d ) :  RealVector
ArrayRealVector.mapDivideToSelf ( double d ) :  RealVector
ArrayRealVector.mapMultiplyToSelf ( double d ) :  RealVector
ArrayRealVector.mapSubtractToSelf ( double d ) :  RealVector
ArrayRealVector.mapToSelf ( UnivariateFunction function ) :  ArrayRealVector
ArrayRealVector.mapToSelf ( UnivariateFunction x0 ) :  RealVector
ArrayRealVector.outerProduct ( RealVector v ) :  RealMatrix
ArrayRealVector.projection ( RealVector v ) :  RealVector
ArrayRealVector.set ( double value ) :  void
ArrayRealVector.setEntry ( int index, double value ) :  void
ArrayRealVector.setSubVector ( int index, double[ ] v ) :  void
ArrayRealVector.setSubVector ( int index, RealVector v ) :  void
ArrayRealVector.subtract ( RealVector v ) :  ArrayRealVector
ArrayRealVector.subtract ( RealVector x0 ) :  RealVector
ArrayRealVector.toArray ( ) :  double[ ]
ArrayRealVector.toString ( ) :  String
ArrayRealVector.unitize ( ) :  void
ArrayRealVector.unitVector ( ) :  RealVector

cdk-1.5.1.jar, Asin.class
package org.apache.commons.math3.analysis.function
Asin.Asin ( )
Asin.derivative ( ) :  UnivariateFunction
Asin.value ( double x ) :  double

cdk-1.5.1.jar, Asinh.class
package org.apache.commons.math3.analysis.function
Asinh.Asinh ( )
Asinh.derivative ( ) :  UnivariateFunction
Asinh.value ( double x ) :  double

cdk-1.5.1.jar, Atan.class
package org.apache.commons.math3.analysis.function
Atan.Atan ( )
Atan.derivative ( ) :  UnivariateFunction
Atan.value ( double x ) :  double

cdk-1.5.1.jar, Atan2.class
package org.apache.commons.math3.analysis.function
Atan2.Atan2 ( )
Atan2.value ( double x, double y ) :  double

cdk-1.5.1.jar, Atanh.class
package org.apache.commons.math3.analysis.function
Atanh.Atanh ( )
Atanh.derivative ( ) :  UnivariateFunction
Atanh.value ( double x ) :  double

cdk-1.5.1.jar, AtomContainerRenderer.class
package org.openscience.cdk.renderer
AtomContainerRenderer.AtomContainerRenderer ( RendererModel rendererModel, List generators, IFontManager fontManager )

cdk-1.5.1.jar, AtomCountDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
AtomCountDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, AtomDegreeDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
AtomDegreeDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, AtomHybridizationDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
AtomHybridizationDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, AtomHybridizationVSEPRDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
AtomHybridizationVSEPRDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, AtomicNumberDifferenceDescriptor.class
package org.openscience.cdk.qsar.descriptors.bond
AtomicNumberDifferenceDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, AtomPlacer.class
package org.openscience.cdk.layout
AtomPlacer.breadthFirstSearch ( IAtomContainer ac, List sphere, IAtomContainer[ ] pathes ) :  void
AtomPlacer.listNumbers ( IAtomContainer mol, List ac ) :  String

cdk-1.5.1.jar, AtomValenceDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
AtomValenceDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, AttachedGroup.class
package org.openscience.cdk.iupac.parser
AttachedGroup.AttachedGroup ( List locations, int length )
AttachedGroup.AttachedGroup ( List locations, String name )
AttachedGroup.getLocations ( ) :  List
AttachedGroup.setLocations ( List locations ) :  void

cdk-1.5.1.jar, AutocorrelationDescriptorCharge.class
package org.openscience.cdk.qsar.descriptors.molecular
AutocorrelationDescriptorCharge.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, AutocorrelationDescriptorMass.class
package org.openscience.cdk.qsar.descriptors.molecular
AutocorrelationDescriptorMass.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, AutocorrelationDescriptorPolarizability.class
package org.openscience.cdk.qsar.descriptors.molecular
AutocorrelationDescriptorPolarizability.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, AverageBondLengthCalculator.class
package org.openscience.cdk.renderer
AverageBondLengthCalculator.AverageBondLengthCalculator ( )

cdk-1.5.1.jar, AVLTree.class
package org.apache.commons.math3.geometry.partitioning.utilities
AVLTree.AVLTree ( )
AVLTree.delete ( Comparable element ) :  boolean
AVLTree.getLargest ( ) :  AVLTree.Node
AVLTree.getNotLarger ( Comparable reference ) :  AVLTree.Node
AVLTree.getNotSmaller ( Comparable reference ) :  AVLTree.Node
AVLTree.getSmallest ( ) :  AVLTree.Node
AVLTree.insert ( Comparable element ) :  void
AVLTree.isEmpty ( ) :  boolean
AVLTree.size ( ) :  int

cdk-1.5.1.jar, BaseAbstractMultivariateOptimizer.class
package org.apache.commons.math3.optimization.direct
BaseAbstractMultivariateOptimizer.BaseAbstractMultivariateOptimizer ( )
BaseAbstractMultivariateOptimizer.BaseAbstractMultivariateOptimizer ( ConvergenceChecker checker )
BaseAbstractMultivariateOptimizer.computeObjectiveValue ( double[ ] point ) :  double
BaseAbstractMultivariateOptimizer.doOptimize ( ) [abstract] :  PointValuePair
BaseAbstractMultivariateOptimizer.getConvergenceChecker ( ) :  ConvergenceChecker
BaseAbstractMultivariateOptimizer.getEvaluations ( ) :  int
BaseAbstractMultivariateOptimizer.getGoalType ( ) :  GoalType
BaseAbstractMultivariateOptimizer.getMaxEvaluations ( ) :  int
BaseAbstractMultivariateOptimizer.getStartPoint ( ) :  double[ ]
BaseAbstractMultivariateOptimizer.optimize ( int maxEval, MultivariateFunction f, GoalType goalType, double[ ] startPoint ) :  PointValuePair

cdk-1.5.1.jar, BaseAbstractMultivariateSimpleBoundsOptimizer.class
package org.apache.commons.math3.optimization.direct
BaseAbstractMultivariateSimpleBoundsOptimizer.BaseAbstractMultivariateSimpleBoundsOptimizer ( )
BaseAbstractMultivariateSimpleBoundsOptimizer.BaseAbstractMultivariateSimpleBoundsOptimizer ( ConvergenceChecker checker )
BaseAbstractMultivariateSimpleBoundsOptimizer.getLowerBound ( ) :  double[ ]
BaseAbstractMultivariateSimpleBoundsOptimizer.getUpperBound ( ) :  double[ ]
BaseAbstractMultivariateSimpleBoundsOptimizer.optimize ( int maxEval, MultivariateFunction f, GoalType goalType, double[ ] startPoint ) :  PointValuePair
BaseAbstractMultivariateSimpleBoundsOptimizer.optimize ( int maxEval, MultivariateFunction f, GoalType goalType, double[ ] startPoint, double[ ] lower, double[ ] upper ) :  PointValuePair

cdk-1.5.1.jar, BaseAbstractMultivariateVectorOptimizer.class
package org.apache.commons.math3.optimization.direct
BaseAbstractMultivariateVectorOptimizer.BaseAbstractMultivariateVectorOptimizer ( )
BaseAbstractMultivariateVectorOptimizer.BaseAbstractMultivariateVectorOptimizer ( ConvergenceChecker checker )
BaseAbstractMultivariateVectorOptimizer.computeObjectiveValue ( double[ ] point ) :  double[ ]
BaseAbstractMultivariateVectorOptimizer.doOptimize ( ) [abstract] :  PointVectorValuePair
BaseAbstractMultivariateVectorOptimizer.getConvergenceChecker ( ) :  ConvergenceChecker
BaseAbstractMultivariateVectorOptimizer.getEvaluations ( ) :  int
BaseAbstractMultivariateVectorOptimizer.getMaxEvaluations ( ) :  int
BaseAbstractMultivariateVectorOptimizer.getStartPoint ( ) :  double[ ]
BaseAbstractMultivariateVectorOptimizer.getTargetRef ( ) :  double[ ]
BaseAbstractMultivariateVectorOptimizer.getWeightRef ( ) :  double[ ]
BaseAbstractMultivariateVectorOptimizer.optimize ( int maxEval, MultivariateVectorFunction f, double[ ] t, double[ ] w, double[ ] startPoint ) :  PointVectorValuePair

cdk-1.5.1.jar, BaseAbstractUnivariateIntegrator.class
package org.apache.commons.math3.analysis.integration
BaseAbstractUnivariateIntegrator.BaseAbstractUnivariateIntegrator ( double relativeAccuracy, double absoluteAccuracy )
BaseAbstractUnivariateIntegrator.BaseAbstractUnivariateIntegrator ( double relativeAccuracy, double absoluteAccuracy, int minimalIterationCount, int maximalIterationCount )
BaseAbstractUnivariateIntegrator.BaseAbstractUnivariateIntegrator ( int minimalIterationCount, int maximalIterationCount )
BaseAbstractUnivariateIntegrator.computeObjectiveValue ( double point ) :  double
BaseAbstractUnivariateIntegrator.doIntegrate ( ) [abstract] :  double
BaseAbstractUnivariateIntegrator.getAbsoluteAccuracy ( ) :  double
BaseAbstractUnivariateIntegrator.getEvaluations ( ) :  int
BaseAbstractUnivariateIntegrator.getIterations ( ) :  int
BaseAbstractUnivariateIntegrator.getMax ( ) :  double
BaseAbstractUnivariateIntegrator.getMaximalIterationCount ( ) :  int
BaseAbstractUnivariateIntegrator.getMin ( ) :  double
BaseAbstractUnivariateIntegrator.getMinimalIterationCount ( ) :  int
BaseAbstractUnivariateIntegrator.getRelativeAccuracy ( ) :  double
BaseAbstractUnivariateIntegrator.integrate ( int maxEval, UnivariateFunction f, double lower, double upper ) :  double
BaseAbstractUnivariateIntegrator.setup ( int maxEval, UnivariateFunction f, double lower, double upper ) :  void

cdk-1.5.1.jar, BaseAbstractUnivariateOptimizer.class
package org.apache.commons.math3.optimization.univariate
BaseAbstractUnivariateOptimizer.BaseAbstractUnivariateOptimizer ( ConvergenceChecker checker )
BaseAbstractUnivariateOptimizer.computeObjectiveValue ( double point ) :  double
BaseAbstractUnivariateOptimizer.doOptimize ( ) [abstract] :  UnivariatePointValuePair
BaseAbstractUnivariateOptimizer.getConvergenceChecker ( ) :  ConvergenceChecker
BaseAbstractUnivariateOptimizer.getEvaluations ( ) :  int
BaseAbstractUnivariateOptimizer.getGoalType ( ) :  GoalType
BaseAbstractUnivariateOptimizer.getMax ( ) :  double
BaseAbstractUnivariateOptimizer.getMaxEvaluations ( ) :  int
BaseAbstractUnivariateOptimizer.getMin ( ) :  double
BaseAbstractUnivariateOptimizer.getStartValue ( ) :  double
BaseAbstractUnivariateOptimizer.optimize ( int maxEval, UnivariateFunction f, GoalType goalType, double min, double max ) :  UnivariatePointValuePair
BaseAbstractUnivariateOptimizer.optimize ( int maxEval, UnivariateFunction f, GoalType goalType, double min, double max, double startValue ) :  UnivariatePointValuePair

cdk-1.5.1.jar, BaseAbstractUnivariateSolver.class
package org.apache.commons.math3.analysis.solvers
BaseAbstractUnivariateSolver.BaseAbstractUnivariateSolver ( double absoluteAccuracy )
BaseAbstractUnivariateSolver.BaseAbstractUnivariateSolver ( double relativeAccuracy, double absoluteAccuracy )
BaseAbstractUnivariateSolver.BaseAbstractUnivariateSolver ( double relativeAccuracy, double absoluteAccuracy, double functionValueAccuracy )
BaseAbstractUnivariateSolver.computeObjectiveValue ( double point ) :  double
BaseAbstractUnivariateSolver.doSolve ( ) [abstract] :  double
BaseAbstractUnivariateSolver.getAbsoluteAccuracy ( ) :  double
BaseAbstractUnivariateSolver.getEvaluations ( ) :  int
BaseAbstractUnivariateSolver.getFunctionValueAccuracy ( ) :  double
BaseAbstractUnivariateSolver.getMax ( ) :  double
BaseAbstractUnivariateSolver.getMaxEvaluations ( ) :  int
BaseAbstractUnivariateSolver.getMin ( ) :  double
BaseAbstractUnivariateSolver.getRelativeAccuracy ( ) :  double
BaseAbstractUnivariateSolver.getStartValue ( ) :  double
BaseAbstractUnivariateSolver.incrementEvaluationCount ( ) :  void
BaseAbstractUnivariateSolver.isBracketing ( double lower, double upper ) :  boolean
BaseAbstractUnivariateSolver.isSequence ( double start, double mid, double end ) :  boolean
BaseAbstractUnivariateSolver.setup ( int maxEval, UnivariateFunction f, double min, double max, double startValue ) :  void
BaseAbstractUnivariateSolver.solve ( int maxEval, UnivariateFunction f, double min, double max ) :  double
BaseAbstractUnivariateSolver.solve ( int maxEval, UnivariateFunction f, double min, double max, double startValue ) :  double
BaseAbstractUnivariateSolver.solve ( int maxEval, UnivariateFunction f, double startValue ) :  double
BaseAbstractUnivariateSolver.verifyBracketing ( double lower, double upper ) :  void
BaseAbstractUnivariateSolver.verifyInterval ( double lower, double upper ) :  void
BaseAbstractUnivariateSolver.verifySequence ( double lower, double initial, double upper ) :  void

cdk-1.5.1.jar, BaseMultivariateMultiStartOptimizer.class
package org.apache.commons.math3.optimization
BaseMultivariateMultiStartOptimizer.BaseMultivariateMultiStartOptimizer ( BaseMultivariateOptimizer optimizer, int starts, RandomVectorGenerator generator )
BaseMultivariateMultiStartOptimizer.getConvergenceChecker ( ) :  ConvergenceChecker
BaseMultivariateMultiStartOptimizer.getEvaluations ( ) :  int
BaseMultivariateMultiStartOptimizer.getMaxEvaluations ( ) :  int
BaseMultivariateMultiStartOptimizer.getOptima ( ) :  PointValuePair[ ]
BaseMultivariateMultiStartOptimizer.optimize ( int maxEval, MultivariateFunction f, GoalType goal, double[ ] startPoint ) :  PointValuePair

cdk-1.5.1.jar, BaseMultivariateOptimizer.class
package org.apache.commons.math3.optimization
BaseMultivariateOptimizer.optimize ( int p1, MultivariateFunction p2, GoalType p3, double[ ] p4 ) [abstract] :  PointValuePair

cdk-1.5.1.jar, BaseMultivariateSimpleBoundsOptimizer.class
package org.apache.commons.math3.optimization
BaseMultivariateSimpleBoundsOptimizer.optimize ( int p1, MultivariateFunction p2, GoalType p3, double[ ] p4, double[ ] p5, double[ ] p6 ) [abstract] :  PointValuePair

cdk-1.5.1.jar, BaseMultivariateVectorMultiStartOptimizer.class
package org.apache.commons.math3.optimization
BaseMultivariateVectorMultiStartOptimizer.BaseMultivariateVectorMultiStartOptimizer ( BaseMultivariateVectorOptimizer optimizer, int starts, RandomVectorGenerator generator )
BaseMultivariateVectorMultiStartOptimizer.getConvergenceChecker ( ) :  ConvergenceChecker
BaseMultivariateVectorMultiStartOptimizer.getEvaluations ( ) :  int
BaseMultivariateVectorMultiStartOptimizer.getMaxEvaluations ( ) :  int
BaseMultivariateVectorMultiStartOptimizer.getOptima ( ) :  PointVectorValuePair[ ]
BaseMultivariateVectorMultiStartOptimizer.optimize ( int maxEval, MultivariateVectorFunction f, double[ ] target, double[ ] weights, double[ ] startPoint ) :  PointVectorValuePair

cdk-1.5.1.jar, BaseMultivariateVectorOptimizer.class
package org.apache.commons.math3.optimization
BaseMultivariateVectorOptimizer.optimize ( int p1, MultivariateVectorFunction p2, double[ ] p3, double[ ] p4, double[ ] p5 ) [abstract] :  PointVectorValuePair

cdk-1.5.1.jar, BaseOptimizer.class
package org.apache.commons.math3.optimization
BaseOptimizer.getConvergenceChecker ( ) [abstract] :  ConvergenceChecker
BaseOptimizer.getEvaluations ( ) [abstract] :  int
BaseOptimizer.getMaxEvaluations ( ) [abstract] :  int

cdk-1.5.1.jar, BaseSecantSolver.class
package org.apache.commons.math3.analysis.solvers
BaseSecantSolver.BaseSecantSolver ( double absoluteAccuracy, BaseSecantSolver.Method method )
BaseSecantSolver.BaseSecantSolver ( double relativeAccuracy, double absoluteAccuracy, BaseSecantSolver.Method method )
BaseSecantSolver.BaseSecantSolver ( double relativeAccuracy, double absoluteAccuracy, double functionValueAccuracy, BaseSecantSolver.Method method )
BaseSecantSolver.doSolve ( ) :  double
BaseSecantSolver.solve ( int maxEval, UnivariateFunction f, double min, double max, AllowedSolution allowedSolution ) :  double
BaseSecantSolver.solve ( int maxEval, UnivariateFunction f, double min, double max, double startValue ) :  double
BaseSecantSolver.solve ( int maxEval, UnivariateFunction f, double min, double max, double startValue, AllowedSolution allowedSolution ) :  double

cdk-1.5.1.jar, BaseUnivariateOptimizer.class
package org.apache.commons.math3.optimization.univariate
BaseUnivariateOptimizer.optimize ( int p1, UnivariateFunction p2, GoalType p3, double p4, double p5 ) [abstract] :  UnivariatePointValuePair
BaseUnivariateOptimizer.optimize ( int p1, UnivariateFunction p2, GoalType p3, double p4, double p5, double p6 ) [abstract] :  UnivariatePointValuePair

cdk-1.5.1.jar, BaseUnivariateSolver.class
package org.apache.commons.math3.analysis.solvers
BaseUnivariateSolver.getAbsoluteAccuracy ( ) [abstract] :  double
BaseUnivariateSolver.getEvaluations ( ) [abstract] :  int
BaseUnivariateSolver.getFunctionValueAccuracy ( ) [abstract] :  double
BaseUnivariateSolver.getMaxEvaluations ( ) [abstract] :  int
BaseUnivariateSolver.getRelativeAccuracy ( ) [abstract] :  double
BaseUnivariateSolver.solve ( int p1, UnivariateFunction p2, double p3 ) [abstract] :  double
BaseUnivariateSolver.solve ( int p1, UnivariateFunction p2, double p3, double p4 ) [abstract] :  double
BaseUnivariateSolver.solve ( int p1, UnivariateFunction p2, double p3, double p4, double p5 ) [abstract] :  double

cdk-1.5.1.jar, BasicGroupCountDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
BasicGroupCountDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, BCUTDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
BCUTDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, Beta.class
package org.apache.commons.math3.special
Beta.logBeta ( double a, double b ) [static] :  double
Beta.logBeta ( double a, double b, double epsilon, int maxIterations ) [static] :  double
Beta.regularizedBeta ( double x, double a, double b ) [static] :  double
Beta.regularizedBeta ( double x, double a, double b, double epsilon ) [static] :  double
Beta.regularizedBeta ( double x, double a, double b, double epsilon, int maxIterations ) [static] :  double
Beta.regularizedBeta ( double x, double a, double b, int maxIterations ) [static] :  double

cdk-1.5.1.jar, BetaDistribution.class
package org.apache.commons.math3.distribution
BetaDistribution.BetaDistribution ( double alpha, double beta )
BetaDistribution.BetaDistribution ( double alpha, double beta, double inverseCumAccuracy )
BetaDistribution.cumulativeProbability ( double x ) :  double
BetaDistribution.density ( double x ) :  double
BetaDistribution.getAlpha ( ) :  double
BetaDistribution.getBeta ( ) :  double
BetaDistribution.getNumericalMean ( ) :  double
BetaDistribution.getNumericalVariance ( ) :  double
BetaDistribution.getSolverAbsoluteAccuracy ( ) :  double
BetaDistribution.getSupportLowerBound ( ) :  double
BetaDistribution.getSupportUpperBound ( ) :  double
BetaDistribution.isSupportConnected ( ) :  boolean
BetaDistribution.isSupportLowerBoundInclusive ( ) :  boolean
BetaDistribution.isSupportUpperBoundInclusive ( ) :  boolean
BetaDistribution.probability ( double x ) :  double

cdk-1.5.1.jar, BicubicSplineInterpolatingFunction.class
package org.apache.commons.math3.analysis.interpolation
BicubicSplineInterpolatingFunction.BicubicSplineInterpolatingFunction ( double[ ] x, double[ ] y, double[ ][ ] f, double[ ][ ] dFdX, double[ ][ ] dFdY, double[ ][ ] d2FdXdY )
BicubicSplineInterpolatingFunction.partialDerivativeX ( double x, double y ) :  double
BicubicSplineInterpolatingFunction.partialDerivativeXX ( double x, double y ) :  double
BicubicSplineInterpolatingFunction.partialDerivativeXY ( double x, double y ) :  double
BicubicSplineInterpolatingFunction.partialDerivativeY ( double x, double y ) :  double
BicubicSplineInterpolatingFunction.partialDerivativeYY ( double x, double y ) :  double
BicubicSplineInterpolatingFunction.value ( double x, double y ) :  double

cdk-1.5.1.jar, BicubicSplineInterpolator.class
package org.apache.commons.math3.analysis.interpolation
BicubicSplineInterpolator.BicubicSplineInterpolator ( )
BicubicSplineInterpolator.interpolate ( double[ ] x0, double[ ] x1, double[ ][ ] x2 ) :  BivariateFunction
BicubicSplineInterpolator.interpolate ( double[ ] xval, double[ ] yval, double[ ][ ] fval ) :  BicubicSplineInterpolatingFunction

cdk-1.5.1.jar, BigFraction.class
package org.apache.commons.math3.fraction
BigFraction.abs ( ) :  BigFraction
BigFraction.add ( BigFraction fraction ) :  BigFraction
BigFraction.add ( BigInteger bg ) :  BigFraction
BigFraction.add ( int i ) :  BigFraction
BigFraction.add ( long l ) :  BigFraction
BigFraction.add ( Object x0 ) :  Object
BigFraction.bigDecimalValue ( ) :  BigDecimal
BigFraction.bigDecimalValue ( int roundingMode ) :  BigDecimal
BigFraction.bigDecimalValue ( int scale, int roundingMode ) :  BigDecimal
BigFraction.BigFraction ( BigInteger num )
BigFraction.BigFraction ( BigInteger num, BigInteger den )
BigFraction.BigFraction ( double value )
BigFraction.BigFraction ( double value, double epsilon, int maxIterations )
BigFraction.BigFraction ( double value, int maxDenominator )
BigFraction.BigFraction ( int num )
BigFraction.BigFraction ( int num, int den )
BigFraction.BigFraction ( long num )
BigFraction.BigFraction ( long num, long den )
BigFraction.compareTo ( BigFraction object ) :  int
BigFraction.compareTo ( Object x0 ) :  int
BigFraction.divide ( BigFraction fraction ) :  BigFraction
BigFraction.divide ( BigInteger bg ) :  BigFraction
BigFraction.divide ( int i ) :  BigFraction
BigFraction.divide ( long l ) :  BigFraction
BigFraction.divide ( Object x0 ) :  Object
BigFraction.doubleValue ( ) :  double
BigFraction.equals ( Object other ) :  boolean
BigFraction.floatValue ( ) :  float
BigFraction.getDenominator ( ) :  BigInteger
BigFraction.getDenominatorAsInt ( ) :  int
BigFraction.getDenominatorAsLong ( ) :  long
BigFraction.getField ( ) :  BigFractionField
BigFraction.getField ( ) :  Field
BigFraction.getNumerator ( ) :  BigInteger
BigFraction.getNumeratorAsInt ( ) :  int
BigFraction.getNumeratorAsLong ( ) :  long
BigFraction.getReducedFraction ( int numerator, int denominator ) [static] :  BigFraction
BigFraction.hashCode ( ) :  int
BigFraction.intValue ( ) :  int
BigFraction.longValue ( ) :  long
BigFraction.multiply ( BigFraction fraction ) :  BigFraction
BigFraction.multiply ( BigInteger bg ) :  BigFraction
BigFraction.multiply ( int i ) :  BigFraction
BigFraction.multiply ( int x0 ) :  Object
BigFraction.multiply ( long l ) :  BigFraction
BigFraction.multiply ( Object x0 ) :  Object
BigFraction.negate ( ) :  BigFraction
BigFraction.negate ( ) :  Object
BigFraction.percentageValue ( ) :  double
BigFraction.pow ( BigInteger exponent ) :  BigFraction
BigFraction.pow ( double exponent ) :  double
BigFraction.pow ( int exponent ) :  BigFraction
BigFraction.pow ( long exponent ) :  BigFraction
BigFraction.reciprocal ( ) :  BigFraction
BigFraction.reciprocal ( ) :  Object
BigFraction.reduce ( ) :  BigFraction
BigFraction.subtract ( BigFraction fraction ) :  BigFraction
BigFraction.subtract ( BigInteger bg ) :  BigFraction
BigFraction.subtract ( int i ) :  BigFraction
BigFraction.subtract ( long l ) :  BigFraction
BigFraction.subtract ( Object x0 ) :  Object
BigFraction.toString ( ) :  String

cdk-1.5.1.jar, BigFractionField.class
package org.apache.commons.math3.fraction
BigFractionField.getInstance ( ) [static] :  BigFractionField
BigFractionField.getOne ( ) :  BigFraction
BigFractionField.getOne ( ) :  Object
BigFractionField.getRuntimeClass ( ) :  Class
BigFractionField.getZero ( ) :  BigFraction
BigFractionField.getZero ( ) :  Object

cdk-1.5.1.jar, BigFractionFormat.class
package org.apache.commons.math3.fraction
BigFractionFormat.BigFractionFormat ( )
BigFractionFormat.BigFractionFormat ( NumberFormat format )
BigFractionFormat.BigFractionFormat ( NumberFormat numeratorFormat, NumberFormat denominatorFormat )
BigFractionFormat.format ( BigFraction BigFraction, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
BigFractionFormat.format ( Object obj, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
BigFractionFormat.formatBigFraction ( BigFraction f ) [static] :  String
BigFractionFormat.getAvailableLocales ( ) [static] :  Locale[ ]
BigFractionFormat.getImproperInstance ( ) [static] :  BigFractionFormat
BigFractionFormat.getImproperInstance ( Locale locale ) [static] :  BigFractionFormat
BigFractionFormat.getProperInstance ( ) [static] :  BigFractionFormat
BigFractionFormat.getProperInstance ( Locale locale ) [static] :  BigFractionFormat
BigFractionFormat.parse ( String source ) :  BigFraction
BigFractionFormat.parse ( String source, ParsePosition pos ) :  BigFraction
BigFractionFormat.parse ( String x0 ) :  Number
BigFractionFormat.parse ( String x0, ParsePosition x1 ) :  Number
BigFractionFormat.parseNextBigInteger ( String source, ParsePosition pos ) :  BigInteger

cdk-1.5.1.jar, BigReal.class
package org.apache.commons.math3.util
BigReal.add ( BigReal a ) :  BigReal
BigReal.add ( Object x0 ) :  Object
BigReal.bigDecimalValue ( ) :  BigDecimal
BigReal.BigReal ( BigDecimal val )
BigReal.BigReal ( BigInteger unscaledVal, int scale )
BigReal.BigReal ( BigInteger unscaledVal, int scale, MathContext mc )
BigReal.BigReal ( BigInteger val )
BigReal.BigReal ( BigInteger val, MathContext mc )
BigReal.BigReal ( char[ ] in )
BigReal.BigReal ( char[ ] in, int offset, int len )
BigReal.BigReal ( char[ ] in, int offset, int len, MathContext mc )
BigReal.BigReal ( char[ ] in, MathContext mc )
BigReal.BigReal ( double val )
BigReal.BigReal ( double val, MathContext mc )
BigReal.BigReal ( int val )
BigReal.BigReal ( int val, MathContext mc )
BigReal.BigReal ( long val )
BigReal.BigReal ( long val, MathContext mc )
BigReal.BigReal ( String val )
BigReal.BigReal ( String val, MathContext mc )
BigReal.compareTo ( BigReal a ) :  int
BigReal.compareTo ( Object x0 ) :  int
BigReal.divide ( BigReal a ) :  BigReal
BigReal.divide ( Object x0 ) :  Object
BigReal.doubleValue ( ) :  double
BigReal.equals ( Object other ) :  boolean
BigReal.getField ( ) :  Field
BigReal.getRoundingMode ( ) :  RoundingMode
BigReal.getScale ( ) :  int
BigReal.hashCode ( ) :  int
BigReal.multiply ( BigReal a ) :  BigReal
BigReal.multiply ( int n ) :  BigReal
BigReal.multiply ( int x0 ) :  Object
BigReal.multiply ( Object x0 ) :  Object
BigReal.negate ( ) :  BigReal
BigReal.negate ( ) :  Object
BigReal.reciprocal ( ) :  BigReal
BigReal.reciprocal ( ) :  Object
BigReal.setRoundingMode ( RoundingMode roundingMode ) :  void
BigReal.setScale ( int scale ) :  void
BigReal.subtract ( BigReal a ) :  BigReal
BigReal.subtract ( Object x0 ) :  Object

cdk-1.5.1.jar, BigRealField.class
package org.apache.commons.math3.util
BigRealField.getInstance ( ) [static] :  BigRealField
BigRealField.getOne ( ) :  BigReal
BigRealField.getOne ( ) :  Object
BigRealField.getRuntimeClass ( ) :  Class
BigRealField.getZero ( ) :  BigReal
BigRealField.getZero ( ) :  Object

cdk-1.5.1.jar, BinaryChromosome.class
package org.apache.commons.math3.genetics
BinaryChromosome.BinaryChromosome ( Integer[ ] representation )
BinaryChromosome.BinaryChromosome ( List representation )
BinaryChromosome.checkValidity ( List chromosomeRepresentation ) :  void
BinaryChromosome.isSame ( Chromosome another ) :  boolean
BinaryChromosome.randomBinaryRepresentation ( int length ) [static] :  List

cdk-1.5.1.jar, BinaryMutation.class
package org.apache.commons.math3.genetics
BinaryMutation.BinaryMutation ( )
BinaryMutation.mutate ( Chromosome original ) :  Chromosome

cdk-1.5.1.jar, BinomialDistribution.class
package org.apache.commons.math3.distribution
BinomialDistribution.BinomialDistribution ( int trials, double p )
BinomialDistribution.cumulativeProbability ( int x ) :  double
BinomialDistribution.getNumberOfTrials ( ) :  int
BinomialDistribution.getNumericalMean ( ) :  double
BinomialDistribution.getNumericalVariance ( ) :  double
BinomialDistribution.getProbabilityOfSuccess ( ) :  double
BinomialDistribution.getSupportLowerBound ( ) :  int
BinomialDistribution.getSupportUpperBound ( ) :  int
BinomialDistribution.isSupportConnected ( ) :  boolean
BinomialDistribution.probability ( int x ) :  double

cdk-1.5.1.jar, BisectionSolver.class
package org.apache.commons.math3.analysis.solvers
BisectionSolver.BisectionSolver ( )
BisectionSolver.BisectionSolver ( double absoluteAccuracy )
BisectionSolver.BisectionSolver ( double relativeAccuracy, double absoluteAccuracy )
BisectionSolver.doSolve ( ) :  double

cdk-1.5.1.jar, BitSetFingerprint.class
package org.openscience.cdk.fingerprint
BitSetFingerprint.and ( IBitFingerprint fingerprint ) :  void
BitSetFingerprint.asBitSet ( ) :  BitSet
BitSetFingerprint.BitSetFingerprint ( )
BitSetFingerprint.BitSetFingerprint ( BitSet bitset )
BitSetFingerprint.BitSetFingerprint ( IBitFingerprint fingerprint )
BitSetFingerprint.BitSetFingerprint ( int size )
BitSetFingerprint.cardinality ( ) :  int
BitSetFingerprint.equals ( Object obj ) :  boolean
BitSetFingerprint.get ( int index ) :  boolean
BitSetFingerprint.getSetbits ( ) :  int[ ]
BitSetFingerprint.hashCode ( ) :  int
BitSetFingerprint.or ( IBitFingerprint fingerprint ) :  void
BitSetFingerprint.set ( int i ) :  void
BitSetFingerprint.set ( int index, boolean b ) :  void
BitSetFingerprint.size ( ) :  long

cdk-1.5.1.jar, BitsStreamGenerator.class
package org.apache.commons.math3.random
BitsStreamGenerator.BitsStreamGenerator ( )
BitsStreamGenerator.clear ( ) :  void
BitsStreamGenerator.next ( int p1 ) [abstract] :  int
BitsStreamGenerator.nextBoolean ( ) :  boolean
BitsStreamGenerator.nextBytes ( byte[ ] bytes ) :  void
BitsStreamGenerator.nextDouble ( ) :  double
BitsStreamGenerator.nextFloat ( ) :  float
BitsStreamGenerator.nextGaussian ( ) :  double
BitsStreamGenerator.nextInt ( ) :  int
BitsStreamGenerator.nextInt ( int n ) :  int
BitsStreamGenerator.nextLong ( ) :  long
BitsStreamGenerator.setSeed ( int p1 ) [abstract] :  void
BitsStreamGenerator.setSeed ( int[ ] p1 ) [abstract] :  void
BitsStreamGenerator.setSeed ( long p1 ) [abstract] :  void

cdk-1.5.1.jar, BivariateFunction.class
package org.apache.commons.math3.analysis
BivariateFunction.value ( double p1, double p2 ) [abstract] :  double

cdk-1.5.1.jar, BivariateGridInterpolator.class
package org.apache.commons.math3.analysis.interpolation
BivariateGridInterpolator.interpolate ( double[ ] p1, double[ ] p2, double[ ][ ] p3 ) [abstract] :  BivariateFunction

cdk-1.5.1.jar, BlockFieldMatrix.class
package org.apache.commons.math3.linear
BlockFieldMatrix.add ( BlockFieldMatrix m ) :  BlockFieldMatrix
BlockFieldMatrix.add ( FieldMatrix m ) :  FieldMatrix
BlockFieldMatrix.addToEntry ( int row, int column, FieldElement increment ) :  void
BlockFieldMatrix.BlockFieldMatrix ( Field field, int rows, int columns )
BlockFieldMatrix.BlockFieldMatrix ( FieldElement[ ][ ] rawData )
BlockFieldMatrix.BlockFieldMatrix ( int rows, int columns, FieldElement[ ][ ] blockData, boolean copyArray )
BlockFieldMatrix.copy ( ) :  FieldMatrix
BlockFieldMatrix.createBlocksLayout ( Field field, int rows, int columns ) [static] :  FieldElement[ ][ ]
BlockFieldMatrix.createMatrix ( int rowDimension, int columnDimension ) :  FieldMatrix
BlockFieldMatrix.getColumn ( int column ) :  FieldElement[ ]
BlockFieldMatrix.getColumnDimension ( ) :  int
BlockFieldMatrix.getColumnMatrix ( int column ) :  FieldMatrix
BlockFieldMatrix.getColumnVector ( int column ) :  FieldVector
BlockFieldMatrix.getData ( ) :  FieldElement[ ][ ]
BlockFieldMatrix.getEntry ( int row, int column ) :  FieldElement
BlockFieldMatrix.getRow ( int row ) :  FieldElement[ ]
BlockFieldMatrix.getRowDimension ( ) :  int
BlockFieldMatrix.getRowMatrix ( int row ) :  FieldMatrix
BlockFieldMatrix.getRowVector ( int row ) :  FieldVector
BlockFieldMatrix.getSubMatrix ( int startRow, int endRow, int startColumn, int endColumn ) :  FieldMatrix
BlockFieldMatrix.multiply ( BlockFieldMatrix m ) :  BlockFieldMatrix
BlockFieldMatrix.multiply ( FieldMatrix m ) :  FieldMatrix
BlockFieldMatrix.multiplyEntry ( int row, int column, FieldElement factor ) :  void
BlockFieldMatrix.operate ( FieldElement[ ] v ) :  FieldElement[ ]
BlockFieldMatrix.preMultiply ( FieldElement[ ] v ) :  FieldElement[ ]
BlockFieldMatrix.scalarAdd ( FieldElement d ) :  FieldMatrix
BlockFieldMatrix.scalarMultiply ( FieldElement d ) :  FieldMatrix
BlockFieldMatrix.setColumn ( int column, FieldElement[ ] array ) :  void
BlockFieldMatrix.setColumnMatrix ( int column, FieldMatrix matrix ) :  void
BlockFieldMatrix.setColumnVector ( int column, FieldVector vector ) :  void
BlockFieldMatrix.setEntry ( int row, int column, FieldElement value ) :  void
BlockFieldMatrix.setRow ( int row, FieldElement[ ] array ) :  void
BlockFieldMatrix.setRowMatrix ( int row, BlockFieldMatrix matrix ) :  void
BlockFieldMatrix.setRowMatrix ( int row, FieldMatrix matrix ) :  void
BlockFieldMatrix.setRowVector ( int row, FieldVector vector ) :  void
BlockFieldMatrix.setSubMatrix ( FieldElement[ ][ ] subMatrix, int row, int column ) :  void
BlockFieldMatrix.subtract ( BlockFieldMatrix m ) :  BlockFieldMatrix
BlockFieldMatrix.subtract ( FieldMatrix m ) :  FieldMatrix
BlockFieldMatrix.toBlocksLayout ( FieldElement[ ][ ] rawData ) [static] :  FieldElement[ ][ ]
BlockFieldMatrix.transpose ( ) :  FieldMatrix
BlockFieldMatrix.walkInOptimizedOrder ( FieldMatrixChangingVisitor visitor ) :  FieldElement
BlockFieldMatrix.walkInOptimizedOrder ( FieldMatrixChangingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  FieldElement
BlockFieldMatrix.walkInOptimizedOrder ( FieldMatrixPreservingVisitor visitor ) :  FieldElement
BlockFieldMatrix.walkInOptimizedOrder ( FieldMatrixPreservingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  FieldElement
BlockFieldMatrix.walkInRowOrder ( FieldMatrixChangingVisitor visitor ) :  FieldElement
BlockFieldMatrix.walkInRowOrder ( FieldMatrixChangingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  FieldElement
BlockFieldMatrix.walkInRowOrder ( FieldMatrixPreservingVisitor visitor ) :  FieldElement
BlockFieldMatrix.walkInRowOrder ( FieldMatrixPreservingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  FieldElement

cdk-1.5.1.jar, BlockRealMatrix.class
package org.apache.commons.math3.linear
BlockRealMatrix.add ( BlockRealMatrix m ) :  BlockRealMatrix
BlockRealMatrix.add ( RealMatrix m ) :  BlockRealMatrix
BlockRealMatrix.add ( RealMatrix x0 ) :  RealMatrix
BlockRealMatrix.addToEntry ( int row, int column, double increment ) :  void
BlockRealMatrix.BlockRealMatrix ( double[ ][ ] rawData )
BlockRealMatrix.BlockRealMatrix ( int rows, int columns )
BlockRealMatrix.BlockRealMatrix ( int rows, int columns, double[ ][ ] blockData, boolean copyArray )
BlockRealMatrix.copy ( ) :  BlockRealMatrix
BlockRealMatrix.copy ( ) :  RealMatrix
BlockRealMatrix.createBlocksLayout ( int rows, int columns ) [static] :  double[ ][ ]
BlockRealMatrix.createMatrix ( int rowDimension, int columnDimension ) :  BlockRealMatrix
BlockRealMatrix.createMatrix ( int x0, int x1 ) :  RealMatrix
BlockRealMatrix.getColumn ( int column ) :  double[ ]
BlockRealMatrix.getColumnDimension ( ) :  int
BlockRealMatrix.getColumnMatrix ( int column ) :  BlockRealMatrix
BlockRealMatrix.getColumnMatrix ( int x0 ) :  RealMatrix
BlockRealMatrix.getColumnVector ( int column ) :  RealVector
BlockRealMatrix.getData ( ) :  double[ ][ ]
BlockRealMatrix.getEntry ( int row, int column ) :  double
BlockRealMatrix.getFrobeniusNorm ( ) :  double
BlockRealMatrix.getNorm ( ) :  double
BlockRealMatrix.getRow ( int row ) :  double[ ]
BlockRealMatrix.getRowDimension ( ) :  int
BlockRealMatrix.getRowMatrix ( int row ) :  BlockRealMatrix
BlockRealMatrix.getRowMatrix ( int x0 ) :  RealMatrix
BlockRealMatrix.getRowVector ( int row ) :  RealVector
BlockRealMatrix.getSubMatrix ( int startRow, int endRow, int startColumn, int endColumn ) :  BlockRealMatrix
BlockRealMatrix.getSubMatrix ( int x0, int x1, int x2, int x3 ) :  RealMatrix
BlockRealMatrix.multiply ( BlockRealMatrix m ) :  BlockRealMatrix
BlockRealMatrix.multiply ( RealMatrix m ) :  BlockRealMatrix
BlockRealMatrix.multiply ( RealMatrix x0 ) :  RealMatrix
BlockRealMatrix.multiplyEntry ( int row, int column, double factor ) :  void
BlockRealMatrix.operate ( double[ ] v ) :  double[ ]
BlockRealMatrix.preMultiply ( double[ ] v ) :  double[ ]
BlockRealMatrix.scalarAdd ( double d ) :  BlockRealMatrix
BlockRealMatrix.scalarAdd ( double x0 ) :  RealMatrix
BlockRealMatrix.scalarMultiply ( double d ) :  RealMatrix
BlockRealMatrix.setColumn ( int column, double[ ] array ) :  void
BlockRealMatrix.setColumnMatrix ( int column, RealMatrix matrix ) :  void
BlockRealMatrix.setColumnVector ( int column, RealVector vector ) :  void
BlockRealMatrix.setEntry ( int row, int column, double value ) :  void
BlockRealMatrix.setRow ( int row, double[ ] array ) :  void
BlockRealMatrix.setRowMatrix ( int row, BlockRealMatrix matrix ) :  void
BlockRealMatrix.setRowMatrix ( int row, RealMatrix matrix ) :  void
BlockRealMatrix.setRowVector ( int row, RealVector vector ) :  void
BlockRealMatrix.setSubMatrix ( double[ ][ ] subMatrix, int row, int column ) :  void
BlockRealMatrix.subtract ( BlockRealMatrix m ) :  BlockRealMatrix
BlockRealMatrix.subtract ( RealMatrix m ) :  BlockRealMatrix
BlockRealMatrix.subtract ( RealMatrix x0 ) :  RealMatrix
BlockRealMatrix.toBlocksLayout ( double[ ][ ] rawData ) [static] :  double[ ][ ]
BlockRealMatrix.transpose ( ) :  BlockRealMatrix
BlockRealMatrix.transpose ( ) :  RealMatrix
BlockRealMatrix.walkInOptimizedOrder ( RealMatrixChangingVisitor visitor ) :  double
BlockRealMatrix.walkInOptimizedOrder ( RealMatrixChangingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  double
BlockRealMatrix.walkInOptimizedOrder ( RealMatrixPreservingVisitor visitor ) :  double
BlockRealMatrix.walkInOptimizedOrder ( RealMatrixPreservingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  double
BlockRealMatrix.walkInRowOrder ( RealMatrixChangingVisitor visitor ) :  double
BlockRealMatrix.walkInRowOrder ( RealMatrixChangingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  double
BlockRealMatrix.walkInRowOrder ( RealMatrixPreservingVisitor visitor ) :  double
BlockRealMatrix.walkInRowOrder ( RealMatrixPreservingVisitor visitor, int startRow, int endRow, int startColumn, int endColumn ) :  double

cdk-1.5.1.jar, BOBYQAOptimizer.class
package org.apache.commons.math3.optimization.direct
BOBYQAOptimizer.BOBYQAOptimizer ( int numberOfInterpolationPoints )
BOBYQAOptimizer.BOBYQAOptimizer ( int numberOfInterpolationPoints, double initialTrustRegionRadius, double stoppingTrustRegionRadius )
BOBYQAOptimizer.doOptimize ( ) :  PointValuePair

cdk-1.5.1.jar, BondCountDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
BondCountDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, BondManipulator.class
package org.openscience.cdk.tools.manipulator
BondManipulator.getMaximumBondOrder ( IBond firstBond, IBond secondBond ) [static] :  IBond.Order
BondManipulator.getMaximumBondOrder ( IBond.Order firstOrder, IBond.Order secondOrder ) [static] :  IBond.Order

cdk-1.5.1.jar, BondPartialPiChargeDescriptor.class
package org.openscience.cdk.qsar.descriptors.bond
BondPartialPiChargeDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, BondPartialSigmaChargeDescriptor.class
package org.openscience.cdk.qsar.descriptors.bond
BondPartialSigmaChargeDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, BondPartialTChargeDescriptor.class
package org.openscience.cdk.qsar.descriptors.bond
BondPartialTChargeDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, BondSigmaElectronegativityDescriptor.class
package org.openscience.cdk.qsar.descriptors.bond
BondSigmaElectronegativityDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, BondsToAtomDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
BondsToAtomDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, BooleanIOSetting.class
package org.openscience.cdk.io.setting
BooleanIOSetting.BooleanIOSetting ( String name, IOSetting.Importance level, String question, String defaultSetting )

cdk-1.5.1.jar, BoundaryAttribute.class
package org.apache.commons.math3.geometry.partitioning
BoundaryAttribute.BoundaryAttribute ( SubHyperplane plusOutside, SubHyperplane plusInside )
BoundaryAttribute.getPlusInside ( ) :  SubHyperplane
BoundaryAttribute.getPlusOutside ( ) :  SubHyperplane

cdk-1.5.1.jar, BPolDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
BPolDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, BracketedUnivariateSolver.class
package org.apache.commons.math3.analysis.solvers
BracketedUnivariateSolver.solve ( int p1, UnivariateFunction p2, double p3, double p4, AllowedSolution p5 ) [abstract] :  double
BracketedUnivariateSolver.solve ( int p1, UnivariateFunction p2, double p3, double p4, double p5, AllowedSolution p6 ) [abstract] :  double

cdk-1.5.1.jar, BracketFinder.class
package org.apache.commons.math3.optimization.univariate
BracketFinder.BracketFinder ( )
BracketFinder.BracketFinder ( double growLimit, int maxEvaluations )
BracketFinder.getEvaluations ( ) :  int
BracketFinder.getFHi ( ) :  double
BracketFinder.getFLo ( ) :  double
BracketFinder.getFMid ( ) :  double
BracketFinder.getHi ( ) :  double
BracketFinder.getLo ( ) :  double
BracketFinder.getMaxEvaluations ( ) :  int
BracketFinder.getMid ( ) :  double
BracketFinder.search ( UnivariateFunction func, GoalType goal, double xA, double xB ) :  void

cdk-1.5.1.jar, BracketingNthOrderBrentSolver.class
package org.apache.commons.math3.analysis.solvers
BracketingNthOrderBrentSolver.BracketingNthOrderBrentSolver ( )
BracketingNthOrderBrentSolver.BracketingNthOrderBrentSolver ( double absoluteAccuracy, int maximalOrder )
BracketingNthOrderBrentSolver.BracketingNthOrderBrentSolver ( double relativeAccuracy, double absoluteAccuracy, double functionValueAccuracy, int maximalOrder )
BracketingNthOrderBrentSolver.BracketingNthOrderBrentSolver ( double relativeAccuracy, double absoluteAccuracy, int maximalOrder )
BracketingNthOrderBrentSolver.doSolve ( ) :  double
BracketingNthOrderBrentSolver.getMaximalOrder ( ) :  int
BracketingNthOrderBrentSolver.solve ( int maxEval, UnivariateFunction f, double min, double max, AllowedSolution allowedSolution ) :  double
BracketingNthOrderBrentSolver.solve ( int maxEval, UnivariateFunction f, double min, double max, double startValue, AllowedSolution allowedSolution ) :  double

cdk-1.5.1.jar, BracketingNthOrderBrentSolverDFP.class
package org.apache.commons.math3.dfp
BracketingNthOrderBrentSolverDFP.BracketingNthOrderBrentSolverDFP ( Dfp relativeAccuracy, Dfp absoluteAccuracy, Dfp functionValueAccuracy, int maximalOrder )
BracketingNthOrderBrentSolverDFP.getAbsoluteAccuracy ( ) :  Dfp
BracketingNthOrderBrentSolverDFP.getEvaluations ( ) :  int
BracketingNthOrderBrentSolverDFP.getFunctionValueAccuracy ( ) :  Dfp
BracketingNthOrderBrentSolverDFP.getMaxEvaluations ( ) :  int
BracketingNthOrderBrentSolverDFP.getMaximalOrder ( ) :  int
BracketingNthOrderBrentSolverDFP.getRelativeAccuracy ( ) :  Dfp
BracketingNthOrderBrentSolverDFP.solve ( int maxEval, UnivariateDfpFunction f, Dfp min, Dfp max, AllowedSolution allowedSolution ) :  Dfp
BracketingNthOrderBrentSolverDFP.solve ( int maxEval, UnivariateDfpFunction f, Dfp min, Dfp max, Dfp startValue, AllowedSolution allowedSolution ) :  Dfp

cdk-1.5.1.jar, BrentOptimizer.class
package org.apache.commons.math3.optimization.univariate
BrentOptimizer.BrentOptimizer ( double rel, double abs )
BrentOptimizer.BrentOptimizer ( double rel, double abs, ConvergenceChecker checker )
BrentOptimizer.doOptimize ( ) :  UnivariatePointValuePair

cdk-1.5.1.jar, BrentSolver.class
package org.apache.commons.math3.analysis.solvers
BrentSolver.BrentSolver ( )
BrentSolver.BrentSolver ( double absoluteAccuracy )
BrentSolver.BrentSolver ( double relativeAccuracy, double absoluteAccuracy )
BrentSolver.BrentSolver ( double relativeAccuracy, double absoluteAccuracy, double functionValueAccuracy )
BrentSolver.doSolve ( ) :  double

cdk-1.5.1.jar, BSPTree.class
package org.apache.commons.math3.geometry.partitioning
BSPTree.BSPTree ( )
BSPTree.BSPTree ( Object attribute )
BSPTree.BSPTree ( SubHyperplane cut, BSPTree plus, BSPTree minus, Object attribute )
BSPTree.copySelf ( ) :  BSPTree
BSPTree.getAttribute ( ) :  Object
BSPTree.getCell ( Vector point ) :  BSPTree
BSPTree.getCut ( ) :  SubHyperplane
BSPTree.getMinus ( ) :  BSPTree
BSPTree.getParent ( ) :  BSPTree
BSPTree.getPlus ( ) :  BSPTree
BSPTree.insertCut ( Hyperplane hyperplane ) :  boolean
BSPTree.insertInTree ( BSPTree parentTree, boolean isPlusChild ) :  void
BSPTree.merge ( BSPTree tree, BSPTree.LeafMerger leafMerger ) :  BSPTree
BSPTree.setAttribute ( Object attribute ) :  void
BSPTree.split ( SubHyperplane sub ) :  BSPTree
BSPTree.visit ( BSPTreeVisitor visitor ) :  void

cdk-1.5.1.jar, BSPTreeVisitor.class
package org.apache.commons.math3.geometry.partitioning
BSPTreeVisitor.visitInternalNode ( BSPTree p1 ) [abstract] :  void
BSPTreeVisitor.visitLeafNode ( BSPTree p1 ) [abstract] :  void
BSPTreeVisitor.visitOrder ( BSPTree p1 ) [abstract] :  BSPTreeVisitor.Order

cdk-1.5.1.jar, CarbonTypesDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
CarbonTypesDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, CardanEulerSingularityException.class
package org.apache.commons.math3.geometry.euclidean.threed
CardanEulerSingularityException.CardanEulerSingularityException ( boolean isCardan )

cdk-1.5.1.jar, CauchyDistribution.class
package org.apache.commons.math3.distribution
CauchyDistribution.CauchyDistribution ( )
CauchyDistribution.CauchyDistribution ( double median, double scale )
CauchyDistribution.CauchyDistribution ( double median, double scale, double inverseCumAccuracy )
CauchyDistribution.cumulativeProbability ( double x ) :  double
CauchyDistribution.density ( double x ) :  double
CauchyDistribution.getMedian ( ) :  double
CauchyDistribution.getNumericalMean ( ) :  double
CauchyDistribution.getNumericalVariance ( ) :  double
CauchyDistribution.getScale ( ) :  double
CauchyDistribution.getSolverAbsoluteAccuracy ( ) :  double
CauchyDistribution.getSupportLowerBound ( ) :  double
CauchyDistribution.getSupportUpperBound ( ) :  double
CauchyDistribution.inverseCumulativeProbability ( double p ) :  double
CauchyDistribution.isSupportConnected ( ) :  boolean
CauchyDistribution.isSupportLowerBoundInclusive ( ) :  boolean
CauchyDistribution.isSupportUpperBoundInclusive ( ) :  boolean
CauchyDistribution.probability ( double x ) :  double

cdk-1.5.1.jar, Cbrt.class
package org.apache.commons.math3.analysis.function
Cbrt.Cbrt ( )
Cbrt.derivative ( ) :  UnivariateFunction
Cbrt.value ( double x ) :  double

cdk-1.5.1.jar, Ceil.class
package org.apache.commons.math3.analysis.function
Ceil.Ceil ( )
Ceil.value ( double x ) :  double

cdk-1.5.1.jar, ChemObject.class
package org.openscience.cdk
ChemObject.getFlagValue ( ) :  Number
ChemObject.getFlagValue ( ) :  Short
package org.openscience.cdk.silent
ChemObject.getFlagValue ( ) :  Number
ChemObject.getFlagValue ( ) :  Short

cdk-1.5.1.jar, ChemObjectIO.class
package org.openscience.cdk.io
ChemObjectIO.addChemObjectIOListener ( IChemObjectIOListener listener ) :  void
ChemObjectIO.addSetting ( IOSetting setting ) :  IOSetting
ChemObjectIO.addSettings ( Collection settings ) :  void
ChemObjectIO.ChemObjectIO ( )
ChemObjectIO.fireIOSettingQuestion ( IOSetting setting ) :  void
ChemObjectIO.getIOSettings ( ) :  IOSetting[ ]
ChemObjectIO.getListeners ( ) :  Collection
ChemObjectIO.getListeners ( ) :  List
ChemObjectIO.getSetting ( String name ) :  IOSetting
ChemObjectIO.getSetting ( String name, Class c ) :  IOSetting
ChemObjectIO.getSettings ( ) :  Collection
ChemObjectIO.hasSetting ( String name ) :  boolean
ChemObjectIO.removeChemObjectIOListener ( IChemObjectIOListener listener ) :  void

cdk-1.5.1.jar, ChiChainDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
ChiChainDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, ChiClusterDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
ChiClusterDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, ChiPathClusterDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
ChiPathClusterDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, ChiPathDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
ChiPathDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, ChiSquaredDistribution.class
package org.apache.commons.math3.distribution
ChiSquaredDistribution.ChiSquaredDistribution ( double degreesOfFreedom )
ChiSquaredDistribution.ChiSquaredDistribution ( double degreesOfFreedom, double inverseCumAccuracy )
ChiSquaredDistribution.cumulativeProbability ( double x ) :  double
ChiSquaredDistribution.density ( double x ) :  double
ChiSquaredDistribution.getDegreesOfFreedom ( ) :  double
ChiSquaredDistribution.getNumericalMean ( ) :  double
ChiSquaredDistribution.getNumericalVariance ( ) :  double
ChiSquaredDistribution.getSolverAbsoluteAccuracy ( ) :  double
ChiSquaredDistribution.getSupportLowerBound ( ) :  double
ChiSquaredDistribution.getSupportUpperBound ( ) :  double
ChiSquaredDistribution.isSupportConnected ( ) :  boolean
ChiSquaredDistribution.isSupportLowerBoundInclusive ( ) :  boolean
ChiSquaredDistribution.isSupportUpperBoundInclusive ( ) :  boolean
ChiSquaredDistribution.probability ( double x ) :  double

cdk-1.5.1.jar, ChiSquareTest.class
package org.apache.commons.math3.stat.inference
ChiSquareTest.chiSquare ( double[ ] expected, long[ ] observed ) :  double
ChiSquareTest.chiSquare ( long[ ][ ] counts ) :  double
ChiSquareTest.chiSquareDataSetsComparison ( long[ ] observed1, long[ ] observed2 ) :  double
ChiSquareTest.ChiSquareTest ( )
ChiSquareTest.chiSquareTest ( double[ ] expected, long[ ] observed ) :  double
ChiSquareTest.chiSquareTest ( double[ ] expected, long[ ] observed, double alpha ) :  boolean
ChiSquareTest.chiSquareTest ( long[ ][ ] counts ) :  double
ChiSquareTest.chiSquareTest ( long[ ][ ] counts, double alpha ) :  boolean
ChiSquareTest.chiSquareTestDataSetsComparison ( long[ ] observed1, long[ ] observed2 ) :  double
ChiSquareTest.chiSquareTestDataSetsComparison ( long[ ] observed1, long[ ] observed2, double alpha ) :  boolean

cdk-1.5.1.jar, CholeskyDecomposition.class
package org.apache.commons.math3.linear
CholeskyDecomposition.CholeskyDecomposition ( RealMatrix matrix )
CholeskyDecomposition.CholeskyDecomposition ( RealMatrix matrix, double relativeSymmetryThreshold, double absolutePositivityThreshold )
CholeskyDecomposition.getDeterminant ( ) :  double
CholeskyDecomposition.getL ( ) :  RealMatrix
CholeskyDecomposition.getLT ( ) :  RealMatrix
CholeskyDecomposition.getSolver ( ) :  DecompositionSolver

cdk-1.5.1.jar, Chromosome.class
package org.apache.commons.math3.genetics
Chromosome.Chromosome ( )
Chromosome.compareTo ( Chromosome another ) :  int
Chromosome.compareTo ( Object x0 ) :  int
Chromosome.findSameChromosome ( Population population ) :  Chromosome
Chromosome.getFitness ( ) :  double
Chromosome.isSame ( Chromosome another ) :  boolean
Chromosome.searchForFitnessUpdate ( Population population ) :  void

cdk-1.5.1.jar, ChromosomePair.class
package org.apache.commons.math3.genetics
ChromosomePair.ChromosomePair ( Chromosome c1, Chromosome c2 )
ChromosomePair.getFirst ( ) :  Chromosome
ChromosomePair.getSecond ( ) :  Chromosome
ChromosomePair.toString ( ) :  String

cdk-1.5.1.jar, ClassicalRungeKuttaIntegrator.class
package org.apache.commons.math3.ode.nonstiff
ClassicalRungeKuttaIntegrator.ClassicalRungeKuttaIntegrator ( double step )

cdk-1.5.1.jar, Cluster.class
package org.apache.commons.math3.stat.clustering
Cluster.addPoint ( Clusterable point ) :  void
Cluster.Cluster ( Clusterable center )
Cluster.getCenter ( ) :  Clusterable
Cluster.getPoints ( ) :  List

cdk-1.5.1.jar, Clusterable.class
package org.apache.commons.math3.stat.clustering
Clusterable.centroidOf ( Collection p1 ) [abstract] :  Object
Clusterable.distanceFrom ( Object p1 ) [abstract] :  double

cdk-1.5.1.jar, CMAESOptimizer.class
package org.apache.commons.math3.optimization.direct
CMAESOptimizer.CMAESOptimizer ( )
CMAESOptimizer.CMAESOptimizer ( int lambda )
CMAESOptimizer.CMAESOptimizer ( int lambda, double[ ] inputSigma )
CMAESOptimizer.CMAESOptimizer ( int lambda, double[ ] inputSigma, int maxIterations, double stopFitness, boolean isActiveCMA, int diagonalOnly, int checkFeasableCount, RandomGenerator random, boolean generateStatistics )
CMAESOptimizer.CMAESOptimizer ( int lambda, double[ ] inputSigma, int maxIterations, double stopFitness, boolean isActiveCMA, int diagonalOnly, int checkFeasableCount, RandomGenerator random, boolean generateStatistics, ConvergenceChecker checker )
CMAESOptimizer.doOptimize ( ) :  PointValuePair
CMAESOptimizer.getStatisticsDHistory ( ) :  List
CMAESOptimizer.getStatisticsFitnessHistory ( ) :  List
CMAESOptimizer.getStatisticsMeanHistory ( ) :  List
CMAESOptimizer.getStatisticsSigmaHistory ( ) :  List

cdk-1.5.1.jar, Complex.class
package org.apache.commons.math3.complex
Complex.abs ( ) :  double
Complex.acos ( ) :  Complex
Complex.add ( Complex addend ) :  Complex
Complex.add ( double addend ) :  Complex
Complex.add ( Object x0 ) :  Object
Complex.asin ( ) :  Complex
Complex.atan ( ) :  Complex
Complex.Complex ( double real )
Complex.Complex ( double real, double imaginary )
Complex.conjugate ( ) :  Complex
Complex.cos ( ) :  Complex
Complex.cosh ( ) :  Complex
Complex.createComplex ( double realPart, double imaginaryPart ) :  Complex
Complex.divide ( Complex divisor ) :  Complex
Complex.divide ( double divisor ) :  Complex
Complex.divide ( Object x0 ) :  Object
Complex.equals ( Object other ) :  boolean
Complex.exp ( ) :  Complex
Complex.getArgument ( ) :  double
Complex.getField ( ) :  ComplexField
Complex.getField ( ) :  Field
Complex.getImaginary ( ) :  double
Complex.getReal ( ) :  double
Complex.hashCode ( ) :  int
Complex.isInfinite ( ) :  boolean
Complex.isNaN ( ) :  boolean
Complex.log ( ) :  Complex
Complex.multiply ( Complex factor ) :  Complex
Complex.multiply ( double factor ) :  Complex
Complex.multiply ( int factor ) :  Complex
Complex.multiply ( int x0 ) :  Object
Complex.multiply ( Object x0 ) :  Object
Complex.negate ( ) :  Complex
Complex.negate ( ) :  Object
Complex.nthRoot ( int n ) :  List
Complex.pow ( Complex x ) :  Complex
Complex.pow ( double x ) :  Complex
Complex.readResolve ( ) :  Object
Complex.reciprocal ( ) :  Complex
Complex.reciprocal ( ) :  Object
Complex.sin ( ) :  Complex
Complex.sinh ( ) :  Complex
Complex.sqrt ( ) :  Complex
Complex.sqrt1z ( ) :  Complex
Complex.subtract ( Complex subtrahend ) :  Complex
Complex.subtract ( double subtrahend ) :  Complex
Complex.subtract ( Object x0 ) :  Object
Complex.tan ( ) :  Complex
Complex.tanh ( ) :  Complex
Complex.toString ( ) :  String
Complex.valueOf ( double realPart ) [static] :  Complex
Complex.valueOf ( double realPart, double imaginaryPart ) [static] :  Complex

cdk-1.5.1.jar, ComplexField.class
package org.apache.commons.math3.complex
ComplexField.getInstance ( ) [static] :  ComplexField
ComplexField.getOne ( ) :  Complex
ComplexField.getOne ( ) :  Object
ComplexField.getRuntimeClass ( ) :  Class
ComplexField.getZero ( ) :  Complex
ComplexField.getZero ( ) :  Object

cdk-1.5.1.jar, ComplexFormat.class
package org.apache.commons.math3.complex
ComplexFormat.ComplexFormat ( )
ComplexFormat.ComplexFormat ( NumberFormat format )
ComplexFormat.ComplexFormat ( NumberFormat realFormat, NumberFormat imaginaryFormat )
ComplexFormat.ComplexFormat ( String imaginaryCharacter )
ComplexFormat.ComplexFormat ( String imaginaryCharacter, NumberFormat format )
ComplexFormat.ComplexFormat ( String imaginaryCharacter, NumberFormat realFormat, NumberFormat imaginaryFormat )
ComplexFormat.format ( Complex c ) :  String
ComplexFormat.format ( Complex complex, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
ComplexFormat.format ( Double c ) :  String
ComplexFormat.format ( Object obj, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
ComplexFormat.getAvailableLocales ( ) [static] :  Locale[ ]
ComplexFormat.getImaginaryCharacter ( ) :  String
ComplexFormat.getImaginaryFormat ( ) :  NumberFormat
ComplexFormat.getInstance ( ) [static] :  ComplexFormat
ComplexFormat.getInstance ( Locale locale ) [static] :  ComplexFormat
ComplexFormat.getInstance ( String imaginaryCharacter, Locale locale ) [static] :  ComplexFormat
ComplexFormat.getRealFormat ( ) :  NumberFormat
ComplexFormat.parse ( String source ) :  Complex
ComplexFormat.parse ( String source, ParsePosition pos ) :  Complex

cdk-1.5.1.jar, ComplexUtils.class
package org.apache.commons.math3.complex
ComplexUtils.polar2Complex ( double r, double theta ) [static] :  Complex

cdk-1.5.1.jar, CompositeFormat.class
package org.apache.commons.math3.util
CompositeFormat.formatDouble ( double value, NumberFormat format, StringBuffer toAppendTo, FieldPosition pos ) [static] :  StringBuffer
CompositeFormat.getDefaultNumberFormat ( ) [static] :  NumberFormat
CompositeFormat.getDefaultNumberFormat ( Locale locale ) [static] :  NumberFormat
CompositeFormat.parseAndIgnoreWhitespace ( String source, ParsePosition pos ) [static] :  void
CompositeFormat.parseFixedstring ( String source, String expected, ParsePosition pos ) [static] :  boolean
CompositeFormat.parseNextCharacter ( String source, ParsePosition pos ) [static] :  char
CompositeFormat.parseNumber ( String source, NumberFormat format, ParsePosition pos ) [static] :  Number

cdk-1.5.1.jar, ConjugateGradient.class
package org.apache.commons.math3.linear
ConjugateGradient.ConjugateGradient ( int maxIterations, double delta, boolean check )
ConjugateGradient.ConjugateGradient ( IterationManager manager, double delta, boolean check )
ConjugateGradient.getCheck ( ) :  boolean
ConjugateGradient.solveInPlace ( RealLinearOperator a, RealLinearOperator minv, RealVector b, RealVector x0 ) :  RealVector

cdk-1.5.1.jar, ConjugateGradientFormula.class
package org.apache.commons.math3.optimization.general
ConjugateGradientFormula.valueOf ( String name ) [static] :  ConjugateGradientFormula
ConjugateGradientFormula.values ( ) [static] :  ConjugateGradientFormula[ ]

cdk-1.5.1.jar, Constant.class
package org.apache.commons.math3.analysis.function
Constant.Constant ( double c )
Constant.derivative ( ) :  DifferentiableUnivariateFunction
Constant.derivative ( ) :  UnivariateFunction
Constant.value ( double x ) :  double

cdk-1.5.1.jar, ContinuedFraction.class
package org.apache.commons.math3.util
ContinuedFraction.ContinuedFraction ( )
ContinuedFraction.evaluate ( double x ) :  double
ContinuedFraction.evaluate ( double x, double epsilon ) :  double
ContinuedFraction.evaluate ( double x, double epsilon, int maxIterations ) :  double
ContinuedFraction.evaluate ( double x, int maxIterations ) :  double
ContinuedFraction.getA ( int p1, double p2 ) [abstract] :  double
ContinuedFraction.getB ( int p1, double p2 ) [abstract] :  double

cdk-1.5.1.jar, ContinuousOutputModel.class
package org.apache.commons.math3.ode
ContinuousOutputModel.append ( ContinuousOutputModel model ) :  void
ContinuousOutputModel.ContinuousOutputModel ( )
ContinuousOutputModel.getFinalTime ( ) :  double
ContinuousOutputModel.getInitialTime ( ) :  double
ContinuousOutputModel.getInterpolatedState ( ) :  double[ ]
ContinuousOutputModel.getInterpolatedTime ( ) :  double
ContinuousOutputModel.handleStep ( StepInterpolator interpolator, boolean isLast ) :  void
ContinuousOutputModel.init ( double t0, double[ ] y0, double t ) :  void
ContinuousOutputModel.setInterpolatedTime ( double time ) :  void

cdk-1.5.1.jar, ConvergenceChecker.class
package org.apache.commons.math3.optimization
ConvergenceChecker.converged ( int p1, Object p2, Object p3 ) [abstract] :  boolean

cdk-1.5.1.jar, ConvergenceException.class
package org.apache.commons.math3.exception
ConvergenceException.ConvergenceException ( )
ConvergenceException.ConvergenceException ( Localizable pattern, Object[ ] args )

cdk-1.5.1.jar, CoordinateCoverage.class
package org.openscience.cdk.geometry
GeometryTools.CoordinateCoverage.valueOf ( String name ) [static] :  GeometryTools.CoordinateCoverage
GeometryTools.CoordinateCoverage.values ( ) [static] :  GeometryTools.CoordinateCoverage[ ]

cdk-1.5.1.jar, CorrelatedRandomVectorGenerator.class
package org.apache.commons.math3.random
CorrelatedRandomVectorGenerator.CorrelatedRandomVectorGenerator ( double[ ] mean, RealMatrix covariance, double small, NormalizedRandomGenerator generator )
CorrelatedRandomVectorGenerator.CorrelatedRandomVectorGenerator ( RealMatrix covariance, double small, NormalizedRandomGenerator generator )
CorrelatedRandomVectorGenerator.getGenerator ( ) :  NormalizedRandomGenerator
CorrelatedRandomVectorGenerator.getRank ( ) :  int
CorrelatedRandomVectorGenerator.getRootMatrix ( ) :  RealMatrix
CorrelatedRandomVectorGenerator.nextVector ( ) :  double[ ]

cdk-1.5.1.jar, Cos.class
package org.apache.commons.math3.analysis.function
Cos.Cos ( )
Cos.derivative ( ) :  UnivariateFunction
Cos.value ( double x ) :  double

cdk-1.5.1.jar, Cosh.class
package org.apache.commons.math3.analysis.function
Cosh.Cosh ( )
Cosh.derivative ( ) :  DifferentiableUnivariateFunction
Cosh.derivative ( ) :  UnivariateFunction
Cosh.value ( double x ) :  double

cdk-1.5.1.jar, CovalentRadiusDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
CovalentRadiusDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, Covariance.class
package org.apache.commons.math3.stat.correlation
Covariance.computeCovarianceMatrix ( double[ ][ ] data ) :  RealMatrix
Covariance.computeCovarianceMatrix ( double[ ][ ] data, boolean biasCorrected ) :  RealMatrix
Covariance.computeCovarianceMatrix ( RealMatrix matrix ) :  RealMatrix
Covariance.computeCovarianceMatrix ( RealMatrix matrix, boolean biasCorrected ) :  RealMatrix
Covariance.Covariance ( )
Covariance.covariance ( double[ ] xArray, double[ ] yArray ) :  double
Covariance.covariance ( double[ ] xArray, double[ ] yArray, boolean biasCorrected ) :  double
Covariance.Covariance ( double[ ][ ] data )
Covariance.Covariance ( double[ ][ ] data, boolean biasCorrected )
Covariance.Covariance ( RealMatrix matrix )
Covariance.Covariance ( RealMatrix matrix, boolean biasCorrected )
Covariance.getCovarianceMatrix ( ) :  RealMatrix
Covariance.getN ( ) :  int

cdk-1.5.1.jar, CPSADescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
CPSADescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, CrossoverPolicy.class
package org.apache.commons.math3.genetics
CrossoverPolicy.crossover ( Chromosome p1, Chromosome p2 ) [abstract] :  ChromosomePair

cdk-1.5.1.jar, CurveFitter.class
package org.apache.commons.math3.optimization.fitting
CurveFitter.addObservedPoint ( double weight, double x, double y ) :  void
CurveFitter.addObservedPoint ( double x, double y ) :  void
CurveFitter.addObservedPoint ( WeightedObservedPoint observed ) :  void
CurveFitter.clearObservations ( ) :  void
CurveFitter.CurveFitter ( DifferentiableMultivariateVectorOptimizer optimizer )
CurveFitter.fit ( int maxEval, ParametricUnivariateFunction f, double[ ] initialGuess ) :  double[ ]
CurveFitter.fit ( ParametricUnivariateFunction f, double[ ] initialGuess ) :  double[ ]
CurveFitter.getObservations ( ) :  WeightedObservedPoint[ ]

cdk-1.5.1.jar, DctNormalization.class
package org.apache.commons.math3.transform
DctNormalization.valueOf ( String name ) [static] :  DctNormalization
DctNormalization.values ( ) [static] :  DctNormalization[ ]

cdk-1.5.1.jar, DecompositionSolver.class
package org.apache.commons.math3.linear
DecompositionSolver.getInverse ( ) [abstract] :  RealMatrix
DecompositionSolver.isNonSingular ( ) [abstract] :  boolean
DecompositionSolver.solve ( RealMatrix p1 ) [abstract] :  RealMatrix
DecompositionSolver.solve ( RealVector p1 ) [abstract] :  RealVector

cdk-1.5.1.jar, DefaultFieldMatrixChangingVisitor.class
package org.apache.commons.math3.linear
DefaultFieldMatrixChangingVisitor.DefaultFieldMatrixChangingVisitor ( FieldElement zero )
DefaultFieldMatrixChangingVisitor.end ( ) :  FieldElement
DefaultFieldMatrixChangingVisitor.start ( int rows, int columns, int startRow, int endRow, int startColumn, int endColumn ) :  void
DefaultFieldMatrixChangingVisitor.visit ( int row, int column, FieldElement value ) :  FieldElement

cdk-1.5.1.jar, DefaultFieldMatrixPreservingVisitor.class
package org.apache.commons.math3.linear
DefaultFieldMatrixPreservingVisitor.DefaultFieldMatrixPreservingVisitor ( FieldElement zero )
DefaultFieldMatrixPreservingVisitor.end ( ) :  FieldElement
DefaultFieldMatrixPreservingVisitor.start ( int rows, int columns, int startRow, int endRow, int startColumn, int endColumn ) :  void
DefaultFieldMatrixPreservingVisitor.visit ( int row, int column, FieldElement value ) :  void

cdk-1.5.1.jar, DefaultIterativeLinearSolverEvent.class
package org.apache.commons.math3.linear
DefaultIterativeLinearSolverEvent.DefaultIterativeLinearSolverEvent ( Object source, int iterations, RealVector x, RealVector b, double rnorm )
DefaultIterativeLinearSolverEvent.DefaultIterativeLinearSolverEvent ( Object source, int iterations, RealVector x, RealVector b, RealVector r, double rnorm )
DefaultIterativeLinearSolverEvent.getNormOfResidual ( ) :  double
DefaultIterativeLinearSolverEvent.getResidual ( ) :  RealVector
DefaultIterativeLinearSolverEvent.getRightHandSideVector ( ) :  RealVector
DefaultIterativeLinearSolverEvent.getSolution ( ) :  RealVector
DefaultIterativeLinearSolverEvent.providesResidual ( ) :  boolean

cdk-1.5.1.jar, DefaultMeasurementModel.class
package org.apache.commons.math3.filter
DefaultMeasurementModel.DefaultMeasurementModel ( double[ ][ ] measMatrix, double[ ][ ] measNoise )
DefaultMeasurementModel.DefaultMeasurementModel ( RealMatrix measMatrix, RealMatrix measNoise )
DefaultMeasurementModel.getMeasurementMatrix ( ) :  RealMatrix
DefaultMeasurementModel.getMeasurementNoise ( ) :  RealMatrix

cdk-1.5.1.jar, DefaultProcessModel.class
package org.apache.commons.math3.filter
DefaultProcessModel.DefaultProcessModel ( double[ ][ ] stateTransition, double[ ][ ] control, double[ ][ ] processNoise )
DefaultProcessModel.DefaultProcessModel ( double[ ][ ] stateTransition, double[ ][ ] control, double[ ][ ] processNoise, double[ ] initialStateEstimate, double[ ][ ] initialErrorCovariance )
DefaultProcessModel.DefaultProcessModel ( RealMatrix stateTransition, RealMatrix control, RealMatrix processNoise, RealVector initialStateEstimate, RealMatrix initialErrorCovariance )
DefaultProcessModel.getControlMatrix ( ) :  RealMatrix
DefaultProcessModel.getInitialErrorCovariance ( ) :  RealMatrix
DefaultProcessModel.getInitialStateEstimate ( ) :  RealVector
DefaultProcessModel.getProcessNoise ( ) :  RealMatrix
DefaultProcessModel.getStateTransitionMatrix ( ) :  RealMatrix

cdk-1.5.1.jar, DefaultRealMatrixChangingVisitor.class
package org.apache.commons.math3.linear
DefaultRealMatrixChangingVisitor.DefaultRealMatrixChangingVisitor ( )
DefaultRealMatrixChangingVisitor.end ( ) :  double
DefaultRealMatrixChangingVisitor.start ( int rows, int columns, int startRow, int endRow, int startColumn, int endColumn ) :  void
DefaultRealMatrixChangingVisitor.visit ( int row, int column, double value ) :  double

cdk-1.5.1.jar, DefaultRealMatrixPreservingVisitor.class
package org.apache.commons.math3.linear
DefaultRealMatrixPreservingVisitor.DefaultRealMatrixPreservingVisitor ( )
DefaultRealMatrixPreservingVisitor.end ( ) :  double
DefaultRealMatrixPreservingVisitor.start ( int rows, int columns, int startRow, int endRow, int startColumn, int endColumn ) :  void
DefaultRealMatrixPreservingVisitor.visit ( int row, int column, double value ) :  void

cdk-1.5.1.jar, DefaultTransformer.class
package org.apache.commons.math3.util
DefaultTransformer.DefaultTransformer ( )
DefaultTransformer.equals ( Object other ) :  boolean
DefaultTransformer.hashCode ( ) :  int
DefaultTransformer.transform ( Object o ) :  double

cdk-1.5.1.jar, DescriptiveStatistics.class
package org.apache.commons.math3.stat.descriptive
DescriptiveStatistics.addValue ( double v ) :  void
DescriptiveStatistics.apply ( UnivariateStatistic stat ) :  double
DescriptiveStatistics.clear ( ) :  void
DescriptiveStatistics.copy ( ) :  DescriptiveStatistics
DescriptiveStatistics.copy ( DescriptiveStatistics source, DescriptiveStatistics dest ) [static] :  void
DescriptiveStatistics.DescriptiveStatistics ( )
DescriptiveStatistics.DescriptiveStatistics ( DescriptiveStatistics original )
DescriptiveStatistics.DescriptiveStatistics ( double[ ] initialDoubleArray )
DescriptiveStatistics.DescriptiveStatistics ( int window )
DescriptiveStatistics.getElement ( int index ) :  double
DescriptiveStatistics.getGeometricMean ( ) :  double
DescriptiveStatistics.getGeometricMeanImpl ( ) :  UnivariateStatistic
DescriptiveStatistics.getKurtosis ( ) :  double
DescriptiveStatistics.getKurtosisImpl ( ) :  UnivariateStatistic
DescriptiveStatistics.getMax ( ) :  double
DescriptiveStatistics.getMaxImpl ( ) :  UnivariateStatistic
DescriptiveStatistics.getMean ( ) :  double
DescriptiveStatistics.getMeanImpl ( ) :  UnivariateStatistic
DescriptiveStatistics.getMin ( ) :  double
DescriptiveStatistics.getMinImpl ( ) :  UnivariateStatistic
DescriptiveStatistics.getN ( ) :  long
DescriptiveStatistics.getPercentile ( double p ) :  double
DescriptiveStatistics.getPercentileImpl ( ) :  UnivariateStatistic
DescriptiveStatistics.getPopulationVariance ( ) :  double
DescriptiveStatistics.getSkewness ( ) :  double
DescriptiveStatistics.getSkewnessImpl ( ) :  UnivariateStatistic
DescriptiveStatistics.getSortedValues ( ) :  double[ ]
DescriptiveStatistics.getStandardDeviation ( ) :  double
DescriptiveStatistics.getSum ( ) :  double
DescriptiveStatistics.getSumImpl ( ) :  UnivariateStatistic
DescriptiveStatistics.getSumsq ( ) :  double
DescriptiveStatistics.getSumsqImpl ( ) :  UnivariateStatistic
DescriptiveStatistics.getValues ( ) :  double[ ]
DescriptiveStatistics.getVariance ( ) :  double
DescriptiveStatistics.getVarianceImpl ( ) :  UnivariateStatistic
DescriptiveStatistics.getWindowSize ( ) :  int
DescriptiveStatistics.removeMostRecentValue ( ) :  void
DescriptiveStatistics.replaceMostRecentValue ( double v ) :  double
DescriptiveStatistics.setGeometricMeanImpl ( UnivariateStatistic geometricMeanImpl ) :  void
DescriptiveStatistics.setKurtosisImpl ( UnivariateStatistic kurtosisImpl ) :  void
DescriptiveStatistics.setMaxImpl ( UnivariateStatistic maxImpl ) :  void
DescriptiveStatistics.setMeanImpl ( UnivariateStatistic meanImpl ) :  void
DescriptiveStatistics.setMinImpl ( UnivariateStatistic minImpl ) :  void
DescriptiveStatistics.setPercentileImpl ( UnivariateStatistic percentileImpl ) :  void
DescriptiveStatistics.setSkewnessImpl ( UnivariateStatistic skewnessImpl ) :  void
DescriptiveStatistics.setSumImpl ( UnivariateStatistic sumImpl ) :  void
DescriptiveStatistics.setSumsqImpl ( UnivariateStatistic sumsqImpl ) :  void
DescriptiveStatistics.setVarianceImpl ( UnivariateStatistic varianceImpl ) :  void
DescriptiveStatistics.setWindowSize ( int windowSize ) :  void
DescriptiveStatistics.toString ( ) :  String

cdk-1.5.1.jar, DescriptorEngine.class
package org.openscience.cdk.qsar
DescriptorEngine.getDictionaryClass ( IImplementationSpecification descriptorSpecification ) :  String[ ]
DescriptorEngine.getDictionaryType ( IImplementationSpecification descriptorSpecification ) :  String

cdk-1.5.1.jar, Dfp.class
package org.apache.commons.math3.dfp
Dfp.abs ( ) :  Dfp
Dfp.add ( Dfp x ) :  Dfp
Dfp.add ( Object x0 ) :  Object
Dfp.align ( int e ) :  int
Dfp.ceil ( ) :  Dfp
Dfp.classify ( ) :  int
Dfp.complement ( int extra ) :  int
Dfp.copysign ( Dfp x, Dfp y ) [static] :  Dfp
Dfp.Dfp ( Dfp d )
Dfp.Dfp ( DfpField field )
Dfp.Dfp ( DfpField field, byte sign, byte nans )
Dfp.Dfp ( DfpField field, byte x )
Dfp.Dfp ( DfpField field, double x )
Dfp.Dfp ( DfpField field, int x )
Dfp.Dfp ( DfpField field, long x )
Dfp.Dfp ( DfpField field, String s )
Dfp.dfp2sci ( ) :  String
Dfp.dfp2string ( ) :  String
Dfp.divide ( Dfp divisor ) :  Dfp
Dfp.divide ( int divisor ) :  Dfp
Dfp.divide ( Object x0 ) :  Object
Dfp.dotrap ( int type, String what, Dfp oper, Dfp result ) :  Dfp
Dfp.equals ( Object other ) :  boolean
Dfp.floor ( ) :  Dfp
Dfp.getField ( ) :  DfpField
Dfp.getField ( ) :  Field
Dfp.getOne ( ) :  Dfp
Dfp.getRadixDigits ( ) :  int
Dfp.getTwo ( ) :  Dfp
Dfp.getZero ( ) :  Dfp
Dfp.greaterThan ( Dfp x ) :  boolean
Dfp.hashCode ( ) :  int
Dfp.intValue ( ) :  int
Dfp.isInfinite ( ) :  boolean
Dfp.isNaN ( ) :  boolean
Dfp.isZero ( ) :  boolean
Dfp.lessThan ( Dfp x ) :  boolean
Dfp.log10 ( ) :  int
Dfp.log10K ( ) :  int
Dfp.multiply ( Dfp x ) :  Dfp
Dfp.multiply ( int x ) :  Dfp
Dfp.multiply ( int x0 ) :  Object
Dfp.multiply ( Object x0 ) :  Object
Dfp.negate ( ) :  Dfp
Dfp.negate ( ) :  Object
Dfp.negativeOrNull ( ) :  boolean
Dfp.newInstance ( ) :  Dfp
Dfp.newInstance ( byte sig, byte code ) :  Dfp
Dfp.newInstance ( byte x ) :  Dfp
Dfp.newInstance ( Dfp d ) :  Dfp
Dfp.newInstance ( double x ) :  Dfp
Dfp.newInstance ( int x ) :  Dfp
Dfp.newInstance ( long x ) :  Dfp
Dfp.newInstance ( String s ) :  Dfp
Dfp.nextAfter ( Dfp x ) :  Dfp
Dfp.positiveOrNull ( ) :  boolean
Dfp.power10 ( int e ) :  Dfp
Dfp.power10K ( int e ) :  Dfp
Dfp.reciprocal ( ) :  Dfp
Dfp.reciprocal ( ) :  Object
Dfp.remainder ( Dfp d ) :  Dfp
Dfp.rint ( ) :  Dfp
Dfp.round ( int n ) :  int
Dfp.shiftLeft ( ) :  void
Dfp.shiftRight ( ) :  void
Dfp.sqrt ( ) :  Dfp
Dfp.strictlyNegative ( ) :  boolean
Dfp.strictlyPositive ( ) :  boolean
Dfp.subtract ( Dfp x ) :  Dfp
Dfp.subtract ( Object x0 ) :  Object
Dfp.toDouble ( ) :  double
Dfp.toSplitDouble ( ) :  double[ ]
Dfp.toString ( ) :  String
Dfp.trap ( int type, String what, Dfp oper, Dfp def, Dfp result ) :  Dfp
Dfp.trunc ( DfpField.RoundingMode rmode ) :  Dfp
Dfp.unequal ( Dfp x ) :  boolean

cdk-1.5.1.jar, DfpDec.class
package org.apache.commons.math3.dfp
DfpDec.DfpDec ( Dfp d )
DfpDec.DfpDec ( DfpField factory )
DfpDec.DfpDec ( DfpField factory, byte sign, byte nans )
DfpDec.DfpDec ( DfpField factory, byte x )
DfpDec.DfpDec ( DfpField factory, double x )
DfpDec.DfpDec ( DfpField factory, int x )
DfpDec.DfpDec ( DfpField factory, long x )
DfpDec.DfpDec ( DfpField factory, String s )
DfpDec.getDecimalDigits ( ) :  int
DfpDec.newInstance ( ) :  Dfp
DfpDec.newInstance ( byte sign, byte nans ) :  Dfp
DfpDec.newInstance ( byte x ) :  Dfp
DfpDec.newInstance ( Dfp d ) :  Dfp
DfpDec.newInstance ( double x ) :  Dfp
DfpDec.newInstance ( int x ) :  Dfp
DfpDec.newInstance ( long x ) :  Dfp
DfpDec.newInstance ( String s ) :  Dfp
DfpDec.nextAfter ( Dfp x ) :  Dfp
DfpDec.round ( int in ) :  int

cdk-1.5.1.jar, DfpField.class
package org.apache.commons.math3.dfp
DfpField.clearIEEEFlags ( ) :  void
DfpField.computeExp ( Dfp a, Dfp one ) [static] :  Dfp
DfpField.computeLn ( Dfp a, Dfp one, Dfp two ) [static] :  Dfp
DfpField.DfpField ( int decimalDigits )
DfpField.getE ( ) :  Dfp
DfpField.getESplit ( ) :  Dfp[ ]
DfpField.getIEEEFlags ( ) :  int
DfpField.getLn10 ( ) :  Dfp
DfpField.getLn2 ( ) :  Dfp
DfpField.getLn2Split ( ) :  Dfp[ ]
DfpField.getLn5 ( ) :  Dfp
DfpField.getLn5Split ( ) :  Dfp[ ]
DfpField.getOne ( ) :  Dfp
DfpField.getOne ( ) :  Object
DfpField.getPi ( ) :  Dfp
DfpField.getPiSplit ( ) :  Dfp[ ]
DfpField.getRadixDigits ( ) :  int
DfpField.getRoundingMode ( ) :  DfpField.RoundingMode
DfpField.getRuntimeClass ( ) :  Class
DfpField.getSqr2 ( ) :  Dfp
DfpField.getSqr2Reciprocal ( ) :  Dfp
DfpField.getSqr2Split ( ) :  Dfp[ ]
DfpField.getSqr3 ( ) :  Dfp
DfpField.getSqr3Reciprocal ( ) :  Dfp
DfpField.getTwo ( ) :  Dfp
DfpField.getZero ( ) :  Dfp
DfpField.getZero ( ) :  Object
DfpField.newDfp ( ) :  Dfp
DfpField.newDfp ( byte sign, byte nans ) :  Dfp
DfpField.newDfp ( byte x ) :  Dfp
DfpField.newDfp ( Dfp d ) :  Dfp
DfpField.newDfp ( double x ) :  Dfp
DfpField.newDfp ( int x ) :  Dfp
DfpField.newDfp ( long x ) :  Dfp
DfpField.newDfp ( String s ) :  Dfp
DfpField.setIEEEFlags ( int flags ) :  void
DfpField.setIEEEFlagsBits ( int bits ) :  void
DfpField.setRoundingMode ( DfpField.RoundingMode mode ) :  void

cdk-1.5.1.jar, DfpMath.class
package org.apache.commons.math3.dfp
DfpMath.acos ( Dfp a ) [static] :  Dfp
DfpMath.asin ( Dfp a ) [static] :  Dfp
DfpMath.atan ( Dfp a ) [static] :  Dfp
DfpMath.atanInternal ( Dfp a ) [static] :  Dfp
DfpMath.cos ( Dfp a ) [static] :  Dfp
DfpMath.cosInternal ( Dfp[ ] a ) [static] :  Dfp
DfpMath.exp ( Dfp a ) [static] :  Dfp
DfpMath.expInternal ( Dfp a ) [static] :  Dfp
DfpMath.log ( Dfp a ) [static] :  Dfp
DfpMath.logInternal ( Dfp[ ] a ) [static] :  Dfp[ ]
DfpMath.pow ( Dfp base, int a ) [static] :  Dfp
DfpMath.pow ( Dfp x, Dfp y ) [static] :  Dfp
DfpMath.sin ( Dfp a ) [static] :  Dfp
DfpMath.sinInternal ( Dfp[ ] a ) [static] :  Dfp
DfpMath.split ( Dfp a ) [static] :  Dfp[ ]
DfpMath.split ( DfpField field, String a ) [static] :  Dfp[ ]
DfpMath.splitDiv ( Dfp[ ] a, Dfp[ ] b ) [static] :  Dfp[ ]
DfpMath.splitMult ( Dfp[ ] a, Dfp[ ] b ) [static] :  Dfp[ ]
DfpMath.splitPow ( Dfp[ ] base, int a ) [static] :  Dfp
DfpMath.tan ( Dfp a ) [static] :  Dfp

cdk-1.5.1.jar, DftNormalization.class
package org.apache.commons.math3.transform
DftNormalization.valueOf ( String name ) [static] :  DftNormalization
DftNormalization.values ( ) [static] :  DftNormalization[ ]

cdk-1.5.1.jar, DifferentiableMultivariateFunction.class
package org.apache.commons.math3.analysis
DifferentiableMultivariateFunction.gradient ( ) [abstract] :  MultivariateVectorFunction
DifferentiableMultivariateFunction.partialDerivative ( int p1 ) [abstract] :  MultivariateFunction

cdk-1.5.1.jar, DifferentiableMultivariateMultiStartOptimizer.class
package org.apache.commons.math3.optimization
DifferentiableMultivariateMultiStartOptimizer.DifferentiableMultivariateMultiStartOptimizer ( DifferentiableMultivariateOptimizer optimizer, int starts, RandomVectorGenerator generator )

cdk-1.5.1.jar, DifferentiableMultivariateVectorFunction.class
package org.apache.commons.math3.analysis
DifferentiableMultivariateVectorFunction.jacobian ( ) [abstract] :  MultivariateMatrixFunction

cdk-1.5.1.jar, DifferentiableMultivariateVectorMultiStartOptimizer.class
package org.apache.commons.math3.optimization
DifferentiableMultivariateVectorMultiStartOptimizer.DifferentiableMultivariateVectorMultiStartOptimizer ( DifferentiableMultivariateVectorOptimizer optimizer, int starts, RandomVectorGenerator generator )

cdk-1.5.1.jar, DifferentiableUnivariateFunction.class
package org.apache.commons.math3.analysis
DifferentiableUnivariateFunction.derivative ( ) [abstract] :  UnivariateFunction

cdk-1.5.1.jar, DifferentiableUnivariateMatrixFunction.class
package org.apache.commons.math3.analysis
DifferentiableUnivariateMatrixFunction.derivative ( ) [abstract] :  UnivariateMatrixFunction

cdk-1.5.1.jar, DifferentiableUnivariateVectorFunction.class
package org.apache.commons.math3.analysis
DifferentiableUnivariateVectorFunction.derivative ( ) [abstract] :  UnivariateVectorFunction

cdk-1.5.1.jar, DimensionMismatchException.class
package org.apache.commons.math3.exception
DimensionMismatchException.DimensionMismatchException ( int wrong, int expected )
DimensionMismatchException.DimensionMismatchException ( Localizable specific, int wrong, int expected )
DimensionMismatchException.getDimension ( ) :  int

cdk-1.5.1.jar, Direction.class
package org.apache.commons.math3.stat.descriptive.moment
SemiVariance.Direction.valueOf ( String name ) [static] :  SemiVariance.Direction
SemiVariance.Direction.values ( ) [static] :  SemiVariance.Direction[ ]

cdk-1.5.1.jar, DistanceToAtomDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
DistanceToAtomDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, Divide.class
package org.apache.commons.math3.analysis.function
Divide.Divide ( )
Divide.value ( double x, double y ) :  double

cdk-1.5.1.jar, DividedDifferenceInterpolator.class
package org.apache.commons.math3.analysis.interpolation
DividedDifferenceInterpolator.computeDividedDifference ( double[ ] x, double[ ] y ) [static] :  double[ ]
DividedDifferenceInterpolator.DividedDifferenceInterpolator ( )
DividedDifferenceInterpolator.interpolate ( double[ ] x, double[ ] y ) :  PolynomialFunctionNewtonForm
DividedDifferenceInterpolator.interpolate ( double[ ] x0, double[ ] x1 ) :  UnivariateFunction

cdk-1.5.1.jar, DormandPrince54Integrator.class
package org.apache.commons.math3.ode.nonstiff
DormandPrince54Integrator.DormandPrince54Integrator ( double minStep, double maxStep, double scalAbsoluteTolerance, double scalRelativeTolerance )
DormandPrince54Integrator.DormandPrince54Integrator ( double minStep, double maxStep, double[ ] vecAbsoluteTolerance, double[ ] vecRelativeTolerance )
DormandPrince54Integrator.estimateError ( double[ ][ ] yDotK, double[ ] y0, double[ ] y1, double h ) :  double
DormandPrince54Integrator.getOrder ( ) :  int

cdk-1.5.1.jar, DormandPrince853Integrator.class
package org.apache.commons.math3.ode.nonstiff
DormandPrince853Integrator.DormandPrince853Integrator ( double minStep, double maxStep, double scalAbsoluteTolerance, double scalRelativeTolerance )
DormandPrince853Integrator.DormandPrince853Integrator ( double minStep, double maxStep, double[ ] vecAbsoluteTolerance, double[ ] vecRelativeTolerance )
DormandPrince853Integrator.estimateError ( double[ ][ ] yDotK, double[ ] y0, double[ ] y1, double h ) :  double
DormandPrince853Integrator.getOrder ( ) :  int

cdk-1.5.1.jar, DoubleArray.class
package org.apache.commons.math3.util
DoubleArray.addElement ( double p1 ) [abstract] :  void
DoubleArray.addElementRolling ( double p1 ) [abstract] :  double
DoubleArray.addElements ( double[ ] p1 ) [abstract] :  void
DoubleArray.clear ( ) [abstract] :  void
DoubleArray.getElement ( int p1 ) [abstract] :  double
DoubleArray.getElements ( ) [abstract] :  double[ ]
DoubleArray.getNumElements ( ) [abstract] :  int
DoubleArray.setElement ( int p1, double p2 ) [abstract] :  void

cdk-1.5.1.jar, DstNormalization.class
package org.apache.commons.math3.transform
DstNormalization.valueOf ( String name ) [static] :  DstNormalization
DstNormalization.values ( ) [static] :  DstNormalization[ ]

cdk-1.5.1.jar, DummyLocalizable.class
package org.apache.commons.math3.exception.util
DummyLocalizable.DummyLocalizable ( String source )
DummyLocalizable.getLocalizedString ( Locale locale ) :  String
DummyLocalizable.getSourceString ( ) :  String
DummyLocalizable.toString ( ) :  String

cdk-1.5.1.jar, DummyStepHandler.class
package org.apache.commons.math3.ode.sampling
DummyStepHandler.getInstance ( ) [static] :  DummyStepHandler
DummyStepHandler.handleStep ( StepInterpolator interpolator, boolean isLast ) :  void
DummyStepHandler.init ( double t0, double[ ] y0, double t ) :  void

cdk-1.5.1.jar, EccentricConnectivityIndexDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
EccentricConnectivityIndexDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, EffectiveAtomPolarizabilityDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
EffectiveAtomPolarizabilityDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, EigenDecomposition.class
package org.apache.commons.math3.linear
EigenDecomposition.EigenDecomposition ( double[ ] main, double[ ] secondary, double splitTolerance )
EigenDecomposition.EigenDecomposition ( RealMatrix matrix, double splitTolerance )
EigenDecomposition.getD ( ) :  RealMatrix
EigenDecomposition.getDeterminant ( ) :  double
EigenDecomposition.getEigenvector ( int i ) :  RealVector
EigenDecomposition.getImagEigenvalue ( int i ) :  double
EigenDecomposition.getImagEigenvalues ( ) :  double[ ]
EigenDecomposition.getRealEigenvalue ( int i ) :  double
EigenDecomposition.getRealEigenvalues ( ) :  double[ ]
EigenDecomposition.getSolver ( ) :  DecompositionSolver
EigenDecomposition.getV ( ) :  RealMatrix
EigenDecomposition.getVT ( ) :  RealMatrix

cdk-1.5.1.jar, ElitisticListPopulation.class
package org.apache.commons.math3.genetics
ElitisticListPopulation.ElitisticListPopulation ( int populationLimit, double elitismRate )
ElitisticListPopulation.ElitisticListPopulation ( List chromosomes, int populationLimit, double elitismRate )
ElitisticListPopulation.getElitismRate ( ) :  double
ElitisticListPopulation.nextGeneration ( ) :  Population
ElitisticListPopulation.setElitismRate ( double elitismRate ) :  void

cdk-1.5.1.jar, EmbeddedRungeKuttaIntegrator.class
package org.apache.commons.math3.ode.nonstiff
EmbeddedRungeKuttaIntegrator.EmbeddedRungeKuttaIntegrator ( String name, boolean fsal, double[ ] c, double[ ][ ] a, double[ ] b, RungeKuttaStepInterpolator prototype, double minStep, double maxStep, double scalAbsoluteTolerance, double scalRelativeTolerance )
EmbeddedRungeKuttaIntegrator.EmbeddedRungeKuttaIntegrator ( String name, boolean fsal, double[ ] c, double[ ][ ] a, double[ ] b, RungeKuttaStepInterpolator prototype, double minStep, double maxStep, double[ ] vecAbsoluteTolerance, double[ ] vecRelativeTolerance )
EmbeddedRungeKuttaIntegrator.estimateError ( double[ ][ ] p1, double[ ] p2, double[ ] p3, double p4 ) [abstract] :  double
EmbeddedRungeKuttaIntegrator.getMaxGrowth ( ) :  double
EmbeddedRungeKuttaIntegrator.getMinReduction ( ) :  double
EmbeddedRungeKuttaIntegrator.getOrder ( ) [abstract] :  int
EmbeddedRungeKuttaIntegrator.getSafety ( ) :  double
EmbeddedRungeKuttaIntegrator.integrate ( ExpandableStatefulODE equations, double t ) :  void
EmbeddedRungeKuttaIntegrator.setMaxGrowth ( double maxGrowth ) :  void
EmbeddedRungeKuttaIntegrator.setMinReduction ( double minReduction ) :  void
EmbeddedRungeKuttaIntegrator.setSafety ( double safety ) :  void

cdk-1.5.1.jar, Embedding.class
package org.apache.commons.math3.geometry.partitioning
Embedding.toSpace ( Vector p1 ) [abstract] :  Vector
Embedding.toSubSpace ( Vector p1 ) [abstract] :  Vector

cdk-1.5.1.jar, EmpiricalDistribution.class
package org.apache.commons.math3.random
EmpiricalDistribution.EmpiricalDistribution ( )
EmpiricalDistribution.EmpiricalDistribution ( int binCount )
EmpiricalDistribution.EmpiricalDistribution ( int binCount, RandomDataImpl randomData )
EmpiricalDistribution.EmpiricalDistribution ( int binCount, RandomGenerator generator )
EmpiricalDistribution.EmpiricalDistribution ( RandomDataImpl randomData )
EmpiricalDistribution.EmpiricalDistribution ( RandomGenerator generator )
EmpiricalDistribution.getBinCount ( ) :  int
EmpiricalDistribution.getBinStats ( ) :  List
EmpiricalDistribution.getGeneratorUpperBounds ( ) :  double[ ]
EmpiricalDistribution.getNextValue ( ) :  double
EmpiricalDistribution.getSampleStats ( ) :  StatisticalSummary
EmpiricalDistribution.getUpperBounds ( ) :  double[ ]
EmpiricalDistribution.isLoaded ( ) :  boolean
EmpiricalDistribution.load ( double[ ] in ) :  void
EmpiricalDistribution.load ( File file ) :  void
EmpiricalDistribution.load ( URL url ) :  void
EmpiricalDistribution.reSeed ( long seed ) :  void

cdk-1.5.1.jar, EmptyClusterStrategy.class
package org.apache.commons.math3.stat.clustering
KMeansPlusPlusClusterer.EmptyClusterStrategy.valueOf ( String name ) [static] :  KMeansPlusPlusClusterer.EmptyClusterStrategy
KMeansPlusPlusClusterer.EmptyClusterStrategy.values ( ) [static] :  KMeansPlusPlusClusterer.EmptyClusterStrategy[ ]

cdk-1.5.1.jar, Entry.class
package org.apache.commons.math3.linear
RealVector.Entry.getIndex ( ) :  int
RealVector.Entry.getValue ( ) :  double
RealVector.Entry.RealVector.Entry ( RealVector p1 )
RealVector.Entry.setIndex ( int index ) :  void
RealVector.Entry.setValue ( double value ) :  void

cdk-1.5.1.jar, EquationsMapper.class
package org.apache.commons.math3.ode
EquationsMapper.EquationsMapper ( int firstIndex, int dimension )
EquationsMapper.extractEquationData ( double[ ] complete, double[ ] equationData ) :  void
EquationsMapper.getDimension ( ) :  int
EquationsMapper.getFirstIndex ( ) :  int
EquationsMapper.insertEquationData ( double[ ] equationData, double[ ] complete ) :  void

cdk-1.5.1.jar, Erf.class
package org.apache.commons.math3.special
Erf.erf ( double x ) [static] :  double
Erf.erf ( double x1, double x2 ) [static] :  double
Erf.erfc ( double x ) [static] :  double

cdk-1.5.1.jar, EStateFingerprinter.class
package org.openscience.cdk.fingerprint
EStateFingerprinter.getBitFingerprint ( IAtomContainer atomContainer ) :  IBitFingerprint
EStateFingerprinter.getCountFingerprint ( IAtomContainer container ) :  ICountFingerprint

cdk-1.5.1.jar, Euclidean1D.class
package org.apache.commons.math3.geometry.euclidean.oned
Euclidean1D.getDimension ( ) :  int
Euclidean1D.getInstance ( ) [static] :  Euclidean1D
Euclidean1D.getSubSpace ( ) :  Space

cdk-1.5.1.jar, Euclidean2D.class
package org.apache.commons.math3.geometry.euclidean.twod
Euclidean2D.getDimension ( ) :  int
Euclidean2D.getInstance ( ) [static] :  Euclidean2D
Euclidean2D.getSubSpace ( ) :  Euclidean1D
Euclidean2D.getSubSpace ( ) :  Space

cdk-1.5.1.jar, Euclidean3D.class
package org.apache.commons.math3.geometry.euclidean.threed
Euclidean3D.getDimension ( ) :  int
Euclidean3D.getInstance ( ) [static] :  Euclidean3D
Euclidean3D.getSubSpace ( ) :  Euclidean2D
Euclidean3D.getSubSpace ( ) :  Space

cdk-1.5.1.jar, EuclideanIntegerPoint.class
package org.apache.commons.math3.stat.clustering
EuclideanIntegerPoint.centroidOf ( Collection points ) :  EuclideanIntegerPoint
EuclideanIntegerPoint.centroidOf ( Collection x0 ) :  Object
EuclideanIntegerPoint.distanceFrom ( EuclideanIntegerPoint p ) :  double
EuclideanIntegerPoint.distanceFrom ( Object x0 ) :  double
EuclideanIntegerPoint.equals ( Object other ) :  boolean
EuclideanIntegerPoint.EuclideanIntegerPoint ( int[ ] point )
EuclideanIntegerPoint.getPoint ( ) :  int[ ]
EuclideanIntegerPoint.hashCode ( ) :  int
EuclideanIntegerPoint.toString ( ) :  String

cdk-1.5.1.jar, EulerIntegrator.class
package org.apache.commons.math3.ode.nonstiff
EulerIntegrator.EulerIntegrator ( double step )

cdk-1.5.1.jar, EventHandler.class
package org.apache.commons.math3.ode.events
EventHandler.eventOccurred ( double p1, double[ ] p2, boolean p3 ) [abstract] :  EventHandler.Action
EventHandler.g ( double p1, double[ ] p2 ) [abstract] :  double
EventHandler.init ( double p1, double[ ] p2, double p3 ) [abstract] :  void
EventHandler.resetState ( double p1, double[ ] p2 ) [abstract] :  void

cdk-1.5.1.jar, EventState.class
package org.apache.commons.math3.ode.events
EventState.evaluateStep ( StepInterpolator interpolator ) :  boolean
EventState.EventState ( EventHandler handler, double maxCheckInterval, double convergence, int maxIterationCount, UnivariateSolver solver )
EventState.getConvergence ( ) :  double
EventState.getEventHandler ( ) :  EventHandler
EventState.getEventTime ( ) :  double
EventState.getMaxCheckInterval ( ) :  double
EventState.getMaxIterationCount ( ) :  int
EventState.reinitializeBegin ( StepInterpolator interpolator ) :  void
EventState.reset ( double t, double[ ] y ) :  boolean
EventState.stepAccepted ( double t, double[ ] y ) :  void
EventState.stop ( ) :  boolean

cdk-1.5.1.jar, ExceptionContext.class
package org.apache.commons.math3.exception.util
ExceptionContext.addMessage ( Localizable pattern, Object[ ] arguments ) :  void
ExceptionContext.ExceptionContext ( Throwable throwable )
ExceptionContext.getKeys ( ) :  Set
ExceptionContext.getLocalizedMessage ( ) :  String
ExceptionContext.getMessage ( ) :  String
ExceptionContext.getMessage ( Locale locale ) :  String
ExceptionContext.getMessage ( Locale locale, String separator ) :  String
ExceptionContext.getThrowable ( ) :  Throwable
ExceptionContext.getValue ( String key ) :  Object
ExceptionContext.setValue ( String key, Object value ) :  void

cdk-1.5.1.jar, ExceptionContextProvider.class
package org.apache.commons.math3.exception.util
ExceptionContextProvider.getContext ( ) [abstract] :  ExceptionContext

cdk-1.5.1.jar, Exp.class
package org.apache.commons.math3.analysis.function
Exp.derivative ( ) :  UnivariateFunction
Exp.Exp ( )
Exp.value ( double x ) :  double

cdk-1.5.1.jar, ExpandableStatefulODE.class
package org.apache.commons.math3.ode
ExpandableStatefulODE.addSecondaryEquations ( SecondaryEquations secondary ) :  int
ExpandableStatefulODE.computeDerivatives ( double t, double[ ] y, double[ ] yDot ) :  void
ExpandableStatefulODE.ExpandableStatefulODE ( FirstOrderDifferentialEquations primary )
ExpandableStatefulODE.getCompleteState ( ) :  double[ ]
ExpandableStatefulODE.getPrimary ( ) :  FirstOrderDifferentialEquations
ExpandableStatefulODE.getPrimaryMapper ( ) :  EquationsMapper
ExpandableStatefulODE.getPrimaryState ( ) :  double[ ]
ExpandableStatefulODE.getPrimaryStateDot ( ) :  double[ ]
ExpandableStatefulODE.getSecondaryMappers ( ) :  EquationsMapper[ ]
ExpandableStatefulODE.getSecondaryState ( int index ) :  double[ ]
ExpandableStatefulODE.getSecondaryStateDot ( int index ) :  double[ ]
ExpandableStatefulODE.getTime ( ) :  double
ExpandableStatefulODE.getTotalDimension ( ) :  int
ExpandableStatefulODE.setCompleteState ( double[ ] completeState ) :  void
ExpandableStatefulODE.setPrimaryState ( double[ ] primaryState ) :  void
ExpandableStatefulODE.setSecondaryState ( int index, double[ ] secondaryState ) :  void
ExpandableStatefulODE.setTime ( double time ) :  void

cdk-1.5.1.jar, Expm1.class
package org.apache.commons.math3.analysis.function
Expm1.derivative ( ) :  UnivariateFunction
Expm1.Expm1 ( )
Expm1.value ( double x ) :  double

cdk-1.5.1.jar, ExponentialDistribution.class
package org.apache.commons.math3.distribution
ExponentialDistribution.cumulativeProbability ( double x ) :  double
ExponentialDistribution.density ( double x ) :  double
ExponentialDistribution.ExponentialDistribution ( double mean )
ExponentialDistribution.ExponentialDistribution ( double mean, double inverseCumAccuracy )
ExponentialDistribution.getMean ( ) :  double
ExponentialDistribution.getNumericalMean ( ) :  double
ExponentialDistribution.getNumericalVariance ( ) :  double
ExponentialDistribution.getSolverAbsoluteAccuracy ( ) :  double
ExponentialDistribution.getSupportLowerBound ( ) :  double
ExponentialDistribution.getSupportUpperBound ( ) :  double
ExponentialDistribution.inverseCumulativeProbability ( double p ) :  double
ExponentialDistribution.isSupportConnected ( ) :  boolean
ExponentialDistribution.isSupportLowerBoundInclusive ( ) :  boolean
ExponentialDistribution.isSupportUpperBoundInclusive ( ) :  boolean
ExponentialDistribution.probability ( double x ) :  double
ExponentialDistribution.sample ( ) :  double

cdk-1.5.1.jar, ExtendedFingerprinter.class
package org.openscience.cdk.fingerprint
ExtendedFingerprinter.getBitFingerprint ( IAtomContainer atomContainer, IRingSet ringSet, List rslist ) :  IBitFingerprint
ExtendedFingerprinter.getBitFingerprint ( IAtomContainer container ) :  IBitFingerprint
ExtendedFingerprinter.getCountFingerprint ( IAtomContainer container ) :  ICountFingerprint

cdk-1.5.1.jar, FastCosineTransformer.class
package org.apache.commons.math3.transform
FastCosineTransformer.FastCosineTransformer ( DctNormalization normalization )
FastCosineTransformer.fct ( double[ ] f ) :  double[ ]
FastCosineTransformer.transform ( double[ ] f, TransformType type ) :  double[ ]
FastCosineTransformer.transform ( UnivariateFunction f, double min, double max, int n, TransformType type ) :  double[ ]

cdk-1.5.1.jar, FastFourierTransformer.class
package org.apache.commons.math3.transform
FastFourierTransformer.FastFourierTransformer ( DftNormalization normalization )
FastFourierTransformer.mdfft ( Object mdca, TransformType type ) :  Object *DEPRECATED*
FastFourierTransformer.transform ( Complex[ ] f, TransformType type ) :  Complex[ ]
FastFourierTransformer.transform ( double[ ] f, TransformType type ) :  Complex[ ]
FastFourierTransformer.transform ( UnivariateFunction f, double min, double max, int n, TransformType type ) :  Complex[ ]
FastFourierTransformer.transformInPlace ( double[ ][ ] dataRI, DftNormalization normalization, TransformType type ) [static] :  void

cdk-1.5.1.jar, FastHadamardTransformer.class
package org.apache.commons.math3.transform
FastHadamardTransformer.FastHadamardTransformer ( )
FastHadamardTransformer.fht ( double[ ] x ) :  double[ ]
FastHadamardTransformer.fht ( int[ ] x ) :  int[ ]
FastHadamardTransformer.transform ( double[ ] f, TransformType type ) :  double[ ]
FastHadamardTransformer.transform ( int[ ] f ) :  int[ ]
FastHadamardTransformer.transform ( UnivariateFunction f, double min, double max, int n, TransformType type ) :  double[ ]

cdk-1.5.1.jar, FastMath.class
package org.apache.commons.math3.util
FastMath.abs ( double x ) [static] :  double
FastMath.abs ( float x ) [static] :  float
FastMath.abs ( int x ) [static] :  int
FastMath.abs ( long x ) [static] :  long
FastMath.acos ( double x ) [static] :  double
FastMath.acosh ( double a ) [static] :  double
FastMath.asin ( double x ) [static] :  double
FastMath.asinh ( double a ) [static] :  double
FastMath.atan ( double x ) [static] :  double
FastMath.atan2 ( double y, double x ) [static] :  double
FastMath.atanh ( double a ) [static] :  double
FastMath.cbrt ( double x ) [static] :  double
FastMath.ceil ( double x ) [static] :  double
FastMath.copySign ( double magnitude, double sign ) [static] :  double
FastMath.copySign ( float magnitude, float sign ) [static] :  float
FastMath.cos ( double x ) [static] :  double
FastMath.cosh ( double x ) [static] :  double
FastMath.exp ( double x ) [static] :  double
FastMath.expm1 ( double x ) [static] :  double
FastMath.floor ( double x ) [static] :  double
FastMath.getExponent ( double d ) [static] :  int
FastMath.getExponent ( float f ) [static] :  int
FastMath.hypot ( double x, double y ) [static] :  double
FastMath.IEEEremainder ( double dividend, double divisor ) [static] :  double
FastMath.log ( double base, double x ) [static] :  double
FastMath.log ( double x ) [static] :  double
FastMath.log10 ( double x ) [static] :  double
FastMath.log1p ( double x ) [static] :  double
FastMath.main ( String[ ] a ) [static] :  void
FastMath.max ( double a, double b ) [static] :  double
FastMath.max ( float a, float b ) [static] :  float
FastMath.max ( int a, int b ) [static] :  int
FastMath.max ( long a, long b ) [static] :  long
FastMath.min ( double a, double b ) [static] :  double
FastMath.min ( float a, float b ) [static] :  float
FastMath.min ( int a, int b ) [static] :  int
FastMath.min ( long a, long b ) [static] :  long
FastMath.nextAfter ( double d, double direction ) [static] :  double
FastMath.nextAfter ( float f, double direction ) [static] :  float
FastMath.nextUp ( double a ) [static] :  double
FastMath.nextUp ( float a ) [static] :  float
FastMath.pow ( double x, double y ) [static] :  double
FastMath.random ( ) [static] :  double
FastMath.rint ( double x ) [static] :  double
FastMath.round ( double x ) [static] :  long
FastMath.round ( float x ) [static] :  int
FastMath.scalb ( double d, int n ) [static] :  double
FastMath.scalb ( float f, int n ) [static] :  float
FastMath.signum ( double a ) [static] :  double
FastMath.signum ( float a ) [static] :  float
FastMath.sin ( double x ) [static] :  double
FastMath.sinh ( double x ) [static] :  double
FastMath.sqrt ( double a ) [static] :  double
FastMath.tan ( double x ) [static] :  double
FastMath.tanh ( double x ) [static] :  double
FastMath.toDegrees ( double x ) [static] :  double
FastMath.toRadians ( double x ) [static] :  double
FastMath.ulp ( double x ) [static] :  double
FastMath.ulp ( float x ) [static] :  float

cdk-1.5.1.jar, FastSineTransformer.class
package org.apache.commons.math3.transform
FastSineTransformer.FastSineTransformer ( DstNormalization normalization )
FastSineTransformer.fst ( double[ ] f ) :  double[ ]
FastSineTransformer.transform ( double[ ] f, TransformType type ) :  double[ ]
FastSineTransformer.transform ( UnivariateFunction f, double min, double max, int n, TransformType type ) :  double[ ]

cdk-1.5.1.jar, FDistribution.class
package org.apache.commons.math3.distribution
FDistribution.calculateNumericalVariance ( ) :  double
FDistribution.cumulativeProbability ( double x ) :  double
FDistribution.density ( double x ) :  double
FDistribution.FDistribution ( double numeratorDegreesOfFreedom, double denominatorDegreesOfFreedom )
FDistribution.FDistribution ( double numeratorDegreesOfFreedom, double denominatorDegreesOfFreedom, double inverseCumAccuracy )
FDistribution.getDenominatorDegreesOfFreedom ( ) :  double
FDistribution.getNumeratorDegreesOfFreedom ( ) :  double
FDistribution.getNumericalMean ( ) :  double
FDistribution.getNumericalVariance ( ) :  double
FDistribution.getSolverAbsoluteAccuracy ( ) :  double
FDistribution.getSupportLowerBound ( ) :  double
FDistribution.getSupportUpperBound ( ) :  double
FDistribution.isSupportConnected ( ) :  boolean
FDistribution.isSupportLowerBoundInclusive ( ) :  boolean
FDistribution.isSupportUpperBoundInclusive ( ) :  boolean
FDistribution.probability ( double x ) :  double

cdk-1.5.1.jar, Field.class
package org.apache.commons.math3
Field.getOne ( ) [abstract] :  Object
Field.getRuntimeClass ( ) [abstract] :  Class
Field.getZero ( ) [abstract] :  Object

cdk-1.5.1.jar, FieldDecompositionSolver.class
package org.apache.commons.math3.linear
FieldDecompositionSolver.getInverse ( ) [abstract] :  FieldMatrix
FieldDecompositionSolver.isNonSingular ( ) [abstract] :  boolean
FieldDecompositionSolver.solve ( FieldMatrix p1 ) [abstract] :  FieldMatrix
FieldDecompositionSolver.solve ( FieldVector p1 ) [abstract] :  FieldVector

cdk-1.5.1.jar, FieldElement.class
package org.apache.commons.math3
FieldElement.add ( Object p1 ) [abstract] :  Object
FieldElement.divide ( Object p1 ) [abstract] :  Object
FieldElement.getField ( ) [abstract] :  Field
FieldElement.multiply ( int p1 ) [abstract] :  Object
FieldElement.multiply ( Object p1 ) [abstract] :  Object
FieldElement.negate ( ) [abstract] :  Object
FieldElement.reciprocal ( ) [abstract] :  Object
FieldElement.subtract ( Object p1 ) [abstract] :  Object

cdk-1.5.1.jar, FieldLUDecomposition.class
package org.apache.commons.math3.linear
FieldLUDecomposition.FieldLUDecomposition ( FieldMatrix matrix )
FieldLUDecomposition.getDeterminant ( ) :  FieldElement
FieldLUDecomposition.getL ( ) :  FieldMatrix
FieldLUDecomposition.getP ( ) :  FieldMatrix
FieldLUDecomposition.getPivot ( ) :  int[ ]
FieldLUDecomposition.getSolver ( ) :  FieldDecompositionSolver
FieldLUDecomposition.getU ( ) :  FieldMatrix

cdk-1.5.1.jar, FieldMatrix.class
package org.apache.commons.math3.linear
FieldMatrix.add ( FieldMatrix p1 ) [abstract] :  FieldMatrix
FieldMatrix.addToEntry ( int p1, int p2, FieldElement p3 ) [abstract] :  void
FieldMatrix.copy ( ) [abstract] :  FieldMatrix
FieldMatrix.copySubMatrix ( int p1, int p2, int p3, int p4, FieldElement[ ][ ] p5 ) [abstract] :  void
FieldMatrix.copySubMatrix ( int[ ] p1, int[ ] p2, FieldElement[ ][ ] p3 ) [abstract] :  void
FieldMatrix.createMatrix ( int p1, int p2 ) [abstract] :  FieldMatrix
FieldMatrix.getColumn ( int p1 ) [abstract] :  FieldElement[ ]
FieldMatrix.getColumnMatrix ( int p1 ) [abstract] :  FieldMatrix
FieldMatrix.getColumnVector ( int p1 ) [abstract] :  FieldVector
FieldMatrix.getData ( ) [abstract] :  FieldElement[ ][ ]
FieldMatrix.getEntry ( int p1, int p2 ) [abstract] :  FieldElement
FieldMatrix.getField ( ) [abstract] :  Field
FieldMatrix.getRow ( int p1 ) [abstract] :  FieldElement[ ]
FieldMatrix.getRowMatrix ( int p1 ) [abstract] :  FieldMatrix
FieldMatrix.getRowVector ( int p1 ) [abstract] :  FieldVector
FieldMatrix.getSubMatrix ( int p1, int p2, int p3, int p4 ) [abstract] :  FieldMatrix
FieldMatrix.getSubMatrix ( int[ ] p1, int[ ] p2 ) [abstract] :  FieldMatrix
FieldMatrix.getTrace ( ) [abstract] :  FieldElement
FieldMatrix.multiply ( FieldMatrix p1 ) [abstract] :  FieldMatrix
FieldMatrix.multiplyEntry ( int p1, int p2, FieldElement p3 ) [abstract] :  void
FieldMatrix.operate ( FieldElement[ ] p1 ) [abstract] :  FieldElement[ ]
FieldMatrix.operate ( FieldVector p1 ) [abstract] :  FieldVector
FieldMatrix.power ( int p1 ) [abstract] :  FieldMatrix
FieldMatrix.preMultiply ( FieldElement[ ] p1 ) [abstract] :  FieldElement[ ]
FieldMatrix.preMultiply ( FieldMatrix p1 ) [abstract] :  FieldMatrix
FieldMatrix.preMultiply ( FieldVector p1 ) [abstract] :  FieldVector
FieldMatrix.scalarAdd ( FieldElement p1 ) [abstract] :  FieldMatrix
FieldMatrix.scalarMultiply ( FieldElement p1 ) [abstract] :  FieldMatrix
FieldMatrix.setColumn ( int p1, FieldElement[ ] p2 ) [abstract] :  void
FieldMatrix.setColumnMatrix ( int p1, FieldMatrix p2 ) [abstract] :  void
FieldMatrix.setColumnVector ( int p1, FieldVector p2 ) [abstract] :  void
FieldMatrix.setEntry ( int p1, int p2, FieldElement p3 ) [abstract] :  void
FieldMatrix.setRow ( int p1, FieldElement[ ] p2 ) [abstract] :  void
FieldMatrix.setRowMatrix ( int p1, FieldMatrix p2 ) [abstract] :  void
FieldMatrix.setRowVector ( int p1, FieldVector p2 ) [abstract] :  void
FieldMatrix.setSubMatrix ( FieldElement[ ][ ] p1, int p2, int p3 ) [abstract] :  void
FieldMatrix.subtract ( FieldMatrix p1 ) [abstract] :  FieldMatrix
FieldMatrix.transpose ( ) [abstract] :  FieldMatrix
FieldMatrix.walkInColumnOrder ( FieldMatrixChangingVisitor p1 ) [abstract] :  FieldElement
FieldMatrix.walkInColumnOrder ( FieldMatrixChangingVisitor p1, int p2, int p3, int p4, int p5 ) [abstract] :  FieldElement
FieldMatrix.walkInColumnOrder ( FieldMatrixPreservingVisitor p1 ) [abstract] :  FieldElement
FieldMatrix.walkInColumnOrder ( FieldMatrixPreservingVisitor p1, int p2, int p3, int p4, int p5 ) [abstract] :  FieldElement
FieldMatrix.walkInOptimizedOrder ( FieldMatrixChangingVisitor p1 ) [abstract] :  FieldElement
FieldMatrix.walkInOptimizedOrder ( FieldMatrixChangingVisitor p1, int p2, int p3, int p4, int p5 ) [abstract] :  FieldElement
FieldMatrix.walkInOptimizedOrder ( FieldMatrixPreservingVisitor p1 ) [abstract] :  FieldElement
FieldMatrix.walkInOptimizedOrder ( FieldMatrixPreservingVisitor p1, int p2, int p3, int p4, int p5 ) [abstract] :  FieldElement
FieldMatrix.walkInRowOrder ( FieldMatrixChangingVisitor p1 ) [abstract] :  FieldElement
FieldMatrix.walkInRowOrder ( FieldMatrixChangingVisitor p1, int p2, int p3, int p4, int p5 ) [abstract] :  FieldElement
FieldMatrix.walkInRowOrder ( FieldMatrixPreservingVisitor p1 ) [abstract] :  FieldElement
FieldMatrix.walkInRowOrder ( FieldMatrixPreservingVisitor p1, int p2, int p3, int p4, int p5 ) [abstract] :  FieldElement

cdk-1.5.1.jar, FieldMatrixChangingVisitor.class
package org.apache.commons.math3.linear
FieldMatrixChangingVisitor.end ( ) [abstract] :  FieldElement
FieldMatrixChangingVisitor.start ( int p1, int p2, int p3, int p4, int p5, int p6 ) [abstract] :  void
FieldMatrixChangingVisitor.visit ( int p1, int p2, FieldElement p3 ) [abstract] :  FieldElement

cdk-1.5.1.jar, FieldMatrixPreservingVisitor.class
package org.apache.commons.math3.linear
FieldMatrixPreservingVisitor.end ( ) [abstract] :  FieldElement
FieldMatrixPreservingVisitor.start ( int p1, int p2, int p3, int p4, int p5, int p6 ) [abstract] :  void
FieldMatrixPreservingVisitor.visit ( int p1, int p2, FieldElement p3 ) [abstract] :  void

cdk-1.5.1.jar, FieldVector.class
package org.apache.commons.math3.linear
FieldVector.add ( FieldVector p1 ) [abstract] :  FieldVector
FieldVector.append ( FieldElement p1 ) [abstract] :  FieldVector
FieldVector.append ( FieldVector p1 ) [abstract] :  FieldVector
FieldVector.copy ( ) [abstract] :  FieldVector
FieldVector.dotProduct ( FieldVector p1 ) [abstract] :  FieldElement
FieldVector.ebeDivide ( FieldVector p1 ) [abstract] :  FieldVector
FieldVector.ebeMultiply ( FieldVector p1 ) [abstract] :  FieldVector
FieldVector.getData ( ) [abstract] :  FieldElement[ ]
FieldVector.getDimension ( ) [abstract] :  int
FieldVector.getEntry ( int p1 ) [abstract] :  FieldElement
FieldVector.getField ( ) [abstract] :  Field
FieldVector.getSubVector ( int p1, int p2 ) [abstract] :  FieldVector
FieldVector.mapAdd ( FieldElement p1 ) [abstract] :  FieldVector
FieldVector.mapAddToSelf ( FieldElement p1 ) [abstract] :  FieldVector
FieldVector.mapDivide ( FieldElement p1 ) [abstract] :  FieldVector
FieldVector.mapDivideToSelf ( FieldElement p1 ) [abstract] :  FieldVector
FieldVector.mapInv ( ) [abstract] :  FieldVector
FieldVector.mapInvToSelf ( ) [abstract] :  FieldVector
FieldVector.mapMultiply ( FieldElement p1 ) [abstract] :  FieldVector
FieldVector.mapMultiplyToSelf ( FieldElement p1 ) [abstract] :  FieldVector
FieldVector.mapSubtract ( FieldElement p1 ) [abstract] :  FieldVector
FieldVector.mapSubtractToSelf ( FieldElement p1 ) [abstract] :  FieldVector
FieldVector.outerProduct ( FieldVector p1 ) [abstract] :  FieldMatrix
FieldVector.projection ( FieldVector p1 ) [abstract] :  FieldVector
FieldVector.set ( FieldElement p1 ) [abstract] :  void
FieldVector.setEntry ( int p1, FieldElement p2 ) [abstract] :  void
FieldVector.setSubVector ( int p1, FieldVector p2 ) [abstract] :  void
FieldVector.subtract ( FieldVector p1 ) [abstract] :  FieldVector
FieldVector.toArray ( ) [abstract] :  FieldElement[ ]

cdk-1.5.1.jar, FiguerasSSSRFinder.class
package org.openscience.cdk.ringsearch
FiguerasSSSRFinder.findSSSR ( IAtomContainer mol ) :  IRingSet

cdk-1.5.1.jar, Fingerprinter.class
package org.openscience.cdk.fingerprint
Fingerprinter.getBitFingerprint ( IAtomContainer container ) :  IBitFingerprint
Fingerprinter.getBitFingerprint ( IAtomContainer container, AllRingsFinder ringFinder ) :  IBitFingerprint
Fingerprinter.getCountFingerprint ( IAtomContainer container ) :  ICountFingerprint

cdk-1.5.1.jar, FirstOrderConverter.class
package org.apache.commons.math3.ode
FirstOrderConverter.computeDerivatives ( double t, double[ ] y, double[ ] yDot ) :  void
FirstOrderConverter.FirstOrderConverter ( SecondOrderDifferentialEquations equations )
FirstOrderConverter.getDimension ( ) :  int

cdk-1.5.1.jar, FirstOrderDifferentialEquations.class
package org.apache.commons.math3.ode
FirstOrderDifferentialEquations.computeDerivatives ( double p1, double[ ] p2, double[ ] p3 ) [abstract] :  void
FirstOrderDifferentialEquations.getDimension ( ) [abstract] :  int

cdk-1.5.1.jar, FirstOrderIntegrator.class
package org.apache.commons.math3.ode
FirstOrderIntegrator.integrate ( FirstOrderDifferentialEquations p1, double p2, double[ ] p3, double p4, double[ ] p5 ) [abstract] :  double

cdk-1.5.1.jar, Fitness.class
package org.apache.commons.math3.genetics
Fitness.fitness ( ) [abstract] :  double

cdk-1.5.1.jar, FixBondOrdersTool.class
package org.openscience.cdk.smiles
FixBondOrdersTool.FixBondOrdersTool ( )
FixBondOrdersTool.isInterrupted ( ) :  boolean
FixBondOrdersTool.kekuliseAromaticRings ( IAtomContainer molecule ) :  IAtomContainer
FixBondOrdersTool.setInterrupted ( boolean interrupted ) :  void

cdk-1.5.1.jar, FixedGenerationCount.class
package org.apache.commons.math3.genetics
FixedGenerationCount.FixedGenerationCount ( int maxGenerations )
FixedGenerationCount.getNumGenerations ( ) :  int
FixedGenerationCount.isSatisfied ( Population population ) :  boolean

cdk-1.5.1.jar, FixedStepHandler.class
package org.apache.commons.math3.ode.sampling
FixedStepHandler.handleStep ( double p1, double[ ] p2, double[ ] p3, boolean p4 ) [abstract] :  void
FixedStepHandler.init ( double p1, double[ ] p2, double p3 ) [abstract] :  void

cdk-1.5.1.jar, Floor.class
package org.apache.commons.math3.analysis.function
Floor.Floor ( )
Floor.value ( double x ) :  double

cdk-1.5.1.jar, FMFDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
FMFDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, Fraction.class
package org.apache.commons.math3.fraction
Fraction.abs ( ) :  Fraction
Fraction.add ( Fraction fraction ) :  Fraction
Fraction.add ( int i ) :  Fraction
Fraction.add ( Object x0 ) :  Object
Fraction.compareTo ( Fraction object ) :  int
Fraction.compareTo ( Object x0 ) :  int
Fraction.divide ( Fraction fraction ) :  Fraction
Fraction.divide ( int i ) :  Fraction
Fraction.divide ( Object x0 ) :  Object
Fraction.doubleValue ( ) :  double
Fraction.equals ( Object other ) :  boolean
Fraction.floatValue ( ) :  float
Fraction.Fraction ( double value )
Fraction.Fraction ( double value, double epsilon, int maxIterations )
Fraction.Fraction ( double value, int maxDenominator )
Fraction.Fraction ( int num )
Fraction.Fraction ( int num, int den )
Fraction.getDenominator ( ) :  int
Fraction.getField ( ) :  Field
Fraction.getField ( ) :  FractionField
Fraction.getNumerator ( ) :  int
Fraction.getReducedFraction ( int numerator, int denominator ) [static] :  Fraction
Fraction.hashCode ( ) :  int
Fraction.intValue ( ) :  int
Fraction.longValue ( ) :  long
Fraction.multiply ( Fraction fraction ) :  Fraction
Fraction.multiply ( int i ) :  Fraction
Fraction.multiply ( int x0 ) :  Object
Fraction.multiply ( Object x0 ) :  Object
Fraction.negate ( ) :  Fraction
Fraction.negate ( ) :  Object
Fraction.percentageValue ( ) :  double
Fraction.reciprocal ( ) :  Fraction
Fraction.reciprocal ( ) :  Object
Fraction.subtract ( Fraction fraction ) :  Fraction
Fraction.subtract ( int i ) :  Fraction
Fraction.subtract ( Object x0 ) :  Object
Fraction.toString ( ) :  String

cdk-1.5.1.jar, FractionConversionException.class
package org.apache.commons.math3.fraction
FractionConversionException.FractionConversionException ( double value, int maxIterations )
FractionConversionException.FractionConversionException ( double value, long p, long q )

cdk-1.5.1.jar, FractionField.class
package org.apache.commons.math3.fraction
FractionField.getInstance ( ) [static] :  FractionField
FractionField.getOne ( ) :  Fraction
FractionField.getOne ( ) :  Object
FractionField.getRuntimeClass ( ) :  Class
FractionField.getZero ( ) :  Fraction
FractionField.getZero ( ) :  Object

cdk-1.5.1.jar, FractionFormat.class
package org.apache.commons.math3.fraction
FractionFormat.format ( Fraction fraction, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
FractionFormat.format ( Object obj, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
FractionFormat.formatFraction ( Fraction f ) [static] :  String
FractionFormat.FractionFormat ( )
FractionFormat.FractionFormat ( NumberFormat format )
FractionFormat.FractionFormat ( NumberFormat numeratorFormat, NumberFormat denominatorFormat )
FractionFormat.getAvailableLocales ( ) [static] :  Locale[ ]
FractionFormat.getDefaultNumberFormat ( ) [static] :  NumberFormat
FractionFormat.getImproperInstance ( ) [static] :  FractionFormat
FractionFormat.getImproperInstance ( Locale locale ) [static] :  FractionFormat
FractionFormat.getProperInstance ( ) [static] :  FractionFormat
FractionFormat.getProperInstance ( Locale locale ) [static] :  FractionFormat
FractionFormat.parse ( String source ) :  Fraction
FractionFormat.parse ( String source, ParsePosition pos ) :  Fraction
FractionFormat.parse ( String x0 ) :  Number
FractionFormat.parse ( String x0, ParsePosition x1 ) :  Number

cdk-1.5.1.jar, FragmentComplexityDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
FragmentComplexityDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, Frequency.class
package org.apache.commons.math3.stat
Frequency.addValue ( char v ) :  void
Frequency.addValue ( Comparable v ) :  void
Frequency.addValue ( int v ) :  void
Frequency.addValue ( long v ) :  void
Frequency.clear ( ) :  void
Frequency.equals ( Object obj ) :  boolean
Frequency.Frequency ( )
Frequency.Frequency ( Comparator comparator )
Frequency.getCount ( char v ) :  long
Frequency.getCount ( Comparable v ) :  long
Frequency.getCount ( int v ) :  long
Frequency.getCount ( long v ) :  long
Frequency.getCumFreq ( char v ) :  long
Frequency.getCumFreq ( Comparable v ) :  long
Frequency.getCumFreq ( int v ) :  long
Frequency.getCumFreq ( long v ) :  long
Frequency.getCumPct ( char v ) :  double
Frequency.getCumPct ( Comparable v ) :  double
Frequency.getCumPct ( int v ) :  double
Frequency.getCumPct ( long v ) :  double
Frequency.getPct ( char v ) :  double
Frequency.getPct ( Comparable v ) :  double
Frequency.getPct ( int v ) :  double
Frequency.getPct ( long v ) :  double
Frequency.getSumFreq ( ) :  long
Frequency.getUniqueCount ( ) :  int
Frequency.hashCode ( ) :  int
Frequency.toString ( ) :  String
Frequency.valuesIterator ( ) :  Iterator

cdk-1.5.1.jar, FunctionUtils.class
package org.apache.commons.math3.analysis
FunctionUtils.add ( DifferentiableUnivariateFunction[ ] f ) [static] :  DifferentiableUnivariateFunction
FunctionUtils.add ( UnivariateFunction[ ] f ) [static] :  UnivariateFunction
FunctionUtils.collector ( BivariateFunction combiner, double initialValue ) [static] :  MultivariateFunction
FunctionUtils.collector ( BivariateFunction combiner, UnivariateFunction f, double initialValue ) [static] :  MultivariateFunction
FunctionUtils.combine ( BivariateFunction combiner, UnivariateFunction f, UnivariateFunction g ) [static] :  UnivariateFunction
FunctionUtils.compose ( DifferentiableUnivariateFunction[ ] f ) [static] :  DifferentiableUnivariateFunction
FunctionUtils.compose ( UnivariateFunction[ ] f ) [static] :  UnivariateFunction
FunctionUtils.fix1stArgument ( BivariateFunction f, double fixed ) [static] :  UnivariateFunction
FunctionUtils.fix2ndArgument ( BivariateFunction f, double fixed ) [static] :  UnivariateFunction
FunctionUtils.multiply ( DifferentiableUnivariateFunction[ ] f ) [static] :  DifferentiableUnivariateFunction
FunctionUtils.multiply ( UnivariateFunction[ ] f ) [static] :  UnivariateFunction
FunctionUtils.sample ( UnivariateFunction f, double min, double max, int n ) [static] :  double[ ]

cdk-1.5.1.jar, Gamma.class
package org.apache.commons.math3.special
Gamma.digamma ( double x ) [static] :  double
Gamma.logGamma ( double x ) [static] :  double
Gamma.regularizedGammaP ( double a, double x ) [static] :  double
Gamma.regularizedGammaP ( double a, double x, double epsilon, int maxIterations ) [static] :  double
Gamma.regularizedGammaQ ( double a, double x ) [static] :  double
Gamma.regularizedGammaQ ( double a, double x, double epsilon, int maxIterations ) [static] :  double
Gamma.trigamma ( double x ) [static] :  double

cdk-1.5.1.jar, GammaDistribution.class
package org.apache.commons.math3.distribution
GammaDistribution.cumulativeProbability ( double x ) :  double
GammaDistribution.density ( double x ) :  double
GammaDistribution.GammaDistribution ( double alpha, double beta )
GammaDistribution.GammaDistribution ( double alpha, double beta, double inverseCumAccuracy )
GammaDistribution.getAlpha ( ) :  double
GammaDistribution.getBeta ( ) :  double
GammaDistribution.getNumericalMean ( ) :  double
GammaDistribution.getNumericalVariance ( ) :  double
GammaDistribution.getSolverAbsoluteAccuracy ( ) :  double
GammaDistribution.getSupportLowerBound ( ) :  double
GammaDistribution.getSupportUpperBound ( ) :  double
GammaDistribution.isSupportConnected ( ) :  boolean
GammaDistribution.isSupportLowerBoundInclusive ( ) :  boolean
GammaDistribution.isSupportUpperBoundInclusive ( ) :  boolean
GammaDistribution.probability ( double x ) :  double

cdk-1.5.1.jar, Gaussian.class
package org.apache.commons.math3.analysis.function
Gaussian.derivative ( ) :  UnivariateFunction
Gaussian.Gaussian ( )
Gaussian.Gaussian ( double mean, double sigma )
Gaussian.Gaussian ( double norm, double mean, double sigma )
Gaussian.value ( double x ) :  double

cdk-1.5.1.jar, GaussianFitter.class
package org.apache.commons.math3.optimization.fitting
GaussianFitter.fit ( ) :  double[ ]
GaussianFitter.fit ( double[ ] initialGuess ) :  double[ ]
GaussianFitter.GaussianFitter ( DifferentiableMultivariateVectorOptimizer optimizer )

cdk-1.5.1.jar, GaussianRandomGenerator.class
package org.apache.commons.math3.random
GaussianRandomGenerator.GaussianRandomGenerator ( RandomGenerator generator )
GaussianRandomGenerator.nextNormalizedDouble ( ) :  double

cdk-1.5.1.jar, GaussNewtonOptimizer.class
package org.apache.commons.math3.optimization.general
GaussNewtonOptimizer.doOptimize ( ) :  PointVectorValuePair
GaussNewtonOptimizer.GaussNewtonOptimizer ( )
GaussNewtonOptimizer.GaussNewtonOptimizer ( boolean useLU )
GaussNewtonOptimizer.GaussNewtonOptimizer ( boolean useLU, ConvergenceChecker checker )
GaussNewtonOptimizer.GaussNewtonOptimizer ( ConvergenceChecker checker )

cdk-1.5.1.jar, GeneticAlgorithm.class
package org.apache.commons.math3.genetics
GeneticAlgorithm.evolve ( Population initial, StoppingCondition condition ) :  Population
GeneticAlgorithm.GeneticAlgorithm ( CrossoverPolicy crossoverPolicy, double crossoverRate, MutationPolicy mutationPolicy, double mutationRate, SelectionPolicy selectionPolicy )
GeneticAlgorithm.getCrossoverPolicy ( ) :  CrossoverPolicy
GeneticAlgorithm.getCrossoverRate ( ) :  double
GeneticAlgorithm.getGenerationsEvolved ( ) :  int
GeneticAlgorithm.getMutationPolicy ( ) :  MutationPolicy
GeneticAlgorithm.getMutationRate ( ) :  double
GeneticAlgorithm.getRandomGenerator ( ) [static] :  RandomGenerator
GeneticAlgorithm.getSelectionPolicy ( ) :  SelectionPolicy
GeneticAlgorithm.nextGeneration ( Population current ) :  Population
GeneticAlgorithm.setRandomGenerator ( RandomGenerator random ) [static] :  void

cdk-1.5.1.jar, GeometricMean.class
package org.apache.commons.math3.stat.descriptive.moment
GeometricMean.clear ( ) :  void
GeometricMean.copy ( ) :  GeometricMean
GeometricMean.copy ( ) :  StorelessUnivariateStatistic
GeometricMean.copy ( ) :  UnivariateStatistic
GeometricMean.copy ( GeometricMean source, GeometricMean dest ) [static] :  void
GeometricMean.evaluate ( double[ ] values, int begin, int length ) :  double
GeometricMean.GeometricMean ( )
GeometricMean.GeometricMean ( GeometricMean original )
GeometricMean.GeometricMean ( SumOfLogs sumOfLogs )
GeometricMean.getN ( ) :  long
GeometricMean.getResult ( ) :  double
GeometricMean.getSumLogImpl ( ) :  StorelessUnivariateStatistic
GeometricMean.increment ( double d ) :  void
GeometricMean.setSumLogImpl ( StorelessUnivariateStatistic sumLogImpl ) :  void

cdk-1.5.1.jar, GeometryTools.class
package org.openscience.cdk.geometry
GeometryTools.get2DCoordinateCoverage ( IAtomContainer container ) [static] :  GeometryTools.CoordinateCoverage
GeometryTools.get3DCoordinateCoverage ( IAtomContainer container ) [static] :  GeometryTools.CoordinateCoverage

cdk-1.5.1.jar, GillIntegrator.class
package org.apache.commons.math3.ode.nonstiff
GillIntegrator.GillIntegrator ( double step )

cdk-1.5.1.jar, GLSMultipleLinearRegression.class
package org.apache.commons.math3.stat.regression
GLSMultipleLinearRegression.calculateBeta ( ) :  RealVector
GLSMultipleLinearRegression.calculateBetaVariance ( ) :  RealMatrix
GLSMultipleLinearRegression.calculateErrorVariance ( ) :  double
GLSMultipleLinearRegression.getOmegaInverse ( ) :  RealMatrix
GLSMultipleLinearRegression.GLSMultipleLinearRegression ( )
GLSMultipleLinearRegression.newCovarianceData ( double[ ][ ] omega ) :  void
GLSMultipleLinearRegression.newSampleData ( double[ ] y, double[ ][ ] x, double[ ][ ] covariance ) :  void

cdk-1.5.1.jar, GoalType.class
package org.apache.commons.math3.optimization
GoalType.valueOf ( String name ) [static] :  GoalType
GoalType.values ( ) [static] :  GoalType[ ]

cdk-1.5.1.jar, GraggBulirschStoerIntegrator.class
package org.apache.commons.math3.ode.nonstiff
GraggBulirschStoerIntegrator.addEventHandler ( EventHandler function, double maxCheckInterval, double convergence, int maxIterationCount, UnivariateSolver solver ) :  void
GraggBulirschStoerIntegrator.addStepHandler ( StepHandler handler ) :  void
GraggBulirschStoerIntegrator.GraggBulirschStoerIntegrator ( double minStep, double maxStep, double scalAbsoluteTolerance, double scalRelativeTolerance )
GraggBulirschStoerIntegrator.GraggBulirschStoerIntegrator ( double minStep, double maxStep, double[ ] vecAbsoluteTolerance, double[ ] vecRelativeTolerance )
GraggBulirschStoerIntegrator.integrate ( ExpandableStatefulODE equations, double t ) :  void
GraggBulirschStoerIntegrator.setControlFactors ( double control1, double control2, double control3, double control4 ) :  void
GraggBulirschStoerIntegrator.setInterpolationControl ( boolean useInterpolationErrorForControl, int mudifControlParameter ) :  void
GraggBulirschStoerIntegrator.setOrderControl ( int maximalOrder, double control1, double control2 ) :  void
GraggBulirschStoerIntegrator.setStabilityCheck ( boolean performStabilityCheck, int maxNumIter, int maxNumChecks, double stepsizeReductionFactor ) :  void

cdk-1.5.1.jar, GraphOnlyFingerprinter.class
package org.openscience.cdk.fingerprint
GraphOnlyFingerprinter.getBitFingerprint ( IAtomContainer container, int size ) :  BitSet

cdk-1.5.1.jar, GravitationalIndexDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
GravitationalIndexDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, HarmonicFitter.class
package org.apache.commons.math3.optimization.fitting
HarmonicFitter.fit ( ) :  double[ ]
HarmonicFitter.fit ( double[ ] initialGuess ) :  double[ ]
HarmonicFitter.HarmonicFitter ( DifferentiableMultivariateVectorOptimizer optimizer )

cdk-1.5.1.jar, HarmonicOscillator.class
package org.apache.commons.math3.analysis.function
HarmonicOscillator.derivative ( ) :  UnivariateFunction
HarmonicOscillator.HarmonicOscillator ( double amplitude, double omega, double phase )
HarmonicOscillator.value ( double x ) :  double

cdk-1.5.1.jar, HBondAcceptorCountDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
HBondAcceptorCountDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, HBondDonorCountDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
HBondDonorCountDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, HighamHall54Integrator.class
package org.apache.commons.math3.ode.nonstiff
HighamHall54Integrator.estimateError ( double[ ][ ] yDotK, double[ ] y0, double[ ] y1, double h ) :  double
HighamHall54Integrator.getOrder ( ) :  int
HighamHall54Integrator.HighamHall54Integrator ( double minStep, double maxStep, double scalAbsoluteTolerance, double scalRelativeTolerance )
HighamHall54Integrator.HighamHall54Integrator ( double minStep, double maxStep, double[ ] vecAbsoluteTolerance, double[ ] vecRelativeTolerance )

cdk-1.5.1.jar, HybridizationFingerprinter.class
package org.openscience.cdk.fingerprint
HybridizationFingerprinter.getBitFingerprint ( IAtomContainer container ) :  IBitFingerprint
HybridizationFingerprinter.getCountFingerprint ( IAtomContainer container ) :  ICountFingerprint

cdk-1.5.1.jar, HybridizationRatioDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
HybridizationRatioDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, HypergeometricDistribution.class
package org.apache.commons.math3.distribution
HypergeometricDistribution.calculateNumericalVariance ( ) :  double
HypergeometricDistribution.cumulativeProbability ( int x ) :  double
HypergeometricDistribution.getNumberOfSuccesses ( ) :  int
HypergeometricDistribution.getNumericalMean ( ) :  double
HypergeometricDistribution.getNumericalVariance ( ) :  double
HypergeometricDistribution.getPopulationSize ( ) :  int
HypergeometricDistribution.getSampleSize ( ) :  int
HypergeometricDistribution.getSupportLowerBound ( ) :  int
HypergeometricDistribution.getSupportUpperBound ( ) :  int
HypergeometricDistribution.HypergeometricDistribution ( int populationSize, int numberOfSuccesses, int sampleSize )
HypergeometricDistribution.isSupportConnected ( ) :  boolean
HypergeometricDistribution.probability ( int x ) :  double
HypergeometricDistribution.upperCumulativeProbability ( int x ) :  double

cdk-1.5.1.jar, Hyperplane.class
package org.apache.commons.math3.geometry.partitioning
Hyperplane.copySelf ( ) [abstract] :  Hyperplane
Hyperplane.getOffset ( Vector p1 ) [abstract] :  double
Hyperplane.sameOrientationAs ( Hyperplane p1 ) [abstract] :  boolean
Hyperplane.wholeHyperplane ( ) [abstract] :  SubHyperplane
Hyperplane.wholeSpace ( ) [abstract] :  Region

cdk-1.5.1.jar, IBitFingerprint.class
package org.openscience.cdk.fingerprint
IBitFingerprint.and ( IBitFingerprint p1 ) [abstract] :  void
IBitFingerprint.asBitSet ( ) [abstract] :  BitSet
IBitFingerprint.cardinality ( ) [abstract] :  int
IBitFingerprint.get ( int p1 ) [abstract] :  boolean
IBitFingerprint.getSetbits ( ) [abstract] :  int[ ]
IBitFingerprint.or ( IBitFingerprint p1 ) [abstract] :  void
IBitFingerprint.set ( int p1 ) [abstract] :  void
IBitFingerprint.set ( int p1, boolean p2 ) [abstract] :  void
IBitFingerprint.size ( ) [abstract] :  long

cdk-1.5.1.jar, IChemObject.class
package org.openscience.cdk.interfaces
IChemObject.getFlagValue ( ) [abstract] :  Number

cdk-1.5.1.jar, IChemObjectIO.class
package org.openscience.cdk.io
IChemObjectIO.addSetting ( IOSetting p1 ) [abstract] :  IOSetting
IChemObjectIO.addSettings ( Collection p1 ) [abstract] :  void
IChemObjectIO.getListeners ( ) [abstract] :  Collection
IChemObjectIO.getSetting ( String p1 ) [abstract] :  IOSetting
IChemObjectIO.getSetting ( String p1, Class p2 ) [abstract] :  IOSetting
IChemObjectIO.getSettings ( ) [abstract] :  Collection
IChemObjectIO.hasSetting ( String p1 ) [abstract] :  boolean

cdk-1.5.1.jar, ICountFingerprint.class
package org.openscience.cdk.fingerprint
ICountFingerprint.getCount ( int p1 ) [abstract] :  int
ICountFingerprint.getCountForHash ( int p1 ) [abstract] :  int
ICountFingerprint.getHash ( int p1 ) [abstract] :  int
ICountFingerprint.hasHash ( int p1 ) [abstract] :  boolean
ICountFingerprint.merge ( ICountFingerprint p1 ) [abstract] :  void
ICountFingerprint.numOfPopulatedbins ( ) [abstract] :  int
ICountFingerprint.setBehaveAsBitFingerprint ( boolean p1 ) [abstract] :  void
ICountFingerprint.size ( ) [abstract] :  long

cdk-1.5.1.jar, Identity.class
package org.apache.commons.math3.analysis.function
Identity.derivative ( ) :  DifferentiableUnivariateFunction
Identity.derivative ( ) :  UnivariateFunction
Identity.Identity ( )
Identity.value ( double x ) :  double

cdk-1.5.1.jar, IdentityPreconditioner.class
package org.apache.commons.math3.optimization.general
NonLinearConjugateGradientOptimizer.IdentityPreconditioner.NonLinearConjugateGradientOptimizer.IdentityPreconditioner ( )
NonLinearConjugateGradientOptimizer.IdentityPreconditioner.precondition ( double[ ] variables, double[ ] r ) :  double[ ]

cdk-1.5.1.jar, IDescriptor.class
package org.openscience.cdk.qsar
IDescriptor.getSpecification ( ) [abstract] :  IImplementationSpecification

cdk-1.5.1.jar, IFingerprinter.class
package org.openscience.cdk.fingerprint
IFingerprinter.getBitFingerprint ( IAtomContainer p1 ) [abstract] :  IBitFingerprint
IFingerprinter.getCountFingerprint ( IAtomContainer p1 ) [abstract] :  ICountFingerprint

cdk-1.5.1.jar, IllConditionedOperatorException.class
package org.apache.commons.math3.linear
IllConditionedOperatorException.IllConditionedOperatorException ( double cond )

cdk-1.5.1.jar, IllinoisSolver.class
package org.apache.commons.math3.analysis.solvers
IllinoisSolver.IllinoisSolver ( )
IllinoisSolver.IllinoisSolver ( double absoluteAccuracy )
IllinoisSolver.IllinoisSolver ( double relativeAccuracy, double absoluteAccuracy )
IllinoisSolver.IllinoisSolver ( double relativeAccuracy, double absoluteAccuracy, double functionValueAccuracy )

cdk-1.5.1.jar, Importance.class
package org.openscience.cdk.io.setting
IOSetting.Importance.valueOf ( String name ) [static] :  IOSetting.Importance
IOSetting.Importance.values ( ) [static] :  IOSetting.Importance[ ]

cdk-1.5.1.jar, Incrementor.class
package org.apache.commons.math3.util
Incrementor.canIncrement ( ) :  boolean
Incrementor.getCount ( ) :  int
Incrementor.getMaximalCount ( ) :  int
Incrementor.incrementCount ( ) :  void
Incrementor.incrementCount ( int value ) :  void
Incrementor.Incrementor ( )
Incrementor.Incrementor ( int max )
Incrementor.Incrementor ( int max, Incrementor.MaxCountExceededCallback cb )
Incrementor.resetCount ( ) :  void
Incrementor.setMaximalCount ( int max ) :  void

cdk-1.5.1.jar, InductiveAtomicHardnessDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
InductiveAtomicHardnessDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, InductiveAtomicSoftnessDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
InductiveAtomicSoftnessDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, IntArrayCountFingerprint.class
package org.openscience.cdk.fingerprint
IntArrayCountFingerprint.getCount ( int index ) :  int
IntArrayCountFingerprint.getCountForHash ( int hash ) :  int
IntArrayCountFingerprint.getHash ( int index ) :  int
IntArrayCountFingerprint.hasHash ( int hash ) :  boolean
IntArrayCountFingerprint.IntArrayCountFingerprint ( )
IntArrayCountFingerprint.IntArrayCountFingerprint ( Map rawFingerprint )
IntArrayCountFingerprint.IntArrayCountFingerprint ( Map rawFingerprint, boolean behaveAsBitFingerprint )
IntArrayCountFingerprint.merge ( ICountFingerprint fp ) :  void
IntArrayCountFingerprint.numOfPopulatedbins ( ) :  int
IntArrayCountFingerprint.setBehaveAsBitFingerprint ( boolean behaveAsBitFingerprint ) :  void
IntArrayCountFingerprint.size ( ) :  long

cdk-1.5.1.jar, IntArrayFingerprint.class
package org.openscience.cdk.fingerprint
IntArrayFingerprint.and ( IBitFingerprint fingerprint ) :  void
IntArrayFingerprint.and ( IntArrayFingerprint fingerprint ) :  void
IntArrayFingerprint.asBitSet ( ) :  BitSet
IntArrayFingerprint.cardinality ( ) :  int
IntArrayFingerprint.equals ( Object obj ) :  boolean
IntArrayFingerprint.get ( int index ) :  boolean
IntArrayFingerprint.getSetbits ( ) :  int[ ]
IntArrayFingerprint.hashCode ( ) :  int
IntArrayFingerprint.IntArrayFingerprint ( )
IntArrayFingerprint.IntArrayFingerprint ( IBitFingerprint fingerprint )
IntArrayFingerprint.IntArrayFingerprint ( int[ ] setBits )
IntArrayFingerprint.IntArrayFingerprint ( Map rawFingerPrint )
IntArrayFingerprint.or ( IBitFingerprint fingerprint ) :  void
IntArrayFingerprint.or ( IntArrayFingerprint fingerprint ) :  void
IntArrayFingerprint.set ( int i ) :  void
IntArrayFingerprint.set ( int index, boolean value ) :  void
IntArrayFingerprint.size ( ) :  long

cdk-1.5.1.jar, IntegerDistribution.class
package org.apache.commons.math3.distribution
IntegerDistribution.cumulativeProbability ( int p1 ) [abstract] :  double
IntegerDistribution.cumulativeProbability ( int p1, int p2 ) [abstract] :  double
IntegerDistribution.getNumericalMean ( ) [abstract] :  double
IntegerDistribution.getNumericalVariance ( ) [abstract] :  double
IntegerDistribution.getSupportLowerBound ( ) [abstract] :  int
IntegerDistribution.getSupportUpperBound ( ) [abstract] :  int
IntegerDistribution.inverseCumulativeProbability ( double p1 ) [abstract] :  int
IntegerDistribution.isSupportConnected ( ) [abstract] :  boolean
IntegerDistribution.probability ( int p1 ) [abstract] :  double
IntegerDistribution.reseedRandomGenerator ( long p1 ) [abstract] :  void
IntegerDistribution.sample ( ) [abstract] :  int
IntegerDistribution.sample ( int p1 ) [abstract] :  int[ ]

cdk-1.5.1.jar, IntegerIOSetting.class
package org.openscience.cdk.io.setting
IntegerIOSetting.IntegerIOSetting ( String name, IOSetting.Importance level, String question, String defaultSetting )

cdk-1.5.1.jar, Interval.class
package org.apache.commons.math3.geometry.euclidean.oned
Interval.getLength ( ) :  double
Interval.getLower ( ) :  double
Interval.getMidPoint ( ) :  double
Interval.getUpper ( ) :  double
Interval.Interval ( double lower, double upper )

cdk-1.5.1.jar, IntervalsSet.class
package org.apache.commons.math3.geometry.euclidean.oned
IntervalsSet.asList ( ) :  List
IntervalsSet.buildNew ( BSPTree tree ) :  IntervalsSet
IntervalsSet.buildNew ( BSPTree x0 ) :  AbstractRegion
IntervalsSet.buildNew ( BSPTree x0 ) :  Region
IntervalsSet.computeGeometricalProperties ( ) :  void
IntervalsSet.getInf ( ) :  double
IntervalsSet.getSup ( ) :  double
IntervalsSet.IntervalsSet ( )
IntervalsSet.IntervalsSet ( BSPTree tree )
IntervalsSet.IntervalsSet ( Collection boundary )
IntervalsSet.IntervalsSet ( double lower, double upper )

cdk-1.5.1.jar, InvalidRepresentationException.class
package org.apache.commons.math3.genetics
InvalidRepresentationException.InvalidRepresentationException ( Localizable pattern, Object[ ] args )

cdk-1.5.1.jar, Inverse.class
package org.apache.commons.math3.analysis.function
Inverse.derivative ( ) :  UnivariateFunction
Inverse.Inverse ( )
Inverse.value ( double x ) :  double

cdk-1.5.1.jar, IOSetting.class
package org.openscience.cdk.io.setting
IOSetting.getLevel ( ) :  IOSetting.Importance
IOSetting.IOSetting ( String name, IOSetting.Importance level, String question, String defaultSetting )

cdk-1.5.1.jar, IPAtomicHOSEDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
IPAtomicHOSEDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, IPAtomicLearningDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
IPAtomicLearningDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, IPBondLearningDescriptor.class
package org.openscience.cdk.qsar.descriptors.bond
IPBondLearningDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, IPMolecularLearningDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
IPMolecularLearningDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, ISAACRandom.class
package org.apache.commons.math3.random
ISAACRandom.ISAACRandom ( )
ISAACRandom.ISAACRandom ( int[ ] seed )
ISAACRandom.ISAACRandom ( long seed )
ISAACRandom.next ( int bits ) :  int
ISAACRandom.setSeed ( int seed ) :  void
ISAACRandom.setSeed ( int[ ] seed ) :  void
ISAACRandom.setSeed ( long seed ) :  void

cdk-1.5.1.jar, ISetting.class
package org.openscience.cdk.interfaces
ISetting.getName ( ) [abstract] :  String

cdk-1.5.1.jar, IsoAlkanes.class
package org.openscience.cdk.templates.saturatedhydrocarbons
IsoAlkanes.getIsobutane ( IChemObjectBuilder builder ) [static] :  IAtomContainer
IsoAlkanes.getIsohexane ( IChemObjectBuilder builder ) [static] :  IAtomContainer
IsoAlkanes.getIsopentane ( IChemObjectBuilder builder ) [static] :  IAtomContainer

cdk-1.5.1.jar, IsProtonInAromaticSystemDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
IsProtonInAromaticSystemDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, IsProtonInConjugatedPiSystemDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
IsProtonInConjugatedPiSystemDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, IteratingSDFReader.class
package org.openscience.cdk.io.iterator
IteratingSDFReader.close ( ) :  void
IteratingSDFReader.customizeJob ( ) :  void
IteratingSDFReader.getFormat ( ) :  IResourceFormat
IteratingSDFReader.hasNext ( ) :  boolean
IteratingSDFReader.IteratingSDFReader ( InputStream in, IChemObjectBuilder builder )
IteratingSDFReader.IteratingSDFReader ( InputStream in, IChemObjectBuilder builder, boolean skip )
IteratingSDFReader.IteratingSDFReader ( Reader in, IChemObjectBuilder builder )
IteratingSDFReader.IteratingSDFReader ( Reader in, IChemObjectBuilder builder, boolean skip )
IteratingSDFReader.next ( ) :  IAtomContainer
IteratingSDFReader.next ( ) :  Object
IteratingSDFReader.remove ( ) :  void
IteratingSDFReader.setReader ( InputStream reader ) :  void
IteratingSDFReader.setReader ( Reader reader ) :  void
IteratingSDFReader.setSkip ( boolean skip ) :  void

cdk-1.5.1.jar, IterationEvent.class
package org.apache.commons.math3.util
IterationEvent.getIterations ( ) :  int
IterationEvent.IterationEvent ( Object source, int iterations )

cdk-1.5.1.jar, IterationListener.class
package org.apache.commons.math3.util
IterationListener.initializationPerformed ( IterationEvent p1 ) [abstract] :  void
IterationListener.iterationPerformed ( IterationEvent p1 ) [abstract] :  void
IterationListener.iterationStarted ( IterationEvent p1 ) [abstract] :  void
IterationListener.terminationPerformed ( IterationEvent p1 ) [abstract] :  void

cdk-1.5.1.jar, IterationManager.class
package org.apache.commons.math3.util
IterationManager.addIterationListener ( IterationListener listener ) :  void
IterationManager.fireInitializationEvent ( IterationEvent e ) :  void
IterationManager.fireIterationPerformedEvent ( IterationEvent e ) :  void
IterationManager.fireIterationStartedEvent ( IterationEvent e ) :  void
IterationManager.fireTerminationEvent ( IterationEvent e ) :  void
IterationManager.getIterations ( ) :  int
IterationManager.getMaxIterations ( ) :  int
IterationManager.incrementIterationCount ( ) :  void
IterationManager.IterationManager ( int maxIterations )
IterationManager.removeIterationListener ( IterationListener listener ) :  void
IterationManager.resetIterationCount ( ) :  void

cdk-1.5.1.jar, IterativeLinearSolver.class
package org.apache.commons.math3.linear
IterativeLinearSolver.checkParameters ( RealLinearOperator a, RealVector b, RealVector x0 ) [static] :  void
IterativeLinearSolver.getIterationManager ( ) :  IterationManager
IterativeLinearSolver.IterativeLinearSolver ( int maxIterations )
IterativeLinearSolver.IterativeLinearSolver ( IterationManager manager )
IterativeLinearSolver.solve ( RealLinearOperator a, RealVector b ) :  RealVector
IterativeLinearSolver.solve ( RealLinearOperator a, RealVector b, RealVector x0 ) :  RealVector
IterativeLinearSolver.solveInPlace ( RealLinearOperator p1, RealVector p2, RealVector p3 ) [abstract] :  RealVector

cdk-1.5.1.jar, IterativeLinearSolverEvent.class
package org.apache.commons.math3.linear
IterativeLinearSolverEvent.getNormOfResidual ( ) [abstract] :  double
IterativeLinearSolverEvent.getResidual ( ) :  RealVector
IterativeLinearSolverEvent.getRightHandSideVector ( ) [abstract] :  RealVector
IterativeLinearSolverEvent.getSolution ( ) [abstract] :  RealVector
IterativeLinearSolverEvent.IterativeLinearSolverEvent ( Object source, int iterations )
IterativeLinearSolverEvent.providesResidual ( ) :  boolean

cdk-1.5.1.jar, Iterator.class
package org.apache.commons.math3.util
MultidimensionalCounter.Iterator.getCount ( ) :  int
MultidimensionalCounter.Iterator.getCount ( int dim ) :  int
MultidimensionalCounter.Iterator.getCounts ( ) :  int[ ]
MultidimensionalCounter.Iterator.hasNext ( ) :  boolean
MultidimensionalCounter.Iterator.next ( ) :  Integer
MultidimensionalCounter.Iterator.next ( ) :  Object
MultidimensionalCounter.Iterator.remove ( ) :  void
OpenIntToDoubleHashMap.Iterator.advance ( ) :  void
OpenIntToDoubleHashMap.Iterator.hasNext ( ) :  boolean
OpenIntToDoubleHashMap.Iterator.key ( ) :  int
OpenIntToDoubleHashMap.Iterator.value ( ) :  double
OpenIntToFieldHashMap.Iterator.advance ( ) :  void
OpenIntToFieldHashMap.Iterator.hasNext ( ) :  boolean
OpenIntToFieldHashMap.Iterator.key ( ) :  int
OpenIntToFieldHashMap.Iterator.value ( ) :  FieldElement

cdk-1.5.1.jar, JacobianMatrices.class
package org.apache.commons.math3.ode
JacobianMatrices.addParameterJacobianProvider ( ParameterJacobianProvider provider ) :  void
JacobianMatrices.getCurrentMainSetJacobian ( double[ ][ ] dYdY0 ) :  void
JacobianMatrices.getCurrentParameterJacobian ( String pName, double[ ] dYdP ) :  void
JacobianMatrices.JacobianMatrices ( FirstOrderDifferentialEquations fode, double[ ] hY, String[ ] parameters )
JacobianMatrices.JacobianMatrices ( MainStateJacobianProvider jode, String[ ] parameters )
JacobianMatrices.registerVariationalEquations ( ExpandableStatefulODE expandable ) :  void
JacobianMatrices.setInitialMainStateJacobian ( double[ ][ ] dYdY0 ) :  void
JacobianMatrices.setInitialParameterJacobian ( String pName, double[ ] dYdP ) :  void
JacobianMatrices.setParameterizedODE ( ParameterizedODE parameterizedOde ) :  void
JacobianMatrices.setParameterStep ( String parameter, double hP ) :  void

cdk-1.5.1.jar, JacobiPreconditioner.class
package org.apache.commons.math3.linear
JacobiPreconditioner.create ( RealLinearOperator a ) [static] :  JacobiPreconditioner
JacobiPreconditioner.getColumnDimension ( ) :  int
JacobiPreconditioner.getRowDimension ( ) :  int
JacobiPreconditioner.JacobiPreconditioner ( double[ ] diag, boolean deep )
JacobiPreconditioner.operate ( RealVector x ) :  RealVector

cdk-1.5.1.jar, JDKRandomGenerator.class
package org.apache.commons.math3.random
JDKRandomGenerator.JDKRandomGenerator ( )
JDKRandomGenerator.setSeed ( int seed ) :  void
JDKRandomGenerator.setSeed ( int[ ] seed ) :  void

cdk-1.5.1.jar, JJTSMARTSParserState.class
package org.openscience.cdk.smiles.smarts.parser
JJTSMARTSParserState.JJTSMARTSParserState ( )

cdk-1.5.1.jar, KalmanFilter.class
package org.apache.commons.math3.filter
KalmanFilter.correct ( double[ ] z ) :  void
KalmanFilter.correct ( RealVector z ) :  void
KalmanFilter.getErrorCovariance ( ) :  double[ ][ ]
KalmanFilter.getErrorCovarianceMatrix ( ) :  RealMatrix
KalmanFilter.getMeasurementDimension ( ) :  int
KalmanFilter.getStateDimension ( ) :  int
KalmanFilter.getStateEstimation ( ) :  double[ ]
KalmanFilter.getStateEstimationVector ( ) :  RealVector
KalmanFilter.KalmanFilter ( ProcessModel process, MeasurementModel measurement )
KalmanFilter.predict ( ) :  void
KalmanFilter.predict ( double[ ] u ) :  void
KalmanFilter.predict ( RealVector u ) :  void

cdk-1.5.1.jar, KappaShapeIndicesDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
KappaShapeIndicesDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, KierHallSmartsDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
KierHallSmartsDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, KMeansPlusPlusClusterer.class
package org.apache.commons.math3.stat.clustering
KMeansPlusPlusClusterer.cluster ( Collection points, int k, int maxIterations ) :  List
KMeansPlusPlusClusterer.cluster ( Collection points, int k, int numTrials, int maxIterationsPerTrial ) :  List
KMeansPlusPlusClusterer.KMeansPlusPlusClusterer ( Random random )
KMeansPlusPlusClusterer.KMeansPlusPlusClusterer ( Random random, KMeansPlusPlusClusterer.EmptyClusterStrategy emptyStrategy )

cdk-1.5.1.jar, KolmogorovSmirnovDistribution.class
package org.apache.commons.math3.distribution
KolmogorovSmirnovDistribution.cdf ( double d ) :  double
KolmogorovSmirnovDistribution.cdf ( double d, boolean exact ) :  double
KolmogorovSmirnovDistribution.cdfExact ( double d ) :  double
KolmogorovSmirnovDistribution.KolmogorovSmirnovDistribution ( int n )

cdk-1.5.1.jar, Kurtosis.class
package org.apache.commons.math3.stat.descriptive.moment
Kurtosis.clear ( ) :  void
Kurtosis.copy ( ) :  Kurtosis
Kurtosis.copy ( ) :  StorelessUnivariateStatistic
Kurtosis.copy ( ) :  UnivariateStatistic
Kurtosis.copy ( Kurtosis source, Kurtosis dest ) [static] :  void
Kurtosis.evaluate ( double[ ] values, int begin, int length ) :  double
Kurtosis.getN ( ) :  long
Kurtosis.getResult ( ) :  double
Kurtosis.increment ( double d ) :  void
Kurtosis.Kurtosis ( )
Kurtosis.Kurtosis ( FourthMoment m4 )
Kurtosis.Kurtosis ( Kurtosis original )

cdk-1.5.1.jar, LaguerreSolver.class
package org.apache.commons.math3.analysis.solvers
LaguerreSolver.doSolve ( ) :  double
LaguerreSolver.laguerre ( double lo, double hi, double fLo, double fHi ) :  double
LaguerreSolver.LaguerreSolver ( )
LaguerreSolver.LaguerreSolver ( double absoluteAccuracy )
LaguerreSolver.LaguerreSolver ( double relativeAccuracy, double absoluteAccuracy )
LaguerreSolver.LaguerreSolver ( double relativeAccuracy, double absoluteAccuracy, double functionValueAccuracy )

cdk-1.5.1.jar, LargestChainDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
LargestChainDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, LargestPiSystemDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
LargestPiSystemDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, LeafMerger.class
package org.apache.commons.math3.geometry.partitioning
BSPTree.LeafMerger.merge ( BSPTree p1, BSPTree p2, BSPTree p3, boolean p4, boolean p5 ) [abstract] :  BSPTree

cdk-1.5.1.jar, LeastSquaresConverter.class
package org.apache.commons.math3.optimization
LeastSquaresConverter.LeastSquaresConverter ( MultivariateVectorFunction function, double[ ] observations )
LeastSquaresConverter.LeastSquaresConverter ( MultivariateVectorFunction function, double[ ] observations, double[ ] weights )
LeastSquaresConverter.LeastSquaresConverter ( MultivariateVectorFunction function, double[ ] observations, RealMatrix scale )
LeastSquaresConverter.value ( double[ ] point ) :  double

cdk-1.5.1.jar, LegendreGaussIntegrator.class
package org.apache.commons.math3.analysis.integration
LegendreGaussIntegrator.doIntegrate ( ) :  double
LegendreGaussIntegrator.LegendreGaussIntegrator ( int n, double relativeAccuracy, double absoluteAccuracy )
LegendreGaussIntegrator.LegendreGaussIntegrator ( int n, double relativeAccuracy, double absoluteAccuracy, int minimalIterationCount, int maximalIterationCount )
LegendreGaussIntegrator.LegendreGaussIntegrator ( int n, int minimalIterationCount, int maximalIterationCount )

cdk-1.5.1.jar, LengthOverBreadthDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
LengthOverBreadthDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, LevenbergMarquardtOptimizer.class
package org.apache.commons.math3.optimization.general
LevenbergMarquardtOptimizer.doOptimize ( ) :  PointVectorValuePair
LevenbergMarquardtOptimizer.LevenbergMarquardtOptimizer ( )
LevenbergMarquardtOptimizer.LevenbergMarquardtOptimizer ( ConvergenceChecker checker )
LevenbergMarquardtOptimizer.LevenbergMarquardtOptimizer ( double costRelativeTolerance, double parRelativeTolerance, double orthoTolerance )
LevenbergMarquardtOptimizer.LevenbergMarquardtOptimizer ( double initialStepBoundFactor, ConvergenceChecker checker, double costRelativeTolerance, double parRelativeTolerance, double orthoTolerance, double threshold )
LevenbergMarquardtOptimizer.LevenbergMarquardtOptimizer ( double initialStepBoundFactor, double costRelativeTolerance, double parRelativeTolerance, double orthoTolerance, double threshold )

cdk-1.5.1.jar, Line.class
package org.apache.commons.math3.geometry.euclidean.threed
Line.closestPoint ( Line line ) :  Vector3D
Line.contains ( Vector3D p ) :  boolean
Line.distance ( Line line ) :  double
Line.distance ( Vector3D p ) :  double
Line.getAbscissa ( Vector3D point ) :  double
Line.getDirection ( ) :  Vector3D
Line.getOrigin ( ) :  Vector3D
Line.intersection ( Line line ) :  Vector3D
Line.isSimilarTo ( Line line ) :  boolean
Line.Line ( Line line )
Line.Line ( Vector3D p1, Vector3D p2 )
Line.pointAt ( double abscissa ) :  Vector3D
Line.reset ( Vector3D p1, Vector3D p2 ) :  void
Line.revert ( ) :  Line
Line.toSpace ( Vector point ) :  Vector3D
Line.toSpace ( Vector x0 ) :  Vector
Line.toSubSpace ( Vector point ) :  Vector1D
Line.toSubSpace ( Vector x0 ) :  Vector
Line.wholeLine ( ) :  SubLine
package org.apache.commons.math3.geometry.euclidean.twod
Line.contains ( Vector2D p ) :  boolean
Line.copySelf ( ) :  Hyperplane
Line.copySelf ( ) :  Line
Line.getAngle ( ) :  double
Line.getOffset ( Line line ) :  double
Line.getOffset ( Vector point ) :  double
Line.getOriginOffset ( ) :  double
Line.getPointAt ( Vector1D abscissa, double offset ) :  Vector2D
Line.getReverse ( ) :  Line
Line.getTransform ( AffineTransform transform ) [static] :  Transform
Line.intersection ( Line other ) :  Vector2D
Line.isParallelTo ( Line line ) :  boolean
Line.Line ( Line line )
Line.Line ( Vector2D p, double angle )
Line.Line ( Vector2D p1, Vector2D p2 )
Line.reset ( Vector2D p, double alpha ) :  void
Line.reset ( Vector2D p1, Vector2D p2 ) :  void
Line.revertSelf ( ) :  void
Line.sameOrientationAs ( Hyperplane other ) :  boolean
Line.setAngle ( double angle ) :  void
Line.setOriginOffset ( double offset ) :  void
Line.toSpace ( Vector point ) :  Vector2D
Line.toSpace ( Vector x0 ) :  Vector
Line.toSubSpace ( Vector point ) :  Vector1D
Line.toSubSpace ( Vector x0 ) :  Vector
Line.translateToPoint ( Vector2D p ) :  void
Line.wholeHyperplane ( ) :  SubHyperplane
Line.wholeHyperplane ( ) :  SubLine
Line.wholeSpace ( ) :  PolygonsSet
Line.wholeSpace ( ) :  Region

cdk-1.5.1.jar, LinearConstraint.class
package org.apache.commons.math3.optimization.linear
LinearConstraint.equals ( Object other ) :  boolean
LinearConstraint.getCoefficients ( ) :  RealVector
LinearConstraint.getRelationship ( ) :  Relationship
LinearConstraint.getValue ( ) :  double
LinearConstraint.hashCode ( ) :  int
LinearConstraint.LinearConstraint ( double[ ] coefficients, Relationship relationship, double value )
LinearConstraint.LinearConstraint ( double[ ] lhsCoefficients, double lhsConstant, Relationship relationship, double[ ] rhsCoefficients, double rhsConstant )
LinearConstraint.LinearConstraint ( RealVector coefficients, Relationship relationship, double value )
LinearConstraint.LinearConstraint ( RealVector lhsCoefficients, double lhsConstant, Relationship relationship, RealVector rhsCoefficients, double rhsConstant )

cdk-1.5.1.jar, LinearInterpolator.class
package org.apache.commons.math3.analysis.interpolation
LinearInterpolator.interpolate ( double[ ] x, double[ ] y ) :  PolynomialSplineFunction
LinearInterpolator.interpolate ( double[ ] x0, double[ ] x1 ) :  UnivariateFunction
LinearInterpolator.LinearInterpolator ( )

cdk-1.5.1.jar, LinearObjectiveFunction.class
package org.apache.commons.math3.optimization.linear
LinearObjectiveFunction.equals ( Object other ) :  boolean
LinearObjectiveFunction.getCoefficients ( ) :  RealVector
LinearObjectiveFunction.getConstantTerm ( ) :  double
LinearObjectiveFunction.getValue ( double[ ] point ) :  double
LinearObjectiveFunction.getValue ( RealVector point ) :  double
LinearObjectiveFunction.hashCode ( ) :  int
LinearObjectiveFunction.LinearObjectiveFunction ( double[ ] coefficients, double constantTerm )
LinearObjectiveFunction.LinearObjectiveFunction ( RealVector coefficients, double constantTerm )

cdk-1.5.1.jar, LinearOptimizer.class
package org.apache.commons.math3.optimization.linear
LinearOptimizer.getIterations ( ) [abstract] :  int
LinearOptimizer.getMaxIterations ( ) [abstract] :  int
LinearOptimizer.optimize ( LinearObjectiveFunction p1, Collection p2, GoalType p3, boolean p4 ) [abstract] :  PointValuePair
LinearOptimizer.setMaxIterations ( int p1 ) [abstract] :  void

cdk-1.5.1.jar, LingoFingerprinter.class
package org.openscience.cdk.fingerprint
LingoFingerprinter.getBitFingerprint ( IAtomContainer iAtomContainer ) :  IBitFingerprint
LingoFingerprinter.getCountFingerprint ( IAtomContainer container ) :  ICountFingerprint

cdk-1.5.1.jar, ListPopulation.class
package org.apache.commons.math3.genetics
ListPopulation.addChromosome ( Chromosome chromosome ) :  void
ListPopulation.getChromosomes ( ) :  List
ListPopulation.getFittestChromosome ( ) :  Chromosome
ListPopulation.getPopulationLimit ( ) :  int
ListPopulation.getPopulationSize ( ) :  int
ListPopulation.iterator ( ) :  Iterator
ListPopulation.ListPopulation ( int populationLimit )
ListPopulation.ListPopulation ( List chromosomes, int populationLimit )
ListPopulation.setChromosomes ( List chromosomes ) :  void
ListPopulation.setPopulationLimit ( int populationLimit ) :  void
ListPopulation.toString ( ) :  String

cdk-1.5.1.jar, Localizable.class
package org.apache.commons.math3.exception.util
Localizable.getLocalizedString ( Locale p1 ) [abstract] :  String
Localizable.getSourceString ( ) [abstract] :  String

cdk-1.5.1.jar, LocalizedFormats.class
package org.apache.commons.math3.exception.util
LocalizedFormats.getLocalizedString ( Locale locale ) :  String
LocalizedFormats.getSourceString ( ) :  String
LocalizedFormats.valueOf ( String name ) [static] :  LocalizedFormats
LocalizedFormats.values ( ) [static] :  LocalizedFormats[ ]

cdk-1.5.1.jar, Location.class
package org.apache.commons.math3.geometry.partitioning
Region.Location.valueOf ( String name ) [static] :  Region.Location
Region.Location.values ( ) [static] :  Region.Location[ ]

cdk-1.5.1.jar, LoessInterpolator.class
package org.apache.commons.math3.analysis.interpolation
LoessInterpolator.interpolate ( double[ ] x0, double[ ] x1 ) :  UnivariateFunction
LoessInterpolator.interpolate ( double[ ] xval, double[ ] yval ) :  PolynomialSplineFunction
LoessInterpolator.LoessInterpolator ( )
LoessInterpolator.LoessInterpolator ( double bandwidth, int robustnessIters )
LoessInterpolator.LoessInterpolator ( double bandwidth, int robustnessIters, double accuracy )
LoessInterpolator.smooth ( double[ ] xval, double[ ] yval ) :  double[ ]
LoessInterpolator.smooth ( double[ ] xval, double[ ] yval, double[ ] weights ) :  double[ ]

cdk-1.5.1.jar, Log.class
package org.apache.commons.math3.analysis.function
Log.derivative ( ) :  UnivariateFunction
Log.Log ( )
Log.value ( double x ) :  double

cdk-1.5.1.jar, Log10.class
package org.apache.commons.math3.analysis.function
Log10.derivative ( ) :  UnivariateFunction
Log10.Log10 ( )
Log10.value ( double x ) :  double

cdk-1.5.1.jar, Log1p.class
package org.apache.commons.math3.analysis.function
Log1p.derivative ( ) :  UnivariateFunction
Log1p.Log1p ( )
Log1p.value ( double x ) :  double

cdk-1.5.1.jar, Logistic.class
package org.apache.commons.math3.analysis.function
Logistic.derivative ( ) :  UnivariateFunction
Logistic.Logistic ( double k, double m, double b, double q, double a, double n )
Logistic.value ( double x ) :  double

cdk-1.5.1.jar, Logit.class
package org.apache.commons.math3.analysis.function
Logit.derivative ( ) :  UnivariateFunction
Logit.Logit ( )
Logit.Logit ( double lo, double hi )
Logit.value ( double x ) :  double

cdk-1.5.1.jar, LogNormalDistribution.class
package org.apache.commons.math3.distribution
LogNormalDistribution.cumulativeProbability ( double x ) :  double
LogNormalDistribution.cumulativeProbability ( double x0, double x1 ) :  double
LogNormalDistribution.density ( double x ) :  double
LogNormalDistribution.getNumericalMean ( ) :  double
LogNormalDistribution.getNumericalVariance ( ) :  double
LogNormalDistribution.getScale ( ) :  double
LogNormalDistribution.getShape ( ) :  double
LogNormalDistribution.getSolverAbsoluteAccuracy ( ) :  double
LogNormalDistribution.getSupportLowerBound ( ) :  double
LogNormalDistribution.getSupportUpperBound ( ) :  double
LogNormalDistribution.isSupportConnected ( ) :  boolean
LogNormalDistribution.isSupportLowerBoundInclusive ( ) :  boolean
LogNormalDistribution.isSupportUpperBoundInclusive ( ) :  boolean
LogNormalDistribution.LogNormalDistribution ( )
LogNormalDistribution.LogNormalDistribution ( double scale, double shape )
LogNormalDistribution.LogNormalDistribution ( double scale, double shape, double inverseCumAccuracy )
LogNormalDistribution.probability ( double x ) :  double
LogNormalDistribution.sample ( ) :  double

cdk-1.5.1.jar, LongestAliphaticChainDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
LongestAliphaticChainDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, LUDecomposition.class
package org.apache.commons.math3.linear
LUDecomposition.getDeterminant ( ) :  double
LUDecomposition.getL ( ) :  RealMatrix
LUDecomposition.getP ( ) :  RealMatrix
LUDecomposition.getPivot ( ) :  int[ ]
LUDecomposition.getSolver ( ) :  DecompositionSolver
LUDecomposition.getU ( ) :  RealMatrix
LUDecomposition.LUDecomposition ( RealMatrix matrix )
LUDecomposition.LUDecomposition ( RealMatrix matrix, double singularityThreshold )

cdk-1.5.1.jar, MACCSFingerprinter.class
package org.openscience.cdk.fingerprint
MACCSFingerprinter.getBitFingerprint ( IAtomContainer atomContainer ) :  IBitFingerprint
MACCSFingerprinter.getCountFingerprint ( IAtomContainer container ) :  ICountFingerprint

cdk-1.5.1.jar, MainStateJacobianProvider.class
package org.apache.commons.math3.ode
MainStateJacobianProvider.computeMainStateJacobian ( double p1, double[ ] p2, double[ ] p3, double[ ][ ] p4 ) [abstract] :  void

cdk-1.5.1.jar, MannholdLogPDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
MannholdLogPDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, MannWhitneyUTest.class
package org.apache.commons.math3.stat.inference
MannWhitneyUTest.mannWhitneyU ( double[ ] x, double[ ] y ) :  double
MannWhitneyUTest.MannWhitneyUTest ( )
MannWhitneyUTest.mannWhitneyUTest ( double[ ] x, double[ ] y ) :  double
MannWhitneyUTest.MannWhitneyUTest ( NaNStrategy nanStrategy, TiesStrategy tiesStrategy )

cdk-1.5.1.jar, MathArithmeticException.class
package org.apache.commons.math3.exception
MathArithmeticException.getContext ( ) :  ExceptionContext
MathArithmeticException.getLocalizedMessage ( ) :  String
MathArithmeticException.getMessage ( ) :  String
MathArithmeticException.MathArithmeticException ( )
MathArithmeticException.MathArithmeticException ( Localizable pattern, Object[ ] args )

cdk-1.5.1.jar, MathArrays.class
package org.apache.commons.math3.util
MathArrays.checkOrder ( double[ ] val ) [static] :  void
MathArrays.checkOrder ( double[ ] val, MathArrays.OrderDirection dir, boolean strict ) [static] :  void
MathArrays.checkOrder ( double[ ] val, MathArrays.OrderDirection dir, boolean strict, boolean abort ) [static] :  boolean
MathArrays.copyOf ( double[ ] source ) [static] :  double[ ]
MathArrays.copyOf ( double[ ] source, int len ) [static] :  double[ ]
MathArrays.copyOf ( int[ ] source ) [static] :  int[ ]
MathArrays.copyOf ( int[ ] source, int len ) [static] :  int[ ]
MathArrays.distance ( double[ ] p1, double[ ] p2 ) [static] :  double
MathArrays.distance ( int[ ] p1, int[ ] p2 ) [static] :  double
MathArrays.distance1 ( double[ ] p1, double[ ] p2 ) [static] :  double
MathArrays.distance1 ( int[ ] p1, int[ ] p2 ) [static] :  int
MathArrays.distanceInf ( double[ ] p1, double[ ] p2 ) [static] :  double
MathArrays.distanceInf ( int[ ] p1, int[ ] p2 ) [static] :  int
MathArrays.equals ( double[ ] x, double[ ] y ) [static] :  boolean
MathArrays.equals ( float[ ] x, float[ ] y ) [static] :  boolean
MathArrays.equalsIncludingNaN ( double[ ] x, double[ ] y ) [static] :  boolean
MathArrays.equalsIncludingNaN ( float[ ] x, float[ ] y ) [static] :  boolean
MathArrays.isMonotonic ( Comparable[ ] val, MathArrays.OrderDirection dir, boolean strict ) [static] :  boolean
MathArrays.isMonotonic ( double[ ] val, MathArrays.OrderDirection dir, boolean strict ) [static] :  boolean
MathArrays.linearCombination ( double a1, double b1, double a2, double b2 ) [static] :  double
MathArrays.linearCombination ( double a1, double b1, double a2, double b2, double a3, double b3 ) [static] :  double
MathArrays.linearCombination ( double a1, double b1, double a2, double b2, double a3, double b3, double a4, double b4 ) [static] :  double
MathArrays.linearCombination ( double[ ] a, double[ ] b ) [static] :  double
MathArrays.normalizeArray ( double[ ] values, double normalizedSum ) [static] :  double[ ]
MathArrays.safeNorm ( double[ ] v ) [static] :  double
MathArrays.sortInPlace ( double[ ] x, double[ ][ ] yList ) [static] :  void
MathArrays.sortInPlace ( double[ ] x, MathArrays.OrderDirection dir, double[ ][ ] yList ) [static] :  void

cdk-1.5.1.jar, MathIllegalArgumentException.class
package org.apache.commons.math3.exception
MathIllegalArgumentException.getContext ( ) :  ExceptionContext
MathIllegalArgumentException.getLocalizedMessage ( ) :  String
MathIllegalArgumentException.getMessage ( ) :  String
MathIllegalArgumentException.MathIllegalArgumentException ( Localizable pattern, Object[ ] args )

cdk-1.5.1.jar, MathIllegalNumberException.class
package org.apache.commons.math3.exception
MathIllegalNumberException.getArgument ( ) :  Number
MathIllegalNumberException.MathIllegalNumberException ( Localizable pattern, Number wrong, Object[ ] arguments )

cdk-1.5.1.jar, MathIllegalStateException.class
package org.apache.commons.math3.exception
MathIllegalStateException.getContext ( ) :  ExceptionContext
MathIllegalStateException.getLocalizedMessage ( ) :  String
MathIllegalStateException.getMessage ( ) :  String
MathIllegalStateException.MathIllegalStateException ( )
MathIllegalStateException.MathIllegalStateException ( Localizable pattern, Object[ ] args )
MathIllegalStateException.MathIllegalStateException ( Throwable cause, Localizable pattern, Object[ ] args )

cdk-1.5.1.jar, MathInternalError.class
package org.apache.commons.math3.exception
MathInternalError.MathInternalError ( )
MathInternalError.MathInternalError ( Localizable pattern, Object[ ] args )
MathInternalError.MathInternalError ( Throwable cause )

cdk-1.5.1.jar, MathParseException.class
package org.apache.commons.math3.exception
MathParseException.MathParseException ( String wrong, int position )
MathParseException.MathParseException ( String wrong, int position, Class type )

cdk-1.5.1.jar, MathUnsupportedOperationException.class
package org.apache.commons.math3.exception
MathUnsupportedOperationException.getContext ( ) :  ExceptionContext
MathUnsupportedOperationException.getLocalizedMessage ( ) :  String
MathUnsupportedOperationException.getMessage ( ) :  String
MathUnsupportedOperationException.MathUnsupportedOperationException ( )
MathUnsupportedOperationException.MathUnsupportedOperationException ( Localizable pattern, Object[ ] args )

cdk-1.5.1.jar, MathUtils.class
package org.apache.commons.math3.util
MathUtils.checkFinite ( double x ) [static] :  void
MathUtils.checkFinite ( double[ ] val ) [static] :  void
MathUtils.checkNotNull ( Object o ) [static] :  void
MathUtils.checkNotNull ( Object o, Localizable pattern, Object[ ] args ) [static] :  void
MathUtils.copySign ( byte magnitude, byte sign ) [static] :  byte
MathUtils.copySign ( int magnitude, int sign ) [static] :  int
MathUtils.copySign ( long magnitude, long sign ) [static] :  long
MathUtils.copySign ( short magnitude, short sign ) [static] :  short
MathUtils.hash ( double value ) [static] :  int
MathUtils.hash ( double[ ] value ) [static] :  int
MathUtils.normalizeAngle ( double a, double center ) [static] :  double
MathUtils.reduce ( double a, double period, double offset ) [static] :  double

cdk-1.5.1.jar, MatrixDimensionMismatchException.class
package org.apache.commons.math3.linear
MatrixDimensionMismatchException.getExpectedColumnDimension ( ) :  int
MatrixDimensionMismatchException.getExpectedRowDimension ( ) :  int
MatrixDimensionMismatchException.getWrongColumnDimension ( ) :  int
MatrixDimensionMismatchException.getWrongRowDimension ( ) :  int
MatrixDimensionMismatchException.MatrixDimensionMismatchException ( int wrongRowDim, int wrongColDim, int expectedRowDim, int expectedColDim )

cdk-1.5.1.jar, MatrixUtils.class
package org.apache.commons.math3.linear
MatrixUtils.bigFractionMatrixToRealMatrix ( FieldMatrix m ) [static] :  Array2DRowRealMatrix
MatrixUtils.checkAdditionCompatible ( AnyMatrix left, AnyMatrix right ) [static] :  void
MatrixUtils.checkColumnIndex ( AnyMatrix m, int column ) [static] :  void
MatrixUtils.checkMatrixIndex ( AnyMatrix m, int row, int column ) [static] :  void
MatrixUtils.checkMultiplicationCompatible ( AnyMatrix left, AnyMatrix right ) [static] :  void
MatrixUtils.checkRowIndex ( AnyMatrix m, int row ) [static] :  void
MatrixUtils.checkSubMatrixIndex ( AnyMatrix m, int startRow, int endRow, int startColumn, int endColumn ) [static] :  void
MatrixUtils.checkSubMatrixIndex ( AnyMatrix m, int[ ] selectedRows, int[ ] selectedColumns ) [static] :  void
MatrixUtils.checkSubtractionCompatible ( AnyMatrix left, AnyMatrix right ) [static] :  void
MatrixUtils.createColumnFieldMatrix ( FieldElement[ ] columnData ) [static] :  FieldMatrix
MatrixUtils.createColumnRealMatrix ( double[ ] columnData ) [static] :  RealMatrix
MatrixUtils.createFieldDiagonalMatrix ( FieldElement[ ] diagonal ) [static] :  FieldMatrix
MatrixUtils.createFieldIdentityMatrix ( Field field, int dimension ) [static] :  FieldMatrix
MatrixUtils.createFieldMatrix ( Field field, int rows, int columns ) [static] :  FieldMatrix
MatrixUtils.createFieldMatrix ( FieldElement[ ][ ] data ) [static] :  FieldMatrix
MatrixUtils.createFieldVector ( FieldElement[ ] data ) [static] :  FieldVector
MatrixUtils.createRealDiagonalMatrix ( double[ ] diagonal ) [static] :  RealMatrix
MatrixUtils.createRealIdentityMatrix ( int dimension ) [static] :  RealMatrix
MatrixUtils.createRealMatrix ( double[ ][ ] data ) [static] :  RealMatrix
MatrixUtils.createRealMatrix ( int rows, int columns ) [static] :  RealMatrix
MatrixUtils.createRealVector ( double[ ] data ) [static] :  RealVector
MatrixUtils.createRowFieldMatrix ( FieldElement[ ] rowData ) [static] :  FieldMatrix
MatrixUtils.createRowRealMatrix ( double[ ] rowData ) [static] :  RealMatrix
MatrixUtils.deserializeRealMatrix ( Object instance, String fieldName, ObjectInputStream ois ) [static] :  void
MatrixUtils.deserializeRealVector ( Object instance, String fieldName, ObjectInputStream ois ) [static] :  void
MatrixUtils.fractionMatrixToRealMatrix ( FieldMatrix m ) [static] :  Array2DRowRealMatrix
MatrixUtils.serializeRealMatrix ( RealMatrix matrix, ObjectOutputStream oos ) [static] :  void
MatrixUtils.serializeRealVector ( RealVector vector, ObjectOutputStream oos ) [static] :  void
MatrixUtils.solveLowerTriangularSystem ( RealMatrix rm, RealVector b ) [static] :  void
MatrixUtils.solveUpperTriangularSystem ( RealMatrix rm, RealVector b ) [static] :  void

cdk-1.5.1.jar, Max.class
package org.apache.commons.math3.analysis.function
Max.Max ( )
Max.value ( double x, double y ) :  double
package org.apache.commons.math3.stat.descriptive.rank
Max.clear ( ) :  void
Max.copy ( ) :  Max
Max.copy ( ) :  StorelessUnivariateStatistic
Max.copy ( ) :  UnivariateStatistic
Max.copy ( Max source, Max dest ) [static] :  void
Max.evaluate ( double[ ] values, int begin, int length ) :  double
Max.getN ( ) :  long
Max.getResult ( ) :  double
Max.increment ( double d ) :  void
Max.Max ( )
Max.Max ( Max original )

cdk-1.5.1.jar, MaxCountExceededCallback.class
package org.apache.commons.math3.util
Incrementor.MaxCountExceededCallback.trigger ( int p1 ) [abstract] :  void

cdk-1.5.1.jar, MaxCountExceededException.class
package org.apache.commons.math3.exception
MaxCountExceededException.getMax ( ) :  Number
MaxCountExceededException.MaxCountExceededException ( Localizable specific, Number max, Object[ ] args )
MaxCountExceededException.MaxCountExceededException ( Number max )

cdk-1.5.1.jar, MDEDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
MDEDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, Mean.class
package org.apache.commons.math3.stat.descriptive.moment
Mean.clear ( ) :  void
Mean.copy ( ) :  Mean
Mean.copy ( ) :  StorelessUnivariateStatistic
Mean.copy ( ) :  UnivariateStatistic
Mean.copy ( Mean source, Mean dest ) [static] :  void
Mean.evaluate ( double[ ] values, double[ ] weights ) :  double
Mean.evaluate ( double[ ] values, double[ ] weights, int begin, int length ) :  double
Mean.evaluate ( double[ ] values, int begin, int length ) :  double
Mean.getN ( ) :  long
Mean.getResult ( ) :  double
Mean.increment ( double d ) :  void
Mean.Mean ( )
Mean.Mean ( FirstMoment m1 )
Mean.Mean ( Mean original )

cdk-1.5.1.jar, MeasurementModel.class
package org.apache.commons.math3.filter
MeasurementModel.getMeasurementMatrix ( ) [abstract] :  RealMatrix
MeasurementModel.getMeasurementNoise ( ) [abstract] :  RealMatrix

cdk-1.5.1.jar, Median.class
package org.apache.commons.math3.stat.descriptive.rank
Median.Median ( )
Median.Median ( Median original )

cdk-1.5.1.jar, MersenneTwister.class
package org.apache.commons.math3.random
MersenneTwister.MersenneTwister ( )
MersenneTwister.MersenneTwister ( int seed )
MersenneTwister.MersenneTwister ( int[ ] seed )
MersenneTwister.MersenneTwister ( long seed )
MersenneTwister.next ( int bits ) :  int
MersenneTwister.setSeed ( int seed ) :  void
MersenneTwister.setSeed ( int[ ] seed ) :  void
MersenneTwister.setSeed ( long seed ) :  void

cdk-1.5.1.jar, Method.class
package org.apache.commons.math3.analysis.solvers
BaseSecantSolver.Method.valueOf ( String name ) [static] :  BaseSecantSolver.Method
BaseSecantSolver.Method.values ( ) [static] :  BaseSecantSolver.Method[ ]

cdk-1.5.1.jar, MicrosphereInterpolatingFunction.class
package org.apache.commons.math3.analysis.interpolation
MicrosphereInterpolatingFunction.MicrosphereInterpolatingFunction ( double[ ][ ] xval, double[ ] yval, int brightnessExponent, int microsphereElements, UnitSphereRandomVectorGenerator rand )
MicrosphereInterpolatingFunction.value ( double[ ] point ) :  double

cdk-1.5.1.jar, MicrosphereInterpolator.class
package org.apache.commons.math3.analysis.interpolation
MicrosphereInterpolator.interpolate ( double[ ][ ] xval, double[ ] yval ) :  MultivariateFunction
MicrosphereInterpolator.MicrosphereInterpolator ( )
MicrosphereInterpolator.MicrosphereInterpolator ( int elements, int exponent )

cdk-1.5.1.jar, MidpointIntegrator.class
package org.apache.commons.math3.ode.nonstiff
MidpointIntegrator.MidpointIntegrator ( double step )

cdk-1.5.1.jar, MillerUpdatingRegression.class
package org.apache.commons.math3.stat.regression
MillerUpdatingRegression.addObservation ( double[ ] x, double y ) :  void
MillerUpdatingRegression.addObservations ( double[ ][ ] x, double[ ] y ) :  void
MillerUpdatingRegression.clear ( ) :  void
MillerUpdatingRegression.getDiagonalOfHatMatrix ( double[ ] row_data ) :  double
MillerUpdatingRegression.getN ( ) :  long
MillerUpdatingRegression.getOrderOfRegressors ( ) :  int[ ]
MillerUpdatingRegression.getPartialCorrelations ( int in ) :  double[ ]
MillerUpdatingRegression.hasIntercept ( ) :  boolean
MillerUpdatingRegression.MillerUpdatingRegression ( int numberOfVariables, boolean includeConstant )
MillerUpdatingRegression.MillerUpdatingRegression ( int numberOfVariables, boolean includeConstant, double errorTolerance )
MillerUpdatingRegression.regress ( ) :  RegressionResults
MillerUpdatingRegression.regress ( int numberOfRegressors ) :  RegressionResults
MillerUpdatingRegression.regress ( int[ ] variablesToInclude ) :  RegressionResults

cdk-1.5.1.jar, Min.class
package org.apache.commons.math3.analysis.function
Min.Min ( )
Min.value ( double x, double y ) :  double
package org.apache.commons.math3.stat.descriptive.rank
Min.clear ( ) :  void
Min.copy ( ) :  Min
Min.copy ( ) :  StorelessUnivariateStatistic
Min.copy ( ) :  UnivariateStatistic
Min.copy ( Min source, Min dest ) [static] :  void
Min.evaluate ( double[ ] values, int begin, int length ) :  double
Min.getN ( ) :  long
Min.getResult ( ) :  double
Min.increment ( double d ) :  void
Min.Min ( )
Min.Min ( Min original )

cdk-1.5.1.jar, Minus.class
package org.apache.commons.math3.analysis.function
Minus.derivative ( ) :  DifferentiableUnivariateFunction
Minus.derivative ( ) :  UnivariateFunction
Minus.Minus ( )
Minus.value ( double x ) :  double

cdk-1.5.1.jar, ModelSpecificationException.class
package org.apache.commons.math3.stat.regression
ModelSpecificationException.ModelSpecificationException ( Localizable pattern, Object[ ] args )

cdk-1.5.1.jar, MolecularFormulaManipulator.class
package org.openscience.cdk.tools.manipulator
MolecularFormulaManipulator.getHTML ( IMolecularFormula formula, String[ ] orderElements, boolean chargeB, boolean isotopeB ) [static] :  String

cdk-1.5.1.jar, MoleculeBuilder.class
package org.openscience.cdk.iupac.parser
MoleculeBuilder.buildMolecule ( int mainChain, List attachedSubstituents, List attachedGroups, boolean isMainCyclic, String name ) :  IAtomContainer

cdk-1.5.1.jar, MomentOfInertiaDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
MomentOfInertiaDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, MOPAC7InputFormat.class
package org.openscience.cdk.io.formats
MOPAC7InputFormat.getFormatName ( ) :  String
MOPAC7InputFormat.getInstance ( ) [static] :  IResourceFormat
MOPAC7InputFormat.getMIMEType ( ) :  String
MOPAC7InputFormat.getNameExtensions ( ) :  String[ ]
MOPAC7InputFormat.getPreferredNameExtension ( ) :  String
MOPAC7InputFormat.getReaderClassName ( ) :  String
MOPAC7InputFormat.getRequiredDataFeatures ( ) :  int
MOPAC7InputFormat.getSupportedDataFeatures ( ) :  int
MOPAC7InputFormat.getWriterClassName ( ) :  String
MOPAC7InputFormat.isXMLBased ( ) :  boolean
MOPAC7InputFormat.matches ( int lineNumber, String line ) :  boolean

cdk-1.5.1.jar, Mopac7Reader.class
package org.openscience.cdk.io
Mopac7Reader.accepts ( Class classObject ) :  boolean
Mopac7Reader.close ( ) :  void
Mopac7Reader.getFormat ( ) :  IResourceFormat
Mopac7Reader.Mopac7Reader ( )
Mopac7Reader.Mopac7Reader ( InputStream input )
Mopac7Reader.Mopac7Reader ( Reader input )
Mopac7Reader.read ( IChemObject object ) :  IChemObject
Mopac7Reader.setReader ( InputStream input ) :  void
Mopac7Reader.setReader ( Reader input ) :  void

cdk-1.5.1.jar, Mopac7Writer.class
package org.openscience.cdk.io.program
Mopac7Writer.accepts ( Class classObject ) :  boolean
Mopac7Writer.close ( ) :  void
Mopac7Writer.getFormat ( ) :  IResourceFormat
Mopac7Writer.Mopac7Writer ( )
Mopac7Writer.Mopac7Writer ( OutputStream out )
Mopac7Writer.Mopac7Writer ( Writer out )
Mopac7Writer.setWriter ( OutputStream writer ) :  void
Mopac7Writer.setWriter ( Writer writer ) :  void
Mopac7Writer.write ( IChemObject arg0 ) :  void

cdk-1.5.1.jar, MullerSolver.class
package org.apache.commons.math3.analysis.solvers
MullerSolver.doSolve ( ) :  double
MullerSolver.MullerSolver ( )
MullerSolver.MullerSolver ( double absoluteAccuracy )
MullerSolver.MullerSolver ( double relativeAccuracy, double absoluteAccuracy )

cdk-1.5.1.jar, MullerSolver2.class
package org.apache.commons.math3.analysis.solvers
MullerSolver2.doSolve ( ) :  double
MullerSolver2.MullerSolver2 ( )
MullerSolver2.MullerSolver2 ( double absoluteAccuracy )
MullerSolver2.MullerSolver2 ( double relativeAccuracy, double absoluteAccuracy )

cdk-1.5.1.jar, MultidimensionalCounter.class
package org.apache.commons.math3.util
MultidimensionalCounter.getCount ( int[ ] c ) :  int
MultidimensionalCounter.getCounts ( int index ) :  int[ ]
MultidimensionalCounter.getDimension ( ) :  int
MultidimensionalCounter.getSize ( ) :  int
MultidimensionalCounter.getSizes ( ) :  int[ ]
MultidimensionalCounter.iterator ( ) :  Iterator
MultidimensionalCounter.iterator ( ) :  MultidimensionalCounter.Iterator
MultidimensionalCounter.MultidimensionalCounter ( int[ ] size )
MultidimensionalCounter.toString ( ) :  String

cdk-1.5.1.jar, MultiDimensionMismatchException.class
package org.apache.commons.math3.exception
MultiDimensionMismatchException.getExpectedDimension ( int index ) :  int
MultiDimensionMismatchException.getExpectedDimensions ( ) :  Integer[ ]
MultiDimensionMismatchException.getWrongDimension ( int index ) :  int
MultiDimensionMismatchException.getWrongDimensions ( ) :  Integer[ ]
MultiDimensionMismatchException.MultiDimensionMismatchException ( Integer[ ] wrong, Integer[ ] expected )
MultiDimensionMismatchException.MultiDimensionMismatchException ( Localizable specific, Integer[ ] wrong, Integer[ ] expected )

cdk-1.5.1.jar, MultiDirectionalSimplex.class
package org.apache.commons.math3.optimization.direct
MultiDirectionalSimplex.iterate ( MultivariateFunction evaluationFunction, Comparator comparator ) :  void
MultiDirectionalSimplex.MultiDirectionalSimplex ( double[ ] steps )
MultiDirectionalSimplex.MultiDirectionalSimplex ( double[ ] steps, double khi, double gamma )
MultiDirectionalSimplex.MultiDirectionalSimplex ( double[ ][ ] referenceSimplex )
MultiDirectionalSimplex.MultiDirectionalSimplex ( double[ ][ ] referenceSimplex, double khi, double gamma )
MultiDirectionalSimplex.MultiDirectionalSimplex ( int n )
MultiDirectionalSimplex.MultiDirectionalSimplex ( int n, double khi, double gamma )
MultiDirectionalSimplex.MultiDirectionalSimplex ( int n, double sideLength )
MultiDirectionalSimplex.MultiDirectionalSimplex ( int n, double sideLength, double khi, double gamma )

cdk-1.5.1.jar, MultipleLinearRegression.class
package org.apache.commons.math3.stat.regression
MultipleLinearRegression.estimateRegressandVariance ( ) [abstract] :  double
MultipleLinearRegression.estimateRegressionParameters ( ) [abstract] :  double[ ]
MultipleLinearRegression.estimateRegressionParametersStandardErrors ( ) [abstract] :  double[ ]
MultipleLinearRegression.estimateRegressionParametersVariance ( ) [abstract] :  double[ ][ ]
MultipleLinearRegression.estimateResiduals ( ) [abstract] :  double[ ]

cdk-1.5.1.jar, Multiply.class
package org.apache.commons.math3.analysis.function
Multiply.Multiply ( )
Multiply.value ( double x, double y ) :  double

cdk-1.5.1.jar, MultistepIntegrator.class
package org.apache.commons.math3.ode
MultistepIntegrator.computeStepGrowShrinkFactor ( double error ) :  double
MultistepIntegrator.getMaxGrowth ( ) :  double
MultistepIntegrator.getMinReduction ( ) :  double
MultistepIntegrator.getSafety ( ) :  double
MultistepIntegrator.getStarterIntegrator ( ) :  ODEIntegrator
MultistepIntegrator.initializeHighOrderDerivatives ( double p1, double[ ] p2, double[ ][ ] p3, double[ ][ ] p4 ) [abstract] :  Array2DRowRealMatrix
MultistepIntegrator.MultistepIntegrator ( String name, int nSteps, int order, double minStep, double maxStep, double scalAbsoluteTolerance, double scalRelativeTolerance )
MultistepIntegrator.MultistepIntegrator ( String name, int nSteps, int order, double minStep, double maxStep, double[ ] vecAbsoluteTolerance, double[ ] vecRelativeTolerance )
MultistepIntegrator.setMaxGrowth ( double maxGrowth ) :  void
MultistepIntegrator.setMinReduction ( double minReduction ) :  void
MultistepIntegrator.setSafety ( double safety ) :  void
MultistepIntegrator.setStarterIntegrator ( FirstOrderIntegrator starterIntegrator ) :  void
MultistepIntegrator.start ( double t0, double[ ] y0, double t ) :  void

cdk-1.5.1.jar, MultivariateFunction.class
package org.apache.commons.math3.analysis
MultivariateFunction.value ( double[ ] p1 ) [abstract] :  double

cdk-1.5.1.jar, MultivariateFunctionMappingAdapter.class
package org.apache.commons.math3.optimization.direct
MultivariateFunctionMappingAdapter.boundedToUnbounded ( double[ ] point ) :  double[ ]
MultivariateFunctionMappingAdapter.MultivariateFunctionMappingAdapter ( MultivariateFunction bounded, double[ ] lower, double[ ] upper )
MultivariateFunctionMappingAdapter.unboundedToBounded ( double[ ] point ) :  double[ ]
MultivariateFunctionMappingAdapter.value ( double[ ] point ) :  double

cdk-1.5.1.jar, MultivariateFunctionPenaltyAdapter.class
package org.apache.commons.math3.optimization.direct
MultivariateFunctionPenaltyAdapter.MultivariateFunctionPenaltyAdapter ( MultivariateFunction bounded, double[ ] lower, double[ ] upper, double offset, double[ ] scale )
MultivariateFunctionPenaltyAdapter.value ( double[ ] point ) :  double

cdk-1.5.1.jar, MultivariateInterpolator.class
package org.apache.commons.math3.analysis.interpolation
MultivariateInterpolator.interpolate ( double[ ][ ] p1, double[ ] p2 ) [abstract] :  MultivariateFunction

cdk-1.5.1.jar, MultivariateMatrixFunction.class
package org.apache.commons.math3.analysis
MultivariateMatrixFunction.value ( double[ ] p1 ) [abstract] :  double[ ][ ]

cdk-1.5.1.jar, MultivariateMultiStartOptimizer.class
package org.apache.commons.math3.optimization
MultivariateMultiStartOptimizer.MultivariateMultiStartOptimizer ( MultivariateOptimizer optimizer, int starts, RandomVectorGenerator generator )

cdk-1.5.1.jar, MultivariateSummaryStatistics.class
package org.apache.commons.math3.stat.descriptive
MultivariateSummaryStatistics.addValue ( double[ ] value ) :  void
MultivariateSummaryStatistics.clear ( ) :  void
MultivariateSummaryStatistics.equals ( Object object ) :  boolean
MultivariateSummaryStatistics.getCovariance ( ) :  RealMatrix
MultivariateSummaryStatistics.getDimension ( ) :  int
MultivariateSummaryStatistics.getGeoMeanImpl ( ) :  StorelessUnivariateStatistic[ ]
MultivariateSummaryStatistics.getGeometricMean ( ) :  double[ ]
MultivariateSummaryStatistics.getMax ( ) :  double[ ]
MultivariateSummaryStatistics.getMaxImpl ( ) :  StorelessUnivariateStatistic[ ]
MultivariateSummaryStatistics.getMean ( ) :  double[ ]
MultivariateSummaryStatistics.getMeanImpl ( ) :  StorelessUnivariateStatistic[ ]
MultivariateSummaryStatistics.getMin ( ) :  double[ ]
MultivariateSummaryStatistics.getMinImpl ( ) :  StorelessUnivariateStatistic[ ]
MultivariateSummaryStatistics.getN ( ) :  long
MultivariateSummaryStatistics.getStandardDeviation ( ) :  double[ ]
MultivariateSummaryStatistics.getSum ( ) :  double[ ]
MultivariateSummaryStatistics.getSumImpl ( ) :  StorelessUnivariateStatistic[ ]
MultivariateSummaryStatistics.getSumLog ( ) :  double[ ]
MultivariateSummaryStatistics.getSumLogImpl ( ) :  StorelessUnivariateStatistic[ ]
MultivariateSummaryStatistics.getSumSq ( ) :  double[ ]
MultivariateSummaryStatistics.getSumsqImpl ( ) :  StorelessUnivariateStatistic[ ]
MultivariateSummaryStatistics.hashCode ( ) :  int
MultivariateSummaryStatistics.MultivariateSummaryStatistics ( int k, boolean isCovarianceBiasCorrected )
MultivariateSummaryStatistics.setGeoMeanImpl ( StorelessUnivariateStatistic[ ] geoMeanImpl ) :  void
MultivariateSummaryStatistics.setMaxImpl ( StorelessUnivariateStatistic[ ] maxImpl ) :  void
MultivariateSummaryStatistics.setMeanImpl ( StorelessUnivariateStatistic[ ] meanImpl ) :  void
MultivariateSummaryStatistics.setMinImpl ( StorelessUnivariateStatistic[ ] minImpl ) :  void
MultivariateSummaryStatistics.setSumImpl ( StorelessUnivariateStatistic[ ] sumImpl ) :  void
MultivariateSummaryStatistics.setSumLogImpl ( StorelessUnivariateStatistic[ ] sumLogImpl ) :  void
MultivariateSummaryStatistics.setSumsqImpl ( StorelessUnivariateStatistic[ ] sumsqImpl ) :  void
MultivariateSummaryStatistics.toString ( ) :  String

cdk-1.5.1.jar, MultivariateVectorFunction.class
package org.apache.commons.math3.analysis
MultivariateVectorFunction.value ( double[ ] p1 ) [abstract] :  double[ ]

cdk-1.5.1.jar, MutationPolicy.class
package org.apache.commons.math3.genetics
MutationPolicy.mutate ( Chromosome p1 ) [abstract] :  Chromosome

cdk-1.5.1.jar, NaNStrategy.class
package org.apache.commons.math3.stat.ranking
NaNStrategy.valueOf ( String name ) [static] :  NaNStrategy
NaNStrategy.values ( ) [static] :  NaNStrategy[ ]

cdk-1.5.1.jar, NaturalElement.class
package org.openscience.cdk.config
NaturalElement.addListener ( IChemObjectListener col ) :  void
NaturalElement.clone ( ) :  Object
NaturalElement.getAtomicNumber ( ) :  Integer
NaturalElement.getBuilder ( ) :  IChemObjectBuilder
NaturalElement.getFlag ( int flag_type ) :  boolean
NaturalElement.getFlags ( ) :  boolean[ ]
NaturalElement.getFlagValue ( ) :  Number
NaturalElement.getID ( ) :  String
NaturalElement.getListenerCount ( ) :  int
NaturalElement.getNotification ( ) :  boolean
NaturalElement.getProperties ( ) :  Map
NaturalElement.getProperty ( Object description ) :  Object
NaturalElement.getSymbol ( ) :  String
NaturalElement.NaturalElement ( String element, Integer atomicNumber )
NaturalElement.notifyChanged ( ) :  void
NaturalElement.notifyChanged ( IChemObjectChangeEvent evt ) :  void
NaturalElement.removeListener ( IChemObjectListener col ) :  void
NaturalElement.removeProperty ( Object description ) :  void
NaturalElement.setAtomicNumber ( Integer atomicNumber ) :  void
NaturalElement.setFlag ( int flag_type, boolean flag_value ) :  void
NaturalElement.setFlags ( boolean[ ] flagsNew ) :  void
NaturalElement.setID ( String identifier ) :  void
NaturalElement.setNotification ( boolean bool ) :  void
NaturalElement.setProperties ( Map properties ) :  void
NaturalElement.setProperty ( Object description, Object property ) :  void
NaturalElement.setSymbol ( String symbol ) :  void

cdk-1.5.1.jar, NaturalRanking.class
package org.apache.commons.math3.stat.ranking
NaturalRanking.getNanStrategy ( ) :  NaNStrategy
NaturalRanking.getTiesStrategy ( ) :  TiesStrategy
NaturalRanking.NaturalRanking ( )
NaturalRanking.NaturalRanking ( NaNStrategy nanStrategy )
NaturalRanking.NaturalRanking ( NaNStrategy nanStrategy, RandomGenerator randomGenerator )
NaturalRanking.NaturalRanking ( NaNStrategy nanStrategy, TiesStrategy tiesStrategy )
NaturalRanking.NaturalRanking ( RandomGenerator randomGenerator )
NaturalRanking.NaturalRanking ( TiesStrategy tiesStrategy )
NaturalRanking.rank ( double[ ] data ) :  double[ ]

cdk-1.5.1.jar, NelderMeadSimplex.class
package org.apache.commons.math3.optimization.direct
NelderMeadSimplex.iterate ( MultivariateFunction evaluationFunction, Comparator comparator ) :  void
NelderMeadSimplex.NelderMeadSimplex ( double[ ] steps )
NelderMeadSimplex.NelderMeadSimplex ( double[ ] steps, double rho, double khi, double gamma, double sigma )
NelderMeadSimplex.NelderMeadSimplex ( double[ ][ ] referenceSimplex )
NelderMeadSimplex.NelderMeadSimplex ( double[ ][ ] referenceSimplex, double rho, double khi, double gamma, double sigma )
NelderMeadSimplex.NelderMeadSimplex ( int n )
NelderMeadSimplex.NelderMeadSimplex ( int n, double rho, double khi, double gamma, double sigma )
NelderMeadSimplex.NelderMeadSimplex ( int n, double sideLength )
NelderMeadSimplex.NelderMeadSimplex ( int n, double sideLength, double rho, double khi, double gamma, double sigma )

cdk-1.5.1.jar, NevilleInterpolator.class
package org.apache.commons.math3.analysis.interpolation
NevilleInterpolator.interpolate ( double[ ] x, double[ ] y ) :  PolynomialFunctionLagrangeForm
NevilleInterpolator.interpolate ( double[ ] x0, double[ ] x1 ) :  UnivariateFunction
NevilleInterpolator.NevilleInterpolator ( )

cdk-1.5.1.jar, NewtonSolver.class
package org.apache.commons.math3.analysis.solvers
NewtonSolver.doSolve ( ) :  double
NewtonSolver.NewtonSolver ( )
NewtonSolver.NewtonSolver ( double absoluteAccuracy )
NewtonSolver.solve ( int maxEval, DifferentiableUnivariateFunction f, double min, double max ) :  double
NewtonSolver.solve ( int x0, UnivariateFunction x1, double x2, double x3 ) :  double

cdk-1.5.1.jar, NoBracketingException.class
package org.apache.commons.math3.exception
NoBracketingException.getFHi ( ) :  double
NoBracketingException.getFLo ( ) :  double
NoBracketingException.getHi ( ) :  double
NoBracketingException.getLo ( ) :  double
NoBracketingException.NoBracketingException ( double lo, double hi, double fLo, double fHi )
NoBracketingException.NoBracketingException ( Localizable specific, double lo, double hi, double fLo, double fHi, Object[ ] args )

cdk-1.5.1.jar, NoDataException.class
package org.apache.commons.math3.exception
NoDataException.NoDataException ( )
NoDataException.NoDataException ( Localizable specific )

cdk-1.5.1.jar, Node.class
package org.apache.commons.math3.geometry.partitioning.utilities
AVLTree.Node.delete ( ) :  void
AVLTree.Node.getElement ( ) :  Comparable
AVLTree.Node.getNext ( ) :  AVLTree.Node
AVLTree.Node.getPrevious ( ) :  AVLTree.Node

cdk-1.5.1.jar, NoFeasibleSolutionException.class
package org.apache.commons.math3.optimization.linear
NoFeasibleSolutionException.NoFeasibleSolutionException ( )

cdk-1.5.1.jar, NomParser.class
package org.openscience.cdk.iupac.parser
NomParser.NomParser ( InputStream stream, String encoding )
NomParser.ReInit ( InputStream stream, String encoding ) :  void

cdk-1.5.1.jar, NonLinearConjugateGradientOptimizer.class
package org.apache.commons.math3.optimization.general
NonLinearConjugateGradientOptimizer.doOptimize ( ) :  PointValuePair
NonLinearConjugateGradientOptimizer.NonLinearConjugateGradientOptimizer ( ConjugateGradientFormula updateFormula )
NonLinearConjugateGradientOptimizer.NonLinearConjugateGradientOptimizer ( ConjugateGradientFormula updateFormula, ConvergenceChecker checker )
NonLinearConjugateGradientOptimizer.NonLinearConjugateGradientOptimizer ( ConjugateGradientFormula updateFormula, ConvergenceChecker checker, UnivariateSolver lineSearchSolver )
NonLinearConjugateGradientOptimizer.NonLinearConjugateGradientOptimizer ( ConjugateGradientFormula updateFormula, ConvergenceChecker checker, UnivariateSolver lineSearchSolver, Preconditioner preconditioner )
NonLinearConjugateGradientOptimizer.setInitialStep ( double initialStep ) :  void

cdk-1.5.1.jar, NonMonotonicSequenceException.class
package org.apache.commons.math3.exception
NonMonotonicSequenceException.getDirection ( ) :  MathArrays.OrderDirection
NonMonotonicSequenceException.getIndex ( ) :  int
NonMonotonicSequenceException.getPrevious ( ) :  Number
NonMonotonicSequenceException.getStrict ( ) :  boolean
NonMonotonicSequenceException.NonMonotonicSequenceException ( Number wrong, Number previous, int index )
NonMonotonicSequenceException.NonMonotonicSequenceException ( Number wrong, Number previous, int index, MathArrays.OrderDirection direction, boolean strict )

cdk-1.5.1.jar, NonPositiveDefiniteMatrixException.class
package org.apache.commons.math3.linear
NonPositiveDefiniteMatrixException.getColumn ( ) :  int
NonPositiveDefiniteMatrixException.getRow ( ) :  int
NonPositiveDefiniteMatrixException.getThreshold ( ) :  double
NonPositiveDefiniteMatrixException.NonPositiveDefiniteMatrixException ( double wrong, int index, double threshold )

cdk-1.5.1.jar, NonPositiveDefiniteOperatorException.class
package org.apache.commons.math3.linear
NonPositiveDefiniteOperatorException.NonPositiveDefiniteOperatorException ( )

cdk-1.5.1.jar, NonSelfAdjointOperatorException.class
package org.apache.commons.math3.linear
NonSelfAdjointOperatorException.NonSelfAdjointOperatorException ( )

cdk-1.5.1.jar, NonSquareMatrixException.class
package org.apache.commons.math3.linear
NonSquareMatrixException.NonSquareMatrixException ( int wrong, int expected )

cdk-1.5.1.jar, NonSquareOperatorException.class
package org.apache.commons.math3.linear
NonSquareOperatorException.NonSquareOperatorException ( int wrong, int expected )

cdk-1.5.1.jar, NonSymmetricMatrixException.class
package org.apache.commons.math3.linear
NonSymmetricMatrixException.getColumn ( ) :  int
NonSymmetricMatrixException.getRow ( ) :  int
NonSymmetricMatrixException.getThreshold ( ) :  double
NonSymmetricMatrixException.NonSymmetricMatrixException ( int row, int column, double threshold )

cdk-1.5.1.jar, NordsieckStepInterpolator.class
package org.apache.commons.math3.ode.sampling
NordsieckStepInterpolator.computeInterpolatedStateAndDerivatives ( double theta, double oneMinusThetaH ) :  void
NordsieckStepInterpolator.doCopy ( ) :  StepInterpolator
NordsieckStepInterpolator.getInterpolatedStateVariation ( ) :  double[ ]
NordsieckStepInterpolator.NordsieckStepInterpolator ( )
NordsieckStepInterpolator.NordsieckStepInterpolator ( NordsieckStepInterpolator interpolator )
NordsieckStepInterpolator.readExternal ( ObjectInput in ) :  void
NordsieckStepInterpolator.reinitialize ( double time, double stepSize, double[ ] scaledDerivative, Array2DRowRealMatrix nordsieckVector ) :  void
NordsieckStepInterpolator.reinitialize ( double[ ] y, boolean forward, EquationsMapper primaryMapper, EquationsMapper[ ] secondaryMappers ) :  void
NordsieckStepInterpolator.rescale ( double stepSize ) :  void
NordsieckStepInterpolator.writeExternal ( ObjectOutput out ) :  void

cdk-1.5.1.jar, NordsieckTransformer.class
package org.apache.commons.math3.ode
MultistepIntegrator.NordsieckTransformer.initializeHighOrderDerivatives ( double p1, double[ ] p2, double[ ][ ] p3, double[ ][ ] p4 ) [abstract] :  Array2DRowRealMatrix

cdk-1.5.1.jar, NormalDistribution.class
package org.apache.commons.math3.distribution
NormalDistribution.cumulativeProbability ( double x ) :  double
NormalDistribution.cumulativeProbability ( double x0, double x1 ) :  double
NormalDistribution.density ( double x ) :  double
NormalDistribution.getMean ( ) :  double
NormalDistribution.getNumericalMean ( ) :  double
NormalDistribution.getNumericalVariance ( ) :  double
NormalDistribution.getSolverAbsoluteAccuracy ( ) :  double
NormalDistribution.getStandardDeviation ( ) :  double
NormalDistribution.getSupportLowerBound ( ) :  double
NormalDistribution.getSupportUpperBound ( ) :  double
NormalDistribution.isSupportConnected ( ) :  boolean
NormalDistribution.isSupportLowerBoundInclusive ( ) :  boolean
NormalDistribution.isSupportUpperBoundInclusive ( ) :  boolean
NormalDistribution.NormalDistribution ( )
NormalDistribution.NormalDistribution ( double mean, double sd )
NormalDistribution.NormalDistribution ( double mean, double sd, double inverseCumAccuracy )
NormalDistribution.probability ( double x ) :  double
NormalDistribution.sample ( ) :  double

cdk-1.5.1.jar, NormalizedRandomGenerator.class
package org.apache.commons.math3.random
NormalizedRandomGenerator.nextNormalizedDouble ( ) [abstract] :  double

cdk-1.5.1.jar, NotARotationMatrixException.class
package org.apache.commons.math3.geometry.euclidean.threed
NotARotationMatrixException.NotARotationMatrixException ( Localizable specifier, Object[ ] parts )

cdk-1.5.1.jar, NotFiniteNumberException.class
package org.apache.commons.math3.exception
NotFiniteNumberException.NotFiniteNumberException ( Localizable specific, Number wrong, Object[ ] args )
NotFiniteNumberException.NotFiniteNumberException ( Number wrong, Object[ ] args )

cdk-1.5.1.jar, NotPositiveException.class
package org.apache.commons.math3.exception
NotPositiveException.NotPositiveException ( Localizable specific, Number value )
NotPositiveException.NotPositiveException ( Number value )

cdk-1.5.1.jar, NotStrictlyPositiveException.class
package org.apache.commons.math3.exception
NotStrictlyPositiveException.NotStrictlyPositiveException ( Localizable specific, Number value )
NotStrictlyPositiveException.NotStrictlyPositiveException ( Number value )

cdk-1.5.1.jar, NullArgumentException.class
package org.apache.commons.math3.exception
NullArgumentException.NullArgumentException ( )
NullArgumentException.NullArgumentException ( Localizable pattern, Object[ ] arguments )

cdk-1.5.1.jar, NumberIsTooLargeException.class
package org.apache.commons.math3.exception
NumberIsTooLargeException.getBoundIsAllowed ( ) :  boolean
NumberIsTooLargeException.getMax ( ) :  Number
NumberIsTooLargeException.NumberIsTooLargeException ( Localizable specific, Number wrong, Number max, boolean boundIsAllowed )
NumberIsTooLargeException.NumberIsTooLargeException ( Number wrong, Number max, boolean boundIsAllowed )

cdk-1.5.1.jar, NumberIsTooSmallException.class
package org.apache.commons.math3.exception
NumberIsTooSmallException.getBoundIsAllowed ( ) :  boolean
NumberIsTooSmallException.getMin ( ) :  Number
NumberIsTooSmallException.NumberIsTooSmallException ( Localizable specific, Number wrong, Number min, boolean boundIsAllowed )
NumberIsTooSmallException.NumberIsTooSmallException ( Number wrong, Number min, boolean boundIsAllowed )

cdk-1.5.1.jar, NumberTransformer.class
package org.apache.commons.math3.util
NumberTransformer.transform ( Object p1 ) [abstract] :  double

cdk-1.5.1.jar, ODEIntegrator.class
package org.apache.commons.math3.ode
ODEIntegrator.addEventHandler ( EventHandler p1, double p2, double p3, int p4 ) [abstract] :  void
ODEIntegrator.addEventHandler ( EventHandler p1, double p2, double p3, int p4, UnivariateSolver p5 ) [abstract] :  void
ODEIntegrator.addStepHandler ( StepHandler p1 ) [abstract] :  void
ODEIntegrator.clearEventHandlers ( ) [abstract] :  void
ODEIntegrator.clearStepHandlers ( ) [abstract] :  void
ODEIntegrator.getCurrentSignedStepsize ( ) [abstract] :  double
ODEIntegrator.getCurrentStepStart ( ) [abstract] :  double
ODEIntegrator.getEvaluations ( ) [abstract] :  int
ODEIntegrator.getEventHandlers ( ) [abstract] :  Collection
ODEIntegrator.getMaxEvaluations ( ) [abstract] :  int
ODEIntegrator.getName ( ) [abstract] :  String
ODEIntegrator.getStepHandlers ( ) [abstract] :  Collection
ODEIntegrator.setMaxEvaluations ( int p1 ) [abstract] :  void

cdk-1.5.1.jar, OLSMultipleLinearRegression.class
package org.apache.commons.math3.stat.regression
OLSMultipleLinearRegression.calculateAdjustedRSquared ( ) :  double
OLSMultipleLinearRegression.calculateBeta ( ) :  RealVector
OLSMultipleLinearRegression.calculateBetaVariance ( ) :  RealMatrix
OLSMultipleLinearRegression.calculateHat ( ) :  RealMatrix
OLSMultipleLinearRegression.calculateResidualSumOfSquares ( ) :  double
OLSMultipleLinearRegression.calculateRSquared ( ) :  double
OLSMultipleLinearRegression.calculateTotalSumOfSquares ( ) :  double
OLSMultipleLinearRegression.newSampleData ( double[ ] data, int nobs, int nvars ) :  void
OLSMultipleLinearRegression.newSampleData ( double[ ] y, double[ ][ ] x ) :  void
OLSMultipleLinearRegression.newXSampleData ( double[ ][ ] x ) :  void
OLSMultipleLinearRegression.OLSMultipleLinearRegression ( )

cdk-1.5.1.jar, OnePointCrossover.class
package org.apache.commons.math3.genetics
OnePointCrossover.crossover ( Chromosome first, Chromosome second ) :  ChromosomePair
OnePointCrossover.OnePointCrossover ( )

cdk-1.5.1.jar, OneWayAnova.class
package org.apache.commons.math3.stat.inference
OneWayAnova.anovaFValue ( Collection categoryData ) :  double
OneWayAnova.anovaPValue ( Collection categoryData ) :  double
OneWayAnova.anovaTest ( Collection categoryData, double alpha ) :  boolean
OneWayAnova.OneWayAnova ( )

cdk-1.5.1.jar, OpenIntToDoubleHashMap.class
package org.apache.commons.math3.util
OpenIntToDoubleHashMap.containsKey ( int key ) :  boolean
OpenIntToDoubleHashMap.get ( int key ) :  double
OpenIntToDoubleHashMap.iterator ( ) :  OpenIntToDoubleHashMap.Iterator
OpenIntToDoubleHashMap.OpenIntToDoubleHashMap ( )
OpenIntToDoubleHashMap.OpenIntToDoubleHashMap ( double missingEntries )
OpenIntToDoubleHashMap.OpenIntToDoubleHashMap ( int expectedSize )
OpenIntToDoubleHashMap.OpenIntToDoubleHashMap ( int expectedSize, double missingEntries )
OpenIntToDoubleHashMap.OpenIntToDoubleHashMap ( OpenIntToDoubleHashMap source )
OpenIntToDoubleHashMap.put ( int key, double value ) :  double
OpenIntToDoubleHashMap.remove ( int key ) :  double
OpenIntToDoubleHashMap.size ( ) :  int

cdk-1.5.1.jar, OpenIntToFieldHashMap.class
package org.apache.commons.math3.util
OpenIntToFieldHashMap.containsKey ( int key ) :  boolean
OpenIntToFieldHashMap.get ( int key ) :  FieldElement
OpenIntToFieldHashMap.iterator ( ) :  OpenIntToFieldHashMap.Iterator
OpenIntToFieldHashMap.OpenIntToFieldHashMap ( Field field )
OpenIntToFieldHashMap.OpenIntToFieldHashMap ( Field field, FieldElement missingEntries )
OpenIntToFieldHashMap.OpenIntToFieldHashMap ( Field field, int expectedSize )
OpenIntToFieldHashMap.OpenIntToFieldHashMap ( Field field, int expectedSize, FieldElement missingEntries )
OpenIntToFieldHashMap.OpenIntToFieldHashMap ( OpenIntToFieldHashMap source )
OpenIntToFieldHashMap.put ( int key, FieldElement value ) :  FieldElement
OpenIntToFieldHashMap.remove ( int key ) :  FieldElement
OpenIntToFieldHashMap.size ( ) :  int

cdk-1.5.1.jar, OpenMapEntry.class
package org.apache.commons.math3.linear
OpenMapRealVector.OpenMapEntry.getIndex ( ) :  int
OpenMapRealVector.OpenMapEntry.getValue ( ) :  double
OpenMapRealVector.OpenMapEntry.OpenMapRealVector.OpenMapEntry ( OpenMapRealVector iter, OpenIntToDoubleHashMap.Iterator p2 )
OpenMapRealVector.OpenMapEntry.setValue ( double value ) :  void

cdk-1.5.1.jar, OpenMapRealMatrix.class
package org.apache.commons.math3.linear
OpenMapRealMatrix.add ( OpenMapRealMatrix m ) :  OpenMapRealMatrix
OpenMapRealMatrix.addToEntry ( int row, int column, double increment ) :  void
OpenMapRealMatrix.copy ( ) :  OpenMapRealMatrix
OpenMapRealMatrix.copy ( ) :  RealMatrix
OpenMapRealMatrix.createMatrix ( int rowDimension, int columnDimension ) :  OpenMapRealMatrix
OpenMapRealMatrix.createMatrix ( int x0, int x1 ) :  RealMatrix
OpenMapRealMatrix.getColumnDimension ( ) :  int
OpenMapRealMatrix.getEntry ( int row, int column ) :  double
OpenMapRealMatrix.getRowDimension ( ) :  int
OpenMapRealMatrix.multiply ( OpenMapRealMatrix m ) :  OpenMapRealMatrix
OpenMapRealMatrix.multiply ( RealMatrix m ) :  RealMatrix
OpenMapRealMatrix.multiplyEntry ( int row, int column, double factor ) :  void
OpenMapRealMatrix.OpenMapRealMatrix ( int rowDimension, int columnDimension )
OpenMapRealMatrix.OpenMapRealMatrix ( OpenMapRealMatrix matrix )
OpenMapRealMatrix.setEntry ( int row, int column, double value ) :  void
OpenMapRealMatrix.subtract ( OpenMapRealMatrix m ) :  OpenMapRealMatrix
OpenMapRealMatrix.subtract ( RealMatrix m ) :  OpenMapRealMatrix
OpenMapRealMatrix.subtract ( RealMatrix x0 ) :  RealMatrix

cdk-1.5.1.jar, OpenMapRealVector.class
package org.apache.commons.math3.linear
OpenMapRealVector.add ( OpenMapRealVector v ) :  OpenMapRealVector
OpenMapRealVector.add ( RealVector v ) :  RealVector
OpenMapRealVector.append ( double d ) :  OpenMapRealVector
OpenMapRealVector.append ( double x0 ) :  RealVector
OpenMapRealVector.append ( OpenMapRealVector v ) :  OpenMapRealVector
OpenMapRealVector.append ( RealVector v ) :  OpenMapRealVector
OpenMapRealVector.append ( RealVector x0 ) :  RealVector
OpenMapRealVector.copy ( ) :  OpenMapRealVector
OpenMapRealVector.copy ( ) :  RealVector
OpenMapRealVector.dotProduct ( OpenMapRealVector v ) :  double
OpenMapRealVector.dotProduct ( RealVector v ) :  double
OpenMapRealVector.ebeDivide ( RealVector v ) :  OpenMapRealVector
OpenMapRealVector.ebeDivide ( RealVector x0 ) :  RealVector
OpenMapRealVector.ebeMultiply ( RealVector v ) :  OpenMapRealVector
OpenMapRealVector.ebeMultiply ( RealVector x0 ) :  RealVector
OpenMapRealVector.equals ( Object obj ) :  boolean
OpenMapRealVector.getDimension ( ) :  int
OpenMapRealVector.getDistance ( OpenMapRealVector v ) :  double
OpenMapRealVector.getDistance ( RealVector v ) :  double
OpenMapRealVector.getEntry ( int index ) :  double
OpenMapRealVector.getL1Distance ( OpenMapRealVector v ) :  double
OpenMapRealVector.getL1Distance ( RealVector v ) :  double
OpenMapRealVector.getLInfDistance ( RealVector v ) :  double
OpenMapRealVector.getSparsity ( ) :  double
OpenMapRealVector.getSubVector ( int index, int n ) :  OpenMapRealVector
OpenMapRealVector.getSubVector ( int x0, int x1 ) :  RealVector
OpenMapRealVector.hashCode ( ) :  int
OpenMapRealVector.isDefaultValue ( double value ) :  boolean
OpenMapRealVector.isInfinite ( ) :  boolean
OpenMapRealVector.isNaN ( ) :  boolean
OpenMapRealVector.mapAdd ( double d ) :  OpenMapRealVector
OpenMapRealVector.mapAdd ( double x0 ) :  RealVector
OpenMapRealVector.mapAddToSelf ( double d ) :  OpenMapRealVector
OpenMapRealVector.mapAddToSelf ( double x0 ) :  RealVector
OpenMapRealVector.OpenMapRealVector ( )
OpenMapRealVector.OpenMapRealVector ( double[ ] values )
OpenMapRealVector.OpenMapRealVector ( Double[ ] values )
OpenMapRealVector.OpenMapRealVector ( Double[ ] values, double epsilon )
OpenMapRealVector.OpenMapRealVector ( double[ ] values, double epsilon )
OpenMapRealVector.OpenMapRealVector ( int dimension )
OpenMapRealVector.OpenMapRealVector ( int dimension, double epsilon )
OpenMapRealVector.OpenMapRealVector ( int dimension, int expectedSize )
OpenMapRealVector.OpenMapRealVector ( int dimension, int expectedSize, double epsilon )
OpenMapRealVector.OpenMapRealVector ( OpenMapRealVector v )
OpenMapRealVector.OpenMapRealVector ( OpenMapRealVector v, int resize )
OpenMapRealVector.OpenMapRealVector ( RealVector v )
OpenMapRealVector.projection ( RealVector v ) :  RealVector
OpenMapRealVector.set ( double value ) :  void
OpenMapRealVector.setEntry ( int index, double value ) :  void
OpenMapRealVector.setSubVector ( int index, RealVector v ) :  void
OpenMapRealVector.sparseIterator ( ) :  Iterator
OpenMapRealVector.subtract ( OpenMapRealVector v ) :  OpenMapRealVector
OpenMapRealVector.subtract ( RealVector v ) :  RealVector
OpenMapRealVector.toArray ( ) :  double[ ]
OpenMapRealVector.unitize ( ) :  void
OpenMapRealVector.unitVector ( ) :  OpenMapRealVector
OpenMapRealVector.unitVector ( ) :  RealVector

cdk-1.5.1.jar, OpenMapSparseIterator.class
package org.apache.commons.math3.linear
OpenMapRealVector.OpenMapSparseIterator.hasNext ( ) :  boolean
OpenMapRealVector.OpenMapSparseIterator.next ( ) :  Object
OpenMapRealVector.OpenMapSparseIterator.next ( ) :  RealVector.Entry
OpenMapRealVector.OpenMapSparseIterator.OpenMapRealVector.OpenMapSparseIterator ( OpenMapRealVector p1 )
OpenMapRealVector.OpenMapSparseIterator.remove ( ) :  void

cdk-1.5.1.jar, OptionIOSetting.class
package org.openscience.cdk.io.setting
OptionIOSetting.OptionIOSetting ( String name, IOSetting.Importance level, String question, List settings, String defaultSetting )

cdk-1.5.1.jar, Order.class
package org.apache.commons.math3.geometry.partitioning
BSPTreeVisitor.Order.valueOf ( String name ) [static] :  BSPTreeVisitor.Order
BSPTreeVisitor.Order.values ( ) [static] :  BSPTreeVisitor.Order[ ]

cdk-1.5.1.jar, OrderDirection.class
package org.apache.commons.math3.util
MathArrays.OrderDirection.valueOf ( String name ) [static] :  MathArrays.OrderDirection
MathArrays.OrderDirection.values ( ) [static] :  MathArrays.OrderDirection[ ]

cdk-1.5.1.jar, OrderedTuple.class
package org.apache.commons.math3.geometry.partitioning.utilities
OrderedTuple.compareTo ( Object x0 ) :  int
OrderedTuple.compareTo ( OrderedTuple ot ) :  int
OrderedTuple.equals ( Object other ) :  boolean
OrderedTuple.getComponents ( ) :  double[ ]
OrderedTuple.hashCode ( ) :  int
OrderedTuple.OrderedTuple ( double[ ] components )

cdk-1.5.1.jar, OrientedPoint.class
package org.apache.commons.math3.geometry.euclidean.oned
OrientedPoint.copySelf ( ) :  Hyperplane
OrientedPoint.copySelf ( ) :  OrientedPoint
OrientedPoint.getLocation ( ) :  Vector1D
OrientedPoint.getOffset ( Vector point ) :  double
OrientedPoint.isDirect ( ) :  boolean
OrientedPoint.OrientedPoint ( Vector1D location, boolean direct )
OrientedPoint.revertSelf ( ) :  void
OrientedPoint.sameOrientationAs ( Hyperplane other ) :  boolean
OrientedPoint.wholeHyperplane ( ) :  SubHyperplane
OrientedPoint.wholeHyperplane ( ) :  SubOrientedPoint
OrientedPoint.wholeSpace ( ) :  IntervalsSet
OrientedPoint.wholeSpace ( ) :  Region

cdk-1.5.1.jar, OutlineExtractor.class
package org.apache.commons.math3.geometry.euclidean.threed
OutlineExtractor.getOutline ( PolyhedronsSet polyhedronsSet ) :  Vector2D[ ][ ]
OutlineExtractor.OutlineExtractor ( Vector3D u, Vector3D v )

cdk-1.5.1.jar, OutOfRangeException.class
package org.apache.commons.math3.exception
OutOfRangeException.getHi ( ) :  Number
OutOfRangeException.getLo ( ) :  Number
OutOfRangeException.OutOfRangeException ( Localizable specific, Number wrong, Number lo, Number hi )
OutOfRangeException.OutOfRangeException ( Number wrong, Number lo, Number hi )

cdk-1.5.1.jar, Pair.class
package org.apache.commons.math3.util
Pair.equals ( Object o ) :  boolean
Pair.getKey ( ) :  Object
Pair.getValue ( ) :  Object
Pair.hashCode ( ) :  int
Pair.Pair ( Object k, Object v )
Pair.Pair ( Pair entry )

cdk-1.5.1.jar, ParameterGuesser.class
package org.apache.commons.math3.optimization.fitting
GaussianFitter.ParameterGuesser.GaussianFitter.ParameterGuesser ( WeightedObservedPoint[ ] observations )
GaussianFitter.ParameterGuesser.guess ( ) :  double[ ]
HarmonicFitter.ParameterGuesser.guess ( ) :  double[ ]
HarmonicFitter.ParameterGuesser.HarmonicFitter.ParameterGuesser ( WeightedObservedPoint[ ] observations )

cdk-1.5.1.jar, Parameterizable.class
package org.apache.commons.math3.ode
Parameterizable.getParametersNames ( ) [abstract] :  Collection
Parameterizable.isSupported ( String p1 ) [abstract] :  boolean

cdk-1.5.1.jar, ParameterizedODE.class
package org.apache.commons.math3.ode
ParameterizedODE.getParameter ( String p1 ) [abstract] :  double
ParameterizedODE.setParameter ( String p1, double p2 ) [abstract] :  void

cdk-1.5.1.jar, ParameterJacobianProvider.class
package org.apache.commons.math3.ode
ParameterJacobianProvider.computeParameterJacobian ( double p1, double[ ] p2, double[ ] p3, String p4, double[ ] p5 ) [abstract] :  void

cdk-1.5.1.jar, Parametric.class
package org.apache.commons.math3.analysis.function
Gaussian.Parametric.Gaussian.Parametric ( )
Gaussian.Parametric.gradient ( double x, double[ ] param ) :  double[ ]
Gaussian.Parametric.value ( double x, double[ ] param ) :  double
HarmonicOscillator.Parametric.gradient ( double x, double[ ] param ) :  double[ ]
HarmonicOscillator.Parametric.HarmonicOscillator.Parametric ( )
HarmonicOscillator.Parametric.value ( double x, double[ ] param ) :  double
Logistic.Parametric.gradient ( double x, double[ ] param ) :  double[ ]
Logistic.Parametric.Logistic.Parametric ( )
Logistic.Parametric.value ( double x, double[ ] param ) :  double
Logit.Parametric.gradient ( double x, double[ ] param ) :  double[ ]
Logit.Parametric.Logit.Parametric ( )
Logit.Parametric.value ( double x, double[ ] param ) :  double
Sigmoid.Parametric.gradient ( double x, double[ ] param ) :  double[ ]
Sigmoid.Parametric.Sigmoid.Parametric ( )
Sigmoid.Parametric.value ( double x, double[ ] param ) :  double
package org.apache.commons.math3.analysis.polynomials
PolynomialFunction.Parametric.gradient ( double x, double[ ] parameters ) :  double[ ]
PolynomialFunction.Parametric.PolynomialFunction.Parametric ( )
PolynomialFunction.Parametric.value ( double x, double[ ] parameters ) :  double

cdk-1.5.1.jar, ParametricUnivariateFunction.class
package org.apache.commons.math3.analysis
ParametricUnivariateFunction.gradient ( double p1, double[ ] p2 ) [abstract] :  double[ ]
ParametricUnivariateFunction.value ( double p1, double[ ] p2 ) [abstract] :  double

cdk-1.5.1.jar, PartialPiChargeDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
PartialPiChargeDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, PartialSigmaChargeDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
PartialSigmaChargeDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, PartialTChargeMMFF94Descriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
PartialTChargeMMFF94Descriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, PartialTChargePEOEDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
PartialTChargePEOEDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, PascalDistribution.class
package org.apache.commons.math3.distribution
PascalDistribution.cumulativeProbability ( int x ) :  double
PascalDistribution.getNumberOfSuccesses ( ) :  int
PascalDistribution.getNumericalMean ( ) :  double
PascalDistribution.getNumericalVariance ( ) :  double
PascalDistribution.getProbabilityOfSuccess ( ) :  double
PascalDistribution.getSupportLowerBound ( ) :  int
PascalDistribution.getSupportUpperBound ( ) :  int
PascalDistribution.isSupportConnected ( ) :  boolean
PascalDistribution.PascalDistribution ( int r, double p )
PascalDistribution.probability ( int x ) :  double

cdk-1.5.1.jar, PearsonsCorrelation.class
package org.apache.commons.math3.stat.correlation
PearsonsCorrelation.computeCorrelationMatrix ( double[ ][ ] data ) :  RealMatrix
PearsonsCorrelation.computeCorrelationMatrix ( RealMatrix matrix ) :  RealMatrix
PearsonsCorrelation.correlation ( double[ ] xArray, double[ ] yArray ) :  double
PearsonsCorrelation.covarianceToCorrelation ( RealMatrix covarianceMatrix ) :  RealMatrix
PearsonsCorrelation.getCorrelationMatrix ( ) :  RealMatrix
PearsonsCorrelation.getCorrelationPValues ( ) :  RealMatrix
PearsonsCorrelation.getCorrelationStandardErrors ( ) :  RealMatrix
PearsonsCorrelation.PearsonsCorrelation ( )
PearsonsCorrelation.PearsonsCorrelation ( Covariance covariance )
PearsonsCorrelation.PearsonsCorrelation ( double[ ][ ] data )
PearsonsCorrelation.PearsonsCorrelation ( RealMatrix covarianceMatrix, int numberOfObservations )
PearsonsCorrelation.PearsonsCorrelation ( RealMatrix matrix )

cdk-1.5.1.jar, PegasusSolver.class
package org.apache.commons.math3.analysis.solvers
PegasusSolver.PegasusSolver ( )
PegasusSolver.PegasusSolver ( double absoluteAccuracy )
PegasusSolver.PegasusSolver ( double relativeAccuracy, double absoluteAccuracy )
PegasusSolver.PegasusSolver ( double relativeAccuracy, double absoluteAccuracy, double functionValueAccuracy )

cdk-1.5.1.jar, Percentile.class
package org.apache.commons.math3.stat.descriptive.rank
Percentile.copy ( ) :  Percentile
Percentile.copy ( ) :  UnivariateStatistic
Percentile.copy ( Percentile source, Percentile dest ) [static] :  void
Percentile.evaluate ( double p ) :  double
Percentile.evaluate ( double[ ] values, double p ) :  double
Percentile.evaluate ( double[ ] values, int begin, int length, double p ) :  double
Percentile.evaluate ( double[ ] values, int start, int length ) :  double
Percentile.getQuantile ( ) :  double
Percentile.Percentile ( )
Percentile.Percentile ( double p )
Percentile.Percentile ( Percentile original )
Percentile.setData ( double[ ] values ) :  void
Percentile.setData ( double[ ] values, int begin, int length ) :  void
Percentile.setQuantile ( double p ) :  void

cdk-1.5.1.jar, PeriodicTablePositionDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
PeriodicTablePositionDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, PermutationChromosome.class
package org.apache.commons.math3.genetics
PermutationChromosome.decode ( List p1 ) [abstract] :  List

cdk-1.5.1.jar, PetitjeanNumberDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
PetitjeanNumberDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, PetitjeanShapeIndexDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
PetitjeanShapeIndexDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, PiContactDetectionDescriptor.class
package org.openscience.cdk.qsar.descriptors.atompair
PiContactDetectionDescriptor.calculate ( IAtom first, IAtom second, IAtomContainer atomContainer ) :  DescriptorValue
PiContactDetectionDescriptor.getDescriptorNames ( ) :  String[ ]
PiContactDetectionDescriptor.getParameterNames ( ) :  String[ ]
PiContactDetectionDescriptor.getParameters ( ) :  Object[ ]
PiContactDetectionDescriptor.getParameterType ( String name ) :  Object
PiContactDetectionDescriptor.getSpecification ( ) :  DescriptorSpecification
PiContactDetectionDescriptor.getSpecification ( ) :  IImplementationSpecification
PiContactDetectionDescriptor.PiContactDetectionDescriptor ( )
PiContactDetectionDescriptor.setParameters ( Object[ ] params ) :  void

cdk-1.5.1.jar, PiElectronegativityDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
PiElectronegativityDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, Plane.class
package org.apache.commons.math3.geometry.euclidean.threed
Plane.contains ( Vector3D p ) :  boolean
Plane.copySelf ( ) :  Hyperplane
Plane.copySelf ( ) :  Plane
Plane.getNormal ( ) :  Vector3D
Plane.getOffset ( Plane plane ) :  double
Plane.getOffset ( Vector point ) :  double
Plane.getOrigin ( ) :  Vector3D
Plane.getPointAt ( Vector2D inPlane, double offset ) :  Vector3D
Plane.getU ( ) :  Vector3D
Plane.getV ( ) :  Vector3D
Plane.intersection ( Line line ) :  Vector3D
Plane.intersection ( Plane other ) :  Line
Plane.intersection ( Plane plane1, Plane plane2, Plane plane3 ) [static] :  Vector3D
Plane.isSimilarTo ( Plane plane ) :  boolean
Plane.Plane ( Plane plane )
Plane.Plane ( Vector3D normal )
Plane.Plane ( Vector3D p, Vector3D normal )
Plane.Plane ( Vector3D p1, Vector3D p2, Vector3D p3 )
Plane.reset ( Plane original ) :  void
Plane.reset ( Vector3D p, Vector3D normal ) :  void
Plane.revertSelf ( ) :  void
Plane.rotate ( Vector3D center, Rotation rotation ) :  Plane
Plane.sameOrientationAs ( Hyperplane other ) :  boolean
Plane.toSpace ( Vector point ) :  Vector3D
Plane.toSpace ( Vector x0 ) :  Vector
Plane.toSubSpace ( Vector point ) :  Vector2D
Plane.toSubSpace ( Vector x0 ) :  Vector
Plane.translate ( Vector3D translation ) :  Plane
Plane.wholeHyperplane ( ) :  SubHyperplane
Plane.wholeHyperplane ( ) :  SubPlane
Plane.wholeSpace ( ) :  PolyhedronsSet
Plane.wholeSpace ( ) :  Region

cdk-1.5.1.jar, PointValuePair.class
package org.apache.commons.math3.optimization
PointValuePair.getPoint ( ) :  double[ ]
PointValuePair.getPointRef ( ) :  double[ ]
PointValuePair.PointValuePair ( double[ ] point, double value )
PointValuePair.PointValuePair ( double[ ] point, double value, boolean copyArray )

cdk-1.5.1.jar, PointVectorValuePair.class
package org.apache.commons.math3.optimization
PointVectorValuePair.getPoint ( ) :  double[ ]
PointVectorValuePair.getPointRef ( ) :  double[ ]
PointVectorValuePair.getValue ( ) :  double[ ]
PointVectorValuePair.getValue ( ) :  Object
PointVectorValuePair.getValueRef ( ) :  double[ ]
PointVectorValuePair.PointVectorValuePair ( double[ ] point, double[ ] value )
PointVectorValuePair.PointVectorValuePair ( double[ ] point, double[ ] value, boolean copyArray )

cdk-1.5.1.jar, PoissonDistribution.class
package org.apache.commons.math3.distribution
PoissonDistribution.cumulativeProbability ( int x ) :  double
PoissonDistribution.getMean ( ) :  double
PoissonDistribution.getNumericalMean ( ) :  double
PoissonDistribution.getNumericalVariance ( ) :  double
PoissonDistribution.getSupportLowerBound ( ) :  int
PoissonDistribution.getSupportUpperBound ( ) :  int
PoissonDistribution.isSupportConnected ( ) :  boolean
PoissonDistribution.normalApproximateProbability ( int x ) :  double
PoissonDistribution.PoissonDistribution ( double p )
PoissonDistribution.PoissonDistribution ( double p, double epsilon )
PoissonDistribution.PoissonDistribution ( double p, double epsilon, int maxIterations )
PoissonDistribution.PoissonDistribution ( double p, int maxIterations )
PoissonDistribution.probability ( int x ) :  double
PoissonDistribution.sample ( ) :  int

cdk-1.5.1.jar, PolygonsSet.class
package org.apache.commons.math3.geometry.euclidean.twod
PolygonsSet.buildNew ( BSPTree tree ) :  PolygonsSet
PolygonsSet.buildNew ( BSPTree x0 ) :  AbstractRegion
PolygonsSet.buildNew ( BSPTree x0 ) :  Region
PolygonsSet.computeGeometricalProperties ( ) :  void
PolygonsSet.getVertices ( ) :  Vector2D[ ][ ]
PolygonsSet.PolygonsSet ( )
PolygonsSet.PolygonsSet ( BSPTree tree )
PolygonsSet.PolygonsSet ( Collection boundary )
PolygonsSet.PolygonsSet ( double xMin, double xMax, double yMin, double yMax )

cdk-1.5.1.jar, PolyhedronsSet.class
package org.apache.commons.math3.geometry.euclidean.threed
PolyhedronsSet.buildNew ( BSPTree tree ) :  PolyhedronsSet
PolyhedronsSet.buildNew ( BSPTree x0 ) :  AbstractRegion
PolyhedronsSet.buildNew ( BSPTree x0 ) :  Region
PolyhedronsSet.computeGeometricalProperties ( ) :  void
PolyhedronsSet.firstIntersection ( Vector3D point, Line line ) :  SubHyperplane
PolyhedronsSet.PolyhedronsSet ( )
PolyhedronsSet.PolyhedronsSet ( BSPTree tree )
PolyhedronsSet.PolyhedronsSet ( Collection boundary )
PolyhedronsSet.PolyhedronsSet ( double xMin, double xMax, double yMin, double yMax, double zMin, double zMax )
PolyhedronsSet.rotate ( Vector3D center, Rotation rotation ) :  PolyhedronsSet
PolyhedronsSet.translate ( Vector3D translation ) :  PolyhedronsSet

cdk-1.5.1.jar, PolynomialFitter.class
package org.apache.commons.math3.optimization.fitting
PolynomialFitter.fit ( ) :  double[ ]
PolynomialFitter.PolynomialFitter ( int degree, DifferentiableMultivariateVectorOptimizer optimizer )

cdk-1.5.1.jar, PolynomialFunction.class
package org.apache.commons.math3.analysis.polynomials
PolynomialFunction.add ( PolynomialFunction p ) :  PolynomialFunction
PolynomialFunction.degree ( ) :  int
PolynomialFunction.derivative ( ) :  UnivariateFunction
PolynomialFunction.differentiate ( double[ ] coefficients ) [static] :  double[ ]
PolynomialFunction.equals ( Object obj ) :  boolean
PolynomialFunction.evaluate ( double[ ] coefficients, double argument ) [static] :  double
PolynomialFunction.getCoefficients ( ) :  double[ ]
PolynomialFunction.hashCode ( ) :  int
PolynomialFunction.multiply ( PolynomialFunction p ) :  PolynomialFunction
PolynomialFunction.negate ( ) :  PolynomialFunction
PolynomialFunction.polynomialDerivative ( ) :  PolynomialFunction
PolynomialFunction.PolynomialFunction ( double[ ] c )
PolynomialFunction.subtract ( PolynomialFunction p ) :  PolynomialFunction
PolynomialFunction.toString ( ) :  String
PolynomialFunction.value ( double x ) :  double

cdk-1.5.1.jar, PolynomialFunctionLagrangeForm.class
package org.apache.commons.math3.analysis.polynomials
PolynomialFunctionLagrangeForm.computeCoefficients ( ) :  void
PolynomialFunctionLagrangeForm.degree ( ) :  int
PolynomialFunctionLagrangeForm.evaluate ( double[ ] x, double[ ] y, double z ) [static] :  double
PolynomialFunctionLagrangeForm.getCoefficients ( ) :  double[ ]
PolynomialFunctionLagrangeForm.getInterpolatingPoints ( ) :  double[ ]
PolynomialFunctionLagrangeForm.getInterpolatingValues ( ) :  double[ ]
PolynomialFunctionLagrangeForm.PolynomialFunctionLagrangeForm ( double[ ] x, double[ ] y )
PolynomialFunctionLagrangeForm.value ( double z ) :  double
PolynomialFunctionLagrangeForm.verifyInterpolationArray ( double[ ] x, double[ ] y, boolean abort ) [static] :  boolean

cdk-1.5.1.jar, PolynomialFunctionNewtonForm.class
package org.apache.commons.math3.analysis.polynomials
PolynomialFunctionNewtonForm.computeCoefficients ( ) :  void
PolynomialFunctionNewtonForm.degree ( ) :  int
PolynomialFunctionNewtonForm.evaluate ( double[ ] a, double[ ] c, double z ) [static] :  double
PolynomialFunctionNewtonForm.getCenters ( ) :  double[ ]
PolynomialFunctionNewtonForm.getCoefficients ( ) :  double[ ]
PolynomialFunctionNewtonForm.getNewtonCoefficients ( ) :  double[ ]
PolynomialFunctionNewtonForm.PolynomialFunctionNewtonForm ( double[ ] a, double[ ] c )
PolynomialFunctionNewtonForm.value ( double z ) :  double
PolynomialFunctionNewtonForm.verifyInputArray ( double[ ] a, double[ ] c ) [static] :  void

cdk-1.5.1.jar, PolynomialSplineFunction.class
package org.apache.commons.math3.analysis.polynomials
PolynomialSplineFunction.derivative ( ) :  UnivariateFunction
PolynomialSplineFunction.getKnots ( ) :  double[ ]
PolynomialSplineFunction.getN ( ) :  int
PolynomialSplineFunction.getPolynomials ( ) :  PolynomialFunction[ ]
PolynomialSplineFunction.polynomialSplineDerivative ( ) :  PolynomialSplineFunction
PolynomialSplineFunction.PolynomialSplineFunction ( double[ ] knots, PolynomialFunction[ ] polynomials )
PolynomialSplineFunction.value ( double v ) :  double

cdk-1.5.1.jar, PolynomialsUtils.class
package org.apache.commons.math3.analysis.polynomials
PolynomialsUtils.createChebyshevPolynomial ( int degree ) [static] :  PolynomialFunction
PolynomialsUtils.createHermitePolynomial ( int degree ) [static] :  PolynomialFunction
PolynomialsUtils.createJacobiPolynomial ( int degree, int v, int w ) [static] :  PolynomialFunction
PolynomialsUtils.createLaguerrePolynomial ( int degree ) [static] :  PolynomialFunction
PolynomialsUtils.createLegendrePolynomial ( int degree ) [static] :  PolynomialFunction
PolynomialsUtils.shift ( double[ ] coefficients, double shift ) [static] :  double[ ]

cdk-1.5.1.jar, Population.class
package org.apache.commons.math3.genetics
Population.addChromosome ( Chromosome p1 ) [abstract] :  void
Population.getFittestChromosome ( ) [abstract] :  Chromosome
Population.getPopulationLimit ( ) [abstract] :  int
Population.getPopulationSize ( ) [abstract] :  int
Population.nextGeneration ( ) [abstract] :  Population

cdk-1.5.1.jar, Pow.class
package org.apache.commons.math3.analysis.function
Pow.Pow ( )
Pow.value ( double x, double y ) :  double

cdk-1.5.1.jar, PowellOptimizer.class
package org.apache.commons.math3.optimization.direct
PowellOptimizer.doOptimize ( ) :  PointValuePair
PowellOptimizer.PowellOptimizer ( double rel, double abs )
PowellOptimizer.PowellOptimizer ( double rel, double abs, ConvergenceChecker checker )

cdk-1.5.1.jar, Power.class
package org.apache.commons.math3.analysis.function
Power.derivative ( ) :  UnivariateFunction
Power.Power ( double p )
Power.value ( double x ) :  double

cdk-1.5.1.jar, Precision.class
package org.apache.commons.math3.util
Precision.compareTo ( double x, double y, double eps ) [static] :  int
Precision.compareTo ( double x, double y, int maxUlps ) [static] :  int
Precision.equals ( double x, double y ) [static] :  boolean
Precision.equals ( double x, double y, double eps ) [static] :  boolean
Precision.equals ( double x, double y, int maxUlps ) [static] :  boolean
Precision.equals ( float x, float y ) [static] :  boolean
Precision.equals ( float x, float y, float eps ) [static] :  boolean
Precision.equals ( float x, float y, int maxUlps ) [static] :  boolean
Precision.equalsIncludingNaN ( double x, double y ) [static] :  boolean
Precision.equalsIncludingNaN ( double x, double y, double eps ) [static] :  boolean
Precision.equalsIncludingNaN ( double x, double y, int maxUlps ) [static] :  boolean
Precision.equalsIncludingNaN ( float x, float y ) [static] :  boolean
Precision.equalsIncludingNaN ( float x, float y, float eps ) [static] :  boolean
Precision.equalsIncludingNaN ( float x, float y, int maxUlps ) [static] :  boolean
Precision.representableDelta ( double x, double originalDelta ) [static] :  double
Precision.round ( double x, int scale ) [static] :  double
Precision.round ( double x, int scale, int roundingMethod ) [static] :  double
Precision.round ( float x, int scale ) [static] :  float
Precision.round ( float x, int scale, int roundingMethod ) [static] :  float

cdk-1.5.1.jar, PreconditionedIterativeLinearSolver.class
package org.apache.commons.math3.linear
PreconditionedIterativeLinearSolver.checkParameters ( RealLinearOperator a, RealLinearOperator minv, RealVector b, RealVector x0 ) [static] :  void
PreconditionedIterativeLinearSolver.PreconditionedIterativeLinearSolver ( int maxIterations )
PreconditionedIterativeLinearSolver.PreconditionedIterativeLinearSolver ( IterationManager manager )
PreconditionedIterativeLinearSolver.solve ( RealLinearOperator a, RealLinearOperator minv, RealVector b ) :  RealVector
PreconditionedIterativeLinearSolver.solve ( RealLinearOperator a, RealLinearOperator minv, RealVector b, RealVector x0 ) :  RealVector
PreconditionedIterativeLinearSolver.solve ( RealLinearOperator a, RealVector b ) :  RealVector
PreconditionedIterativeLinearSolver.solve ( RealLinearOperator a, RealVector b, RealVector x0 ) :  RealVector
PreconditionedIterativeLinearSolver.solveInPlace ( RealLinearOperator a, RealVector b, RealVector x0 ) :  RealVector
PreconditionedIterativeLinearSolver.solveInPlace ( RealLinearOperator p1, RealLinearOperator p2, RealVector p3, RealVector p4 ) [abstract] :  RealVector

cdk-1.5.1.jar, Preconditioner.class
package org.apache.commons.math3.optimization.general
Preconditioner.precondition ( double[ ] p1, double[ ] p2 ) [abstract] :  double[ ]

cdk-1.5.1.jar, ProcessModel.class
package org.apache.commons.math3.filter
ProcessModel.getControlMatrix ( ) [abstract] :  RealMatrix
ProcessModel.getInitialErrorCovariance ( ) [abstract] :  RealMatrix
ProcessModel.getInitialStateEstimate ( ) [abstract] :  RealVector
ProcessModel.getProcessNoise ( ) [abstract] :  RealMatrix
ProcessModel.getStateTransitionMatrix ( ) [abstract] :  RealMatrix

cdk-1.5.1.jar, Product.class
package org.apache.commons.math3.stat.descriptive.summary
Product.clear ( ) :  void
Product.copy ( ) :  Product
Product.copy ( ) :  StorelessUnivariateStatistic
Product.copy ( ) :  UnivariateStatistic
Product.copy ( Product source, Product dest ) [static] :  void
Product.evaluate ( double[ ] values, double[ ] weights ) :  double
Product.evaluate ( double[ ] values, double[ ] weights, int begin, int length ) :  double
Product.evaluate ( double[ ] values, int begin, int length ) :  double
Product.getN ( ) :  long
Product.getResult ( ) :  double
Product.increment ( double d ) :  void
Product.Product ( )
Product.Product ( Product original )

cdk-1.5.1.jar, ProperBigFractionFormat.class
package org.apache.commons.math3.fraction
ProperBigFractionFormat.format ( BigFraction fraction, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
ProperBigFractionFormat.getWholeFormat ( ) :  NumberFormat
ProperBigFractionFormat.parse ( String source, ParsePosition pos ) :  BigFraction
ProperBigFractionFormat.parse ( String x0, ParsePosition x1 ) :  Number
ProperBigFractionFormat.ProperBigFractionFormat ( )
ProperBigFractionFormat.ProperBigFractionFormat ( NumberFormat format )
ProperBigFractionFormat.ProperBigFractionFormat ( NumberFormat wholeFormat, NumberFormat numeratorFormat, NumberFormat denominatorFormat )
ProperBigFractionFormat.setWholeFormat ( NumberFormat format ) :  void

cdk-1.5.1.jar, ProperFractionFormat.class
package org.apache.commons.math3.fraction
ProperFractionFormat.format ( Fraction fraction, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
ProperFractionFormat.getWholeFormat ( ) :  NumberFormat
ProperFractionFormat.parse ( String source, ParsePosition pos ) :  Fraction
ProperFractionFormat.parse ( String x0, ParsePosition x1 ) :  Number
ProperFractionFormat.ProperFractionFormat ( )
ProperFractionFormat.ProperFractionFormat ( NumberFormat format )
ProperFractionFormat.ProperFractionFormat ( NumberFormat wholeFormat, NumberFormat numeratorFormat, NumberFormat denominatorFormat )
ProperFractionFormat.setWholeFormat ( NumberFormat format ) :  void

cdk-1.5.1.jar, ProtonAffinityHOSEDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
ProtonAffinityHOSEDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, ProtonTotalPartialChargeDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
ProtonTotalPartialChargeDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, PubchemFingerprinter.class
package org.openscience.cdk.fingerprint
PubchemFingerprinter.getBitFingerprint ( IAtomContainer atomContainer ) :  IBitFingerprint
PubchemFingerprinter.getBitFingerprintAsBytes ( ) :  byte[ ]
PubchemFingerprinter.getCountFingerprint ( IAtomContainer container ) :  ICountFingerprint

cdk-1.5.1.jar, QRDecomposition.class
package org.apache.commons.math3.linear
QRDecomposition.getH ( ) :  RealMatrix
QRDecomposition.getQ ( ) :  RealMatrix
QRDecomposition.getQT ( ) :  RealMatrix
QRDecomposition.getR ( ) :  RealMatrix
QRDecomposition.getSolver ( ) :  DecompositionSolver
QRDecomposition.QRDecomposition ( RealMatrix matrix )
QRDecomposition.QRDecomposition ( RealMatrix matrix, double threshold )

cdk-1.5.1.jar, QueryChemObject.class
package org.openscience.cdk.isomorphism.matchers
QueryChemObject.getFlagValue ( ) :  Number
QueryChemObject.getFlagValue ( ) :  Short

cdk-1.5.1.jar, RandomAdaptor.class
package org.apache.commons.math3.random
RandomAdaptor.createAdaptor ( RandomGenerator randomGenerator ) [static] :  Random
RandomAdaptor.nextBoolean ( ) :  boolean
RandomAdaptor.nextBytes ( byte[ ] bytes ) :  void
RandomAdaptor.nextDouble ( ) :  double
RandomAdaptor.nextFloat ( ) :  float
RandomAdaptor.nextGaussian ( ) :  double
RandomAdaptor.nextInt ( ) :  int
RandomAdaptor.nextInt ( int n ) :  int
RandomAdaptor.nextLong ( ) :  long
RandomAdaptor.RandomAdaptor ( RandomGenerator randomGenerator )
RandomAdaptor.setSeed ( int seed ) :  void
RandomAdaptor.setSeed ( int[ ] seed ) :  void
RandomAdaptor.setSeed ( long seed ) :  void

cdk-1.5.1.jar, RandomData.class
package org.apache.commons.math3.random
RandomData.nextExponential ( double p1 ) [abstract] :  double
RandomData.nextGaussian ( double p1, double p2 ) [abstract] :  double
RandomData.nextHexString ( int p1 ) [abstract] :  String
RandomData.nextInt ( int p1, int p2 ) [abstract] :  int
RandomData.nextLong ( long p1, long p2 ) [abstract] :  long
RandomData.nextPermutation ( int p1, int p2 ) [abstract] :  int[ ]
RandomData.nextPoisson ( double p1 ) [abstract] :  long
RandomData.nextSample ( Collection p1, int p2 ) [abstract] :  Object[ ]
RandomData.nextSecureHexString ( int p1 ) [abstract] :  String
RandomData.nextSecureInt ( int p1, int p2 ) [abstract] :  int
RandomData.nextSecureLong ( long p1, long p2 ) [abstract] :  long
RandomData.nextUniform ( double p1, double p2 ) [abstract] :  double
RandomData.nextUniform ( double p1, double p2, boolean p3 ) [abstract] :  double

cdk-1.5.1.jar, RandomDataImpl.class
package org.apache.commons.math3.random
RandomDataImpl.nextBeta ( double alpha, double beta ) :  double
RandomDataImpl.nextBinomial ( int numberOfTrials, double probabilityOfSuccess ) :  int
RandomDataImpl.nextCauchy ( double median, double scale ) :  double
RandomDataImpl.nextChiSquare ( double df ) :  double
RandomDataImpl.nextExponential ( double mean ) :  double
RandomDataImpl.nextF ( double numeratorDf, double denominatorDf ) :  double
RandomDataImpl.nextGamma ( double shape, double scale ) :  double
RandomDataImpl.nextGaussian ( double mu, double sigma ) :  double
RandomDataImpl.nextHexString ( int len ) :  String
RandomDataImpl.nextHypergeometric ( int populationSize, int numberOfSuccesses, int sampleSize ) :  int
RandomDataImpl.nextInt ( int lower, int upper ) :  int
RandomDataImpl.nextInversionDeviate ( IntegerDistribution distribution ) :  int
RandomDataImpl.nextInversionDeviate ( RealDistribution distribution ) :  double
RandomDataImpl.nextLong ( long lower, long upper ) :  long
RandomDataImpl.nextPascal ( int r, double p ) :  int
RandomDataImpl.nextPermutation ( int n, int k ) :  int[ ]
RandomDataImpl.nextPoisson ( double mean ) :  long
RandomDataImpl.nextSample ( Collection c, int k ) :  Object[ ]
RandomDataImpl.nextSecureHexString ( int len ) :  String
RandomDataImpl.nextSecureInt ( int lower, int upper ) :  int
RandomDataImpl.nextSecureLong ( long lower, long upper ) :  long
RandomDataImpl.nextT ( double df ) :  double
RandomDataImpl.nextUniform ( double lower, double upper ) :  double
RandomDataImpl.nextUniform ( double lower, double upper, boolean lowerInclusive ) :  double
RandomDataImpl.nextWeibull ( double shape, double scale ) :  double
RandomDataImpl.nextZipf ( int numberOfElements, double exponent ) :  int
RandomDataImpl.RandomDataImpl ( )
RandomDataImpl.RandomDataImpl ( RandomGenerator rand )
RandomDataImpl.reSeed ( ) :  void
RandomDataImpl.reSeed ( long seed ) :  void
RandomDataImpl.reSeedSecure ( ) :  void
RandomDataImpl.reSeedSecure ( long seed ) :  void
RandomDataImpl.setSecureAlgorithm ( String algorithm, String provider ) :  void

cdk-1.5.1.jar, RandomGenerator.class
package org.apache.commons.math3.random
RandomGenerator.nextBoolean ( ) [abstract] :  boolean
RandomGenerator.nextBytes ( byte[ ] p1 ) [abstract] :  void
RandomGenerator.nextDouble ( ) [abstract] :  double
RandomGenerator.nextFloat ( ) [abstract] :  float
RandomGenerator.nextGaussian ( ) [abstract] :  double
RandomGenerator.nextInt ( ) [abstract] :  int
RandomGenerator.nextInt ( int p1 ) [abstract] :  int
RandomGenerator.nextLong ( ) [abstract] :  long
RandomGenerator.setSeed ( int p1 ) [abstract] :  void
RandomGenerator.setSeed ( int[ ] p1 ) [abstract] :  void
RandomGenerator.setSeed ( long p1 ) [abstract] :  void

cdk-1.5.1.jar, RandomKey.class
package org.apache.commons.math3.genetics
RandomKey.checkValidity ( List chromosomeRepresentation ) :  void
RandomKey.comparatorPermutation ( List data, Comparator comparator ) [static] :  List
RandomKey.decode ( List sequence ) :  List
RandomKey.identityPermutation ( int l ) [static] :  List
RandomKey.inducedPermutation ( List originalData, List permutedData ) [static] :  List
RandomKey.isSame ( Chromosome another ) :  boolean
RandomKey.RandomKey ( Double[ ] representation )
RandomKey.RandomKey ( List representation )
RandomKey.randomPermutation ( int l ) [static] :  List
RandomKey.toString ( ) :  String

cdk-1.5.1.jar, RandomKeyMutation.class
package org.apache.commons.math3.genetics
RandomKeyMutation.mutate ( Chromosome original ) :  Chromosome
RandomKeyMutation.RandomKeyMutation ( )

cdk-1.5.1.jar, RandomNumber.class
package org.openscience.cdk.fingerprint
RandomNumber.generateMersenneTwisterRandomNumber ( int maximum, long hashCode ) [static] :  int
RandomNumber.RandomNumber ( )

cdk-1.5.1.jar, RandomVectorGenerator.class
package org.apache.commons.math3.random
RandomVectorGenerator.nextVector ( ) [abstract] :  double[ ]

cdk-1.5.1.jar, RankingAlgorithm.class
package org.apache.commons.math3.stat.ranking
RankingAlgorithm.rank ( double[ ] p1 ) [abstract] :  double[ ]

cdk-1.5.1.jar, RDFProtonDescriptor_G3R.class
package org.openscience.cdk.qsar.descriptors.atomic
RDFProtonDescriptor_G3R.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, RDFProtonDescriptor_GDR.class
package org.openscience.cdk.qsar.descriptors.atomic
RDFProtonDescriptor_GDR.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, RDFProtonDescriptor_GHR.class
package org.openscience.cdk.qsar.descriptors.atomic
RDFProtonDescriptor_GHR.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, RDFProtonDescriptor_GHR_topol.class
package org.openscience.cdk.qsar.descriptors.atomic
RDFProtonDescriptor_GHR_topol.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, RDFProtonDescriptor_GSR.class
package org.openscience.cdk.qsar.descriptors.atomic
RDFProtonDescriptor_GSR.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, RealDistribution.class
package org.apache.commons.math3.distribution
RealDistribution.cumulativeProbability ( double p1 ) [abstract] :  double
RealDistribution.cumulativeProbability ( double p1, double p2 ) [abstract] :  double
RealDistribution.density ( double p1 ) [abstract] :  double
RealDistribution.getNumericalMean ( ) [abstract] :  double
RealDistribution.getNumericalVariance ( ) [abstract] :  double
RealDistribution.getSupportLowerBound ( ) [abstract] :  double
RealDistribution.getSupportUpperBound ( ) [abstract] :  double
RealDistribution.inverseCumulativeProbability ( double p1 ) [abstract] :  double
RealDistribution.isSupportConnected ( ) [abstract] :  boolean
RealDistribution.isSupportLowerBoundInclusive ( ) [abstract] :  boolean
RealDistribution.isSupportUpperBoundInclusive ( ) [abstract] :  boolean
RealDistribution.probability ( double p1 ) [abstract] :  double
RealDistribution.reseedRandomGenerator ( long p1 ) [abstract] :  void
RealDistribution.sample ( ) [abstract] :  double
RealDistribution.sample ( int p1 ) [abstract] :  double[ ]

cdk-1.5.1.jar, RealLinearOperator.class
package org.apache.commons.math3.linear
RealLinearOperator.getColumnDimension ( ) [abstract] :  int
RealLinearOperator.getRowDimension ( ) [abstract] :  int
RealLinearOperator.isTransposable ( ) :  boolean
RealLinearOperator.operate ( RealVector p1 ) [abstract] :  RealVector
RealLinearOperator.operateTranspose ( RealVector x ) :  RealVector
RealLinearOperator.RealLinearOperator ( )

cdk-1.5.1.jar, RealMatrix.class
package org.apache.commons.math3.linear
RealMatrix.add ( RealMatrix p1 ) [abstract] :  RealMatrix
RealMatrix.addToEntry ( int p1, int p2, double p3 ) [abstract] :  void
RealMatrix.copy ( ) [abstract] :  RealMatrix
RealMatrix.copySubMatrix ( int p1, int p2, int p3, int p4, double[ ][ ] p5 ) [abstract] :  void
RealMatrix.copySubMatrix ( int[ ] p1, int[ ] p2, double[ ][ ] p3 ) [abstract] :  void
RealMatrix.createMatrix ( int p1, int p2 ) [abstract] :  RealMatrix
RealMatrix.getColumn ( int p1 ) [abstract] :  double[ ]
RealMatrix.getColumnMatrix ( int p1 ) [abstract] :  RealMatrix
RealMatrix.getColumnVector ( int p1 ) [abstract] :  RealVector
RealMatrix.getData ( ) [abstract] :  double[ ][ ]
RealMatrix.getEntry ( int p1, int p2 ) [abstract] :  double
RealMatrix.getFrobeniusNorm ( ) [abstract] :  double
RealMatrix.getNorm ( ) [abstract] :  double
RealMatrix.getRow ( int p1 ) [abstract] :  double[ ]
RealMatrix.getRowMatrix ( int p1 ) [abstract] :  RealMatrix
RealMatrix.getRowVector ( int p1 ) [abstract] :  RealVector
RealMatrix.getSubMatrix ( int p1, int p2, int p3, int p4 ) [abstract] :  RealMatrix
RealMatrix.getSubMatrix ( int[ ] p1, int[ ] p2 ) [abstract] :  RealMatrix
RealMatrix.getTrace ( ) [abstract] :  double
RealMatrix.multiply ( RealMatrix p1 ) [abstract] :  RealMatrix
RealMatrix.multiplyEntry ( int p1, int p2, double p3 ) [abstract] :  void
RealMatrix.operate ( double[ ] p1 ) [abstract] :  double[ ]
RealMatrix.operate ( RealVector p1 ) [abstract] :  RealVector
RealMatrix.power ( int p1 ) [abstract] :  RealMatrix
RealMatrix.preMultiply ( double[ ] p1 ) [abstract] :  double[ ]
RealMatrix.preMultiply ( RealMatrix p1 ) [abstract] :  RealMatrix
RealMatrix.preMultiply ( RealVector p1 ) [abstract] :  RealVector
RealMatrix.scalarAdd ( double p1 ) [abstract] :  RealMatrix
RealMatrix.scalarMultiply ( double p1 ) [abstract] :  RealMatrix
RealMatrix.setColumn ( int p1, double[ ] p2 ) [abstract] :  void
RealMatrix.setColumnMatrix ( int p1, RealMatrix p2 ) [abstract] :  void
RealMatrix.setColumnVector ( int p1, RealVector p2 ) [abstract] :  void
RealMatrix.setEntry ( int p1, int p2, double p3 ) [abstract] :  void
RealMatrix.setRow ( int p1, double[ ] p2 ) [abstract] :  void
RealMatrix.setRowMatrix ( int p1, RealMatrix p2 ) [abstract] :  void
RealMatrix.setRowVector ( int p1, RealVector p2 ) [abstract] :  void
RealMatrix.setSubMatrix ( double[ ][ ] p1, int p2, int p3 ) [abstract] :  void
RealMatrix.subtract ( RealMatrix p1 ) [abstract] :  RealMatrix
RealMatrix.transpose ( ) [abstract] :  RealMatrix
RealMatrix.walkInColumnOrder ( RealMatrixChangingVisitor p1 ) [abstract] :  double
RealMatrix.walkInColumnOrder ( RealMatrixChangingVisitor p1, int p2, int p3, int p4, int p5 ) [abstract] :  double
RealMatrix.walkInColumnOrder ( RealMatrixPreservingVisitor p1 ) [abstract] :  double
RealMatrix.walkInColumnOrder ( RealMatrixPreservingVisitor p1, int p2, int p3, int p4, int p5 ) [abstract] :  double
RealMatrix.walkInOptimizedOrder ( RealMatrixChangingVisitor p1 ) [abstract] :  double
RealMatrix.walkInOptimizedOrder ( RealMatrixChangingVisitor p1, int p2, int p3, int p4, int p5 ) [abstract] :  double
RealMatrix.walkInOptimizedOrder ( RealMatrixPreservingVisitor p1 ) [abstract] :  double
RealMatrix.walkInOptimizedOrder ( RealMatrixPreservingVisitor p1, int p2, int p3, int p4, int p5 ) [abstract] :  double
RealMatrix.walkInRowOrder ( RealMatrixChangingVisitor p1 ) [abstract] :  double
RealMatrix.walkInRowOrder ( RealMatrixChangingVisitor p1, int p2, int p3, int p4, int p5 ) [abstract] :  double
RealMatrix.walkInRowOrder ( RealMatrixPreservingVisitor p1 ) [abstract] :  double
RealMatrix.walkInRowOrder ( RealMatrixPreservingVisitor p1, int p2, int p3, int p4, int p5 ) [abstract] :  double

cdk-1.5.1.jar, RealMatrixChangingVisitor.class
package org.apache.commons.math3.linear
RealMatrixChangingVisitor.end ( ) [abstract] :  double
RealMatrixChangingVisitor.start ( int p1, int p2, int p3, int p4, int p5, int p6 ) [abstract] :  void
RealMatrixChangingVisitor.visit ( int p1, int p2, double p3 ) [abstract] :  double

cdk-1.5.1.jar, RealMatrixPreservingVisitor.class
package org.apache.commons.math3.linear
RealMatrixPreservingVisitor.end ( ) [abstract] :  double
RealMatrixPreservingVisitor.start ( int p1, int p2, int p3, int p4, int p5, int p6 ) [abstract] :  void
RealMatrixPreservingVisitor.visit ( int p1, int p2, double p3 ) [abstract] :  void

cdk-1.5.1.jar, RealTransformer.class
package org.apache.commons.math3.transform
RealTransformer.transform ( double[ ] p1, TransformType p2 ) [abstract] :  double[ ]
RealTransformer.transform ( UnivariateFunction p1, double p2, double p3, int p4, TransformType p5 ) [abstract] :  double[ ]

cdk-1.5.1.jar, RealVector.class
package org.apache.commons.math3.linear
RealVector.add ( RealVector v ) :  RealVector
RealVector.addToEntry ( int index, double increment ) :  void
RealVector.append ( double p1 ) [abstract] :  RealVector
RealVector.append ( RealVector p1 ) [abstract] :  RealVector
RealVector.checkIndex ( int index ) :  void
RealVector.checkVectorDimensions ( int n ) :  void
RealVector.checkVectorDimensions ( RealVector v ) :  void
RealVector.combine ( double a, double b, RealVector y ) :  RealVector
RealVector.combineToSelf ( double a, double b, RealVector y ) :  RealVector
RealVector.copy ( ) [abstract] :  RealVector
RealVector.cosine ( RealVector v ) :  double
RealVector.dotProduct ( RealVector v ) :  double
RealVector.ebeDivide ( RealVector p1 ) [abstract] :  RealVector
RealVector.ebeMultiply ( RealVector p1 ) [abstract] :  RealVector
RealVector.getDimension ( ) [abstract] :  int
RealVector.getDistance ( RealVector v ) :  double
RealVector.getEntry ( int p1 ) [abstract] :  double
RealVector.getL1Distance ( RealVector v ) :  double
RealVector.getL1Norm ( ) :  double
RealVector.getLInfDistance ( RealVector v ) :  double
RealVector.getLInfNorm ( ) :  double
RealVector.getMaxIndex ( ) :  int
RealVector.getMaxValue ( ) :  double
RealVector.getMinIndex ( ) :  int
RealVector.getMinValue ( ) :  double
RealVector.getNorm ( ) :  double
RealVector.getSubVector ( int p1, int p2 ) [abstract] :  RealVector
RealVector.isInfinite ( ) [abstract] :  boolean
RealVector.isNaN ( ) [abstract] :  boolean
RealVector.iterator ( ) :  Iterator
RealVector.map ( UnivariateFunction function ) :  RealVector
RealVector.mapAdd ( double d ) :  RealVector
RealVector.mapAddToSelf ( double d ) :  RealVector
RealVector.mapDivide ( double d ) :  RealVector
RealVector.mapDivideToSelf ( double d ) :  RealVector
RealVector.mapMultiply ( double d ) :  RealVector
RealVector.mapMultiplyToSelf ( double d ) :  RealVector
RealVector.mapSubtract ( double d ) :  RealVector
RealVector.mapSubtractToSelf ( double d ) :  RealVector
RealVector.mapToSelf ( UnivariateFunction function ) :  RealVector
RealVector.outerProduct ( RealVector v ) :  RealMatrix
RealVector.projection ( RealVector p1 ) [abstract] :  RealVector
RealVector.RealVector ( )
RealVector.set ( double value ) :  void
RealVector.setEntry ( int p1, double p2 ) [abstract] :  void
RealVector.setSubVector ( int p1, RealVector p2 ) [abstract] :  void
RealVector.sparseIterator ( ) :  Iterator
RealVector.subtract ( RealVector v ) :  RealVector
RealVector.toArray ( ) :  double[ ]
RealVector.unitize ( ) :  void
RealVector.unitVector ( ) :  RealVector
RealVector.unmodifiableRealVector ( RealVector v ) [static] :  RealVector

cdk-1.5.1.jar, RealVectorFormat.class
package org.apache.commons.math3.linear
RealVectorFormat.format ( RealVector v ) :  String
RealVectorFormat.format ( RealVector vector, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
RealVectorFormat.getAvailableLocales ( ) [static] :  Locale[ ]
RealVectorFormat.getFormat ( ) :  NumberFormat
RealVectorFormat.getInstance ( ) [static] :  RealVectorFormat
RealVectorFormat.getInstance ( Locale locale ) [static] :  RealVectorFormat
RealVectorFormat.getPrefix ( ) :  String
RealVectorFormat.getSeparator ( ) :  String
RealVectorFormat.getSuffix ( ) :  String
RealVectorFormat.parse ( String source ) :  ArrayRealVector
RealVectorFormat.parse ( String source, ParsePosition pos ) :  ArrayRealVector
RealVectorFormat.RealVectorFormat ( )
RealVectorFormat.RealVectorFormat ( NumberFormat format )
RealVectorFormat.RealVectorFormat ( String prefix, String suffix, String separator )
RealVectorFormat.RealVectorFormat ( String prefix, String suffix, String separator, NumberFormat format )

cdk-1.5.1.jar, RectangularCholeskyDecomposition.class
package org.apache.commons.math3.linear
RectangularCholeskyDecomposition.getRank ( ) :  int
RectangularCholeskyDecomposition.getRootMatrix ( ) :  RealMatrix
RectangularCholeskyDecomposition.RectangularCholeskyDecomposition ( RealMatrix matrix, double small )

cdk-1.5.1.jar, Region.class
package org.apache.commons.math3.geometry.partitioning
Region.buildNew ( BSPTree p1 ) [abstract] :  Region
Region.checkPoint ( Vector p1 ) [abstract] :  Region.Location
Region.contains ( Region p1 ) [abstract] :  boolean
Region.copySelf ( ) [abstract] :  Region
Region.getBarycenter ( ) [abstract] :  Vector
Region.getBoundarySize ( ) [abstract] :  double
Region.getSize ( ) [abstract] :  double
Region.getTree ( boolean p1 ) [abstract] :  BSPTree
Region.intersection ( SubHyperplane p1 ) [abstract] :  SubHyperplane
Region.isEmpty ( ) [abstract] :  boolean
Region.isEmpty ( BSPTree p1 ) [abstract] :  boolean
Region.side ( Hyperplane p1 ) [abstract] :  Side

cdk-1.5.1.jar, RegionFactory.class
package org.apache.commons.math3.geometry.partitioning
RegionFactory.buildConvex ( Hyperplane[ ] hyperplanes ) :  Region
RegionFactory.difference ( Region region1, Region region2 ) :  Region
RegionFactory.getComplement ( Region region ) :  Region
RegionFactory.intersection ( Region region1, Region region2 ) :  Region
RegionFactory.RegionFactory ( )
RegionFactory.union ( Region region1, Region region2 ) :  Region
RegionFactory.xor ( Region region1, Region region2 ) :  Region

cdk-1.5.1.jar, RegressionResults.class
package org.apache.commons.math3.stat.regression
RegressionResults.getAdjustedRSquared ( ) :  double
RegressionResults.getCovarianceOfParameters ( int i, int j ) :  double
RegressionResults.getErrorSumSquares ( ) :  double
RegressionResults.getMeanSquareError ( ) :  double
RegressionResults.getN ( ) :  long
RegressionResults.getNumberOfParameters ( ) :  int
RegressionResults.getParameterEstimate ( int index ) :  double
RegressionResults.getParameterEstimates ( ) :  double[ ]
RegressionResults.getRegressionSumSquares ( ) :  double
RegressionResults.getRSquared ( ) :  double
RegressionResults.getStdErrorOfEstimate ( int index ) :  double
RegressionResults.getStdErrorOfEstimates ( ) :  double[ ]
RegressionResults.getTotalSumSquares ( ) :  double
RegressionResults.hasIntercept ( ) :  boolean
RegressionResults.RegressionResults ( double[ ] parameters, double[ ][ ] varcov, boolean isSymmetricCompressed, long nobs, int rank, double sumy, double sumysq, double sse, boolean containsConstant, boolean copyData )

cdk-1.5.1.jar, RegulaFalsiSolver.class
package org.apache.commons.math3.analysis.solvers
RegulaFalsiSolver.RegulaFalsiSolver ( )
RegulaFalsiSolver.RegulaFalsiSolver ( double absoluteAccuracy )
RegulaFalsiSolver.RegulaFalsiSolver ( double relativeAccuracy, double absoluteAccuracy )
RegulaFalsiSolver.RegulaFalsiSolver ( double relativeAccuracy, double absoluteAccuracy, double functionValueAccuracy )

cdk-1.5.1.jar, Relationship.class
package org.apache.commons.math3.optimization.linear
Relationship.oppositeRelationship ( ) :  Relationship
Relationship.toString ( ) :  String
Relationship.valueOf ( String name ) [static] :  Relationship
Relationship.values ( ) [static] :  Relationship[ ]

cdk-1.5.1.jar, ResizableDoubleArray.class
package org.apache.commons.math3.util
ResizableDoubleArray.addElement ( double value ) :  void
ResizableDoubleArray.addElementRolling ( double value ) :  double
ResizableDoubleArray.addElements ( double[ ] values ) :  void
ResizableDoubleArray.checkContractExpand ( float contraction, float expansion ) :  void
ResizableDoubleArray.clear ( ) :  void
ResizableDoubleArray.contract ( ) :  void
ResizableDoubleArray.copy ( ) :  ResizableDoubleArray
ResizableDoubleArray.copy ( ResizableDoubleArray source, ResizableDoubleArray dest ) [static] :  void
ResizableDoubleArray.discardFrontElements ( int i ) :  void
ResizableDoubleArray.discardMostRecentElements ( int i ) :  void
ResizableDoubleArray.equals ( Object object ) :  boolean
ResizableDoubleArray.expand ( ) :  void
ResizableDoubleArray.getContractionCriteria ( ) :  float
ResizableDoubleArray.getElement ( int index ) :  double
ResizableDoubleArray.getElements ( ) :  double[ ]
ResizableDoubleArray.getExpansionFactor ( ) :  float
ResizableDoubleArray.getExpansionMode ( ) :  int
ResizableDoubleArray.getInternalValues ( ) :  double[ ]
ResizableDoubleArray.getNumElements ( ) :  int
ResizableDoubleArray.hashCode ( ) :  int
ResizableDoubleArray.ResizableDoubleArray ( )
ResizableDoubleArray.ResizableDoubleArray ( double[ ] initialArray )
ResizableDoubleArray.ResizableDoubleArray ( int initialCapacity )
ResizableDoubleArray.ResizableDoubleArray ( int initialCapacity, float expansionFactor )
ResizableDoubleArray.ResizableDoubleArray ( int initialCapacity, float expansionFactor, float contractionCriteria )
ResizableDoubleArray.ResizableDoubleArray ( int initialCapacity, float expansionFactor, float contractionCriteria, int expansionMode )
ResizableDoubleArray.ResizableDoubleArray ( ResizableDoubleArray original )
ResizableDoubleArray.setContractionCriteria ( float contractionCriteria ) :  void
ResizableDoubleArray.setElement ( int index, double value ) :  void
ResizableDoubleArray.setExpansionFactor ( float expansionFactor ) :  void
ResizableDoubleArray.setExpansionMode ( int expansionMode ) :  void
ResizableDoubleArray.setInitialCapacity ( int initialCapacity ) :  void
ResizableDoubleArray.setNumElements ( int i ) :  void
ResizableDoubleArray.start ( ) :  int
ResizableDoubleArray.substituteMostRecentElement ( double value ) :  double

cdk-1.5.1.jar, RiddersSolver.class
package org.apache.commons.math3.analysis.solvers
RiddersSolver.doSolve ( ) :  double
RiddersSolver.RiddersSolver ( )
RiddersSolver.RiddersSolver ( double absoluteAccuracy )
RiddersSolver.RiddersSolver ( double relativeAccuracy, double absoluteAccuracy )

cdk-1.5.1.jar, Rint.class
package org.apache.commons.math3.analysis.function
Rint.Rint ( )
Rint.value ( double x ) :  double

cdk-1.5.1.jar, RombergIntegrator.class
package org.apache.commons.math3.analysis.integration
RombergIntegrator.doIntegrate ( ) :  double
RombergIntegrator.RombergIntegrator ( )
RombergIntegrator.RombergIntegrator ( double relativeAccuracy, double absoluteAccuracy, int minimalIterationCount, int maximalIterationCount )
RombergIntegrator.RombergIntegrator ( int minimalIterationCount, int maximalIterationCount )

cdk-1.5.1.jar, RootsOfUnity.class
package org.apache.commons.math3.complex
RootsOfUnity.computeRoots ( int n ) :  void
RootsOfUnity.getImaginary ( int k ) :  double
RootsOfUnity.getNumberOfRoots ( ) :  int
RootsOfUnity.getReal ( int k ) :  double
RootsOfUnity.isCounterClockWise ( ) :  boolean
RootsOfUnity.RootsOfUnity ( )

cdk-1.5.1.jar, RotatableBondsCountDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
RotatableBondsCountDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, Rotation.class
package org.apache.commons.math3.geometry.euclidean.threed
Rotation.applyInverseTo ( double[ ] in, double[ ] out ) :  void
Rotation.applyInverseTo ( Rotation r ) :  Rotation
Rotation.applyInverseTo ( Vector3D u ) :  Vector3D
Rotation.applyTo ( double[ ] in, double[ ] out ) :  void
Rotation.applyTo ( Rotation r ) :  Rotation
Rotation.applyTo ( Vector3D u ) :  Vector3D
Rotation.distance ( Rotation r1, Rotation r2 ) [static] :  double
Rotation.getAngle ( ) :  double
Rotation.getAngles ( RotationOrder order ) :  double[ ]
Rotation.getAxis ( ) :  Vector3D
Rotation.getMatrix ( ) :  double[ ][ ]
Rotation.getQ0 ( ) :  double
Rotation.getQ1 ( ) :  double
Rotation.getQ2 ( ) :  double
Rotation.getQ3 ( ) :  double
Rotation.revert ( ) :  Rotation
Rotation.Rotation ( double q0, double q1, double q2, double q3, boolean needsNormalization )
Rotation.Rotation ( double[ ][ ] m, double threshold )
Rotation.Rotation ( RotationOrder order, double alpha1, double alpha2, double alpha3 )
Rotation.Rotation ( Vector3D axis, double angle )
Rotation.Rotation ( Vector3D u, Vector3D v )
Rotation.Rotation ( Vector3D u1, Vector3D u2, Vector3D v1, Vector3D v2 )

cdk-1.5.1.jar, RotationOrder.class
package org.apache.commons.math3.geometry.euclidean.threed
RotationOrder.getA1 ( ) :  Vector3D
RotationOrder.getA2 ( ) :  Vector3D
RotationOrder.getA3 ( ) :  Vector3D
RotationOrder.toString ( ) :  String

cdk-1.5.1.jar, RoundingMode.class
package org.apache.commons.math3.dfp
DfpField.RoundingMode.valueOf ( String name ) [static] :  DfpField.RoundingMode
DfpField.RoundingMode.values ( ) [static] :  DfpField.RoundingMode[ ]

cdk-1.5.1.jar, RuleOfFiveDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
RuleOfFiveDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, RungeKuttaIntegrator.class
package org.apache.commons.math3.ode.nonstiff
RungeKuttaIntegrator.integrate ( ExpandableStatefulODE equations, double t ) :  void
RungeKuttaIntegrator.RungeKuttaIntegrator ( String name, double[ ] c, double[ ][ ] a, double[ ] b, RungeKuttaStepInterpolator prototype, double step )

cdk-1.5.1.jar, SecantSolver.class
package org.apache.commons.math3.analysis.solvers
SecantSolver.doSolve ( ) :  double
SecantSolver.SecantSolver ( )
SecantSolver.SecantSolver ( double absoluteAccuracy )
SecantSolver.SecantSolver ( double relativeAccuracy, double absoluteAccuracy )

cdk-1.5.1.jar, SecondaryEquations.class
package org.apache.commons.math3.ode
SecondaryEquations.computeDerivatives ( double p1, double[ ] p2, double[ ] p3, double[ ] p4, double[ ] p5 ) [abstract] :  void
SecondaryEquations.getDimension ( ) [abstract] :  int

cdk-1.5.1.jar, SecondMoment.class
package org.apache.commons.math3.stat.descriptive.moment
SecondMoment.clear ( ) :  void
SecondMoment.copy ( ) :  FirstMoment
SecondMoment.copy ( ) :  SecondMoment
SecondMoment.copy ( ) :  StorelessUnivariateStatistic
SecondMoment.copy ( ) :  UnivariateStatistic
SecondMoment.copy ( SecondMoment source, SecondMoment dest ) [static] :  void
SecondMoment.getN ( ) :  long
SecondMoment.getResult ( ) :  double
SecondMoment.increment ( double d ) :  void
SecondMoment.SecondMoment ( )
SecondMoment.SecondMoment ( SecondMoment original )

cdk-1.5.1.jar, SecondOrderDifferentialEquations.class
package org.apache.commons.math3.ode
SecondOrderDifferentialEquations.computeSecondDerivatives ( double p1, double[ ] p2, double[ ] p3, double[ ] p4 ) [abstract] :  void
SecondOrderDifferentialEquations.getDimension ( ) [abstract] :  int

cdk-1.5.1.jar, SecondOrderIntegrator.class
package org.apache.commons.math3.ode
SecondOrderIntegrator.integrate ( SecondOrderDifferentialEquations p1, double p2, double[ ] p3, double[ ] p4, double p5, double[ ] p6, double[ ] p7 ) [abstract] :  void

cdk-1.5.1.jar, Segment.class
package org.apache.commons.math3.geometry.euclidean.threed
Segment.getEnd ( ) :  Vector3D
Segment.getLine ( ) :  Line
Segment.getStart ( ) :  Vector3D
Segment.Segment ( Vector3D start, Vector3D end, Line line )
package org.apache.commons.math3.geometry.euclidean.twod
Segment.getEnd ( ) :  Vector2D
Segment.getLine ( ) :  Line
Segment.getStart ( ) :  Vector2D
Segment.Segment ( Vector2D start, Vector2D end, Line line )

cdk-1.5.1.jar, SelectionPolicy.class
package org.apache.commons.math3.genetics
SelectionPolicy.select ( Population p1 ) [abstract] :  ChromosomePair

cdk-1.5.1.jar, SemiVariance.class
package org.apache.commons.math3.stat.descriptive.moment
SemiVariance.copy ( ) :  SemiVariance
SemiVariance.copy ( ) :  UnivariateStatistic
SemiVariance.copy ( SemiVariance source, SemiVariance dest ) [static] :  void
SemiVariance.evaluate ( double[ ] values ) :  double
SemiVariance.evaluate ( double[ ] values, double cutoff ) :  double
SemiVariance.evaluate ( double[ ] values, double cutoff, SemiVariance.Direction direction ) :  double
SemiVariance.evaluate ( double[ ] values, double cutoff, SemiVariance.Direction direction, boolean corrected, int start, int length ) :  double
SemiVariance.evaluate ( double[ ] values, int start, int length ) :  double
SemiVariance.evaluate ( double[ ] values, SemiVariance.Direction direction ) :  double
SemiVariance.getVarianceDirection ( ) :  SemiVariance.Direction
SemiVariance.isBiasCorrected ( ) :  boolean
SemiVariance.SemiVariance ( )
SemiVariance.SemiVariance ( boolean biasCorrected )
SemiVariance.SemiVariance ( boolean corrected, SemiVariance.Direction direction )
SemiVariance.SemiVariance ( SemiVariance original )
SemiVariance.SemiVariance ( SemiVariance.Direction direction )
SemiVariance.setBiasCorrected ( boolean biasCorrected ) :  void
SemiVariance.setVarianceDirection ( SemiVariance.Direction varianceDirection ) :  void

cdk-1.5.1.jar, SettingManager.class
package org.openscience.cdk.io.setting
SettingManager.add ( ISetting setting ) :  ISetting
SettingManager.get ( String name ) :  ISetting
SettingManager.get ( String name, Class c ) :  ISetting
SettingManager.getSettings ( ) :  Collection
SettingManager.has ( String name ) :  boolean
SettingManager.SettingManager ( )
SettingManager.toArray ( ISetting[ ] c ) :  ISetting[ ]

cdk-1.5.1.jar, ShortestPathFingerprinter.class
package org.openscience.cdk.fingerprint
ShortestPathFingerprinter.getBitFingerprint ( IAtomContainer ac ) :  IBitFingerprint
ShortestPathFingerprinter.getCountFingerprint ( IAtomContainer iac ) :  ICountFingerprint
ShortestPathFingerprinter.getRawFingerprint ( IAtomContainer ac ) :  Map
ShortestPathFingerprinter.getSize ( ) :  int
ShortestPathFingerprinter.ShortestPathFingerprinter ( )
ShortestPathFingerprinter.ShortestPathFingerprinter ( int fingerprintLength )

cdk-1.5.1.jar, Side.class
package org.apache.commons.math3.geometry.partitioning
Side.valueOf ( String name ) [static] :  Side
Side.values ( ) [static] :  Side[ ]

cdk-1.5.1.jar, SigmaElectronegativityDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
SigmaElectronegativityDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, Sigmoid.class
package org.apache.commons.math3.analysis.function
Sigmoid.derivative ( ) :  UnivariateFunction
Sigmoid.Sigmoid ( )
Sigmoid.Sigmoid ( double lo, double hi )
Sigmoid.value ( double x ) :  double

cdk-1.5.1.jar, SignatureFingerprinter.class
package org.openscience.cdk.fingerprint
SignatureFingerprinter.getBitFingerprint ( IAtomContainer atomContainer ) :  IBitFingerprint
SignatureFingerprinter.getCountFingerprint ( IAtomContainer container ) :  ICountFingerprint

cdk-1.5.1.jar, Signum.class
package org.apache.commons.math3.analysis.function
Signum.Signum ( )
Signum.value ( double x ) :  double

cdk-1.5.1.jar, SimpleAtomCanonicalisation.class
package org.openscience.cdk.fingerprint
SimpleAtomCanonicalisation.canonicalizeAtoms ( IAtomContainer container ) :  Collection
SimpleAtomCanonicalisation.SimpleAtomCanonicalisation ( )

cdk-1.5.1.jar, SimpleCharStream.class
package org.openscience.cdk.iupac.parser
SimpleCharStream.getTabSize ( int i ) :  int
SimpleCharStream.ReInit ( InputStream dstream, String encoding ) :  void
SimpleCharStream.ReInit ( InputStream dstream, String encoding, int startline, int startcolumn ) :  void
SimpleCharStream.ReInit ( InputStream dstream, String encoding, int startline, int startcolumn, int buffersize ) :  void
SimpleCharStream.setTabSize ( int i ) :  void
SimpleCharStream.SimpleCharStream ( InputStream dstream, String encoding )
SimpleCharStream.SimpleCharStream ( InputStream dstream, String encoding, int startline, int startcolumn )
SimpleCharStream.SimpleCharStream ( InputStream dstream, String encoding, int startline, int startcolumn, int buffersize )
package org.openscience.cdk.smiles.smarts.parser
SimpleCharStream.getTabSize ( int i ) :  int
SimpleCharStream.ReInit ( InputStream dstream, String encoding ) :  void
SimpleCharStream.ReInit ( InputStream dstream, String encoding, int startline, int startcolumn ) :  void
SimpleCharStream.ReInit ( InputStream dstream, String encoding, int startline, int startcolumn, int buffersize ) :  void
SimpleCharStream.setTabSize ( int i ) :  void
SimpleCharStream.SimpleCharStream ( InputStream dstream, String encoding )
SimpleCharStream.SimpleCharStream ( InputStream dstream, String encoding, int startline, int startcolumn )
SimpleCharStream.SimpleCharStream ( InputStream dstream, String encoding, int startline, int startcolumn, int buffersize )

cdk-1.5.1.jar, SimplePointChecker.class
package org.apache.commons.math3.optimization
SimplePointChecker.converged ( int iteration, Pair previous, Pair current ) :  boolean
SimplePointChecker.converged ( int x0, Object x1, Object x2 ) :  boolean
SimplePointChecker.SimplePointChecker ( )
SimplePointChecker.SimplePointChecker ( double relativeThreshold, double absoluteThreshold )

cdk-1.5.1.jar, SimpleRegression.class
package org.apache.commons.math3.stat.regression
SimpleRegression.addData ( double x, double y ) :  void
SimpleRegression.addData ( double[ ][ ] data ) :  void
SimpleRegression.addObservation ( double[ ] x, double y ) :  void
SimpleRegression.addObservations ( double[ ][ ] x, double[ ] y ) :  void
SimpleRegression.clear ( ) :  void
SimpleRegression.getIntercept ( ) :  double
SimpleRegression.getInterceptStdErr ( ) :  double
SimpleRegression.getMeanSquareError ( ) :  double
SimpleRegression.getN ( ) :  long
SimpleRegression.getR ( ) :  double
SimpleRegression.getRegressionSumSquares ( ) :  double
SimpleRegression.getRSquare ( ) :  double
SimpleRegression.getSignificance ( ) :  double
SimpleRegression.getSlope ( ) :  double
SimpleRegression.getSlopeConfidenceInterval ( ) :  double
SimpleRegression.getSlopeConfidenceInterval ( double alpha ) :  double
SimpleRegression.getSlopeStdErr ( ) :  double
SimpleRegression.getSumOfCrossProducts ( ) :  double
SimpleRegression.getSumSquaredErrors ( ) :  double
SimpleRegression.getTotalSumSquares ( ) :  double
SimpleRegression.getXSumSquares ( ) :  double
SimpleRegression.hasIntercept ( ) :  boolean
SimpleRegression.predict ( double x ) :  double
SimpleRegression.regress ( ) :  RegressionResults
SimpleRegression.regress ( int[ ] variablesToInclude ) :  RegressionResults
SimpleRegression.removeData ( double x, double y ) :  void
SimpleRegression.removeData ( double[ ][ ] data ) :  void
SimpleRegression.SimpleRegression ( )
SimpleRegression.SimpleRegression ( boolean includeIntercept )

cdk-1.5.1.jar, SimpleValueChecker.class
package org.apache.commons.math3.optimization
SimpleValueChecker.converged ( int iteration, PointValuePair previous, PointValuePair current ) :  boolean
SimpleValueChecker.converged ( int x0, Object x1, Object x2 ) :  boolean
SimpleValueChecker.SimpleValueChecker ( )
SimpleValueChecker.SimpleValueChecker ( double relativeThreshold, double absoluteThreshold )

cdk-1.5.1.jar, SimpleVectorValueChecker.class
package org.apache.commons.math3.optimization
SimpleVectorValueChecker.converged ( int iteration, PointVectorValuePair previous, PointVectorValuePair current ) :  boolean
SimpleVectorValueChecker.converged ( int x0, Object x1, Object x2 ) :  boolean
SimpleVectorValueChecker.SimpleVectorValueChecker ( )
SimpleVectorValueChecker.SimpleVectorValueChecker ( double relativeThreshold, double absoluteThreshold )

cdk-1.5.1.jar, SimplexOptimizer.class
package org.apache.commons.math3.optimization.direct
SimplexOptimizer.doOptimize ( ) :  PointValuePair
SimplexOptimizer.setSimplex ( AbstractSimplex simplex ) :  void
SimplexOptimizer.SimplexOptimizer ( )
SimplexOptimizer.SimplexOptimizer ( ConvergenceChecker checker )
SimplexOptimizer.SimplexOptimizer ( double rel, double abs )

cdk-1.5.1.jar, SimplexSolver.class
package org.apache.commons.math3.optimization.linear
SimplexSolver.doIteration ( SimplexTableau tableau ) :  void
SimplexSolver.doOptimize ( ) :  PointValuePair
SimplexSolver.SimplexSolver ( )
SimplexSolver.SimplexSolver ( double epsilon, int maxUlps )
SimplexSolver.solvePhase1 ( SimplexTableau tableau ) :  void

cdk-1.5.1.jar, SimpsonIntegrator.class
package org.apache.commons.math3.analysis.integration
SimpsonIntegrator.doIntegrate ( ) :  double
SimpsonIntegrator.SimpsonIntegrator ( )
SimpsonIntegrator.SimpsonIntegrator ( double relativeAccuracy, double absoluteAccuracy, int minimalIterationCount, int maximalIterationCount )
SimpsonIntegrator.SimpsonIntegrator ( int minimalIterationCount, int maximalIterationCount )

cdk-1.5.1.jar, Sin.class
package org.apache.commons.math3.analysis.function
Sin.derivative ( ) :  DifferentiableUnivariateFunction
Sin.derivative ( ) :  UnivariateFunction
Sin.Sin ( )
Sin.value ( double x ) :  double

cdk-1.5.1.jar, Sinc.class
package org.apache.commons.math3.analysis.function
Sinc.derivative ( ) :  UnivariateFunction
Sinc.Sinc ( )
Sinc.Sinc ( boolean normalized )
Sinc.value ( double x ) :  double

cdk-1.5.1.jar, SingularMatrixException.class
package org.apache.commons.math3.linear
SingularMatrixException.SingularMatrixException ( )

cdk-1.5.1.jar, SingularOperatorException.class
package org.apache.commons.math3.linear
SingularOperatorException.SingularOperatorException ( )

cdk-1.5.1.jar, SingularValueDecomposition.class
package org.apache.commons.math3.linear
SingularValueDecomposition.getConditionNumber ( ) :  double
SingularValueDecomposition.getCovariance ( double minSingularValue ) :  RealMatrix
SingularValueDecomposition.getInverseConditionNumber ( ) :  double
SingularValueDecomposition.getNorm ( ) :  double
SingularValueDecomposition.getRank ( ) :  int
SingularValueDecomposition.getS ( ) :  RealMatrix
SingularValueDecomposition.getSingularValues ( ) :  double[ ]
SingularValueDecomposition.getSolver ( ) :  DecompositionSolver
SingularValueDecomposition.getU ( ) :  RealMatrix
SingularValueDecomposition.getUT ( ) :  RealMatrix
SingularValueDecomposition.getV ( ) :  RealMatrix
SingularValueDecomposition.getVT ( ) :  RealMatrix
SingularValueDecomposition.SingularValueDecomposition ( RealMatrix matrix )

cdk-1.5.1.jar, Sinh.class
package org.apache.commons.math3.analysis.function
Sinh.derivative ( ) :  DifferentiableUnivariateFunction
Sinh.derivative ( ) :  UnivariateFunction
Sinh.Sinh ( )
Sinh.value ( double x ) :  double

cdk-1.5.1.jar, Skewness.class
package org.apache.commons.math3.stat.descriptive.moment
Skewness.clear ( ) :  void
Skewness.copy ( ) :  Skewness
Skewness.copy ( ) :  StorelessUnivariateStatistic
Skewness.copy ( ) :  UnivariateStatistic
Skewness.copy ( Skewness source, Skewness dest ) [static] :  void
Skewness.evaluate ( double[ ] values, int begin, int length ) :  double
Skewness.getN ( ) :  long
Skewness.getResult ( ) :  double
Skewness.increment ( double d ) :  void
Skewness.Skewness ( )
Skewness.Skewness ( Skewness original )
Skewness.Skewness ( ThirdMoment m3 )

cdk-1.5.1.jar, SMARTSParser.class
package org.openscience.cdk.smiles.smarts.parser
SMARTSParser.ReInit ( InputStream stream, String encoding ) :  void
SMARTSParser.SMARTSParser ( InputStream stream, String encoding )

cdk-1.5.1.jar, SmoothingPolynomialBicubicSplineInterpolator.class
package org.apache.commons.math3.analysis.interpolation
SmoothingPolynomialBicubicSplineInterpolator.interpolate ( double[ ] x0, double[ ] x1, double[ ][ ] x2 ) :  BivariateFunction
SmoothingPolynomialBicubicSplineInterpolator.interpolate ( double[ ] xval, double[ ] yval, double[ ][ ] fval ) :  BicubicSplineInterpolatingFunction
SmoothingPolynomialBicubicSplineInterpolator.SmoothingPolynomialBicubicSplineInterpolator ( )
SmoothingPolynomialBicubicSplineInterpolator.SmoothingPolynomialBicubicSplineInterpolator ( int degree )
SmoothingPolynomialBicubicSplineInterpolator.SmoothingPolynomialBicubicSplineInterpolator ( int xDegree, int yDegree )

cdk-1.5.1.jar, Space.class
package org.apache.commons.math3.geometry
Space.getDimension ( ) [abstract] :  int
Space.getSubSpace ( ) [abstract] :  Space

cdk-1.5.1.jar, SparseEntryIterator.class
package org.apache.commons.math3.linear
RealVector.SparseEntryIterator.advance ( RealVector.Entry e ) :  void
RealVector.SparseEntryIterator.hasNext ( ) :  boolean
RealVector.SparseEntryIterator.next ( ) :  Object
RealVector.SparseEntryIterator.next ( ) :  RealVector.Entry
RealVector.SparseEntryIterator.RealVector.SparseEntryIterator ( RealVector p1 )
RealVector.SparseEntryIterator.remove ( ) :  void

cdk-1.5.1.jar, SparseFieldMatrix.class
package org.apache.commons.math3.linear
SparseFieldMatrix.addToEntry ( int row, int column, FieldElement increment ) :  void
SparseFieldMatrix.copy ( ) :  FieldMatrix
SparseFieldMatrix.createMatrix ( int rowDimension, int columnDimension ) :  FieldMatrix
SparseFieldMatrix.getColumnDimension ( ) :  int
SparseFieldMatrix.getEntry ( int row, int column ) :  FieldElement
SparseFieldMatrix.getRowDimension ( ) :  int
SparseFieldMatrix.multiplyEntry ( int row, int column, FieldElement factor ) :  void
SparseFieldMatrix.setEntry ( int row, int column, FieldElement value ) :  void
SparseFieldMatrix.SparseFieldMatrix ( Field field )
SparseFieldMatrix.SparseFieldMatrix ( Field field, int rowDimension, int columnDimension )
SparseFieldMatrix.SparseFieldMatrix ( FieldMatrix other )
SparseFieldMatrix.SparseFieldMatrix ( SparseFieldMatrix other )

cdk-1.5.1.jar, SparseFieldVector.class
package org.apache.commons.math3.linear
SparseFieldVector.add ( FieldVector v ) :  FieldVector
SparseFieldVector.add ( SparseFieldVector v ) :  FieldVector
SparseFieldVector.append ( FieldElement d ) :  FieldVector
SparseFieldVector.append ( FieldVector v ) :  FieldVector
SparseFieldVector.append ( SparseFieldVector v ) :  FieldVector
SparseFieldVector.checkVectorDimensions ( int n ) :  void
SparseFieldVector.copy ( ) :  FieldVector
SparseFieldVector.dotProduct ( FieldVector v ) :  FieldElement
SparseFieldVector.ebeDivide ( FieldVector v ) :  FieldVector
SparseFieldVector.ebeMultiply ( FieldVector v ) :  FieldVector
SparseFieldVector.equals ( Object obj ) :  boolean
SparseFieldVector.getData ( ) :  FieldElement[ ]
SparseFieldVector.getDimension ( ) :  int
SparseFieldVector.getEntry ( int index ) :  FieldElement
SparseFieldVector.getField ( ) :  Field
SparseFieldVector.getSubVector ( int index, int n ) :  FieldVector
SparseFieldVector.hashCode ( ) :  int
SparseFieldVector.mapAdd ( FieldElement d ) :  FieldVector
SparseFieldVector.mapAddToSelf ( FieldElement d ) :  FieldVector
SparseFieldVector.mapDivide ( FieldElement d ) :  FieldVector
SparseFieldVector.mapDivideToSelf ( FieldElement d ) :  FieldVector
SparseFieldVector.mapInv ( ) :  FieldVector
SparseFieldVector.mapInvToSelf ( ) :  FieldVector
SparseFieldVector.mapMultiply ( FieldElement d ) :  FieldVector
SparseFieldVector.mapMultiplyToSelf ( FieldElement d ) :  FieldVector
SparseFieldVector.mapSubtract ( FieldElement d ) :  FieldVector
SparseFieldVector.mapSubtractToSelf ( FieldElement d ) :  FieldVector
SparseFieldVector.outerProduct ( FieldVector v ) :  FieldMatrix
SparseFieldVector.outerProduct ( SparseFieldVector v ) :  FieldMatrix
SparseFieldVector.projection ( FieldVector v ) :  FieldVector
SparseFieldVector.set ( FieldElement value ) :  void
SparseFieldVector.setEntry ( int index, FieldElement value ) :  void
SparseFieldVector.setSubVector ( int index, FieldVector v ) :  void
SparseFieldVector.SparseFieldVector ( Field field )
SparseFieldVector.SparseFieldVector ( Field field, FieldElement[ ] values )
SparseFieldVector.SparseFieldVector ( Field field, int dimension )
SparseFieldVector.SparseFieldVector ( Field field, int dimension, int expectedSize )
SparseFieldVector.SparseFieldVector ( SparseFieldVector v )
SparseFieldVector.SparseFieldVector ( SparseFieldVector v, int resize )
SparseFieldVector.subtract ( FieldVector v ) :  FieldVector
SparseFieldVector.subtract ( SparseFieldVector v ) :  SparseFieldVector
SparseFieldVector.toArray ( ) :  FieldElement[ ]

cdk-1.5.1.jar, SparseRealVector.class
package org.apache.commons.math3.linear
SparseRealVector.SparseRealVector ( )

cdk-1.5.1.jar, SpearmansCorrelation.class
package org.apache.commons.math3.stat.correlation
SpearmansCorrelation.computeCorrelationMatrix ( double[ ][ ] matrix ) :  RealMatrix
SpearmansCorrelation.computeCorrelationMatrix ( RealMatrix matrix ) :  RealMatrix
SpearmansCorrelation.correlation ( double[ ] xArray, double[ ] yArray ) :  double
SpearmansCorrelation.getCorrelationMatrix ( ) :  RealMatrix
SpearmansCorrelation.getRankCorrelation ( ) :  PearsonsCorrelation
SpearmansCorrelation.SpearmansCorrelation ( )
SpearmansCorrelation.SpearmansCorrelation ( RealMatrix dataMatrix )
SpearmansCorrelation.SpearmansCorrelation ( RealMatrix dataMatrix, RankingAlgorithm rankingAlgorithm )

cdk-1.5.1.jar, SplineInterpolator.class
package org.apache.commons.math3.analysis.interpolation
SplineInterpolator.interpolate ( double[ ] x, double[ ] y ) :  PolynomialSplineFunction
SplineInterpolator.interpolate ( double[ ] x0, double[ ] x1 ) :  UnivariateFunction
SplineInterpolator.SplineInterpolator ( )

cdk-1.5.1.jar, SplitSubHyperplane.class
package org.apache.commons.math3.geometry.partitioning
SubHyperplane.SplitSubHyperplane.getMinus ( ) :  SubHyperplane
SubHyperplane.SplitSubHyperplane.getPlus ( ) :  SubHyperplane
SubHyperplane.SplitSubHyperplane.SubHyperplane.SplitSubHyperplane ( SubHyperplane plus, SubHyperplane minus )

cdk-1.5.1.jar, Sqrt.class
package org.apache.commons.math3.analysis.function
Sqrt.derivative ( ) :  UnivariateFunction
Sqrt.Sqrt ( )
Sqrt.value ( double x ) :  double

cdk-1.5.1.jar, StabilizationPlusChargeDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
StabilizationPlusChargeDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, StableRandomGenerator.class
package org.apache.commons.math3.random
StableRandomGenerator.nextNormalizedDouble ( ) :  double
StableRandomGenerator.StableRandomGenerator ( RandomGenerator generator, double alpha, double beta )

cdk-1.5.1.jar, StandardDeviation.class
package org.apache.commons.math3.stat.descriptive.moment
StandardDeviation.clear ( ) :  void
StandardDeviation.copy ( ) :  StandardDeviation
StandardDeviation.copy ( ) :  StorelessUnivariateStatistic
StandardDeviation.copy ( ) :  UnivariateStatistic
StandardDeviation.copy ( StandardDeviation source, StandardDeviation dest ) [static] :  void
StandardDeviation.evaluate ( double[ ] values ) :  double
StandardDeviation.evaluate ( double[ ] values, double mean ) :  double
StandardDeviation.evaluate ( double[ ] values, double mean, int begin, int length ) :  double
StandardDeviation.evaluate ( double[ ] values, int begin, int length ) :  double
StandardDeviation.getN ( ) :  long
StandardDeviation.getResult ( ) :  double
StandardDeviation.increment ( double d ) :  void
StandardDeviation.isBiasCorrected ( ) :  boolean
StandardDeviation.setBiasCorrected ( boolean isBiasCorrected ) :  void
StandardDeviation.StandardDeviation ( )
StandardDeviation.StandardDeviation ( boolean isBiasCorrected )
StandardDeviation.StandardDeviation ( boolean isBiasCorrected, SecondMoment m2 )
StandardDeviation.StandardDeviation ( SecondMoment m2 )
StandardDeviation.StandardDeviation ( StandardDeviation original )

cdk-1.5.1.jar, StatisticalMultivariateSummary.class
package org.apache.commons.math3.stat.descriptive
StatisticalMultivariateSummary.getCovariance ( ) [abstract] :  RealMatrix
StatisticalMultivariateSummary.getDimension ( ) [abstract] :  int
StatisticalMultivariateSummary.getGeometricMean ( ) [abstract] :  double[ ]
StatisticalMultivariateSummary.getMax ( ) [abstract] :  double[ ]
StatisticalMultivariateSummary.getMean ( ) [abstract] :  double[ ]
StatisticalMultivariateSummary.getMin ( ) [abstract] :  double[ ]
StatisticalMultivariateSummary.getN ( ) [abstract] :  long
StatisticalMultivariateSummary.getStandardDeviation ( ) [abstract] :  double[ ]
StatisticalMultivariateSummary.getSum ( ) [abstract] :  double[ ]
StatisticalMultivariateSummary.getSumLog ( ) [abstract] :  double[ ]
StatisticalMultivariateSummary.getSumSq ( ) [abstract] :  double[ ]

cdk-1.5.1.jar, StatisticalSummary.class
package org.apache.commons.math3.stat.descriptive
StatisticalSummary.getMax ( ) [abstract] :  double
StatisticalSummary.getMean ( ) [abstract] :  double
StatisticalSummary.getMin ( ) [abstract] :  double
StatisticalSummary.getN ( ) [abstract] :  long
StatisticalSummary.getStandardDeviation ( ) [abstract] :  double
StatisticalSummary.getSum ( ) [abstract] :  double
StatisticalSummary.getVariance ( ) [abstract] :  double

cdk-1.5.1.jar, StatisticalSummaryValues.class
package org.apache.commons.math3.stat.descriptive
StatisticalSummaryValues.equals ( Object object ) :  boolean
StatisticalSummaryValues.getMax ( ) :  double
StatisticalSummaryValues.getMean ( ) :  double
StatisticalSummaryValues.getMin ( ) :  double
StatisticalSummaryValues.getN ( ) :  long
StatisticalSummaryValues.getStandardDeviation ( ) :  double
StatisticalSummaryValues.getSum ( ) :  double
StatisticalSummaryValues.getVariance ( ) :  double
StatisticalSummaryValues.hashCode ( ) :  int
StatisticalSummaryValues.StatisticalSummaryValues ( double mean, double variance, long n, double max, double min, double sum )
StatisticalSummaryValues.toString ( ) :  String

cdk-1.5.1.jar, StatUtils.class
package org.apache.commons.math3.stat
StatUtils.geometricMean ( double[ ] values ) [static] :  double
StatUtils.geometricMean ( double[ ] values, int begin, int length ) [static] :  double
StatUtils.max ( double[ ] values ) [static] :  double
StatUtils.max ( double[ ] values, int begin, int length ) [static] :  double
StatUtils.mean ( double[ ] values ) [static] :  double
StatUtils.mean ( double[ ] values, int begin, int length ) [static] :  double
StatUtils.meanDifference ( double[ ] sample1, double[ ] sample2 ) [static] :  double
StatUtils.min ( double[ ] values ) [static] :  double
StatUtils.min ( double[ ] values, int begin, int length ) [static] :  double
StatUtils.normalize ( double[ ] sample ) [static] :  double[ ]
StatUtils.percentile ( double[ ] values, double p ) [static] :  double
StatUtils.percentile ( double[ ] values, int begin, int length, double p ) [static] :  double
StatUtils.populationVariance ( double[ ] values ) [static] :  double
StatUtils.populationVariance ( double[ ] values, double mean ) [static] :  double
StatUtils.populationVariance ( double[ ] values, double mean, int begin, int length ) [static] :  double
StatUtils.populationVariance ( double[ ] values, int begin, int length ) [static] :  double
StatUtils.product ( double[ ] values ) [static] :  double
StatUtils.product ( double[ ] values, int begin, int length ) [static] :  double
StatUtils.sum ( double[ ] values ) [static] :  double
StatUtils.sum ( double[ ] values, int begin, int length ) [static] :  double
StatUtils.sumDifference ( double[ ] sample1, double[ ] sample2 ) [static] :  double
StatUtils.sumLog ( double[ ] values ) [static] :  double
StatUtils.sumLog ( double[ ] values, int begin, int length ) [static] :  double
StatUtils.sumSq ( double[ ] values ) [static] :  double
StatUtils.sumSq ( double[ ] values, int begin, int length ) [static] :  double
StatUtils.variance ( double[ ] values ) [static] :  double
StatUtils.variance ( double[ ] values, double mean ) [static] :  double
StatUtils.variance ( double[ ] values, double mean, int begin, int length ) [static] :  double
StatUtils.variance ( double[ ] values, int begin, int length ) [static] :  double
StatUtils.varianceDifference ( double[ ] sample1, double[ ] sample2, double meanDifference ) [static] :  double

cdk-1.5.1.jar, StepFunction.class
package org.apache.commons.math3.analysis.function
StepFunction.StepFunction ( double[ ] x, double[ ] y )
StepFunction.value ( double x ) :  double

cdk-1.5.1.jar, StepHandler.class
package org.apache.commons.math3.ode.sampling
StepHandler.handleStep ( StepInterpolator p1, boolean p2 ) [abstract] :  void
StepHandler.init ( double p1, double[ ] p2, double p3 ) [abstract] :  void

cdk-1.5.1.jar, StepInterpolator.class
package org.apache.commons.math3.ode.sampling
StepInterpolator.copy ( ) [abstract] :  StepInterpolator
StepInterpolator.getCurrentTime ( ) [abstract] :  double
StepInterpolator.getInterpolatedDerivatives ( ) [abstract] :  double[ ]
StepInterpolator.getInterpolatedSecondaryDerivatives ( int p1 ) [abstract] :  double[ ]
StepInterpolator.getInterpolatedSecondaryState ( int p1 ) [abstract] :  double[ ]
StepInterpolator.getInterpolatedState ( ) [abstract] :  double[ ]
StepInterpolator.getInterpolatedTime ( ) [abstract] :  double
StepInterpolator.getPreviousTime ( ) [abstract] :  double
StepInterpolator.isForward ( ) [abstract] :  boolean
StepInterpolator.setInterpolatedTime ( double p1 ) [abstract] :  void

cdk-1.5.1.jar, StepNormalizer.class
package org.apache.commons.math3.ode.sampling
StepNormalizer.handleStep ( StepInterpolator interpolator, boolean isLast ) :  void
StepNormalizer.init ( double t0, double[ ] y0, double t ) :  void
StepNormalizer.StepNormalizer ( double h, FixedStepHandler handler )
StepNormalizer.StepNormalizer ( double h, FixedStepHandler handler, StepNormalizerBounds bounds )
StepNormalizer.StepNormalizer ( double h, FixedStepHandler handler, StepNormalizerMode mode )
StepNormalizer.StepNormalizer ( double h, FixedStepHandler handler, StepNormalizerMode mode, StepNormalizerBounds bounds )

cdk-1.5.1.jar, StepNormalizerBounds.class
package org.apache.commons.math3.ode.sampling
StepNormalizerBounds.firstIncluded ( ) :  boolean
StepNormalizerBounds.lastIncluded ( ) :  boolean
StepNormalizerBounds.valueOf ( String name ) [static] :  StepNormalizerBounds
StepNormalizerBounds.values ( ) [static] :  StepNormalizerBounds[ ]

cdk-1.5.1.jar, StepNormalizerMode.class
package org.apache.commons.math3.ode.sampling
StepNormalizerMode.valueOf ( String name ) [static] :  StepNormalizerMode
StepNormalizerMode.values ( ) [static] :  StepNormalizerMode[ ]

cdk-1.5.1.jar, StoppingCondition.class
package org.apache.commons.math3.genetics
StoppingCondition.isSatisfied ( Population p1 ) [abstract] :  boolean

cdk-1.5.1.jar, StorelessCovariance.class
package org.apache.commons.math3.stat.correlation
StorelessCovariance.getCovariance ( int xIndex, int yIndex ) :  double
StorelessCovariance.getCovarianceMatrix ( ) :  RealMatrix
StorelessCovariance.getData ( ) :  double[ ][ ]
StorelessCovariance.getN ( ) :  int
StorelessCovariance.increment ( double[ ] data ) :  void
StorelessCovariance.StorelessCovariance ( int dim )
StorelessCovariance.StorelessCovariance ( int dim, boolean biasCorrected )

cdk-1.5.1.jar, StorelessUnivariateStatistic.class
package org.apache.commons.math3.stat.descriptive
StorelessUnivariateStatistic.clear ( ) [abstract] :  void
StorelessUnivariateStatistic.copy ( ) [abstract] :  StorelessUnivariateStatistic
StorelessUnivariateStatistic.getN ( ) [abstract] :  long
StorelessUnivariateStatistic.getResult ( ) [abstract] :  double
StorelessUnivariateStatistic.increment ( double p1 ) [abstract] :  void
StorelessUnivariateStatistic.incrementAll ( double[ ] p1 ) [abstract] :  void
StorelessUnivariateStatistic.incrementAll ( double[ ] p1, int p2, int p3 ) [abstract] :  void

cdk-1.5.1.jar, StringIOSetting.class
package org.openscience.cdk.io.setting
StringIOSetting.StringIOSetting ( String name, IOSetting.Importance level, String question, String defaultSetting )

cdk-1.5.1.jar, SubHyperplane.class
package org.apache.commons.math3.geometry.partitioning
SubHyperplane.copySelf ( ) [abstract] :  SubHyperplane
SubHyperplane.getHyperplane ( ) [abstract] :  Hyperplane
SubHyperplane.getSize ( ) [abstract] :  double
SubHyperplane.isEmpty ( ) [abstract] :  boolean
SubHyperplane.reunite ( SubHyperplane p1 ) [abstract] :  SubHyperplane
SubHyperplane.side ( Hyperplane p1 ) [abstract] :  Side
SubHyperplane.split ( Hyperplane p1 ) [abstract] :  SubHyperplane.SplitSubHyperplane

cdk-1.5.1.jar, SubLine.class
package org.apache.commons.math3.geometry.euclidean.threed
SubLine.getSegments ( ) :  List
SubLine.intersection ( SubLine subLine, boolean includeEndPoints ) :  Vector3D
SubLine.SubLine ( Line line, IntervalsSet remainingRegion )
SubLine.SubLine ( Segment segment )
SubLine.SubLine ( Vector3D start, Vector3D end )
package org.apache.commons.math3.geometry.euclidean.twod
SubLine.buildNew ( Hyperplane hyperplane, Region remainingRegion ) :  AbstractSubHyperplane
SubLine.getSegments ( ) :  List
SubLine.intersection ( SubLine subLine, boolean includeEndPoints ) :  Vector2D
SubLine.side ( Hyperplane hyperplane ) :  Side
SubLine.split ( Hyperplane hyperplane ) :  SubHyperplane.SplitSubHyperplane
SubLine.SubLine ( Hyperplane hyperplane, Region remainingRegion )
SubLine.SubLine ( Segment segment )
SubLine.SubLine ( Vector2D start, Vector2D end )

cdk-1.5.1.jar, SubOrientedPoint.class
package org.apache.commons.math3.geometry.euclidean.oned
SubOrientedPoint.buildNew ( Hyperplane hyperplane, Region remainingRegion ) :  AbstractSubHyperplane
SubOrientedPoint.getSize ( ) :  double
SubOrientedPoint.side ( Hyperplane hyperplane ) :  Side
SubOrientedPoint.split ( Hyperplane hyperplane ) :  SubHyperplane.SplitSubHyperplane
SubOrientedPoint.SubOrientedPoint ( Hyperplane hyperplane, Region remainingRegion )

cdk-1.5.1.jar, SubPlane.class
package org.apache.commons.math3.geometry.euclidean.threed
SubPlane.buildNew ( Hyperplane hyperplane, Region remainingRegion ) :  AbstractSubHyperplane
SubPlane.side ( Hyperplane hyperplane ) :  Side
SubPlane.split ( Hyperplane hyperplane ) :  SubHyperplane.SplitSubHyperplane
SubPlane.SubPlane ( Hyperplane hyperplane, Region remainingRegion )

cdk-1.5.1.jar, SubstructureFingerprinter.class
package org.openscience.cdk.fingerprint
SubstructureFingerprinter.getBitFingerprint ( IAtomContainer atomContainer ) :  IBitFingerprint
SubstructureFingerprinter.getCountFingerprint ( IAtomContainer container ) :  ICountFingerprint

cdk-1.5.1.jar, Subtract.class
package org.apache.commons.math3.analysis.function
Subtract.Subtract ( )
Subtract.value ( double x, double y ) :  double

cdk-1.5.1.jar, Sum.class
package org.apache.commons.math3.stat.descriptive.summary
Sum.clear ( ) :  void
Sum.copy ( ) :  StorelessUnivariateStatistic
Sum.copy ( ) :  Sum
Sum.copy ( ) :  UnivariateStatistic
Sum.copy ( Sum source, Sum dest ) [static] :  void
Sum.evaluate ( double[ ] values, double[ ] weights ) :  double
Sum.evaluate ( double[ ] values, double[ ] weights, int begin, int length ) :  double
Sum.evaluate ( double[ ] values, int begin, int length ) :  double
Sum.getN ( ) :  long
Sum.getResult ( ) :  double
Sum.increment ( double d ) :  void
Sum.Sum ( )
Sum.Sum ( Sum original )

cdk-1.5.1.jar, SummaryStatistics.class
package org.apache.commons.math3.stat.descriptive
SummaryStatistics.addValue ( double value ) :  void
SummaryStatistics.clear ( ) :  void
SummaryStatistics.copy ( ) :  SummaryStatistics
SummaryStatistics.copy ( SummaryStatistics source, SummaryStatistics dest ) [static] :  void
SummaryStatistics.equals ( Object object ) :  boolean
SummaryStatistics.getGeoMeanImpl ( ) :  StorelessUnivariateStatistic
SummaryStatistics.getGeometricMean ( ) :  double
SummaryStatistics.getMax ( ) :  double
SummaryStatistics.getMaxImpl ( ) :  StorelessUnivariateStatistic
SummaryStatistics.getMean ( ) :  double
SummaryStatistics.getMeanImpl ( ) :  StorelessUnivariateStatistic
SummaryStatistics.getMin ( ) :  double
SummaryStatistics.getMinImpl ( ) :  StorelessUnivariateStatistic
SummaryStatistics.getN ( ) :  long
SummaryStatistics.getPopulationVariance ( ) :  double
SummaryStatistics.getSecondMoment ( ) :  double
SummaryStatistics.getStandardDeviation ( ) :  double
SummaryStatistics.getSum ( ) :  double
SummaryStatistics.getSumImpl ( ) :  StorelessUnivariateStatistic
SummaryStatistics.getSumLogImpl ( ) :  StorelessUnivariateStatistic
SummaryStatistics.getSummary ( ) :  StatisticalSummary
SummaryStatistics.getSumOfLogs ( ) :  double
SummaryStatistics.getSumsq ( ) :  double
SummaryStatistics.getSumsqImpl ( ) :  StorelessUnivariateStatistic
SummaryStatistics.getVariance ( ) :  double
SummaryStatistics.getVarianceImpl ( ) :  StorelessUnivariateStatistic
SummaryStatistics.hashCode ( ) :  int
SummaryStatistics.setGeoMeanImpl ( StorelessUnivariateStatistic geoMeanImpl ) :  void
SummaryStatistics.setMaxImpl ( StorelessUnivariateStatistic maxImpl ) :  void
SummaryStatistics.setMeanImpl ( StorelessUnivariateStatistic meanImpl ) :  void
SummaryStatistics.setMinImpl ( StorelessUnivariateStatistic minImpl ) :  void
SummaryStatistics.setSumImpl ( StorelessUnivariateStatistic sumImpl ) :  void
SummaryStatistics.setSumLogImpl ( StorelessUnivariateStatistic sumLogImpl ) :  void
SummaryStatistics.setSumsqImpl ( StorelessUnivariateStatistic sumsqImpl ) :  void
SummaryStatistics.setVarianceImpl ( StorelessUnivariateStatistic varianceImpl ) :  void
SummaryStatistics.SummaryStatistics ( )
SummaryStatistics.SummaryStatistics ( SummaryStatistics original )
SummaryStatistics.toString ( ) :  String

cdk-1.5.1.jar, SumOfLogs.class
package org.apache.commons.math3.stat.descriptive.summary
SumOfLogs.clear ( ) :  void
SumOfLogs.copy ( ) :  StorelessUnivariateStatistic
SumOfLogs.copy ( ) :  SumOfLogs
SumOfLogs.copy ( ) :  UnivariateStatistic
SumOfLogs.copy ( SumOfLogs source, SumOfLogs dest ) [static] :  void
SumOfLogs.evaluate ( double[ ] values, int begin, int length ) :  double
SumOfLogs.getN ( ) :  long
SumOfLogs.getResult ( ) :  double
SumOfLogs.increment ( double d ) :  void
SumOfLogs.SumOfLogs ( )
SumOfLogs.SumOfLogs ( SumOfLogs original )

cdk-1.5.1.jar, SumOfSquares.class
package org.apache.commons.math3.stat.descriptive.summary
SumOfSquares.clear ( ) :  void
SumOfSquares.copy ( ) :  StorelessUnivariateStatistic
SumOfSquares.copy ( ) :  SumOfSquares
SumOfSquares.copy ( ) :  UnivariateStatistic
SumOfSquares.copy ( SumOfSquares source, SumOfSquares dest ) [static] :  void
SumOfSquares.evaluate ( double[ ] values, int begin, int length ) :  double
SumOfSquares.getN ( ) :  long
SumOfSquares.getResult ( ) :  double
SumOfSquares.increment ( double d ) :  void
SumOfSquares.SumOfSquares ( )
SumOfSquares.SumOfSquares ( SumOfSquares original )

cdk-1.5.1.jar, SwingGUIListener.class
package org.openscience.cdk.io.listener
SwingGUIListener.setLevel ( IOSetting.Importance level ) :  void
SwingGUIListener.SwingGUIListener ( Component frame, IOSetting.Importance level )

cdk-1.5.1.jar, SymmLQ.class
package org.apache.commons.math3.linear
SymmLQ.getCheck ( ) :  boolean
SymmLQ.solve ( RealLinearOperator a, RealLinearOperator minv, RealVector b ) :  RealVector
SymmLQ.solve ( RealLinearOperator a, RealLinearOperator minv, RealVector b, boolean goodb, double shift ) :  RealVector
SymmLQ.solve ( RealLinearOperator a, RealLinearOperator minv, RealVector b, RealVector x ) :  RealVector
SymmLQ.solve ( RealLinearOperator a, RealVector b ) :  RealVector
SymmLQ.solve ( RealLinearOperator a, RealVector b, boolean goodb, double shift ) :  RealVector
SymmLQ.solve ( RealLinearOperator a, RealVector b, RealVector x ) :  RealVector
SymmLQ.solveInPlace ( RealLinearOperator a, RealLinearOperator minv, RealVector b, RealVector x ) :  RealVector
SymmLQ.solveInPlace ( RealLinearOperator a, RealLinearOperator minv, RealVector b, RealVector x, boolean goodb, double shift ) :  RealVector
SymmLQ.solveInPlace ( RealLinearOperator a, RealVector b, RealVector x ) :  RealVector
SymmLQ.SymmLQ ( int maxIterations, double delta, boolean check )
SymmLQ.SymmLQ ( IterationManager manager, double delta, boolean check )

cdk-1.5.1.jar, SynchronizedDescriptiveStatistics.class
package org.apache.commons.math3.stat.descriptive
SynchronizedDescriptiveStatistics.addValue ( double v ) :  void
SynchronizedDescriptiveStatistics.apply ( UnivariateStatistic stat ) :  double
SynchronizedDescriptiveStatistics.clear ( ) :  void
SynchronizedDescriptiveStatistics.copy ( ) :  DescriptiveStatistics
SynchronizedDescriptiveStatistics.copy ( ) :  SynchronizedDescriptiveStatistics
SynchronizedDescriptiveStatistics.copy ( SynchronizedDescriptiveStatistics source, SynchronizedDescriptiveStatistics dest ) [static] :  void
SynchronizedDescriptiveStatistics.getElement ( int index ) :  double
SynchronizedDescriptiveStatistics.getN ( ) :  long
SynchronizedDescriptiveStatistics.getStandardDeviation ( ) :  double
SynchronizedDescriptiveStatistics.getValues ( ) :  double[ ]
SynchronizedDescriptiveStatistics.getWindowSize ( ) :  int
SynchronizedDescriptiveStatistics.setWindowSize ( int windowSize ) :  void
SynchronizedDescriptiveStatistics.SynchronizedDescriptiveStatistics ( )
SynchronizedDescriptiveStatistics.SynchronizedDescriptiveStatistics ( int window )
SynchronizedDescriptiveStatistics.SynchronizedDescriptiveStatistics ( SynchronizedDescriptiveStatistics original )
SynchronizedDescriptiveStatistics.toString ( ) :  String

cdk-1.5.1.jar, SynchronizedMultivariateSummaryStatistics.class
package org.apache.commons.math3.stat.descriptive
SynchronizedMultivariateSummaryStatistics.addValue ( double[ ] value ) :  void
SynchronizedMultivariateSummaryStatistics.clear ( ) :  void
SynchronizedMultivariateSummaryStatistics.equals ( Object object ) :  boolean
SynchronizedMultivariateSummaryStatistics.getCovariance ( ) :  RealMatrix
SynchronizedMultivariateSummaryStatistics.getDimension ( ) :  int
SynchronizedMultivariateSummaryStatistics.getGeoMeanImpl ( ) :  StorelessUnivariateStatistic[ ]
SynchronizedMultivariateSummaryStatistics.getGeometricMean ( ) :  double[ ]
SynchronizedMultivariateSummaryStatistics.getMax ( ) :  double[ ]
SynchronizedMultivariateSummaryStatistics.getMaxImpl ( ) :  StorelessUnivariateStatistic[ ]
SynchronizedMultivariateSummaryStatistics.getMean ( ) :  double[ ]
SynchronizedMultivariateSummaryStatistics.getMeanImpl ( ) :  StorelessUnivariateStatistic[ ]
SynchronizedMultivariateSummaryStatistics.getMin ( ) :  double[ ]
SynchronizedMultivariateSummaryStatistics.getMinImpl ( ) :  StorelessUnivariateStatistic[ ]
SynchronizedMultivariateSummaryStatistics.getN ( ) :  long
SynchronizedMultivariateSummaryStatistics.getStandardDeviation ( ) :  double[ ]
SynchronizedMultivariateSummaryStatistics.getSum ( ) :  double[ ]
SynchronizedMultivariateSummaryStatistics.getSumImpl ( ) :  StorelessUnivariateStatistic[ ]
SynchronizedMultivariateSummaryStatistics.getSumLog ( ) :  double[ ]
SynchronizedMultivariateSummaryStatistics.getSumLogImpl ( ) :  StorelessUnivariateStatistic[ ]
SynchronizedMultivariateSummaryStatistics.getSumSq ( ) :  double[ ]
SynchronizedMultivariateSummaryStatistics.getSumsqImpl ( ) :  StorelessUnivariateStatistic[ ]
SynchronizedMultivariateSummaryStatistics.hashCode ( ) :  int
SynchronizedMultivariateSummaryStatistics.setGeoMeanImpl ( StorelessUnivariateStatistic[ ] geoMeanImpl ) :  void
SynchronizedMultivariateSummaryStatistics.setMaxImpl ( StorelessUnivariateStatistic[ ] maxImpl ) :  void
SynchronizedMultivariateSummaryStatistics.setMeanImpl ( StorelessUnivariateStatistic[ ] meanImpl ) :  void
SynchronizedMultivariateSummaryStatistics.setMinImpl ( StorelessUnivariateStatistic[ ] minImpl ) :  void
SynchronizedMultivariateSummaryStatistics.setSumImpl ( StorelessUnivariateStatistic[ ] sumImpl ) :  void
SynchronizedMultivariateSummaryStatistics.setSumLogImpl ( StorelessUnivariateStatistic[ ] sumLogImpl ) :  void
SynchronizedMultivariateSummaryStatistics.setSumsqImpl ( StorelessUnivariateStatistic[ ] sumsqImpl ) :  void
SynchronizedMultivariateSummaryStatistics.SynchronizedMultivariateSummaryStatistics ( int k, boolean isCovarianceBiasCorrected )
SynchronizedMultivariateSummaryStatistics.toString ( ) :  String

cdk-1.5.1.jar, SynchronizedSummaryStatistics.class
package org.apache.commons.math3.stat.descriptive
SynchronizedSummaryStatistics.addValue ( double value ) :  void
SynchronizedSummaryStatistics.clear ( ) :  void
SynchronizedSummaryStatistics.copy ( ) :  SummaryStatistics
SynchronizedSummaryStatistics.copy ( ) :  SynchronizedSummaryStatistics
SynchronizedSummaryStatistics.copy ( SynchronizedSummaryStatistics source, SynchronizedSummaryStatistics dest ) [static] :  void
SynchronizedSummaryStatistics.equals ( Object object ) :  boolean
SynchronizedSummaryStatistics.getGeoMeanImpl ( ) :  StorelessUnivariateStatistic
SynchronizedSummaryStatistics.getGeometricMean ( ) :  double
SynchronizedSummaryStatistics.getMax ( ) :  double
SynchronizedSummaryStatistics.getMaxImpl ( ) :  StorelessUnivariateStatistic
SynchronizedSummaryStatistics.getMean ( ) :  double
SynchronizedSummaryStatistics.getMeanImpl ( ) :  StorelessUnivariateStatistic
SynchronizedSummaryStatistics.getMin ( ) :  double
SynchronizedSummaryStatistics.getMinImpl ( ) :  StorelessUnivariateStatistic
SynchronizedSummaryStatistics.getN ( ) :  long
SynchronizedSummaryStatistics.getPopulationVariance ( ) :  double
SynchronizedSummaryStatistics.getStandardDeviation ( ) :  double
SynchronizedSummaryStatistics.getSum ( ) :  double
SynchronizedSummaryStatistics.getSumImpl ( ) :  StorelessUnivariateStatistic
SynchronizedSummaryStatistics.getSumLogImpl ( ) :  StorelessUnivariateStatistic
SynchronizedSummaryStatistics.getSummary ( ) :  StatisticalSummary
SynchronizedSummaryStatistics.getSumsq ( ) :  double
SynchronizedSummaryStatistics.getSumsqImpl ( ) :  StorelessUnivariateStatistic
SynchronizedSummaryStatistics.getVariance ( ) :  double
SynchronizedSummaryStatistics.getVarianceImpl ( ) :  StorelessUnivariateStatistic
SynchronizedSummaryStatistics.hashCode ( ) :  int
SynchronizedSummaryStatistics.setGeoMeanImpl ( StorelessUnivariateStatistic geoMeanImpl ) :  void
SynchronizedSummaryStatistics.setMaxImpl ( StorelessUnivariateStatistic maxImpl ) :  void
SynchronizedSummaryStatistics.setMeanImpl ( StorelessUnivariateStatistic meanImpl ) :  void
SynchronizedSummaryStatistics.setMinImpl ( StorelessUnivariateStatistic minImpl ) :  void
SynchronizedSummaryStatistics.setSumImpl ( StorelessUnivariateStatistic sumImpl ) :  void
SynchronizedSummaryStatistics.setSumLogImpl ( StorelessUnivariateStatistic sumLogImpl ) :  void
SynchronizedSummaryStatistics.setSumsqImpl ( StorelessUnivariateStatistic sumsqImpl ) :  void
SynchronizedSummaryStatistics.setVarianceImpl ( StorelessUnivariateStatistic varianceImpl ) :  void
SynchronizedSummaryStatistics.SynchronizedSummaryStatistics ( )
SynchronizedSummaryStatistics.SynchronizedSummaryStatistics ( SynchronizedSummaryStatistics original )
SynchronizedSummaryStatistics.toString ( ) :  String

cdk-1.5.1.jar, TaeAminoAcidDescriptor.class
package org.openscience.cdk.qsar.descriptors.protein
TaeAminoAcidDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, Tan.class
package org.apache.commons.math3.analysis.function
Tan.derivative ( ) :  UnivariateFunction
Tan.Tan ( )
Tan.value ( double x ) :  double

cdk-1.5.1.jar, Tanh.class
package org.apache.commons.math3.analysis.function
Tanh.derivative ( ) :  UnivariateFunction
Tanh.Tanh ( )
Tanh.value ( double x ) :  double

cdk-1.5.1.jar, Tanimoto.class
package org.openscience.cdk.similarity
Tanimoto.calculate ( IBitFingerprint fingerprint1, IBitFingerprint fingerprint2 ) [static] :  double
Tanimoto.calculate ( ICountFingerprint fp1, ICountFingerprint fp2 ) [static] :  double
Tanimoto.method1 ( ICountFingerprint fp1, ICountFingerprint fp2 ) [static] :  double
Tanimoto.method2 ( ICountFingerprint fp1, ICountFingerprint fp2 ) [static] :  double

cdk-1.5.1.jar, TDistribution.class
package org.apache.commons.math3.distribution
TDistribution.cumulativeProbability ( double x ) :  double
TDistribution.density ( double x ) :  double
TDistribution.getDegreesOfFreedom ( ) :  double
TDistribution.getNumericalMean ( ) :  double
TDistribution.getNumericalVariance ( ) :  double
TDistribution.getSolverAbsoluteAccuracy ( ) :  double
TDistribution.getSupportLowerBound ( ) :  double
TDistribution.getSupportUpperBound ( ) :  double
TDistribution.isSupportConnected ( ) :  boolean
TDistribution.isSupportLowerBoundInclusive ( ) :  boolean
TDistribution.isSupportUpperBoundInclusive ( ) :  boolean
TDistribution.probability ( double x ) :  double
TDistribution.TDistribution ( double degreesOfFreedom )
TDistribution.TDistribution ( double degreesOfFreedom, double inverseCumAccuracy )

cdk-1.5.1.jar, TestUtils.class
package org.apache.commons.math3.stat.inference
TestUtils.chiSquare ( double[ ] expected, long[ ] observed ) [static] :  double
TestUtils.chiSquare ( long[ ][ ] counts ) [static] :  double
TestUtils.chiSquareDataSetsComparison ( long[ ] observed1, long[ ] observed2 ) [static] :  double
TestUtils.chiSquareTest ( double[ ] expected, long[ ] observed ) [static] :  double
TestUtils.chiSquareTest ( double[ ] expected, long[ ] observed, double alpha ) [static] :  boolean
TestUtils.chiSquareTest ( long[ ][ ] counts ) [static] :  double
TestUtils.chiSquareTest ( long[ ][ ] counts, double alpha ) [static] :  boolean
TestUtils.chiSquareTestDataSetsComparison ( long[ ] observed1, long[ ] observed2 ) [static] :  double
TestUtils.chiSquareTestDataSetsComparison ( long[ ] observed1, long[ ] observed2, double alpha ) [static] :  boolean
TestUtils.homoscedasticT ( double[ ] sample1, double[ ] sample2 ) [static] :  double
TestUtils.homoscedasticT ( StatisticalSummary sampleStats1, StatisticalSummary sampleStats2 ) [static] :  double
TestUtils.homoscedasticTTest ( double[ ] sample1, double[ ] sample2 ) [static] :  double
TestUtils.homoscedasticTTest ( double[ ] sample1, double[ ] sample2, double alpha ) [static] :  boolean
TestUtils.homoscedasticTTest ( StatisticalSummary sampleStats1, StatisticalSummary sampleStats2 ) [static] :  double
TestUtils.oneWayAnovaFValue ( Collection categoryData ) [static] :  double
TestUtils.oneWayAnovaPValue ( Collection categoryData ) [static] :  double
TestUtils.oneWayAnovaTest ( Collection categoryData, double alpha ) [static] :  boolean
TestUtils.pairedT ( double[ ] sample1, double[ ] sample2 ) [static] :  double
TestUtils.pairedTTest ( double[ ] sample1, double[ ] sample2 ) [static] :  double
TestUtils.pairedTTest ( double[ ] sample1, double[ ] sample2, double alpha ) [static] :  boolean
TestUtils.t ( double mu, double[ ] observed ) [static] :  double
TestUtils.t ( double mu, StatisticalSummary sampleStats ) [static] :  double
TestUtils.t ( double[ ] sample1, double[ ] sample2 ) [static] :  double
TestUtils.t ( StatisticalSummary sampleStats1, StatisticalSummary sampleStats2 ) [static] :  double
TestUtils.tTest ( double mu, double[ ] sample ) [static] :  double
TestUtils.tTest ( double mu, double[ ] sample, double alpha ) [static] :  boolean
TestUtils.tTest ( double mu, StatisticalSummary sampleStats ) [static] :  double
TestUtils.tTest ( double mu, StatisticalSummary sampleStats, double alpha ) [static] :  boolean
TestUtils.tTest ( double[ ] sample1, double[ ] sample2 ) [static] :  double
TestUtils.tTest ( double[ ] sample1, double[ ] sample2, double alpha ) [static] :  boolean
TestUtils.tTest ( StatisticalSummary sampleStats1, StatisticalSummary sampleStats2 ) [static] :  double
TestUtils.tTest ( StatisticalSummary sampleStats1, StatisticalSummary sampleStats2, double alpha ) [static] :  boolean

cdk-1.5.1.jar, TextGUIListener.class
package org.openscience.cdk.io.listener
TextGUIListener.setLevel ( IOSetting.Importance level ) :  void
TextGUIListener.TextGUIListener ( IOSetting.Importance level )

cdk-1.5.1.jar, ThreeEighthesIntegrator.class
package org.apache.commons.math3.ode.nonstiff
ThreeEighthesIntegrator.ThreeEighthesIntegrator ( double step )

cdk-1.5.1.jar, TiesStrategy.class
package org.apache.commons.math3.stat.ranking
TiesStrategy.valueOf ( String name ) [static] :  TiesStrategy
TiesStrategy.values ( ) [static] :  TiesStrategy[ ]

cdk-1.5.1.jar, Token.class
package org.openscience.cdk.iupac.parser
Token.getValue ( ) :  Object
Token.newToken ( int ofKind, String image ) [static] :  Token
Token.Token ( int kind )
Token.Token ( int kind, String image )
package org.openscience.cdk.smiles.smarts.parser
Token.getValue ( ) :  Object
Token.newToken ( int ofKind, String image ) [static] :  Token
Token.Token ( int kind )
Token.Token ( int kind, String image )

cdk-1.5.1.jar, TooManyEvaluationsException.class
package org.apache.commons.math3.exception
TooManyEvaluationsException.TooManyEvaluationsException ( Number max )

cdk-1.5.1.jar, TournamentSelection.class
package org.apache.commons.math3.genetics
TournamentSelection.getArity ( ) :  int
TournamentSelection.select ( Population population ) :  ChromosomePair
TournamentSelection.setArity ( int arity ) :  void
TournamentSelection.TournamentSelection ( int arity )

cdk-1.5.1.jar, TPSADescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
TPSADescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, Transform.class
package org.apache.commons.math3.geometry.partitioning
Transform.apply ( Hyperplane p1 ) [abstract] :  Hyperplane
Transform.apply ( SubHyperplane p1, Hyperplane p2, Hyperplane p3 ) [abstract] :  SubHyperplane
Transform.apply ( Vector p1 ) [abstract] :  Vector

cdk-1.5.1.jar, TransformerMap.class
package org.apache.commons.math3.util
TransformerMap.classes ( ) :  Set
TransformerMap.clear ( ) :  void
TransformerMap.containsClass ( Class key ) :  boolean
TransformerMap.containsTransformer ( NumberTransformer value ) :  boolean
TransformerMap.equals ( Object other ) :  boolean
TransformerMap.getTransformer ( Class key ) :  NumberTransformer
TransformerMap.hashCode ( ) :  int
TransformerMap.putTransformer ( Class key, NumberTransformer transformer ) :  NumberTransformer
TransformerMap.removeTransformer ( Class key ) :  NumberTransformer
TransformerMap.transform ( Object o ) :  double
TransformerMap.TransformerMap ( )
TransformerMap.transformers ( ) :  Collection

cdk-1.5.1.jar, TransformType.class
package org.apache.commons.math3.transform
TransformType.valueOf ( String name ) [static] :  TransformType
TransformType.values ( ) [static] :  TransformType[ ]

cdk-1.5.1.jar, TransformUtils.class
package org.apache.commons.math3.transform
TransformUtils.createComplexArray ( double[ ][ ] dataRI ) [static] :  Complex[ ]
TransformUtils.createRealImaginaryArray ( Complex[ ] dataC ) [static] :  double[ ][ ]
TransformUtils.exactLog2 ( int n ) [static] :  int
TransformUtils.scaleArray ( Complex[ ] f, double d ) [static] :  Complex[ ]
TransformUtils.scaleArray ( double[ ] f, double d ) [static] :  double[ ]

cdk-1.5.1.jar, TrapezoidIntegrator.class
package org.apache.commons.math3.analysis.integration
TrapezoidIntegrator.doIntegrate ( ) :  double
TrapezoidIntegrator.TrapezoidIntegrator ( )
TrapezoidIntegrator.TrapezoidIntegrator ( double relativeAccuracy, double absoluteAccuracy, int minimalIterationCount, int maximalIterationCount )
TrapezoidIntegrator.TrapezoidIntegrator ( int minimalIterationCount, int maximalIterationCount )

cdk-1.5.1.jar, TriangularDistribution.class
package org.apache.commons.math3.distribution
TriangularDistribution.cumulativeProbability ( double x ) :  double
TriangularDistribution.density ( double x ) :  double
TriangularDistribution.getMode ( ) :  double
TriangularDistribution.getNumericalMean ( ) :  double
TriangularDistribution.getNumericalVariance ( ) :  double
TriangularDistribution.getSolverAbsoluteAccuracy ( ) :  double
TriangularDistribution.getSupportLowerBound ( ) :  double
TriangularDistribution.getSupportUpperBound ( ) :  double
TriangularDistribution.inverseCumulativeProbability ( double p ) :  double
TriangularDistribution.isSupportConnected ( ) :  boolean
TriangularDistribution.isSupportLowerBoundInclusive ( ) :  boolean
TriangularDistribution.isSupportUpperBoundInclusive ( ) :  boolean
TriangularDistribution.probability ( double x ) :  double
TriangularDistribution.TriangularDistribution ( double a, double c, double b )

cdk-1.5.1.jar, TricubicSplineInterpolatingFunction.class
package org.apache.commons.math3.analysis.interpolation
TricubicSplineInterpolatingFunction.TricubicSplineInterpolatingFunction ( double[ ] x, double[ ] y, double[ ] z, double[ ][ ][ ] f, double[ ][ ][ ] dFdX, double[ ][ ][ ] dFdY, double[ ][ ][ ] dFdZ, double[ ][ ][ ] d2FdXdY, double[ ][ ][ ] d2FdXdZ, double[ ][ ][ ] d2FdYdZ, double[ ][ ][ ] d3FdXdYdZ )
TricubicSplineInterpolatingFunction.value ( double x, double y, double z ) :  double

cdk-1.5.1.jar, TricubicSplineInterpolator.class
package org.apache.commons.math3.analysis.interpolation
TricubicSplineInterpolator.interpolate ( double[ ] x0, double[ ] x1, double[ ] x2, double[ ][ ][ ] x3 ) :  TrivariateFunction
TricubicSplineInterpolator.interpolate ( double[ ] xval, double[ ] yval, double[ ] zval, double[ ][ ][ ] fval ) :  TricubicSplineInterpolatingFunction
TricubicSplineInterpolator.TricubicSplineInterpolator ( )

cdk-1.5.1.jar, TrivariateFunction.class
package org.apache.commons.math3.analysis
TrivariateFunction.value ( double p1, double p2, double p3 ) [abstract] :  double

cdk-1.5.1.jar, TrivariateGridInterpolator.class
package org.apache.commons.math3.analysis.interpolation
TrivariateGridInterpolator.interpolate ( double[ ] p1, double[ ] p2, double[ ] p3, double[ ][ ][ ] p4 ) [abstract] :  TrivariateFunction

cdk-1.5.1.jar, TTest.class
package org.apache.commons.math3.stat.inference
TTest.df ( double v1, double v2, double n1, double n2 ) :  double
TTest.homoscedasticT ( double m1, double m2, double v1, double v2, double n1, double n2 ) :  double
TTest.homoscedasticT ( double[ ] sample1, double[ ] sample2 ) :  double
TTest.homoscedasticT ( StatisticalSummary sampleStats1, StatisticalSummary sampleStats2 ) :  double
TTest.homoscedasticTTest ( double m1, double m2, double v1, double v2, double n1, double n2 ) :  double
TTest.homoscedasticTTest ( double[ ] sample1, double[ ] sample2 ) :  double
TTest.homoscedasticTTest ( double[ ] sample1, double[ ] sample2, double alpha ) :  boolean
TTest.homoscedasticTTest ( StatisticalSummary sampleStats1, StatisticalSummary sampleStats2 ) :  double
TTest.pairedT ( double[ ] sample1, double[ ] sample2 ) :  double
TTest.pairedTTest ( double[ ] sample1, double[ ] sample2 ) :  double
TTest.pairedTTest ( double[ ] sample1, double[ ] sample2, double alpha ) :  boolean
TTest.t ( double m, double mu, double v, double n ) :  double
TTest.t ( double m1, double m2, double v1, double v2, double n1, double n2 ) :  double
TTest.t ( double mu, double[ ] observed ) :  double
TTest.t ( double mu, StatisticalSummary sampleStats ) :  double
TTest.t ( double[ ] sample1, double[ ] sample2 ) :  double
TTest.t ( StatisticalSummary sampleStats1, StatisticalSummary sampleStats2 ) :  double
TTest.TTest ( )
TTest.tTest ( double m, double mu, double v, double n ) :  double
TTest.tTest ( double m1, double m2, double v1, double v2, double n1, double n2 ) :  double
TTest.tTest ( double mu, double[ ] sample ) :  double
TTest.tTest ( double mu, double[ ] sample, double alpha ) :  boolean
TTest.tTest ( double mu, StatisticalSummary sampleStats ) :  double
TTest.tTest ( double mu, StatisticalSummary sampleStats, double alpha ) :  boolean
TTest.tTest ( double[ ] sample1, double[ ] sample2 ) :  double
TTest.tTest ( double[ ] sample1, double[ ] sample2, double alpha ) :  boolean
TTest.tTest ( StatisticalSummary sampleStats1, StatisticalSummary sampleStats2 ) :  double
TTest.tTest ( StatisticalSummary sampleStats1, StatisticalSummary sampleStats2, double alpha ) :  boolean

cdk-1.5.1.jar, Ulp.class
package org.apache.commons.math3.analysis.function
Ulp.Ulp ( )
Ulp.value ( double x ) :  double

cdk-1.5.1.jar, UnboundedSolutionException.class
package org.apache.commons.math3.optimization.linear
UnboundedSolutionException.UnboundedSolutionException ( )

cdk-1.5.1.jar, UncorrelatedRandomVectorGenerator.class
package org.apache.commons.math3.random
UncorrelatedRandomVectorGenerator.nextVector ( ) :  double[ ]
UncorrelatedRandomVectorGenerator.UncorrelatedRandomVectorGenerator ( double[ ] mean, double[ ] standardDeviation, NormalizedRandomGenerator generator )
UncorrelatedRandomVectorGenerator.UncorrelatedRandomVectorGenerator ( int dimension, NormalizedRandomGenerator generator )

cdk-1.5.1.jar, UniformIntegerDistribution.class
package org.apache.commons.math3.distribution
UniformIntegerDistribution.cumulativeProbability ( int x ) :  double
UniformIntegerDistribution.getNumericalMean ( ) :  double
UniformIntegerDistribution.getNumericalVariance ( ) :  double
UniformIntegerDistribution.getSupportLowerBound ( ) :  int
UniformIntegerDistribution.getSupportUpperBound ( ) :  int
UniformIntegerDistribution.isSupportConnected ( ) :  boolean
UniformIntegerDistribution.probability ( int x ) :  double
UniformIntegerDistribution.sample ( ) :  int
UniformIntegerDistribution.UniformIntegerDistribution ( int lower, int upper )

cdk-1.5.1.jar, UniformRandomGenerator.class
package org.apache.commons.math3.random
UniformRandomGenerator.nextNormalizedDouble ( ) :  double
UniformRandomGenerator.UniformRandomGenerator ( RandomGenerator generator )

cdk-1.5.1.jar, UniformRealDistribution.class
package org.apache.commons.math3.distribution
UniformRealDistribution.cumulativeProbability ( double x ) :  double
UniformRealDistribution.density ( double x ) :  double
UniformRealDistribution.getNumericalMean ( ) :  double
UniformRealDistribution.getNumericalVariance ( ) :  double
UniformRealDistribution.getSolverAbsoluteAccuracy ( ) :  double
UniformRealDistribution.getSupportLowerBound ( ) :  double
UniformRealDistribution.getSupportUpperBound ( ) :  double
UniformRealDistribution.isSupportConnected ( ) :  boolean
UniformRealDistribution.isSupportLowerBoundInclusive ( ) :  boolean
UniformRealDistribution.isSupportUpperBoundInclusive ( ) :  boolean
UniformRealDistribution.probability ( double x ) :  double
UniformRealDistribution.sample ( ) :  double
UniformRealDistribution.UniformRealDistribution ( )
UniformRealDistribution.UniformRealDistribution ( double lower, double upper )
UniformRealDistribution.UniformRealDistribution ( double lower, double upper, double inverseCumAccuracy )

cdk-1.5.1.jar, UnitSphereRandomVectorGenerator.class
package org.apache.commons.math3.random
UnitSphereRandomVectorGenerator.nextVector ( ) :  double[ ]
UnitSphereRandomVectorGenerator.UnitSphereRandomVectorGenerator ( int dimension )
UnitSphereRandomVectorGenerator.UnitSphereRandomVectorGenerator ( int dimension, RandomGenerator rand )

cdk-1.5.1.jar, UnivariateDfpFunction.class
package org.apache.commons.math3.dfp
UnivariateDfpFunction.value ( Dfp p1 ) [abstract] :  Dfp

cdk-1.5.1.jar, UnivariateFunction.class
package org.apache.commons.math3.analysis
UnivariateFunction.value ( double p1 ) [abstract] :  double

cdk-1.5.1.jar, UnivariateIntegrator.class
package org.apache.commons.math3.analysis.integration
UnivariateIntegrator.getAbsoluteAccuracy ( ) [abstract] :  double
UnivariateIntegrator.getEvaluations ( ) [abstract] :  int
UnivariateIntegrator.getIterations ( ) [abstract] :  int
UnivariateIntegrator.getMaximalIterationCount ( ) [abstract] :  int
UnivariateIntegrator.getMinimalIterationCount ( ) [abstract] :  int
UnivariateIntegrator.getRelativeAccuracy ( ) [abstract] :  double
UnivariateIntegrator.integrate ( int p1, UnivariateFunction p2, double p3, double p4 ) [abstract] :  double

cdk-1.5.1.jar, UnivariateInterpolator.class
package org.apache.commons.math3.analysis.interpolation
UnivariateInterpolator.interpolate ( double[ ] p1, double[ ] p2 ) [abstract] :  UnivariateFunction

cdk-1.5.1.jar, UnivariateMatrixFunction.class
package org.apache.commons.math3.analysis
UnivariateMatrixFunction.value ( double p1 ) [abstract] :  double[ ][ ]

cdk-1.5.1.jar, UnivariateMultiStartOptimizer.class
package org.apache.commons.math3.optimization.univariate
UnivariateMultiStartOptimizer.getConvergenceChecker ( ) :  ConvergenceChecker
UnivariateMultiStartOptimizer.getEvaluations ( ) :  int
UnivariateMultiStartOptimizer.getMaxEvaluations ( ) :  int
UnivariateMultiStartOptimizer.getOptima ( ) :  UnivariatePointValuePair[ ]
UnivariateMultiStartOptimizer.optimize ( int maxEval, UnivariateFunction f, GoalType goal, double min, double max ) :  UnivariatePointValuePair
UnivariateMultiStartOptimizer.optimize ( int maxEval, UnivariateFunction f, GoalType goal, double min, double max, double startValue ) :  UnivariatePointValuePair
UnivariateMultiStartOptimizer.UnivariateMultiStartOptimizer ( BaseUnivariateOptimizer optimizer, int starts, RandomGenerator generator )

cdk-1.5.1.jar, UnivariatePeriodicInterpolator.class
package org.apache.commons.math3.analysis.interpolation
UnivariatePeriodicInterpolator.interpolate ( double[ ] xval, double[ ] yval ) :  UnivariateFunction
UnivariatePeriodicInterpolator.UnivariatePeriodicInterpolator ( UnivariateInterpolator interpolator, double period )
UnivariatePeriodicInterpolator.UnivariatePeriodicInterpolator ( UnivariateInterpolator interpolator, double period, int extend )

cdk-1.5.1.jar, UnivariatePointValuePair.class
package org.apache.commons.math3.optimization.univariate
UnivariatePointValuePair.getPoint ( ) :  double
UnivariatePointValuePair.getValue ( ) :  double
UnivariatePointValuePair.UnivariatePointValuePair ( double point, double value )

cdk-1.5.1.jar, UnivariateSolverUtils.class
package org.apache.commons.math3.analysis.solvers
UnivariateSolverUtils.bracket ( UnivariateFunction function, double initial, double lowerBound, double upperBound ) [static] :  double[ ]
UnivariateSolverUtils.bracket ( UnivariateFunction function, double initial, double lowerBound, double upperBound, int maximumIterations ) [static] :  double[ ]
UnivariateSolverUtils.forceSide ( int maxEval, UnivariateFunction f, BracketedUnivariateSolver bracketing, double baseRoot, double min, double max, AllowedSolution allowedSolution ) [static] :  double
UnivariateSolverUtils.isBracketing ( UnivariateFunction function, double lower, double upper ) [static] :  boolean
UnivariateSolverUtils.isSequence ( double start, double mid, double end ) [static] :  boolean
UnivariateSolverUtils.midpoint ( double a, double b ) [static] :  double
UnivariateSolverUtils.solve ( UnivariateFunction function, double x0, double x1 ) [static] :  double
UnivariateSolverUtils.solve ( UnivariateFunction function, double x0, double x1, double absoluteAccuracy ) [static] :  double
UnivariateSolverUtils.verifyBracketing ( UnivariateFunction function, double lower, double upper ) [static] :  void
UnivariateSolverUtils.verifyInterval ( double lower, double upper ) [static] :  void
UnivariateSolverUtils.verifySequence ( double lower, double initial, double upper ) [static] :  void

cdk-1.5.1.jar, UnivariateStatistic.class
package org.apache.commons.math3.stat.descriptive
UnivariateStatistic.copy ( ) [abstract] :  UnivariateStatistic
UnivariateStatistic.evaluate ( double[ ] p1 ) [abstract] :  double
UnivariateStatistic.evaluate ( double[ ] p1, int p2, int p3 ) [abstract] :  double

cdk-1.5.1.jar, UnivariateVectorFunction.class
package org.apache.commons.math3.analysis
UnivariateVectorFunction.value ( double p1 ) [abstract] :  double[ ]

cdk-1.5.1.jar, UpdatingMultipleLinearRegression.class
package org.apache.commons.math3.stat.regression
UpdatingMultipleLinearRegression.addObservation ( double[ ] p1, double p2 ) [abstract] :  void
UpdatingMultipleLinearRegression.addObservations ( double[ ][ ] p1, double[ ] p2 ) [abstract] :  void
UpdatingMultipleLinearRegression.clear ( ) [abstract] :  void
UpdatingMultipleLinearRegression.getN ( ) [abstract] :  long
UpdatingMultipleLinearRegression.hasIntercept ( ) [abstract] :  boolean
UpdatingMultipleLinearRegression.regress ( ) [abstract] :  RegressionResults
UpdatingMultipleLinearRegression.regress ( int[ ] p1 ) [abstract] :  RegressionResults

cdk-1.5.1.jar, VABCDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
VABCDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, VAdjMaDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
VAdjMaDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, ValueServer.class
package org.apache.commons.math3.random
ValueServer.closeReplayFile ( ) :  void
ValueServer.computeDistribution ( ) :  void
ValueServer.computeDistribution ( int binCount ) :  void
ValueServer.fill ( double[ ] values ) :  void
ValueServer.fill ( int length ) :  double[ ]
ValueServer.getEmpiricalDistribution ( ) :  EmpiricalDistribution
ValueServer.getMode ( ) :  int
ValueServer.getMu ( ) :  double
ValueServer.getNext ( ) :  double
ValueServer.getSigma ( ) :  double
ValueServer.getValuesFileURL ( ) :  URL
ValueServer.reSeed ( long seed ) :  void
ValueServer.resetReplayFile ( ) :  void
ValueServer.setMode ( int mode ) :  void
ValueServer.setMu ( double mu ) :  void
ValueServer.setSigma ( double sigma ) :  void
ValueServer.setValuesFileURL ( String url ) :  void
ValueServer.setValuesFileURL ( URL url ) :  void
ValueServer.ValueServer ( )
ValueServer.ValueServer ( RandomDataImpl randomData )

cdk-1.5.1.jar, Variance.class
package org.apache.commons.math3.stat.descriptive.moment
Variance.clear ( ) :  void
Variance.copy ( ) :  StorelessUnivariateStatistic
Variance.copy ( ) :  UnivariateStatistic
Variance.copy ( ) :  Variance
Variance.copy ( Variance source, Variance dest ) [static] :  void
Variance.evaluate ( double[ ] values ) :  double
Variance.evaluate ( double[ ] values, double mean ) :  double
Variance.evaluate ( double[ ] values, double mean, int begin, int length ) :  double
Variance.evaluate ( double[ ] values, double[ ] weights ) :  double
Variance.evaluate ( double[ ] values, double[ ] weights, double mean ) :  double
Variance.evaluate ( double[ ] values, double[ ] weights, double mean, int begin, int length ) :  double
Variance.evaluate ( double[ ] values, double[ ] weights, int begin, int length ) :  double
Variance.evaluate ( double[ ] values, int begin, int length ) :  double
Variance.getN ( ) :  long
Variance.getResult ( ) :  double
Variance.increment ( double d ) :  void
Variance.isBiasCorrected ( ) :  boolean
Variance.setBiasCorrected ( boolean biasCorrected ) :  void
Variance.Variance ( )
Variance.Variance ( boolean isBiasCorrected )
Variance.Variance ( boolean isBiasCorrected, SecondMoment m2 )
Variance.Variance ( SecondMoment m2 )
Variance.Variance ( Variance original )

cdk-1.5.1.jar, VdWRadiusDescriptor.class
package org.openscience.cdk.qsar.descriptors.atomic
VdWRadiusDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, Vector.class
package org.apache.commons.math3.geometry
Vector.add ( double p1, Vector p2 ) [abstract] :  Vector
Vector.add ( Vector p1 ) [abstract] :  Vector
Vector.distance ( Vector p1 ) [abstract] :  double
Vector.distance1 ( Vector p1 ) [abstract] :  double
Vector.distanceInf ( Vector p1 ) [abstract] :  double
Vector.distanceSq ( Vector p1 ) [abstract] :  double
Vector.dotProduct ( Vector p1 ) [abstract] :  double
Vector.getNorm ( ) [abstract] :  double
Vector.getNorm1 ( ) [abstract] :  double
Vector.getNormInf ( ) [abstract] :  double
Vector.getNormSq ( ) [abstract] :  double
Vector.getSpace ( ) [abstract] :  Space
Vector.getZero ( ) [abstract] :  Vector
Vector.isInfinite ( ) [abstract] :  boolean
Vector.isNaN ( ) [abstract] :  boolean
Vector.negate ( ) [abstract] :  Vector
Vector.normalize ( ) [abstract] :  Vector
Vector.scalarMultiply ( double p1 ) [abstract] :  Vector
Vector.subtract ( double p1, Vector p2 ) [abstract] :  Vector
Vector.subtract ( Vector p1 ) [abstract] :  Vector
Vector.toString ( NumberFormat p1 ) [abstract] :  String

cdk-1.5.1.jar, Vector1D.class
package org.apache.commons.math3.geometry.euclidean.oned
Vector1D.add ( double factor, Vector v ) :  Vector1D
Vector1D.add ( double x0, Vector x1 ) :  Vector
Vector1D.add ( Vector v ) :  Vector1D
Vector1D.add ( Vector x0 ) :  Vector
Vector1D.distance ( Vector p ) :  double
Vector1D.distance ( Vector1D p1, Vector1D p2 ) [static] :  double
Vector1D.distance1 ( Vector p ) :  double
Vector1D.distanceInf ( Vector p ) :  double
Vector1D.distanceInf ( Vector1D p1, Vector1D p2 ) [static] :  double
Vector1D.distanceSq ( Vector p ) :  double
Vector1D.distanceSq ( Vector1D p1, Vector1D p2 ) [static] :  double
Vector1D.dotProduct ( Vector v ) :  double
Vector1D.equals ( Object other ) :  boolean
Vector1D.getNorm ( ) :  double
Vector1D.getNorm1 ( ) :  double
Vector1D.getNormInf ( ) :  double
Vector1D.getNormSq ( ) :  double
Vector1D.getSpace ( ) :  Space
Vector1D.getX ( ) :  double
Vector1D.getZero ( ) :  Vector
Vector1D.getZero ( ) :  Vector1D
Vector1D.hashCode ( ) :  int
Vector1D.isInfinite ( ) :  boolean
Vector1D.isNaN ( ) :  boolean
Vector1D.negate ( ) :  Vector
Vector1D.negate ( ) :  Vector1D
Vector1D.normalize ( ) :  Vector
Vector1D.normalize ( ) :  Vector1D
Vector1D.scalarMultiply ( double a ) :  Vector1D
Vector1D.scalarMultiply ( double x0 ) :  Vector
Vector1D.subtract ( double factor, Vector v ) :  Vector1D
Vector1D.subtract ( double x0, Vector x1 ) :  Vector
Vector1D.subtract ( Vector p ) :  Vector1D
Vector1D.subtract ( Vector x0 ) :  Vector
Vector1D.toString ( ) :  String
Vector1D.toString ( NumberFormat format ) :  String
Vector1D.Vector1D ( double a, Vector1D u )
Vector1D.Vector1D ( double a1, Vector1D u1, double a2, Vector1D u2 )
Vector1D.Vector1D ( double a1, Vector1D u1, double a2, Vector1D u2, double a3, Vector1D u3 )
Vector1D.Vector1D ( double a1, Vector1D u1, double a2, Vector1D u2, double a3, Vector1D u3, double a4, Vector1D u4 )
Vector1D.Vector1D ( double x )

cdk-1.5.1.jar, Vector1DFormat.class
package org.apache.commons.math3.geometry.euclidean.oned
Vector1DFormat.format ( Vector vector, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
Vector1DFormat.getInstance ( ) [static] :  Vector1DFormat
Vector1DFormat.getInstance ( Locale locale ) [static] :  Vector1DFormat
Vector1DFormat.parse ( String source ) :  Vector1D
Vector1DFormat.parse ( String source, ParsePosition pos ) :  Vector1D
Vector1DFormat.parse ( String x0 ) :  Vector
Vector1DFormat.parse ( String x0, ParsePosition x1 ) :  Vector
Vector1DFormat.Vector1DFormat ( )
Vector1DFormat.Vector1DFormat ( NumberFormat format )
Vector1DFormat.Vector1DFormat ( String prefix, String suffix )
Vector1DFormat.Vector1DFormat ( String prefix, String suffix, NumberFormat format )

cdk-1.5.1.jar, Vector2D.class
package org.apache.commons.math3.geometry.euclidean.twod
Vector2D.add ( double factor, Vector v ) :  Vector2D
Vector2D.add ( double x0, Vector x1 ) :  Vector
Vector2D.add ( Vector v ) :  Vector2D
Vector2D.add ( Vector x0 ) :  Vector
Vector2D.distance ( Vector p ) :  double
Vector2D.distance ( Vector2D p1, Vector2D p2 ) [static] :  double
Vector2D.distance1 ( Vector p ) :  double
Vector2D.distanceInf ( Vector p ) :  double
Vector2D.distanceInf ( Vector2D p1, Vector2D p2 ) [static] :  double
Vector2D.distanceSq ( Vector p ) :  double
Vector2D.distanceSq ( Vector2D p1, Vector2D p2 ) [static] :  double
Vector2D.dotProduct ( Vector v ) :  double
Vector2D.equals ( Object other ) :  boolean
Vector2D.getNorm ( ) :  double
Vector2D.getNorm1 ( ) :  double
Vector2D.getNormInf ( ) :  double
Vector2D.getNormSq ( ) :  double
Vector2D.getSpace ( ) :  Space
Vector2D.getX ( ) :  double
Vector2D.getY ( ) :  double
Vector2D.getZero ( ) :  Vector
Vector2D.getZero ( ) :  Vector2D
Vector2D.hashCode ( ) :  int
Vector2D.isInfinite ( ) :  boolean
Vector2D.isNaN ( ) :  boolean
Vector2D.negate ( ) :  Vector
Vector2D.negate ( ) :  Vector2D
Vector2D.normalize ( ) :  Vector
Vector2D.normalize ( ) :  Vector2D
Vector2D.scalarMultiply ( double a ) :  Vector2D
Vector2D.scalarMultiply ( double x0 ) :  Vector
Vector2D.subtract ( double factor, Vector v ) :  Vector2D
Vector2D.subtract ( double x0, Vector x1 ) :  Vector
Vector2D.subtract ( Vector p ) :  Vector2D
Vector2D.subtract ( Vector x0 ) :  Vector
Vector2D.toArray ( ) :  double[ ]
Vector2D.toString ( ) :  String
Vector2D.toString ( NumberFormat format ) :  String
Vector2D.Vector2D ( double a, Vector2D u )
Vector2D.Vector2D ( double a1, Vector2D u1, double a2, Vector2D u2 )
Vector2D.Vector2D ( double a1, Vector2D u1, double a2, Vector2D u2, double a3, Vector2D u3 )
Vector2D.Vector2D ( double a1, Vector2D u1, double a2, Vector2D u2, double a3, Vector2D u3, double a4, Vector2D u4 )
Vector2D.Vector2D ( double x, double y )
Vector2D.Vector2D ( double[ ] v )

cdk-1.5.1.jar, Vector2DFormat.class
package org.apache.commons.math3.geometry.euclidean.twod
Vector2DFormat.format ( Vector vector, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
Vector2DFormat.getInstance ( ) [static] :  Vector2DFormat
Vector2DFormat.getInstance ( Locale locale ) [static] :  Vector2DFormat
Vector2DFormat.parse ( String source ) :  Vector2D
Vector2DFormat.parse ( String source, ParsePosition pos ) :  Vector2D
Vector2DFormat.parse ( String x0 ) :  Vector
Vector2DFormat.parse ( String x0, ParsePosition x1 ) :  Vector
Vector2DFormat.Vector2DFormat ( )
Vector2DFormat.Vector2DFormat ( NumberFormat format )
Vector2DFormat.Vector2DFormat ( String prefix, String suffix, String separator )
Vector2DFormat.Vector2DFormat ( String prefix, String suffix, String separator, NumberFormat format )

cdk-1.5.1.jar, Vector3D.class
package org.apache.commons.math3.geometry.euclidean.threed
Vector3D.add ( double factor, Vector v ) :  Vector3D
Vector3D.add ( double x0, Vector x1 ) :  Vector
Vector3D.add ( Vector v ) :  Vector3D
Vector3D.add ( Vector x0 ) :  Vector
Vector3D.angle ( Vector3D v1, Vector3D v2 ) [static] :  double
Vector3D.crossProduct ( Vector v ) :  Vector3D
Vector3D.crossProduct ( Vector3D v1, Vector3D v2 ) [static] :  Vector3D
Vector3D.distance ( Vector v ) :  double
Vector3D.distance ( Vector3D v1, Vector3D v2 ) [static] :  double
Vector3D.distance1 ( Vector v ) :  double
Vector3D.distance1 ( Vector3D v1, Vector3D v2 ) [static] :  double
Vector3D.distanceInf ( Vector v ) :  double
Vector3D.distanceInf ( Vector3D v1, Vector3D v2 ) [static] :  double
Vector3D.distanceSq ( Vector v ) :  double
Vector3D.distanceSq ( Vector3D v1, Vector3D v2 ) [static] :  double
Vector3D.dotProduct ( Vector v ) :  double
Vector3D.dotProduct ( Vector3D v1, Vector3D v2 ) [static] :  double
Vector3D.equals ( Object other ) :  boolean
Vector3D.getAlpha ( ) :  double
Vector3D.getDelta ( ) :  double
Vector3D.getNorm ( ) :  double
Vector3D.getNorm1 ( ) :  double
Vector3D.getNormInf ( ) :  double
Vector3D.getNormSq ( ) :  double
Vector3D.getSpace ( ) :  Space
Vector3D.getX ( ) :  double
Vector3D.getY ( ) :  double
Vector3D.getZ ( ) :  double
Vector3D.getZero ( ) :  Vector
Vector3D.getZero ( ) :  Vector3D
Vector3D.hashCode ( ) :  int
Vector3D.isInfinite ( ) :  boolean
Vector3D.isNaN ( ) :  boolean
Vector3D.negate ( ) :  Vector
Vector3D.negate ( ) :  Vector3D
Vector3D.normalize ( ) :  Vector
Vector3D.normalize ( ) :  Vector3D
Vector3D.orthogonal ( ) :  Vector3D
Vector3D.scalarMultiply ( double a ) :  Vector3D
Vector3D.scalarMultiply ( double x0 ) :  Vector
Vector3D.subtract ( double factor, Vector v ) :  Vector3D
Vector3D.subtract ( double x0, Vector x1 ) :  Vector
Vector3D.subtract ( Vector v ) :  Vector3D
Vector3D.subtract ( Vector x0 ) :  Vector
Vector3D.toArray ( ) :  double[ ]
Vector3D.toString ( ) :  String
Vector3D.toString ( NumberFormat format ) :  String
Vector3D.Vector3D ( double a, Vector3D u )
Vector3D.Vector3D ( double a1, Vector3D u1, double a2, Vector3D u2 )
Vector3D.Vector3D ( double a1, Vector3D u1, double a2, Vector3D u2, double a3, Vector3D u3 )
Vector3D.Vector3D ( double a1, Vector3D u1, double a2, Vector3D u2, double a3, Vector3D u3, double a4, Vector3D u4 )
Vector3D.Vector3D ( double alpha, double delta )
Vector3D.Vector3D ( double x, double y, double z )
Vector3D.Vector3D ( double[ ] v )

cdk-1.5.1.jar, Vector3DFormat.class
package org.apache.commons.math3.geometry.euclidean.threed
Vector3DFormat.format ( Vector vector, StringBuffer toAppendTo, FieldPosition pos ) :  StringBuffer
Vector3DFormat.getInstance ( ) [static] :  Vector3DFormat
Vector3DFormat.getInstance ( Locale locale ) [static] :  Vector3DFormat
Vector3DFormat.parse ( String source ) :  Vector3D
Vector3DFormat.parse ( String source, ParsePosition pos ) :  Vector3D
Vector3DFormat.parse ( String x0 ) :  Vector
Vector3DFormat.parse ( String x0, ParsePosition x1 ) :  Vector
Vector3DFormat.Vector3DFormat ( )
Vector3DFormat.Vector3DFormat ( NumberFormat format )
Vector3DFormat.Vector3DFormat ( String prefix, String suffix, String separator )
Vector3DFormat.Vector3DFormat ( String prefix, String suffix, String separator, NumberFormat format )

cdk-1.5.1.jar, VectorFormat.class
package org.apache.commons.math3.geometry
VectorFormat.format ( StringBuffer toAppendTo, FieldPosition pos, double[ ] coordinates ) :  StringBuffer
VectorFormat.format ( Vector p1, StringBuffer p2, FieldPosition p3 ) [abstract] :  StringBuffer
VectorFormat.format ( Vector vector ) :  String
VectorFormat.getAvailableLocales ( ) [static] :  Locale[ ]
VectorFormat.getFormat ( ) :  NumberFormat
VectorFormat.getPrefix ( ) :  String
VectorFormat.getSeparator ( ) :  String
VectorFormat.getSuffix ( ) :  String
VectorFormat.parse ( String p1 ) [abstract] :  Vector
VectorFormat.parse ( String p1, ParsePosition p2 ) [abstract] :  Vector
VectorFormat.parseCoordinates ( int dimension, String source, ParsePosition pos ) :  double[ ]
VectorFormat.VectorFormat ( )
VectorFormat.VectorFormat ( NumberFormat format )
VectorFormat.VectorFormat ( String prefix, String suffix, String separator )
VectorFormat.VectorFormat ( String prefix, String suffix, String separator, NumberFormat format )

cdk-1.5.1.jar, VectorialCovariance.class
package org.apache.commons.math3.stat.descriptive.moment
VectorialCovariance.clear ( ) :  void
VectorialCovariance.equals ( Object obj ) :  boolean
VectorialCovariance.getN ( ) :  long
VectorialCovariance.getResult ( ) :  RealMatrix
VectorialCovariance.hashCode ( ) :  int
VectorialCovariance.increment ( double[ ] v ) :  void
VectorialCovariance.VectorialCovariance ( int dimension, boolean isBiasCorrected )

cdk-1.5.1.jar, VectorialMean.class
package org.apache.commons.math3.stat.descriptive.moment
VectorialMean.equals ( Object obj ) :  boolean
VectorialMean.getN ( ) :  long
VectorialMean.getResult ( ) :  double[ ]
VectorialMean.hashCode ( ) :  int
VectorialMean.increment ( double[ ] v ) :  void
VectorialMean.VectorialMean ( int dimension )

cdk-1.5.1.jar, WeibullDistribution.class
package org.apache.commons.math3.distribution
WeibullDistribution.calculateNumericalMean ( ) :  double
WeibullDistribution.calculateNumericalVariance ( ) :  double
WeibullDistribution.cumulativeProbability ( double x ) :  double
WeibullDistribution.density ( double x ) :  double
WeibullDistribution.getNumericalMean ( ) :  double
WeibullDistribution.getNumericalVariance ( ) :  double
WeibullDistribution.getScale ( ) :  double
WeibullDistribution.getShape ( ) :  double
WeibullDistribution.getSolverAbsoluteAccuracy ( ) :  double
WeibullDistribution.getSupportLowerBound ( ) :  double
WeibullDistribution.getSupportUpperBound ( ) :  double
WeibullDistribution.inverseCumulativeProbability ( double p ) :  double
WeibullDistribution.isSupportConnected ( ) :  boolean
WeibullDistribution.isSupportLowerBoundInclusive ( ) :  boolean
WeibullDistribution.isSupportUpperBoundInclusive ( ) :  boolean
WeibullDistribution.probability ( double x ) :  double
WeibullDistribution.WeibullDistribution ( double alpha, double beta )
WeibullDistribution.WeibullDistribution ( double alpha, double beta, double inverseCumAccuracy )

cdk-1.5.1.jar, WeightDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
WeightDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, WeightedEvaluation.class
package org.apache.commons.math3.stat.descriptive
WeightedEvaluation.evaluate ( double[ ] p1, double[ ] p2 ) [abstract] :  double
WeightedEvaluation.evaluate ( double[ ] p1, double[ ] p2, int p3, int p4 ) [abstract] :  double

cdk-1.5.1.jar, WeightedObservedPoint.class
package org.apache.commons.math3.optimization.fitting
WeightedObservedPoint.getWeight ( ) :  double
WeightedObservedPoint.getX ( ) :  double
WeightedObservedPoint.getY ( ) :  double
WeightedObservedPoint.WeightedObservedPoint ( double weight, double x, double y )

cdk-1.5.1.jar, WeightedPathDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
WeightedPathDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, Well1024a.class
package org.apache.commons.math3.random
Well1024a.next ( int bits ) :  int
Well1024a.Well1024a ( )
Well1024a.Well1024a ( int seed )
Well1024a.Well1024a ( int[ ] seed )
Well1024a.Well1024a ( long seed )

cdk-1.5.1.jar, Well19937a.class
package org.apache.commons.math3.random
Well19937a.next ( int bits ) :  int
Well19937a.Well19937a ( )
Well19937a.Well19937a ( int seed )
Well19937a.Well19937a ( int[ ] seed )
Well19937a.Well19937a ( long seed )

cdk-1.5.1.jar, Well19937c.class
package org.apache.commons.math3.random
Well19937c.next ( int bits ) :  int
Well19937c.Well19937c ( )
Well19937c.Well19937c ( int seed )
Well19937c.Well19937c ( int[ ] seed )
Well19937c.Well19937c ( long seed )

cdk-1.5.1.jar, Well44497a.class
package org.apache.commons.math3.random
Well44497a.next ( int bits ) :  int
Well44497a.Well44497a ( )
Well44497a.Well44497a ( int seed )
Well44497a.Well44497a ( int[ ] seed )
Well44497a.Well44497a ( long seed )

cdk-1.5.1.jar, Well44497b.class
package org.apache.commons.math3.random
Well44497b.next ( int bits ) :  int
Well44497b.Well44497b ( )
Well44497b.Well44497b ( int seed )
Well44497b.Well44497b ( int[ ] seed )
Well44497b.Well44497b ( long seed )

cdk-1.5.1.jar, Well512a.class
package org.apache.commons.math3.random
Well512a.next ( int bits ) :  int
Well512a.Well512a ( )
Well512a.Well512a ( int seed )
Well512a.Well512a ( int[ ] seed )
Well512a.Well512a ( long seed )

cdk-1.5.1.jar, WHIMDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
WHIMDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, WienerNumbersDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
WienerNumbersDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, WilcoxonSignedRankTest.class
package org.apache.commons.math3.stat.inference
WilcoxonSignedRankTest.wilcoxonSignedRank ( double[ ] x, double[ ] y ) :  double
WilcoxonSignedRankTest.WilcoxonSignedRankTest ( )
WilcoxonSignedRankTest.wilcoxonSignedRankTest ( double[ ] x, double[ ] y, boolean exactPValue ) :  double
WilcoxonSignedRankTest.WilcoxonSignedRankTest ( NaNStrategy nanStrategy, TiesStrategy tiesStrategy )

cdk-1.5.1.jar, XLogPDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
XLogPDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, ZagrebIndexDescriptor.class
package org.openscience.cdk.qsar.descriptors.molecular
ZagrebIndexDescriptor.getSpecification ( ) :  IImplementationSpecification

cdk-1.5.1.jar, ZeroException.class
package org.apache.commons.math3.exception
ZeroException.ZeroException ( )
ZeroException.ZeroException ( Localizable specific, Object[ ] arguments )

cdk-1.5.1.jar, ZipfDistribution.class
package org.apache.commons.math3.distribution
ZipfDistribution.calculateNumericalMean ( ) :  double
ZipfDistribution.calculateNumericalVariance ( ) :  double
ZipfDistribution.cumulativeProbability ( int x ) :  double
ZipfDistribution.getExponent ( ) :  double
ZipfDistribution.getNumberOfElements ( ) :  int
ZipfDistribution.getNumericalMean ( ) :  double
ZipfDistribution.getNumericalVariance ( ) :  double
ZipfDistribution.getSupportLowerBound ( ) :  int
ZipfDistribution.getSupportUpperBound ( ) :  int
ZipfDistribution.isSupportConnected ( ) :  boolean
ZipfDistribution.probability ( int x ) :  double
ZipfDistribution.ZipfDistribution ( int numberOfElements, double exponent )

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Removed Methods (58)

cdk-1.5.0.jar, AbstractRenderer.class
package org.openscience.cdk.renderer
AbstractRenderer.AbstractRenderer ( )

cdk-1.5.0.jar, AtomPlacer.class
package org.openscience.cdk.layout
AtomPlacer.breadthFirstSearch ( IAtomContainer ac, Vector sphere, IAtomContainer[ ] pathes ) :  void
AtomPlacer.listNumbers ( IAtomContainer mol, Vector ac ) :  String

cdk-1.5.0.jar, AttachedGroup.class
package org.openscience.cdk.iupac.parser
AttachedGroup.AttachedGroup ( Vector locations, int length )
AttachedGroup.AttachedGroup ( Vector locations, String name )
AttachedGroup.getLocations ( ) :  Vector
AttachedGroup.setLocations ( Vector locations ) :  void

cdk-1.5.0.jar, BooleanIOSetting.class
package org.openscience.cdk.io.setting
BooleanIOSetting.BooleanIOSetting ( String name, int level, String question, String defaultSetting )

cdk-1.5.0.jar, DescriptorEngine.class
package org.openscience.cdk.qsar
DescriptorEngine.getDictionaryClass ( DescriptorSpecification descriptorSpecification ) :  String[ ]
DescriptorEngine.getDictionaryType ( DescriptorSpecification descriptorSpecification ) :  String

cdk-1.5.0.jar, EStateFingerprinter.class
package org.openscience.cdk.fingerprint
EStateFingerprinter.getFingerprint ( IAtomContainer atomContainer ) :  BitSet

cdk-1.5.0.jar, ExtendedFingerprinter.class
package org.openscience.cdk.fingerprint
ExtendedFingerprinter.getFingerprint ( IAtomContainer atomContainer, IRingSet ringSet, List rslist ) :  BitSet
ExtendedFingerprinter.getFingerprint ( IAtomContainer container ) :  BitSet

cdk-1.5.0.jar, FiguerasSSSRFinder.class
package org.openscience.cdk.ringsearch
FiguerasSSSRFinder.findSSSR ( IAtomContainer mol ) :  RingSet

cdk-1.5.0.jar, Fingerprinter.class
package org.openscience.cdk.fingerprint
Fingerprinter.getFingerprint ( IAtomContainer container ) :  BitSet
Fingerprinter.getFingerprint ( IAtomContainer container, AllRingsFinder ringFinder ) :  BitSet

cdk-1.5.0.jar, FixedSizeStack.class
package org.openscience.cdk.tools
FixedSizeStack.FixedSizeStack ( int size )
FixedSizeStack.pop ( ) :  Object
FixedSizeStack.push ( Object O ) :  void

cdk-1.5.0.jar, GraphOnlyFingerprinter.class
package org.openscience.cdk.fingerprint
GraphOnlyFingerprinter.getFingerprint ( IAtomContainer container, int size ) :  BitSet

cdk-1.5.0.jar, HybridizationFingerprinter.class
package org.openscience.cdk.fingerprint
HybridizationFingerprinter.getFingerprint ( IAtomContainer container ) :  BitSet

cdk-1.5.0.jar, IDescriptor.class
package org.openscience.cdk.qsar
IDescriptor.getSpecification ( ) [abstract] :  DescriptorSpecification

cdk-1.5.0.jar, IFingerprinter.class
package org.openscience.cdk.fingerprint
IFingerprinter.getFingerprint ( IAtomContainer p1 ) [abstract] :  BitSet

cdk-1.5.0.jar, IntegerIOSetting.class
package org.openscience.cdk.io.setting
IntegerIOSetting.IntegerIOSetting ( String name, int level, String question, String defaultSetting )

cdk-1.5.0.jar, IOSetting.class
package org.openscience.cdk.io.setting
IOSetting.getLevel ( ) :  int
IOSetting.IOSetting ( String name, int level, String question, String defaultSetting )

cdk-1.5.0.jar, IsoAlkanes.class
package org.openscience.cdk.templates.saturatedhydrocarbons
IsoAlkanes.getIsobutane ( ) [static] :  IAtomContainer
IsoAlkanes.getIsohexane ( ) [static] :  IAtomContainer
IsoAlkanes.getIsopentane ( ) [static] :  IAtomContainer

cdk-1.5.0.jar, IteratingMDLReader.class
package org.openscience.cdk.io.iterator
IteratingMDLReader.close ( ) :  void
IteratingMDLReader.customizeJob ( ) :  void
IteratingMDLReader.getFormat ( ) :  IResourceFormat
IteratingMDLReader.getIOSettings ( ) :  IOSetting[ ]
IteratingMDLReader.hasNext ( ) :  boolean
IteratingMDLReader.IteratingMDLReader ( InputStream in, IChemObjectBuilder builder )
IteratingMDLReader.IteratingMDLReader ( Reader in, IChemObjectBuilder builder )
IteratingMDLReader.next ( ) :  IAtomContainer
IteratingMDLReader.next ( ) :  Object
IteratingMDLReader.processIOSettingQuestion ( IOSetting setting ) :  void
IteratingMDLReader.remove ( ) :  void
IteratingMDLReader.setReader ( InputStream reader ) :  void
IteratingMDLReader.setReader ( Reader reader ) :  void

cdk-1.5.0.jar, LingoFingerprinter.class
package org.openscience.cdk.fingerprint
LingoFingerprinter.getFingerprint ( IAtomContainer iAtomContainer ) :  BitSet

cdk-1.5.0.jar, MACCSFingerprinter.class
package org.openscience.cdk.fingerprint
MACCSFingerprinter.getFingerprint ( IAtomContainer atomContainer ) :  BitSet

cdk-1.5.0.jar, MDLV3000Reader.class
package org.openscience.cdk.io
MDLV3000Reader.accepts ( IChemObject object ) :  boolean

cdk-1.5.0.jar, MoleculeBuilder.class
package org.openscience.cdk.iupac.parser
MoleculeBuilder.buildMolecule ( int mainChain, Vector attachedSubstituents, Vector attachedGroups, boolean isMainCyclic, String name ) :  IAtomContainer

cdk-1.5.0.jar, OptionIOSetting.class
package org.openscience.cdk.io.setting
OptionIOSetting.OptionIOSetting ( String name, int level, String question, List settings, String defaultSetting )

cdk-1.5.0.jar, ParseException.class
package org.openscience.cdk.iupac.parser
ParseException.getMessage ( ) :  String
package org.openscience.cdk.smiles.smarts.parser
ParseException.getMessage ( ) :  String

cdk-1.5.0.jar, PubchemFingerprinter.class
package org.openscience.cdk.fingerprint
PubchemFingerprinter.getFingerprint ( IAtomContainer atomContainer ) :  BitSet
PubchemFingerprinter.getFingerprintAsBytes ( ) :  byte[ ]

cdk-1.5.0.jar, SignatureFingerprinter.class
package org.openscience.cdk.fingerprint
SignatureFingerprinter.getFingerprint ( IAtomContainer iAtomContainer ) :  BitSet

cdk-1.5.0.jar, StringIOSetting.class
package org.openscience.cdk.io.setting
StringIOSetting.StringIOSetting ( String name, int level, String question, String defaultSetting )

cdk-1.5.0.jar, SubstructureFingerprinter.class
package org.openscience.cdk.fingerprint
SubstructureFingerprinter.getFingerprint ( IAtomContainer atomContainer ) :  BitSet

cdk-1.5.0.jar, SwingGUIListener.class
package org.openscience.cdk.io.listener
SwingGUIListener.setLevel ( int level ) :  void
SwingGUIListener.SwingGUIListener ( Component frame, int level )

cdk-1.5.0.jar, TextGUIListener.class
package org.openscience.cdk.io.listener
TextGUIListener.setLevel ( int level ) :  void
TextGUIListener.TextGUIListener ( int level )

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Problems with Data Types, High Severity (10)

	Change	Effect
1	Abstract method getFingerprint ( IAtomContainer ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

	Change	Effect
1	Type of field level has been changed from int to IOSetting.Importance.	A client program may be interrupted by NoSuchFieldError exception.
2	Field HIGH of type int has been removed from this class.	A client program may be interrupted by NoSuchFieldError exception.

	Change	Effect
1	Field lookingAhead of type boolean has been removed from this class.	A client program may be interrupted by NoSuchFieldError exception.

	Change	Effect
1	Field specialConstructor of type boolean has been removed from this class.	A client program may be interrupted by NoSuchFieldError exception.

	Change	Effect
1	Abstract method getSpecification ( ) has been removed from this interface.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Field specialConstructor of type boolean has been removed from this class.	A client program may be interrupted by NoSuchFieldError exception.

	Change	Effect
1	Field lookingAhead of type boolean has been removed from this class.	A client program may be interrupted by NoSuchFieldError exception.

	Change	Effect
1	This class has been removed.	A client program may be interrupted by NoClassDefFoundError exception.

cdk-1.5.0.jar
package org.openscience.cdk.fingerprint
[+] IFingerprinter (1)

package org.openscience.cdk.io.iterator
[+] IteratingMDLReader (1)

package org.openscience.cdk.io.setting
[+] IOSetting (2)

package org.openscience.cdk.iupac.parser
[+] NomParser (1)
[+] ParseException (1)

package org.openscience.cdk.qsar
[+] IDescriptor (1)

package org.openscience.cdk.smiles.smarts.parser
[+] ParseException (1)
[+] SMARTSParser (1)

package org.openscience.cdk.tools
[+] FixedSizeStack (1)

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Problems with Methods, High Severity (16)

	Change	Effect
1	Method became static.	A client program may be interrupted by NoSuchMethodError exception.
2	Access level has been changed from protected to package-private.	A client program may be interrupted by IllegalAccessError exception.

	Change	Effect
1	Method became static.	A client program may be interrupted by NoSuchMethodError exception.
2	Access level has been changed from protected to package-private.	A client program may be interrupted by IllegalAccessError exception.

	Change	Effect
1	Method became non-static.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Method became non-static.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Method became non-static.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Method became non-static.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Method became non-static.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Method became non-static.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Method became non-static.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Method became non-static.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Method became non-static.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Method became non-static.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Method became non-static.	A client program may be interrupted by NoSuchMethodError exception.

	Change	Effect
1	Method became non-static.	A client program may be interrupted by NoSuchMethodError exception.

cdk-1.5.0.jar, ParseException
package org.openscience.cdk.iupac.parser
[+] ParseException.add_escapes ( String str ) :  String (2)
package org.openscience.cdk.smiles.smarts.parser
[+] ParseException.add_escapes ( String str ) :  String (2)

cdk-1.5.0.jar, UniversalIsomorphismTester
package org.openscience.cdk.isomorphism
[+] UniversalIsomorphismTester.getIsomorphAtomsMap ( IAtomContainer g1, IAtomContainer g2 ) [static] :  List (1)
[+] UniversalIsomorphismTester.getIsomorphMap ( IAtomContainer g1, IAtomContainer g2 ) [static] :  List (1)
[+] UniversalIsomorphismTester.getIsomorphMaps ( IAtomContainer g1, IAtomContainer g2 ) [static] :  List (1)
[+] UniversalIsomorphismTester.getOverlaps ( IAtomContainer g1, IAtomContainer g2 ) [static] :  List (1)
[+] UniversalIsomorphismTester.getSubgraphAtomsMap ( IAtomContainer g1, IAtomContainer g2 ) [static] :  List (1)
[+] UniversalIsomorphismTester.getSubgraphAtomsMaps ( IAtomContainer g1, IAtomContainer g2 ) [static] :  List (1)
[+] UniversalIsomorphismTester.getSubgraphMap ( IAtomContainer g1, IAtomContainer g2 ) [static] :  List (1)
[+] UniversalIsomorphismTester.getSubgraphMaps ( IAtomContainer g1, IAtomContainer g2 ) [static] :  List (1)
[+] UniversalIsomorphismTester.isIsomorph ( IAtomContainer g1, IAtomContainer g2 ) [static] :  boolean (1)
[+] UniversalIsomorphismTester.isSubgraph ( IAtomContainer g1, IAtomContainer g2 ) [static] :  boolean (1)
[+] UniversalIsomorphismTester.search ( IAtomContainer g1, IAtomContainer g2, BitSet c1, BitSet c2, boolean findAllStructure, boolean findAllMap ) [static] :  List (1)
[+] UniversalIsomorphismTester.setTimeout ( long timeout ) [static] :  void (1)

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Problems with Data Types, Medium Severity (17)

	Change	Effect
1	Value of final field ISALIPHATIC (int) has been changed from 3 to 8.	Old value of the field will be inlined to the client code at compile-time and will be used instead of a new one.
2	Value of final field ISAROMATIC (int) has been changed from 5 to 32.	Old value of the field will be inlined to the client code at compile-time and will be used instead of a new one.
3	Value of final field ISCONJUGATED (int) has been changed from 6 to 64.	Old value of the field will be inlined to the client code at compile-time and will be used instead of a new one.
4	Value of final field ISINRING (int) has been changed from 1 to 2.	Old value of the field will be inlined to the client code at compile-time and will be used instead of a new one.
5	Value of final field ISNOTINRING (int) has been changed from 2 to 4.	Old value of the field will be inlined to the client code at compile-time and will be used instead of a new one.
6	Value of final field IS_HYDROGENBOND_ACCEPTOR (int) has been changed from 9 to 512.	Old value of the field will be inlined to the client code at compile-time and will be used instead of a new one.
7	Value of final field IS_HYDROGENBOND_DONOR (int) has been changed from 8 to 256.	Old value of the field will be inlined to the client code at compile-time and will be used instead of a new one.
8	Value of final field IS_TYPEABLE (int) has been changed from 11 to 2048.	Old value of the field will be inlined to the client code at compile-time and will be used instead of a new one.
9	Value of final field MAPPED (int) has been changed from 7 to 128.	Old value of the field will be inlined to the client code at compile-time and will be used instead of a new one.
10	Value of final field MAX_FLAG_INDEX (int) has been changed from 12 to 13.	Old value of the field will be inlined to the client code at compile-time and will be used instead of a new one.
11	Value of final field REACTIVE_CENTER (int) has been changed from 10 to 1024.	Old value of the field will be inlined to the client code at compile-time and will be used instead of a new one.
12	Value of final field VISITED (int) has been changed from 4 to 16.	Old value of the field will be inlined to the client code at compile-time and will be used instead of a new one.

	Change	Effect
1	Abstract method getBitFingerprint ( IAtomContainer ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method makeFingerprintsFromSdf ( boolean, boolean, Map, BufferedReader, int ) and may not be implemented by old clients.

	Change	Effect
1	Field FP_SIZE became final.	A client program may be interrupted by IllegalAccessError exception when attempt to assign new values to the field.

	Change	Effect
1	Abstract method getFlagValue ( ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method ChemObject ( IChemObject ) and may not be implemented by old clients.

	Change	Effect
1	Added super-interface org.openscience.cdk.interfaces.ISetting.	If abstract methods from an added super-interface must be implemented by client then it may be interrupted by AbstractMethodError exception. Abstract method getLevel () from the added super-interface is called by the method processIOSettingQuestion ( IOSetting ) in 2nd library version and may not be implemented by old clients.

	Change	Effect
1	Abstract method getSpecification ( ) has been added to this interface.	A client program may be interrupted by AbstractMethodError exception. Added abstract method is called in 2nd library version by the method initializeSpecifications ( List ) and may not be implemented by old clients.

cdk-1.5.0.jar
package org.openscience.cdk
[+] CDKConstants (12)

package org.openscience.cdk.fingerprint
[+] IFingerprinter (1)
[+] PubchemFingerprinter (1)

package org.openscience.cdk.interfaces
[+] IChemObject (1)

package org.openscience.cdk.io.setting
[+] IOSetting (1)

package org.openscience.cdk.qsar
[+] IDescriptor (1)

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Problems with Data Types, Low Severity (37)

	Change	Effect
1	Field LARGE_FIRST (int) with the compile-time constant value 1 has been removed from this class.	A client program may change behavior.
2	Field SMALL_FIRST (int) with the compile-time constant value 2 has been removed from this class.	A client program may change behavior.

	Change	Effect
1	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.

	Change	Effect
1	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.

	Change	Effect
1	Added super-class ChemObjectIO.	A static field from a super-interface of a client class may hide a field (with the same name) inherited from new super-class and cause IncompatibleClassChangeError exception.
2	Method addChemObjectIOListener ( IChemObjectIOListener ) has been moved up type hierarchy to addChemObjectIOListener ( IChemObjectIOListener )	Method addChemObjectIOListener ( IChemObjectIOListener ) will be called instead of addChemObjectIOListener ( IChemObjectIOListener ) in a client program.
3	Method fireIOSettingQuestion ( IOSetting ) has been moved up type hierarchy to fireIOSettingQuestion ( IOSetting )	Method fireIOSettingQuestion ( IOSetting ) will be called instead of fireIOSettingQuestion ( IOSetting ) in a client program.
4	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.
5	Method removeChemObjectIOListener ( IChemObjectIOListener ) has been moved up type hierarchy to removeChemObjectIOListener ( IChemObjectIOListener )	Method removeChemObjectIOListener ( IChemObjectIOListener ) will be called instead of removeChemObjectIOListener ( IChemObjectIOListener ) in a client program.

	Change	Effect
1	Added super-class ChemObjectIO.	A static field from a super-interface of a client class may hide a field (with the same name) inherited from new super-class and cause IncompatibleClassChangeError exception.
2	Method addChemObjectIOListener ( IChemObjectIOListener ) has been moved up type hierarchy to addChemObjectIOListener ( IChemObjectIOListener )	Method addChemObjectIOListener ( IChemObjectIOListener ) will be called instead of addChemObjectIOListener ( IChemObjectIOListener ) in a client program.
3	Method fireIOSettingQuestion ( IOSetting ) has been moved up type hierarchy to fireIOSettingQuestion ( IOSetting )	Method fireIOSettingQuestion ( IOSetting ) will be called instead of fireIOSettingQuestion ( IOSetting ) in a client program.
4	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.
5	Method removeChemObjectIOListener ( IChemObjectIOListener ) has been moved up type hierarchy to removeChemObjectIOListener ( IChemObjectIOListener )	Method removeChemObjectIOListener ( IChemObjectIOListener ) will be called instead of removeChemObjectIOListener ( IChemObjectIOListener ) in a client program.

	Change	Effect
1	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.

	Change	Effect
1	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.

	Change	Effect
1	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.

	Change	Effect
1	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.

	Change	Effect
1	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.

	Change	Effect
1	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.

	Change	Effect
1	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.

	Change	Effect
1	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.

	Change	Effect
1	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.

	Change	Effect
1	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.

	Change	Effect
1	Added super-class org.openscience.cdk.io.ChemObjectIO.	A static field from a super-interface of a client class may hide a field (with the same name) inherited from new super-class and cause IncompatibleClassChangeError exception.
2	Method addChemObjectIOListener ( IChemObjectIOListener ) has been moved up type hierarchy to addChemObjectIOListener ( IChemObjectIOListener )	Method addChemObjectIOListener ( IChemObjectIOListener ) will be called instead of addChemObjectIOListener ( IChemObjectIOListener ) in a client program.
3	Method fireIOSettingQuestion ( IOSetting ) has been moved up type hierarchy to fireIOSettingQuestion ( IOSetting )	Method fireIOSettingQuestion ( IOSetting ) will be called instead of fireIOSettingQuestion ( IOSetting ) in a client program.
4	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.
5	Method removeChemObjectIOListener ( IChemObjectIOListener ) has been moved up type hierarchy to removeChemObjectIOListener ( IChemObjectIOListener )	Method removeChemObjectIOListener ( IChemObjectIOListener ) will be called instead of removeChemObjectIOListener ( IChemObjectIOListener ) in a client program.

	Change	Effect
1	Added super-class org.openscience.cdk.io.ChemObjectIO.	A static field from a super-interface of a client class may hide a field (with the same name) inherited from new super-class and cause IncompatibleClassChangeError exception.
2	Method addChemObjectIOListener ( IChemObjectIOListener ) has been moved up type hierarchy to addChemObjectIOListener ( IChemObjectIOListener )	Method addChemObjectIOListener ( IChemObjectIOListener ) will be called instead of addChemObjectIOListener ( IChemObjectIOListener ) in a client program.
3	Method fireIOSettingQuestion ( IOSetting ) has been moved up type hierarchy to fireIOSettingQuestion ( IOSetting )	Method fireIOSettingQuestion ( IOSetting ) will be called instead of fireIOSettingQuestion ( IOSetting ) in a client program.
4	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.
5	Method removeChemObjectIOListener ( IChemObjectIOListener ) has been moved up type hierarchy to removeChemObjectIOListener ( IChemObjectIOListener )	Method removeChemObjectIOListener ( IChemObjectIOListener ) will be called instead of removeChemObjectIOListener ( IChemObjectIOListener ) in a client program.

	Change	Effect
1	Method getIOSettings ( ) has been moved up type hierarchy to getIOSettings ( )	Method getIOSettings ( ) will be called instead of getIOSettings ( ) in a client program.

cdk-1.5.0.jar
package org.openscience.cdk
[+] RingSet (2)

package org.openscience.cdk.io
[+] CDKSourceCodeWriter (1)
[+] CMLWriter (1)
[+] DefaultChemObjectReader (5)
[+] DefaultChemObjectWriter (5)
[+] Gaussian98Reader (1)
[+] MDLReader (1)
[+] MDLRXNV3000Reader (1)
[+] MDLV2000Reader (1)
[+] MDLV2000Writer (1)
[+] MDLV3000Reader (1)
[+] PDBReader (1)
[+] PDBWriter (1)
[+] SDFWriter (1)
[+] SMILESWriter (1)

package org.openscience.cdk.io.iterator
[+] DefaultIteratingChemObjectReader (5)

package org.openscience.cdk.io.iterator.event
[+] DefaultEventChemObjectReader (5)

package org.openscience.cdk.io.program
[+] GaussianInputWriter (1)

package org.openscience.cdk.io.setting
[+] IOSetting (2)

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Other Changes in Data Types (17)

cdk-1.5.0.jar
package org.openscience.cdk
[+] CDKConstants (3)

package org.openscience.cdk.fingerprint
[+] IFingerprinter (1)

package org.openscience.cdk.interfaces
[+] IBond.Order (1)

package org.openscience.cdk.io
[+] IChemObjectIO (7)

package org.openscience.cdk.io.cml
[+] CMLCoreModule (1)

package org.openscience.cdk.iupac.parser
[+] SimpleCharStream (1)

package org.openscience.cdk.qsar
[+] DescriptorEngine (1)

package org.openscience.cdk.smiles.smarts.parser
[+] SimpleCharStream (1)
[+] SMARTSParserTokenManager (1)

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Java ARchives (1)

cdk-1.5.0.jar

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	Change	Effect
1	Field FLAG_MASKS has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class and cause IncompatibleClassChangeError exception.
2	Field SINGLE_ELECTRON_COUNT has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class and cause IncompatibleClassChangeError exception.
3	Field SINGLE_OR_DOUBLE has been added to this class.	No effect. NOTE: A static field from a super-interface of a client class may hide an added field (with the same name) inherited from the super-class of a client class and cause IncompatibleClassChangeError exception.

	Change	Effect
1	Abstract method addSetting ( IOSetting ) has been added to this interface.	No effect.
2	Abstract method addSettings ( Collection ) has been added to this interface.	No effect.
3	Abstract method getListeners ( ) has been added to this interface.	No effect.
4	Abstract method getSetting ( String ) has been added to this interface.	No effect.
5	Abstract method getSetting ( String, Class ) has been added to this interface.	No effect.
6	Abstract method getSettings ( ) has been added to this interface.	No effect.
7	Abstract method hasSetting ( String ) has been added to this interface.	No effect.

	Change	Effect
1	Field LOW (int) with the compile-time constant value 2 has been removed from this class.	A client program may change behavior.
2	Field MEDIUM (int) with the compile-time constant value 1 has been removed from this class.	A client program may change behavior.