Serialized Form

Package meshi.applications.corpus

Class meshi.applications.corpus.LoopResultVector extends java.util.Vector<LoopResults> implements Serializable

serialVersionUID: 314159L

Package meshi.applications.prediction

Class meshi.applications.prediction.ModelData extends java.util.ArrayList<Pair> implements Serializable

Class meshi.applications.prediction.PredictionSequenceAlignment extends SequenceAlignment implements Serializable

Serialized Fields

debug

boolean debug

A sequenceAlignment is extracted from a file whose name is referred to by the command line starting with key. The first sequence of the alignment is assumed to be a subsequence of the reference sequence. The reference sequence is used to correct the start field of the aligned sequences. The reference itself is assummed to have correct start field (that is, it indicates the correct residue numbers).

Package meshi.applications.prediction.beautify.unWarpEnergy

Class meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElementsList extends java.util.ArrayList<UnWarpEnergyElement> implements Serializable

Serialized Fields

numberOfUpdates

int numberOfUpdates

Package meshi.applications.prediction.beautify.warpEnergy

Class meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElementsList extends java.util.ArrayList<WarpEnergyElement> implements Serializable

Serialized Fields

numberOfUpdates

int numberOfUpdates

Package meshi.applications.prediction.homology.gui

Class meshi.applications.prediction.homology.gui.DistanceConstrainsDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

templateDistanceConstrainsWeightLabel

javax.swing.JLabel templateDistanceConstrainsWeightLabel

templateDistanceConstrainsWeightText

javax.swing.JTextField templateDistanceConstrainsWeightText

templateDistanceConstrainsSaturationLabel

javax.swing.JLabel templateDistanceConstrainsSaturationLabel

templateDistanceConstrainsInterSegmentToleranceLabel

javax.swing.JLabel templateDistanceConstrainsInterSegmentToleranceLabel

templateDistanceConstrainsInterSegmentFactorLabel

javax.swing.JLabel templateDistanceConstrainsInterSegmentFactorLabel

templateDistanceConstrainsIntraSegmentToleranceLabel

javax.swing.JLabel templateDistanceConstrainsIntraSegmentToleranceLabel

templateDistanceConstrainsIntraSegmentFactorLabel

javax.swing.JLabel templateDistanceConstrainsIntraSegmentFactorLabel

templateDistanceConstrainsInterSegmentFactorText

javax.swing.JTextField templateDistanceConstrainsInterSegmentFactorText

templateDistanceConstrainsIntraSegmentToleranceText

javax.swing.JTextField templateDistanceConstrainsIntraSegmentToleranceText

templateDistanceConstrainsIntraSegmentFactorText

javax.swing.JTextField templateDistanceConstrainsIntraSegmentFactorText

templateDistanceConstrainsSaturationText

javax.swing.JTextField templateDistanceConstrainsSaturationText

templateDistanceConstrainsInterSegmentToleranceText

javax.swing.JTextField templateDistanceConstrainsInterSegmentToleranceText

templateDistanceConstrainsUpToCutoffLabel

javax.swing.JLabel templateDistanceConstrainsUpToCutoffLabel

templateDistanceConstrainsUnsatisfiedCutoffLabel

javax.swing.JLabel templateDistanceConstrainsUnsatisfiedCutoffLabel

templateDistanceConstrainsUpToCutoffText

javax.swing.JTextField templateDistanceConstrainsUpToCutoffText

templateDistanceConstrainsUnsatisfiedCutoffText

javax.swing.JTextField templateDistanceConstrainsUnsatisfiedCutoffText

doneDistanceConstrainsWin

javax.swing.JButton doneDistanceConstrainsWin

Class meshi.applications.prediction.homology.gui.HomologyFrame extends javax.swing.JFrame implements Serializable

Serialized Fields

meshiExplanationLabel

javax.swing.JLabel meshiExplanationLabel

targetFilePathText

javax.swing.JTextField targetFilePathText

alnFiltPathText

javax.swing.JTextField alnFiltPathText

outputFilePathText

javax.swing.JTextField outputFilePathText

submit

javax.swing.JButton submit

commandsButton

javax.swing.JButton commandsButton

statusLabel

javax.swing.JLabel statusLabel

targetFileButton

javax.swing.JButton targetFileButton

alnFileButton

javax.swing.JButton alnFileButton

templateFilePathText

javax.swing.JTextField templateFilePathText

templateFileButton

javax.swing.JButton templateFileButton

outputDirectoryButton

javax.swing.JButton outputDirectoryButton

textSecondaryStructure

javax.swing.JTextField textSecondaryStructure

buttonSecondaryStructure

javax.swing.JButton buttonSecondaryStructure

textTargetName

javax.swing.JTextField textTargetName

labelTargetName

javax.swing.JLabel labelTargetName

buttonReset

javax.swing.JButton buttonReset

buttonExitSave

javax.swing.JButton buttonExitSave

buttonParameters

javax.swing.JButton buttonParameters

textfieldParameters

javax.swing.JTextField textfieldParameters

labelParameters

javax.swing.JLabel labelParameters

Class meshi.applications.prediction.homology.gui.InflateParametersDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

labelInflateEnergyWeight

javax.swing.JLabel labelInflateEnergyWeight

textInflateEnergyWeight

javax.swing.JTextField textInflateEnergyWeight

labelInflateEnergyRmsTarget

javax.swing.JLabel labelInflateEnergyRmsTarget

textInflateEnergyRmsTarget

javax.swing.JTextField textInflateEnergyRmsTarget

doneInflateParameters

javax.swing.JButton doneInflateParameters

Class meshi.applications.prediction.homology.gui.MinimizeParametersFullDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

labelMinimizeMaxSteps

javax.swing.JLabel labelMinimizeMaxSteps

labelLoopNIterationsAllAtoms

javax.swing.JLabel labelLoopNIterationsAllAtoms

labelLoopNIterationsBackbone

javax.swing.JLabel labelLoopNIterationsBackbone

labelLoopNIterationsCA

javax.swing.JLabel labelLoopNIterationsCA

labelMinimizeReportEvery

javax.swing.JLabel labelMinimizeReportEvery

labelMinimizeTolerane

javax.swing.JLabel labelMinimizeTolerane

doneMinimizeParametersFullDialog

javax.swing.JButton doneMinimizeParametersFullDialog

textLoopNIterationsAllAtoms

javax.swing.JTextField textLoopNIterationsAllAtoms

textLoopNIterationsBackbone

javax.swing.JTextField textLoopNIterationsBackbone

textLoopNIterationsCA

javax.swing.JTextField textLoopNIterationsCA

textMinimizeReportEvery

javax.swing.JTextField textMinimizeReportEvery

textMinimizeTolerane

javax.swing.JTextField textMinimizeTolerane

textMinimizeMaxSteps

javax.swing.JTextField textMinimizeMaxSteps

Class meshi.applications.prediction.homology.gui.MinimizeParametersShortDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

relaxToleranceLabel

javax.swing.JLabel relaxToleranceLabel

relaxToleranceText

javax.swing.JTextField relaxToleranceText

relaxReportEveryLabel

javax.swing.JLabel relaxReportEveryLabel

relaxMaxStepsLabel

javax.swing.JLabel relaxMaxStepsLabel

relaxReportEveryText

javax.swing.JTextField relaxReportEveryText

relaxMaxStepsText

javax.swing.JTextField relaxMaxStepsText

doneMiniParaShort

javax.swing.JButton doneMiniParaShort

Class meshi.applications.prediction.homology.gui.NonFrozenRangeDialog extends javax.swing.JFrame implements Serializable

Serialized Fields

textLoosenEdgeLength

javax.swing.JTextField textLoosenEdgeLength

labelNonFrozenRadius

javax.swing.JLabel labelNonFrozenRadius

labelLoosenEdgeLength

javax.swing.JLabel labelLoosenEdgeLength

textNonFrozenRadius

javax.swing.JTextField textNonFrozenRadius

buttonDoneNonFrozenRange

javax.swing.JButton buttonDoneNonFrozenRange

labelNonFrozenBondDepth

javax.swing.JLabel labelNonFrozenBondDepth

textNonFrozenBondDepth

javax.swing.JTextField textNonFrozenBondDepth

Class meshi.applications.prediction.homology.gui.OptionDialog extends javax.swing.JDialog implements Serializable

Serialized Fields

parametersExplanationLabel

javax.swing.JLabel parametersExplanationLabel

numberOfModelsLabel

javax.swing.JLabel numberOfModelsLabel

labelSeedNumber

javax.swing.JLabel labelSeedNumber

numberOfModelsText

javax.swing.JTextField numberOfModelsText

buttonDistanceConstrainParameters

javax.swing.JButton buttonDistanceConstrainParameters

buttonMinimizationParametersShort

javax.swing.JButton buttonMinimizationParametersShort

buttonMinimizationParametersFull

javax.swing.JButton buttonMinimizationParametersFull

buttonDoneOptionDialog

javax.swing.JButton buttonDoneOptionDialog

textSeedNumber

javax.swing.JTextField textSeedNumber

buttonEnergyWeights

javax.swing.JButton buttonEnergyWeights

buttonInflate

javax.swing.JButton buttonInflate

buttonParametersForChainCompletion

javax.swing.JButton buttonParametersForChainCompletion

buttonNonFrozenRange

javax.swing.JButton buttonNonFrozenRange

Class meshi.applications.prediction.homology.gui.ParametersForChainCompletion extends javax.swing.JFrame implements Serializable

Serialized Fields

clashDistanceLabel

javax.swing.JLabel clashDistanceLabel

clashDistanceText

javax.swing.JTextField clashDistanceText

nTraysLabel

javax.swing.JLabel nTraysLabel

maxNumberOfClashesLabel

javax.swing.JLabel maxNumberOfClashesLabel

nTraysText

javax.swing.JTextField nTraysText

maxNumberOfClashesText

javax.swing.JTextField maxNumberOfClashesText

doneParaForChainCompleteWin

javax.swing.JButton doneParaForChainCompleteWin

Class meshi.applications.prediction.homology.gui.WeightsForEnergyTerms extends javax.swing.JFrame implements Serializable

Serialized Fields

labelBondedEnergyWeight

javax.swing.JLabel labelBondedEnergyWeight

textBondedEnergyWeight

javax.swing.JTextField textBondedEnergyWeight

labelTwoTorsionsEnergyWeight

javax.swing.JLabel labelTwoTorsionsEnergyWeight

labelPlaneEnergyWeight

javax.swing.JLabel labelPlaneEnergyWeight

labelAngleEnergyWeight

javax.swing.JLabel labelAngleEnergyWeight

labelLennardJonesWeight

javax.swing.JLabel labelLennardJonesWeight

labelLennardJonesCaWeight

javax.swing.JLabel labelLennardJonesCaWeight

textAngleEnergyWeight

javax.swing.JTextField textAngleEnergyWeight

textLennardJonesWeight

javax.swing.JTextField textLennardJonesWeight

textLennardJonesCaWeight

javax.swing.JTextField textLennardJonesCaWeight

textTwoTorsionsEnergyWeight

javax.swing.JTextField textTwoTorsionsEnergyWeight

textPlaneEnergyWeight

javax.swing.JTextField textPlaneEnergyWeight

labelSolvateCA100EnergyWeight

javax.swing.JLabel labelSolvateCA100EnergyWeight

labelPropensityTorsionEnergyWeight

javax.swing.JLabel labelPropensityTorsionEnergyWeight

labelFlatRamachEnergyWeight

javax.swing.JLabel labelFlatRamachEnergyWeight

textSolvateCA100EnergyWeight

javax.swing.JTextField textSolvateCA100EnergyWeight

textPropensityTorsionEnergyWeight

javax.swing.JTextField textPropensityTorsionEnergyWeight

textFlatRamachEnergyWeight

javax.swing.JTextField textFlatRamachEnergyWeight

doneWeightsForEnergyTerms

javax.swing.JButton doneWeightsForEnergyTerms

labelSolventBb60

javax.swing.JLabel labelSolventBb60

textSolventBb60

javax.swing.JTextField textSolventBb60

textSolventAa40

javax.swing.JTextField textSolventAa40

labelSolventAa40

javax.swing.JLabel labelSolventAa40

labelOutOfPlaneEnergyWeight

javax.swing.JLabel labelOutOfPlaneEnergyWeight

textOutOfPlaneEnergyWeight

javax.swing.JTextField textOutOfPlaneEnergyWeight

labelAlphaAngleEnergyWeight

javax.swing.JLabel labelAlphaAngleEnergyWeight

textAlphaAngleEnergyWeight

javax.swing.JTextField textAlphaAngleEnergyWeight

labelAlphaTorsionEnergyWeight

javax.swing.JLabel labelAlphaTorsionEnergyWeight

textAlphaTorsionEnergyWeight

javax.swing.JTextField textAlphaTorsionEnergyWeight

labelHydrogenBondsWeight

javax.swing.JLabel labelHydrogenBondsWeight

textHydrogenBondsWeight

javax.swing.JTextField textHydrogenBondsWeight

labelHydrogenBondsPairsWeight

javax.swing.JLabel labelHydrogenBondsPairsWeight

textHydrogenBondsPairsWeight

javax.swing.JTextField textHydrogenBondsPairsWeight

labelExcludedVolumeWeight

javax.swing.JLabel labelExcludedVolumeWeight

textExcludedVolumeWeight

javax.swing.JTextField textExcludedVolumeWeight

Package meshi.energy

Class meshi.energy.AbstractEnergy.UpdateableList extends java.util.ArrayList<Updateable> implements Serializable

Package meshi.energy.hydrogenBond

Class meshi.energy.hydrogenBond.HydrogenBondsParametersList extends LennardJonesParametersList implements Serializable

Serialized Fields

nitrogens

AtomList nitrogens

Class meshi.energy.hydrogenBond.LennardJonesParametersList extends ParametersList implements Serializable

Class meshi.energy.hydrogenBond.SynchronizedUpdateException extends java.lang.IllegalStateException implements Serializable

Package meshi.energy.hydrogenBondsPairs

Class meshi.energy.hydrogenBondsPairs.BetaParametersList extends HydrogenBondsPairsParametersList implements Serializable

Class meshi.energy.hydrogenBondsPairs.HelixParametersList extends HydrogenBondsPairsParametersList implements Serializable

Class meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParametersList extends ParametersList implements Serializable

Serialized Fields

nonExsisting

Parameters nonExsisting

searchCounter

int searchCounter

Class meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList extends java.util.ArrayList<PairOfHydrogenBondsElements> implements Serializable

Serialized Fields

insertion

int insertion

deletions

int deletions

hBondList

HBondList hBondList

numberOfUpdates

int numberOfUpdates

debug

boolean debug

isWithinRmax

PairsOfHBEElementsList.IsWithInRmax isWithinRmax

Package meshi.energy.pairwiseNonBondedTerms.ExcludedVol

Class meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParametersList extends java.util.ArrayList<ExcludedVolParameters> implements Serializable

Package meshi.energy.sideChainModelingSolvate

Class meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList extends java.util.ArrayList implements Serializable

Serialized Fields

NTsai

int NTsai

atomicTypeConverter

int[] atomicTypeConverter

maxEnd

double maxEnd

atomTypeSplines

Spline1D[] atomTypeSplines

Cend

double[][] Cend

Cp1

double[][] Cp1

Cp2

double[][] Cp2

CvalAtp1

double[][] CvalAtp1

CvalAtp2

double[][] CvalAtp2

HBend

double[][] HBend

HBp1

double[][] HBp1

HBp2

double[][] HBp2

HBvalAtp1

double[][] HBvalAtp1

HBvalAtp2

double[][] HBvalAtp2

Package meshi.energy.simpleEnergyTerms

Class meshi.energy.simpleEnergyTerms.ParametersList extends java.util.ArrayList<Parameters> implements Serializable

Serialized Fields

sortable

boolean sortable

True if the list is sortable.

sorted

boolean sorted

True if the list is sorted.

Package meshi.energy.simpleEnergyTerms.alphaAngle

Class meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParametersList extends ParametersList implements Serializable

Package meshi.energy.simpleEnergyTerms.alphaTorsion

Class meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionParametersList extends ParametersList implements Serializable

Package meshi.energy.simpleEnergyTerms.angle

Class meshi.energy.simpleEnergyTerms.angle.AngleParametersList extends ParametersList implements Serializable

Package meshi.energy.simpleEnergyTerms.bond

Class meshi.energy.simpleEnergyTerms.bond.BondParametersList extends ParametersList implements Serializable

Package meshi.energy.simpleEnergyTerms.compositeTorsions

Class meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList extends java.util.ArrayList<ResidueTorsions> implements Serializable

Serialized Fields

numberOfUpdates

int numberOfUpdates

Package meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity

Class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityParametersList extends ParametersList implements Serializable

Package meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP

Class meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DParametersList extends ParametersList implements Serializable

Serialized Fields

spl

SplinedPolynomialsLoader spl

Package meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran

Class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranParametersList extends ParametersList implements Serializable

Serialized Fields

spl

SplinedPolynomialsLoader spl

Package meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain

Class meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersList extends ParametersList implements Serializable

Package meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary

Class meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersList extends ParametersList implements Serializable

Package meshi.energy.simpleEnergyTerms.inflate

Class meshi.energy.simpleEnergyTerms.inflate.InflateParametersList extends ParametersList implements Serializable

Package meshi.energy.simpleEnergyTerms.outOfPlane

Class meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParametersList extends ParametersList implements Serializable

Package meshi.energy.simpleEnergyTerms.plane

Class meshi.energy.simpleEnergyTerms.plane.PlaneParametersList extends ParametersList implements Serializable

Package meshi.energy.templateEnergy

Class meshi.energy.templateEnergy.TemplateEnergyElementsList extends java.util.ArrayList<TemplateEnergyElement> implements Serializable

Serialized Fields

numberOfUpdates

int numberOfUpdates

Package meshi.geometry

Class meshi.geometry.AngleList extends java.util.ArrayList<Angle> implements Serializable

Serialized Fields

numberOfUpdates

int numberOfUpdates

Class meshi.geometry.GridCell extends java.util.ArrayList<AtomCore> implements Serializable

Class meshi.geometry.QuickAndDirtyAngleList extends AngleList implements Serializable

Class meshi.geometry.QuickAndDirtyTorsionList extends TorsionList implements Serializable

Class meshi.geometry.TorsionList extends java.util.ArrayList<Torsion> implements Serializable

Serialized Fields

numberOfUpdates

int numberOfUpdates

Class meshi.geometry.TorsionPairList extends java.util.ArrayList<TorsionPair> implements Serializable

Serialized Fields

numberOfUpdates

int numberOfUpdates

Package meshi.geometry.putH

Class meshi.geometry.putH.NotEnoughBoundAtomsException extends java.lang.Exception implements Serializable

Package meshi.molecularElements

Class meshi.molecularElements.Chain extends ResidueList implements Serializable

Serialized Fields

name

java.lang.String name

The first Non Dummy Residue (may but also may not be number 1).

protein

Protein protein

Class meshi.molecularElements.ChainList extends java.util.ArrayList<Chain> implements Serializable

Serialized Fields

protein

Protein protein

Class meshi.molecularElements.ResidueList extends java.util.ArrayList<Residue> implements Serializable

Package meshi.molecularElements.atoms

Class meshi.molecularElements.atoms.AtomList extends java.util.ArrayList<Atom> implements Serializable

Serialized Fields

sourceFile

MeshiLineReader sourceFile

molecularSystem

MolecularSystem molecularSystem

comment

java.lang.String comment

Class meshi.molecularElements.atoms.AtomPairList extends java.util.ArrayList<AtomPair> implements Serializable

Class meshi.molecularElements.atoms.MolecularSystem extends java.util.ArrayList<AtomCore> implements Serializable

Serialized Fields

ID

int ID

numberOfAtoms

int numberOfAtoms

Package meshi.optimizers

Class meshi.optimizers.LineSearchException extends java.lang.Exception implements Serializable

Serialized Fields

code

int code

Class meshi.optimizers.NoConvergenceException extends java.lang.Exception implements Serializable

Class meshi.optimizers.OptimizerException extends java.lang.Exception implements Serializable

Package meshi.PDB

Class meshi.PDB.UnknownAtomTypeException extends java.lang.Exception implements Serializable

Package meshi.sequences

Class meshi.sequences.AccesibilitySequence extends Sequence implements Serializable

Class meshi.sequences.AtomAlignment extends java.util.ArrayList<AtomAlignmentColumn> implements Serializable

Class meshi.sequences.FastaList extends SequenceList implements Serializable

Class meshi.sequences.ResidueAlignment extends java.util.ArrayList<ResidueAlignmentColumn> implements Serializable

Serialized Fields

lastColumn

ResidueAlignmentColumn lastColumn

comments

StringList comments

Class meshi.sequences.ResidueAlignmentOfModels extends ResidueAlignment implements Serializable

Class meshi.sequences.ResidueSequence extends Sequence implements Serializable

Class meshi.sequences.ResidueTypeException extends java.lang.RuntimeException implements Serializable

Class meshi.sequences.SecondaryStructureSequence extends Sequence implements Serializable

Class meshi.sequences.Sequence extends SequenceAlignment implements Serializable

Serialized Fields

charFilter

SequenceCharFilter charFilter

Class meshi.sequences.SequenceAlignment extends java.util.ArrayList<SequenceAlignmentColumn> implements Serializable

Serialized Fields

score

java.lang.Double score

comments

StringList comments

Class meshi.sequences.SequenceList extends java.util.ArrayList<Sequence> implements Serializable

Serialized Fields

fileName

java.lang.String fileName

Package meshi.sequences.aligner

Class meshi.sequences.aligner.AminoAcidSubstitutionMatrix extends java.lang.Object implements Serializable

Class meshi.sequences.aligner.FastaReader extends java.lang.Object implements Serializable

Class meshi.sequences.aligner.FileToString extends java.lang.Object implements Serializable

Class meshi.sequences.aligner.FWriter extends java.lang.Object implements Serializable

Package meshi.symmetryComplex.energy.cylinder

Class meshi.symmetryComplex.energy.cylinder.CylinderParametersList extends ParametersList implements Serializable

Serialized Fields

height

double height

innerR

double innerR

outerR

double outerR

Package meshi.symmetryComplex.energy.edmEnergy

Class meshi.symmetryComplex.energy.edmEnergy.EDMEnergyParametersList extends ParametersList implements Serializable

Serialized Fields

ep

EDMEnergyParameters ep

Package meshi.symmetryComplex.molecularImageElements

Class meshi.symmetryComplex.molecularImageElements.ImageAtomList extends AtomList implements Serializable

Serialized Fields

transformation

Transformation transformation

Class meshi.symmetryComplex.molecularImageElements.ImageChain extends Chain implements Serializable

Serialized Fields

transformation

Transformation transformation

source

Chain source

Package meshi.util

Class meshi.util.CommandList extends java.util.ArrayList<Command> implements Serializable

Serialized Fields

comment

java.lang.String comment

The file from which the comands were read. Usefull for debugging.

debug

boolean debug

commandsException

CommandsException commandsException

Class meshi.util.MeshiException extends java.lang.RuntimeException implements Serializable

Class meshi.util.MeshiInitException extends java.lang.Exception implements Serializable

Serialized Fields

message

java.lang.String message

Class meshi.util.UpdateableException extends java.lang.Exception implements Serializable

Package meshi.util.mathTools.Jama

Class meshi.util.mathTools.Jama.CholeskyDecomposition extends java.lang.Object implements Serializable

Serialized Fields

L

double[][] L

Array for internal storage of decomposition.

internal array storage.

n

int n

Row and column dimension (square matrix).

matrix dimension.

isspd

boolean isspd

Symmetric and positive definite flag.

is symmetric and positive definite flag.

Class meshi.util.mathTools.Jama.EigenvalueDecomposition extends java.lang.Object implements Serializable

Serialized Fields

n

int n

Row and column dimension (square matrix).

matrix dimension.

issymmetric

boolean issymmetric

Symmetry flag.

internal symmetry flag.

d

double[] d

Arrays for internal storage of eigenvalues.

internal storage of eigenvalues.

e

double[] e

Arrays for internal storage of eigenvalues.

internal storage of eigenvalues.

V

double[][] V

Array for internal storage of eigenvectors.

internal storage of eigenvectors.

H

double[][] H

Array for internal storage of nonsymmetric Hessenberg form.

internal storage of nonsymmetric Hessenberg form.

ort

double[] ort

Working storage for nonsymmetric algorithm.

working storage for nonsymmetric algorithm.

Class meshi.util.mathTools.Jama.LUDecomposition extends java.lang.Object implements Serializable

Serialized Fields

LU

double[][] LU

Array for internal storage of decomposition.

internal array storage.

m

int m

Row and column dimensions, and pivot sign.

column dimension.

n

int n

Row and column dimensions, and pivot sign.

column dimension.

pivsign

int pivsign

Row and column dimensions, and pivot sign.

column dimension.

piv

int[] piv

Internal storage of pivot vector.

pivot vector.

Class meshi.util.mathTools.Jama.Matrix extends java.lang.Object implements Serializable

Serialized Fields

A

double[][] A

Array for internal storage of elements.

internal array storage.

m

int m

Row and column dimensions.

row dimension.

n

int n

Row and column dimensions.

row dimension.

Class meshi.util.mathTools.Jama.QRDecomposition extends java.lang.Object implements Serializable

Serialized Fields

QR

double[][] QR

Array for internal storage of decomposition.

internal array storage.

m

int m

Row and column dimensions.

column dimension.

n

int n

Row and column dimensions.

column dimension.

Rdiag

double[] Rdiag

Array for internal storage of diagonal of R.

diagonal of R.

Class meshi.util.mathTools.Jama.SingularValueDecomposition extends java.lang.Object implements Serializable

Serialized Fields

U

double[][] U

Arrays for internal storage of U and V.

internal storage of U.

V

double[][] V

Arrays for internal storage of U and V.

internal storage of U.

s

double[] s

Array for internal storage of singular values.

internal storage of singular values.

m

int m

Row and column dimensions.

row dimension.

n

int n

Row and column dimensions.

row dimension.

Package meshi.util.overlap

Class meshi.util.overlap.RmsException extends java.lang.Exception implements Serializable

Package meshi.util.string

Class meshi.util.string.StringList extends java.util.ArrayList<java.lang.String> implements Serializable

Serialized Fields

comment

java.lang.String comment