Hierarchy For All Packages

Package Hierarchies:

aligner, meshi.applications.corpus, meshi.applications.hubbard, meshi.applications.prediction, meshi.applications.prediction.beautify, meshi.applications.prediction.beautify.unWarpEnergy, meshi.applications.prediction.beautify.warpEnergy, meshi.applications.prediction.homology, meshi.applications.prediction.homology.gui, meshi.energy, meshi.energy.hydrogenBond, meshi.energy.hydrogenBondsAngle, meshi.energy.hydrogenBondsPairs, meshi.energy.linearRG, meshi.energy.pairwiseNonBondedTerms, meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma, meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics, meshi.energy.pairwiseNonBondedTerms.evRot1BB, meshi.energy.pairwiseNonBondedTerms.excludedVol, meshi.energy.pairwiseNonBondedTerms.ExcludedVol, meshi.energy.pairwiseNonBondedTerms.excludedVolOLD, meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol, meshi.energy.pairwiseNonBondedTerms.LennardJones, meshi.energy.RG, meshi.energy.sideChainModelingSolvate, meshi.energy.simpleEnergyTerms, meshi.energy.simpleEnergyTerms.alphaAngle, meshi.energy.simpleEnergyTerms.alphaTorsion, meshi.energy.simpleEnergyTerms.angle, meshi.energy.simpleEnergyTerms.bond, meshi.energy.simpleEnergyTerms.compositeTorsions, meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity, meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP, meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran, meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain, meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary, meshi.energy.simpleEnergyTerms.inflate, meshi.energy.simpleEnergyTerms.inflate.simpleInflate, meshi.energy.simpleEnergyTerms.outOfPlane, meshi.energy.simpleEnergyTerms.plane, meshi.energy.simpleEnergyTerms.tether, meshi.energy.solvate, meshi.energy.solvate.hydrogenBonds, meshi.energy.solvateRot1, meshi.energy.templateEnergy, meshi.geometry, meshi.geometry.fragments, meshi.geometry.putH, meshi.geometry.rotamers, meshi.molecularElements, meshi.molecularElements.allAtoms, meshi.molecularElements.atoms, meshi.molecularElements.ca, meshi.molecularElements.extendedAtoms, meshi.optimizers, meshi.parameters, meshi.PDB, meshi.sequences, meshi.sequences.aligner, meshi.symmetryComplex.energy, meshi.symmetryComplex.energy.cylinder, meshi.symmetryComplex.energy.edmEnergy, meshi.symmetryComplex.geometryImage, meshi.symmetryComplex.molecularImageElements, meshi.symmetryComplex.proteinsGJ, meshi.symmetryComplex.topologyMap, meshi.symmetryComplex.transformations, meshi.symmetryComplex.utils, meshi.util, meshi.util.alignmentTools, meshi.util.dssp, meshi.util.file, meshi.util.filters, meshi.util.formats, meshi.util.histogram, meshi.util.mathTools, meshi.util.mathTools.Jama, meshi.util.overlap, meshi.util.rotamericTools, meshi.util.string

Class Hierarchy

• java.lang.Object
  • • meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameters
  • meshi.applications.prediction.AbitSmarterLoopBuilder
  • meshi.applications.prediction.AbitSmarterLoopBuilder.LoopComperator (implements java.util.Comparator<T>)
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • meshi.energy.AbstractEnergy.UpdateableList
        • meshi.geometry.AngleList (implements meshi.util.Updateable)
          • meshi.geometry.QuickAndDirtyAngleList
        • meshi.sequences.AtomAlignment
        • meshi.molecularElements.atoms.AtomList
          • meshi.symmetryComplex.molecularImageElements.ImageAtomList
        • meshi.molecularElements.atoms.AtomPairList
        • CalculateEnergyFromStructuresListAverages.GaussianAttributes (implements meshi.util.MeshiAttribute)
        • meshi.molecularElements.ChainList
        • ColorByEnergy.GaussianAttributes (implements meshi.util.MeshiAttribute)
        • meshi.util.CommandList (implements meshi.util.KeyWords)
        • meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParametersList
        • meshi.geometry.GridCell
        • meshi.util.MeshiProgram.GlobalElementList
        • meshi.applications.prediction.ModelData
        • meshi.molecularElements.atoms.MolecularSystem
        • meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList (implements meshi.util.Updateable)
        • meshi.energy.simpleEnergyTerms.ParametersList
          • meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParametersList
          • meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionParametersList (implements meshi.parameters.MeshiPotential)
          • meshi.energy.simpleEnergyTerms.angle.AngleParametersList
          • meshi.energy.simpleEnergyTerms.bond.BondParametersList
          • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DParametersList (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions, meshi.energy.Parameters)
          • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityParametersList (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
          • meshi.symmetryComplex.energy.cylinder.CylinderParametersList
          • meshi.symmetryComplex.energy.edmEnergy.EDMEnergyParametersList
          • meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParametersList
            • meshi.energy.hydrogenBondsPairs.BetaParametersList
            • meshi.energy.hydrogenBondsPairs.HelixParametersList
          • meshi.energy.simpleEnergyTerms.inflate.InflateParametersList
          • meshi.energy.hydrogenBond.LennardJonesParametersList
            • meshi.energy.hydrogenBond.HydrogenBondsParametersList
          • meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParametersList
          • meshi.energy.simpleEnergyTerms.plane.PlaneParametersList
          • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranParametersList (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
          • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersList (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
          • meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersList (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
        • meshi.sequences.ResidueAlignment
          • meshi.sequences.ResidueAlignmentOfModels
        • meshi.molecularElements.ResidueList
          • meshi.applications.prediction.AbitSmarterLoopBuilder.Loop
          • meshi.molecularElements.Chain
            • meshi.symmetryComplex.molecularImageElements.ImageChain
            • Pdb2Fasta.MyChain
          • HomologyModeling.Loop
        • meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList (implements meshi.util.Updateable)
        • meshi.sequences.SequenceAlignment
          • meshi.applications.prediction.PredictionSequenceAlignment
          • meshi.sequences.Sequence
            • meshi.sequences.AccesibilitySequence
            • meshi.sequences.ResidueSequence
            • meshi.sequences.SecondaryStructureSequence
        • meshi.sequences.SequenceList (implements meshi.util.KeyWords)
          • meshi.sequences.FastaList
        • meshi.energy.sideChainModelingSolvate.SideChainSolvateParametersList (implements meshi.energy.Parameters)
        • meshi.util.string.StringList
          • AbInitio.AbInitioLogger (implements meshi.util.Logger)
          • Optimize.OptimizeLogger (implements meshi.util.Logger)
          • Refine.RefineLogger (implements meshi.util.Logger)
        • meshi.energy.templateEnergy.TemplateEnergyElementsList (implements meshi.util.Updateable)
        • meshi.geometry.TorsionList (implements meshi.util.Updateable)
          • meshi.geometry.QuickAndDirtyTorsionList
        • meshi.geometry.TorsionPairList (implements meshi.util.Updateable)
        • meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElementsList (implements meshi.util.Updateable)
        • meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElementsList (implements meshi.util.Updateable)
      • java.util.Vector<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • meshi.applications.corpus.LoopResultVector
  • meshi.energy.AbstractEnergy (implements meshi.util.Attributable, meshi.util.Updateable)
    • meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSumma
    • meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSumma
    • meshi.energy.CooperativeEnergyTerm
      • meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBEnergy (implements meshi.util.rotamericTools.Rot1Arrays)
      • meshi.energy.linearRG.LinearRgEnergy
      • meshi.energy.RG.RgEnergy
      • meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy
      • meshi.energy.solvate.SolvateEnergy
      • meshi.energy.solvateRot1.SolvateRot1Energy (implements meshi.util.rotamericTools.Rot1Arrays)
    • meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSumma
    • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityEnergy (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
    • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandran (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
    • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityEnergy (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
    • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandran (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
    • meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSumma
    • meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyTerm
      • meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergy
        • meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergy
        • meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergy
      • meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostatics
      • meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVol
      • meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVol (implements meshi.util.Classes)
      • meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolOLD
      • meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVol
      • meshi.energy.hydrogenBond.HydrogenBondsEnergy
      • meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergy
      • meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJones
    • meshi.energy.simpleEnergyTerms.SimpleEnergyTerm
      • meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergy
      • meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergy
      • meshi.energy.simpleEnergyTerms.angle.AngleEnergy
      • meshi.energy.simpleEnergyTerms.bond.BondEnergy
      • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DEnergy (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
      • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergy (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
      • meshi.symmetryComplex.energy.cylinder.CylinderEnergy
      • meshi.symmetryComplex.energy.edmEnergy.EDMEnergy
      • meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergy
      • meshi.energy.simpleEnergyTerms.plane.PlaneEnergy
      • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranEnergy (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
      • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergy (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
      • meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate
      • meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergy (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
      • meshi.symmetryComplex.energy.SymmetryEnergy
      • meshi.energy.simpleEnergyTerms.tether.TetherEnergy
    • meshi.energy.templateEnergy.TemplateEnergy (implements meshi.util.Updateable)
    • meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergy (implements meshi.util.Updateable)
    • meshi.applications.prediction.beautify.warpEnergy.WarpEnergy (implements meshi.util.Updateable)
  • meshi.energy.AbstractEnergy.IsEnergy (implements meshi.util.filters.Filter)
  • meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBond
    • meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyat (implements meshi.energy.solvate.hydrogenBonds.DahiyatImplementationConstants)
  • meshi.energy.solvate.hydrogenBonds.AbstractHydrogenBondList (implements meshi.util.Updateable)
    • meshi.energy.solvate.hydrogenBonds.HydrogenBondDahiyatList
  • meshi.util.filters.AcceptAll (implements meshi.util.filters.Filter)
  • meshi.sequences.AlignmentCell (implements meshi.util.Attributable)
    • meshi.sequences.AtomAlignmentCell
    • meshi.sequences.ResidueAlignmentCell
    • meshi.sequences.SequenceAlignmentCell (implements meshi.util.MeshiAttribute)
  • meshi.sequences.AlignmentColumn
    • meshi.sequences.AtomAlignmentColumn
    • meshi.sequences.ResidueAlignmentColumn
    • meshi.sequences.SequenceAlignmentColumn (implements meshi.util.MeshiAttribute)
  • meshi.util.alignmentTools.AlignmentTools (implements meshi.util.KeyWords)
  • meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleParameters (implements meshi.energy.Parameters)
  • meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionParameters (implements meshi.energy.Parameters)
  • aligner.AminoAcidSubstitutionMatrix (implements aligner.SubstitutionMatrix)
  • meshi.geometry.Angle (implements meshi.util.Updateable)
    • meshi.geometry.QuickAndDirtyAngle
  • meshi.energy.simpleEnergyTerms.angle.AngleParameters (implements java.lang.Comparable<T>, meshi.energy.Parameters)
  • meshi.energy.simpleEnergyTerms.angle.AngleParameters.isA (implements meshi.util.filters.Filter)
  • meshi.geometry.ArcCos
  • meshi.molecularElements.atoms.Atom (implements meshi.util.Attributable, java.lang.Comparable<T>, meshi.util.Verbose)
    • meshi.symmetryComplex.molecularImageElements.ImageAtom
    • Pdb2Fasta.MyAtom
  • meshi.sequences.AtomAlignment.IsAlignmentColumn (implements meshi.util.filters.Filter)
  • meshi.molecularElements.atoms.AtomComparator (implements java.util.Comparator<T>)
  • meshi.molecularElements.atoms.AtomCore
  • meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaParameters (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
  • meshi.molecularElements.atoms.AtomList.AcceptChainFilter (implements meshi.util.filters.Filter)
  • meshi.molecularElements.atoms.AtomList.BackboneFilter (implements meshi.util.filters.Filter)
  • meshi.molecularElements.atoms.AtomList.IsAtom (implements meshi.util.filters.Filter)
  • meshi.molecularElements.atoms.AtomList.IsDefrostedFilter (implements meshi.util.filters.Filter)
  • meshi.molecularElements.atoms.AtomList.IsFrozenFilter (implements meshi.util.filters.Filter)
  • meshi.molecularElements.atoms.AtomList.NonHydrogen (implements meshi.util.filters.Filter)
  • meshi.molecularElements.atoms.AtomList.RejectChainFilter (implements meshi.util.filters.Filter)
  • meshi.molecularElements.atoms.AtomPair (implements java.lang.Comparable<T>)
  • meshi.molecularElements.atoms.AtomPairList.IsAtomPair (implements meshi.util.filters.Filter)
  • meshi.util.AttributesRack
  • meshi.util.filters.BackboneFilter (implements meshi.util.filters.Filter)
  • meshi.applications.corpus.BasicLoopResult
  • Beautify.BeautifyLogger (implements meshi.util.Logger)
  • meshi.applications.prediction.beautify.BeautifyAttribute (implements meshi.util.MeshiAttribute)
  • meshi.energy.hydrogenBondsPairs.BetaParametersList.IsHydrogenBondsPairsParameters (implements meshi.util.filters.Filter)
  • meshi.energy.simpleEnergyTerms.bond.BondParameters (implements java.lang.Comparable<T>, meshi.energy.Parameters)
  • meshi.energy.simpleEnergyTerms.bond.BondParameters.isA (implements meshi.util.filters.Filter)
  • meshi.symmetryComplex.topologyMap.BoundariesMap (implements meshi.util.KeyWords)
  • meshi.applications.prediction.homology.CaAtomFilter (implements meshi.util.filters.Filter)
  • meshi.util.filters.CaFilter (implements meshi.util.filters.Filter)
  • CalculateEnergyFromStructuresListAverages.AveragesAndMaxs
  • CalculateEnergyFromStructuresListAverages.DistanceFromCatalyticAttribute (implements meshi.util.MeshiAttribute)
  • CalculateEnergyFromStructuresListAverages.GaussianAttribute
  • meshi.sequences.aligner.Cell
  • meshi.molecularElements.Chain.IsResidue (implements meshi.util.filters.Filter)
  • meshi.molecularElements.ChainList.IsChain (implements meshi.util.filters.Filter)
  • meshi.util.mathTools.Jama.CholeskyDecomposition (implements java.io.Serializable)
  • meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CoefficientsMatrixForAtomPairSpline
  • ColorByEnergy.DistanceFromCatalyticAttribute (implements meshi.util.MeshiAttribute)
  • ColorByEnergy.GaussianAttribute
  • meshi.util.Command (implements meshi.util.KeyWords)
  • meshi.util.CommandsException
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • meshi.applications.prediction.homology.gui.DistanceConstrainsDialog
            • meshi.applications.prediction.homology.gui.InflateParametersDialog
            • meshi.applications.prediction.homology.gui.MinimizeParametersFullDialog
            • meshi.applications.prediction.homology.gui.MinimizeParametersShortDialog
            • meshi.applications.prediction.homology.gui.OptionDialog
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • meshi.applications.prediction.homology.gui.HomologyFrame
            • meshi.applications.prediction.homology.gui.NonFrozenRangeDialog
            • meshi.applications.prediction.homology.gui.ParametersForChainCompletion
            • meshi.applications.prediction.homology.gui.WeightsForEnergyTerms
  • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DParameters (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions, meshi.energy.Parameters)
  • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityParameters (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions, meshi.energy.Parameters)
  • meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSummaParameters (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
  • meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSummaParameters (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
  • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityParameters (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
  • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandranParameters (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
  • meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZParameters (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
  • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityParameters (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
  • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandranParameters (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
  • meshi.geometry.Coordinates
    • meshi.geometry.FrozenCoordinates
  • meshi.symmetryComplex.proteinsGJ.CoordinatesAssigner (implements meshi.util.KeyWords)
  • meshi.applications.corpus.Corpus (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions, meshi.util.KeyWords, meshi.parameters.MeshiPotential)
  • meshi.applications.corpus.CorrectRottenRamachandrans
  • meshi.symmetryComplex.energy.cylinder.CylinderParameters (implements meshi.energy.Parameters)
  • meshi.util.filters.Differs (implements meshi.util.filters.Filter)
  • meshi.geometry.Distance (implements meshi.util.Attributable)
    • meshi.geometry.BondedDistance
    • meshi.geometry.DistanceMirror
    • meshi.geometry.FreeDistance
    • meshi.geometry.FrozenDistance
      • meshi.geometry.BondedFrozenDistance
  • meshi.applications.prediction.homology.gui.DistanceConstrainsDialogLayout (implements java.awt.LayoutManager)
  • meshi.geometry.DistanceList (implements java.lang.Iterable<T>)
    • meshi.energy.hydrogenBond.HBdistanceList
      • meshi.energy.hydrogenBond.HBondList (implements meshi.util.Updateable)
    • meshi.geometry.MatrixRow
      • meshi.geometry.MatrixRowCaOnly
      • meshi.symmetryComplex.geometryImage.MatrixRowNoImageAtoms
  • meshi.geometry.DistanceList.DistanceIterator (implements java.util.Iterator<E>)
  • meshi.geometry.DistanceMatrix.Indicator
  • meshi.geometry.DistanceMatrix.RowIterator (implements java.util.Iterator<E>)
  • meshi.geometry.DistanceMatrixBondedOnly.DistanceComparator (implements java.util.Comparator<T>)
  • meshi.util.DoNothingExceptionHandler (implements meshi.util.ExceptionHandler)
  • meshi.sequences.aligner.DpMatrix
  • meshi.geometry.fragments.DresserFullFrag (implements meshi.util.KeyWords)
  • meshi.util.dssp.DSSP
  • meshi.geometry.rotamers.DunbrackLib (implements meshi.util.KeyWords)
  • meshi.symmetryComplex.energy.edmEnergy.EDMEnergyParameters (implements meshi.energy.Parameters)
  • meshi.symmetryComplex.energy.edmEnergy.EDMSplinedPolynomial
  • meshi.util.mathTools.Jama.EigenvalueDecomposition (implements java.io.Serializable)
  • meshi.energy.EnergyCreator (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
    • meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.AtomicPairwisePMFSummaCreator (implements meshi.util.KeyWords)
    • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DCreator (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
    • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityCreator (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
    • meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeAtomicPairwisePMFSummaCreator (implements meshi.util.KeyWords)
    • meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativePerAtomSummaCreator (implements meshi.util.KeyWords)
    • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativePropensityCreator (implements meshi.util.KeyWords)
    • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeRamachandranCreator (implements meshi.util.KeyWords)
    • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CooperativeZPropensityCreator (implements meshi.util.KeyWords)
    • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.CooperativeZRamachandranCreator (implements meshi.util.KeyWords)
    • meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.CooperativeZSummaCreator (implements meshi.util.KeyWords)
    • meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticCreator (implements meshi.util.KeyWords)
    • meshi.symmetryComplex.energy.cylinder.CylinderCreator (implements meshi.util.KeyWords)
    • meshi.symmetryComplex.energy.edmEnergy.EDMEnergyCreator (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
    • meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBCreator (implements meshi.util.KeyWords)
    • meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolCreator (implements meshi.util.KeyWords)
    • meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolCreator (implements meshi.util.KeyWords)
    • meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolCreatorOLD (implements meshi.util.KeyWords)
    • meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolCreator (implements meshi.util.KeyWords)
    • meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleCreator
    • meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleCreator
    • meshi.energy.hydrogenBond.HydrogenBondsCreator (implements meshi.util.KeyWords)
    • meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsCreator
    • meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesCreator (implements meshi.util.KeyWords)
      • HeliumClusterMinimization.HeliumLennardJonesCreator (implements meshi.util.KeyWords)
      • meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesCreatorCa
    • meshi.energy.linearRG.LinearRgCreator (implements meshi.util.KeyWords)
    • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranCreator (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
    • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyCreator (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
    • meshi.energy.RG.RgCreator (implements meshi.util.KeyWords)
    • meshi.energy.sideChainModelingSolvate.SideChainSolvateCreator (implements meshi.util.KeyWords)
    • meshi.energy.simpleEnergyTerms.SimpleEnergyCreator
      • meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleCreator (implements meshi.util.KeyWords)
      • meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionCreator (implements meshi.util.KeyWords)
      • meshi.energy.simpleEnergyTerms.angle.AngleCreator (implements meshi.util.KeyWords)
      • meshi.energy.simpleEnergyTerms.bond.BondCreator (implements meshi.util.KeyWords)
      • meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneCreator (implements meshi.util.KeyWords)
      • meshi.energy.simpleEnergyTerms.plane.PlaneCreator (implements meshi.util.KeyWords)
      • meshi.energy.simpleEnergyTerms.tether.TetherCreator (implements meshi.util.KeyWords)
    • meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateCreator (implements meshi.util.KeyWords)
    • meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyCreator (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
    • meshi.energy.solvate.SolvateCreatorHBforMinimization (implements meshi.util.KeyWords)
    • meshi.energy.solvate.SolvateCreatorLongHB (implements meshi.util.KeyWords)
    • meshi.energy.solvate.SolvateCreatorRegularHB (implements meshi.util.KeyWords)
    • meshi.energy.solvateRot1.SolvateRot1Creator (implements meshi.util.KeyWords)
    • meshi.symmetryComplex.energy.SymmetryCreator (implements meshi.util.KeyWords)
    • meshi.energy.templateEnergy.TemplateEnergyCreator
    • meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyCreator
    • meshi.applications.prediction.beautify.warpEnergy.WarpEnergyCreator
  • meshi.energy.EnergyElement
    • meshi.energy.simpleEnergyTerms.alphaAngle.AlphaAngleEnergyElement (implements meshi.parameters.MeshiPotential)
    • meshi.energy.simpleEnergyTerms.alphaTorsion.AlphaTorsionEnergyElement (implements meshi.parameters.MeshiPotential)
    • meshi.energy.simpleEnergyTerms.angle.AngleEnergyElement
    • meshi.energy.simpleEnergyTerms.bond.BondEnergyElement
    • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity2DwithPP.CompositePropensity2DEnergyElement (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
    • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.CompositePropensityEnergyElement (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
    • meshi.symmetryComplex.energy.cylinder.CylinderEnergyElement
    • meshi.symmetryComplex.energy.edmEnergy.EDMEnergyElement
    • meshi.energy.pairwiseNonBondedTerms.NonBondedEnergyElement
      • meshi.energy.hydrogenBondsAngle.AbstractPunishAngleEnergyElement
        • meshi.energy.hydrogenBondsAngle.HbondsPunishHOCAngleEnergyElement
        • meshi.energy.hydrogenBondsAngle.HBondsPunishOHNAngleEnergyElement
      • meshi.energy.pairwiseNonBondedTerms.CoulombElectrostatics.CoulombElectrostaticEnergyElement
      • meshi.energy.pairwiseNonBondedTerms.excludedVol.ExcludedVolEnergyElement
      • meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolEnergyElement
      • meshi.energy.pairwiseNonBondedTerms.excludedVolOLD.ExcludedVolEnergyElementOLD
      • meshi.energy.pairwiseNonBondedTerms.finiteExcludedVol.FiniteExcludedVolEnergyElement
      • meshi.energy.hydrogenBond.HydrogenBondsEnergyElement
      • meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsEnergyElement
      • meshi.energy.pairwiseNonBondedTerms.LennardJones.LennardJonesEnergyElement
    • meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneEnergyElement
    • meshi.energy.simpleEnergyTerms.plane.PlaneEnergyElement
    • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranEnergyElement (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
    • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElement
      • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi0 (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
      • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi1 (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
      • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi2 (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
      • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi3 (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
      • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainEnergyElementChi4 (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
    • meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflateEnergyElement
    • meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElement
      • meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi0 (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
      • meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi1 (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
      • meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi2 (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
      • meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi3 (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
      • meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryEnergyElementChi4 (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
    • meshi.symmetryComplex.energy.SymmetryEnergyElement
    • meshi.energy.templateEnergy.TemplateEnergyElement
    • meshi.energy.simpleEnergyTerms.tether.TetherEnergyElement
    • meshi.applications.prediction.beautify.unWarpEnergy.UnWarpEnergyElement
    • meshi.applications.prediction.beautify.warpEnergy.WarpEnergyElement
  • meshi.util.filters.Equals (implements meshi.util.filters.Filter)
  • meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameters.isA (implements meshi.util.filters.Filter)
  • meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters (implements meshi.energy.Parameters)
  • meshi.energy.pairwiseNonBondedTerms.ExcludedVol.ExcludedVolParameters.isA (implements meshi.util.filters.Filter)
  • ExtractChain
  • aligner.FastaReader
  • meshi.util.file.File2StringArray
  • javax.swing.filechooser.FileFilter
    • meshi.applications.prediction.homology.gui.HomologyFileFilter
  • aligner.FileToString
  • meshi.util.formats.Format
    • meshi.util.formats.Fdouble
    • meshi.util.formats.Fint
  • aligner.FWriter
  • meshi.util.GDTcalculator
  • meshi.symmetryComplex.utils.GJFilters
  • meshi.symmetryComplex.utils.GJFilters.AcceptChainFilter (implements meshi.util.filters.Filter)
  • meshi.symmetryComplex.utils.GJFilters.AndFilter (implements meshi.util.filters.Filter)
    • meshi.symmetryComplex.proteinsGJ.GJModeller.HBRangesAndGoodResiduesFilter
  • meshi.symmetryComplex.utils.GJFilters.RejectChainFilter (implements meshi.util.filters.Filter)
  • meshi.symmetryComplex.utils.GJFilters.ResidueRangeFilter (implements meshi.util.filters.Filter)
  • meshi.symmetryComplex.proteinsGJ.GJModeller (implements meshi.util.KeyWords)
    • meshi.symmetryComplex.proteinsGJ.BackboneCompleterAndMinimizer
      • meshi.symmetryComplex.proteinsGJ.BackboneMCM
      • meshi.symmetryComplex.proteinsGJ.FullModeller
  • meshi.symmetryComplex.proteinsGJ.GJModeller.HBRangesFilter (implements meshi.util.filters.Filter)
  • meshi.symmetryComplex.proteinsGJ.GJModeller.SpecialHBPairs (implements meshi.util.filters.Filter)
  • meshi.symmetryComplex.utils.GJUtils
  • meshi.energy.simpleEnergyTerms.GoodBonds (implements meshi.util.filters.Filter)
  • meshi.energy.hydrogenBond.GoodResiduesForHB (implements meshi.util.filters.Filter)
  • meshi.energy.hydrogenBond.GoodResiduesForHB.GoodSS (implements meshi.util.filters.Filter)
  • meshi.energy.hydrogenBond.GoodResiduesForHB.IsNot13 (implements meshi.util.filters.Filter)
  • meshi.geometry.Grid
  • meshi.energy.hydrogenBond.HB_AtomAttribute (implements meshi.util.MeshiAttribute)
  • meshi.energy.hydrogenBond.HB_DistanceAttribute (implements meshi.util.MeshiAttribute)
  • meshi.energy.hydrogenBond.HBondList.IsAlive (implements meshi.util.filters.Filter)
  • meshi.energy.hydrogenBond.HBondList.IsWithInRmax (implements meshi.util.filters.Filter)
  • meshi.energy.hydrogenBond.HBondList.WithinRmaxIterator (implements java.util.Iterator<E>)
  • meshi.util.filters.HeavyAtomsFilter (implements meshi.util.filters.Filter)
  • meshi.energy.hydrogenBondsPairs.HelixParametersList.IsHydrogenBondsPairsParameters (implements meshi.util.filters.Filter)
  • meshi.util.histogram.Histogram.BinCreator
  • meshi.util.histogram.Histogram.IsBin (implements meshi.util.filters.Filter)
  • meshi.util.histogram.Histogram.RepresentativesIterator (implements java.util.Iterator<E>)
  • meshi.util.histogram.Histogram.RepresentativesIterator.ThresholdFilter (implements meshi.util.filters.Filter)
  • meshi.util.histogram.HistogramBin (implements java.lang.Comparable<T>)
  • meshi.applications.prediction.homology.gui.HomologyFrame11Layout (implements java.awt.LayoutManager)
  • HomologyModeling (implements meshi.util.KeyWords)
  • HomologyModeling.HomologyLogger (implements meshi.util.Logger)
  • HomologyModeling.LoopAttribute (implements meshi.util.MeshiAttribute)
  • HomologyModeling.LoopComperator (implements java.util.Comparator<T>)
  • HomologyModeling.Three
  • HomologyModeling.TimeTerminator
  • meshi.applications.hubbard.HubbardPosition
  • meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParameters (implements java.lang.Comparable<T>, meshi.energy.Parameters)
  • meshi.energy.hydrogenBondsPairs.HydrogenBondsPairsParametersList.NoElements (implements meshi.util.filters.Filter)
  • HydrogenTest.ResWithSSFilter (implements meshi.util.filters.Filter)
  • meshi.sequences.aligner.Identity (implements meshi.sequences.aligner.CellScorer)
  • meshi.symmetryComplex.molecularImageElements.ImageChain.IsImageChain (implements meshi.util.filters.Filter)
  • meshi.energy.simpleEnergyTerms.inflate.InflateParameters (implements meshi.energy.Parameters)
  • meshi.applications.prediction.homology.gui.InflateParametersLayout (implements java.awt.LayoutManager)
  • meshi.PDB.isAPdbFile (implements meshi.util.filters.Filter)
  • meshi.util.filters.IsClass (implements meshi.util.filters.Filter)
  • meshi.energy.hydrogenBond.IsHO (implements meshi.util.filters.Filter)
  • meshi.util.Key
  • meshi.util.filters.KolDichfin (implements meshi.util.filters.Filter)
  • meshi.optimizers.LBFGS.Element
  • meshi.energy.hydrogenBond.LennardJonesParameters (implements meshi.util.MeshiAttribute, meshi.energy.Parameters)
    • meshi.energy.hydrogenBond.HydrogenBondsParameters
  • meshi.energy.hydrogenBond.LennardJonesParameters.isA (implements meshi.util.filters.Filter)
  • meshi.optimizers.LineSearch
    • meshi.optimizers.SimpleStepLength
    • meshi.optimizers.WolfConditionLineSearch
  • meshi.applications.corpus.LocalFragmentLib (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions, meshi.util.KeyWords, meshi.parameters.MeshiPotential)
  • meshi.symmetryComplex.topologyMap.Loop (implements meshi.util.KeyWords)
  • meshi.applications.corpus.LoopResults
  • meshi.symmetryComplex.utils.LoopUtils
  • meshi.symmetryComplex.utils.LoopUtils.Line
  • meshi.symmetryComplex.utils.LoopUtils.Point
  • meshi.util.mathTools.Jama.LUDecomposition (implements java.io.Serializable)
  • meshi.util.mathTools.Jama.Maths
  • meshi.util.mathTools.Jama.Matrix (implements java.lang.Cloneable, java.io.Serializable)
  • meshi.symmetryComplex.transformations.Matrix1D (implements meshi.symmetryComplex.transformations.Matrix)
    • meshi.symmetryComplex.transformations.Transformation
      • meshi.symmetryComplex.transformations.SingleAxisRotationTransformation
  • meshi.util.MeshiProgram
    • AbInitio (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
    • Beautify (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
    • CalcGDT (implements meshi.util.KeyWords)
    • CalculateEnergyFromStructuresListAverages (implements meshi.util.KeyWords)
    • ChooseTemplate (implements meshi.util.KeyWords)
    • ColorByEnergy (implements meshi.util.KeyWords)
    • meshi.geometry.DistanceMatrix (implements meshi.util.Updateable)
      • meshi.geometry.DistanceMatrixBondedOnly
      • meshi.geometry.DistanceMatrixCaOnly
      • meshi.symmetryComplex.geometryImage.DistanceMatrixNoImageAtoms
      • meshi.molecularElements.allAtoms.DistanceMatrixWhichUpdateOnlyMovingAtoms
      • meshi.geometry.OldDistanceMatrix
    • EnergyStatistics (implements meshi.util.KeyWords)
    • EnergyStatisticsForAtom (implements meshi.util.KeyWords)
    • HeliumClusterMinimization (implements meshi.util.KeyWords)
    • HydrogenTest (implements meshi.util.KeyWords)
    • InitialEvaluation (implements meshi.util.KeyWords)
    • meshi.applications.corpus.MergeCorpora
    • MinimizeProtein (implements meshi.util.KeyWords)
    • ModelRanker (implements meshi.util.KeyWords)
    • Optimize (implements meshi.util.KeyWords)
    • Pdb2Fasta
    • Refine (implements meshi.util.KeyWords)
    • RoisFirstMeshiProgram (implements meshi.util.KeyWords)
    • meshi.applications.corpus.RunThreadingExperiment
    • meshi.util.Scmod (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
    • SCMOD (implements meshi.util.KeyWords)
    • SelectForCASP (implements meshi.util.KeyWords)
    • SimplestMinimizeProtein (implements meshi.util.KeyWords)
    • TestElectrostatics (implements meshi.util.KeyWords)
  • meshi.util.MeshiProgram.GlobalElement
  • meshi.applications.prediction.homology.gui.MinimizeParametersFullDialogLayout (implements java.awt.LayoutManager)
  • meshi.applications.prediction.homology.gui.MinimizeParametersShortLayout (implements java.awt.LayoutManager)
  • meshi.applications.prediction.ModelData.TermComparator (implements java.util.Comparator<T>)
  • meshi.applications.prediction.homology.gui.NonFrozenRangeDialogLayout (implements java.awt.LayoutManager)
  • meshi.applications.prediction.homology.NonFrozensRadiusFilter (implements meshi.util.filters.Filter)
  • meshi.geometry.OldDistanceMatrix.Indicator
  • meshi.geometry.OldDistanceMatrix.RowIterator (implements java.util.Iterator<E>)
  • meshi.geometry.OldGrid
  • meshi.PDB.OneOfTwenty (implements meshi.util.filters.Filter)
  • meshi.optimizers.Optimizer
    • meshi.optimizers.MCM
    • meshi.optimizers.Minimizer
      • meshi.optimizers.BFGS
      • meshi.optimizers.ConjugateGradient
      • meshi.optimizers.LBFGS
      • meshi.optimizers.SteepestDecent
  • meshi.applications.prediction.homology.gui.OptionDialog3Layout (implements java.awt.LayoutManager)
  • meshi.applications.prediction.OriginalAtom (implements meshi.util.MeshiAttribute)
  • meshi.applications.prediction.OriginalAtom.OriginalAtomFilter (implements meshi.util.filters.Filter)
  • meshi.util.filters.OriginalAtoms (implements meshi.util.filters.Filter)
  • meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters (implements java.lang.Comparable<T>, meshi.energy.Parameters)
  • meshi.energy.simpleEnergyTerms.outOfPlane.OutOfPlaneParameters.isA (implements meshi.util.filters.Filter)
  • meshi.util.overlap.Overlap
  • meshi.util.Pair
  • meshi.energy.hydrogenBondsPairs.PairOfHydrogenBondsElements
  • meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList.IsWithInRmax (implements meshi.util.filters.Filter)
  • meshi.energy.hydrogenBondsPairs.PairsOfHBEElementsList.WithinRmaxPairsIterator (implements java.util.Iterator<E>)
  • meshi.applications.prediction.homology.gui.ParametersForChainCompletionLayout (implements java.awt.LayoutManager)
  • ParametersList
    • meshi.energy.pairwiseNonBondedTerms.evRot1BB.EVRot1BBParameterList
  • Pdb2Fasta.MyFilter (implements meshi.util.filters.Filter)
  • meshi.PDB.PdbLine
  • meshi.PDB.PdbLineFilter (implements meshi.util.filters.Filter)
    • meshi.PDB.PdbLineATOM
    • meshi.PDB.PdbLineATOMorHETATOM
    • meshi.PDB.PdbLineSEQRES
  • meshi.optimizers.Perturbation (implements meshi.util.KeyWords)
  • meshi.energy.simpleEnergyTerms.plane.PlaneParameters (implements java.lang.Comparable<T>, meshi.energy.Parameters)
  • meshi.energy.simpleEnergyTerms.plane.PlaneParameters.isA (implements meshi.util.filters.Filter)
  • meshi.molecularElements.Protein
    • meshi.molecularElements.extendedAtoms.ExtendedAtomsProtein
    • HydrogenTest.PolyAla
    • meshi.symmetryComplex.molecularImageElements.SymmetricComplex (implements meshi.util.Updateable)
      • meshi.symmetryComplex.molecularImageElements.SymmetricComplexCompleter (implements meshi.util.KeyWords)
  • meshi.molecularElements.Protein.BackboneFilter (implements meshi.util.filters.Filter)
  • meshi.geometry.putH.PutHpos
  • meshi.geometry.putH.PutHposLog
  • meshi.util.mathTools.Jama.QRDecomposition (implements java.io.Serializable)
  • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandran.RamachandranParameters (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions, meshi.energy.Parameters)
  • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParameters (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions, meshi.energy.Parameters)
    • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi0
    • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi1
    • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi2
    • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi3
    • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.RamachandranSidechainParametersChi4
  • meshi.util.mathTools.Ramp
  • java.io.Reader (implements java.io.Closeable, java.lang.Readable)
    • java.io.BufferedReader
      • java.io.LineNumberReader
        • meshi.util.file.MeshiLineReader
          • meshi.PDB.PdbReader
  • meshi.molecularElements.Residue (implements meshi.util.Attributable, java.lang.Comparable<T>, meshi.util.MeshiAttribute, meshi.parameters.MeshiPotential, meshi.molecularElements.ResidueCreator)
    • meshi.molecularElements.ca.CaResidue
    • meshi.symmetryComplex.molecularImageElements.ImageResidue
    • Pdb2Fasta.MyResidue
    • meshi.molecularElements.extendedAtoms.ResidueExtendedAtoms
      • meshi.molecularElements.extendedAtoms.Ala
      • meshi.molecularElements.extendedAtoms.Arg
      • meshi.molecularElements.extendedAtoms.Asn
      • meshi.molecularElements.extendedAtoms.Asp
      • meshi.molecularElements.extendedAtoms.BackboneResidue (implements meshi.molecularElements.ResidueCreator)
      • meshi.molecularElements.extendedAtoms.Cys
      • meshi.molecularElements.extendedAtoms.Gln
      • meshi.molecularElements.extendedAtoms.Glu
      • meshi.molecularElements.extendedAtoms.Gly
      • meshi.molecularElements.extendedAtoms.His
      • meshi.molecularElements.extendedAtoms.Ile
      • meshi.molecularElements.extendedAtoms.Leu
      • meshi.molecularElements.extendedAtoms.Lys
      • meshi.molecularElements.extendedAtoms.Met
      • meshi.molecularElements.extendedAtoms.Phe
      • meshi.molecularElements.extendedAtoms.Pro
      • meshi.molecularElements.extendedAtoms.Ser
      • meshi.molecularElements.extendedAtoms.Thr
      • meshi.molecularElements.extendedAtoms.Trp
      • meshi.molecularElements.extendedAtoms.Tyr
      • meshi.molecularElements.extendedAtoms.Val
  • meshi.geometry.ResidueBuilder
  • meshi.molecularElements.extendedAtoms.ResidueExtendedAtomsCreator (implements meshi.molecularElements.ResidueCreator)
  • meshi.molecularElements.ResidueIdentifier (implements java.lang.Comparable<T>)
  • meshi.molecularElements.ResidueList.NonDummyFilter (implements meshi.util.filters.Filter)
  • meshi.util.ResidueNameConvertor
  • meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsions (implements meshi.util.Attributable, meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions, meshi.util.Updateable)
  • meshi.energy.simpleEnergyTerms.compositeTorsions.ramachandranSidechain.ResidueTorsionsAttribute (implements meshi.util.MeshiAttribute)
  • meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList.CompleteResidueFilter (implements meshi.util.filters.Filter)
  • meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList.IncompleteResidueFilter (implements meshi.util.filters.Filter)
  • meshi.energy.simpleEnergyTerms.compositeTorsions.ResidueTorsionsList.PhiPsiResidueFilter (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions, meshi.util.filters.Filter)
  • meshi.energy.simpleEnergyTerms.compositeTorsions.compositePropensity.ResidueTorsionsPropensityAttribute (implements meshi.util.MeshiAttribute)
  • meshi.util.RgCalculator (implements meshi.util.Updateable)
  • meshi.util.Rms (implements meshi.util.KeyWords)
  • meshi.util.rotamericTools.RotamericTools (implements meshi.util.KeyWords, meshi.util.rotamericTools.Rot1Arrays)
  • meshi.symmetryComplex.proteinsGJ.RunBackboneCompleterAndMinimizer
  • meshi.symmetryComplex.proteinsGJ.RunBackboneMCM
  • meshi.symmetryComplex.proteinsGJ.RunFullModeller
  • SelectModels
  • SelectModels.ModelComparator (implements java.util.Comparator<T>)
  • meshi.sequences.SequenceCharFilter (implements meshi.util.filters.Filter)
    • meshi.sequences.AccesibilitySequence.AccesibilitySequenceCharFilter
    • meshi.sequences.ResidueSequence.ResidueSequenceCharFilter
    • meshi.sequences.SecondaryStructureSequence.SecondaryStructureSequenceCharFilter
    • meshi.sequences.Sequence.kolDichfin
    • meshi.sequences.SequenceList.AcceptAll
  • meshi.sequences.SequenceList.IsSequenceFilter (implements meshi.util.filters.Filter)
  • meshi.energy.sideChainModelingSolvate.SideChainSolvateDistanceAttribute (implements meshi.util.MeshiAttribute)
  • meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle
  • meshi.util.mathTools.Sigma
  • meshi.energy.solvate.SigmaParameters
  • meshi.energy.simpleEnergyTerms.SimpleEnergyCreator.HaveParametersFilter (implements meshi.util.filters.Filter)
  • meshi.energy.simpleEnergyTerms.inflate.simpleInflate.SimpleInflate.TargetFilter (implements meshi.util.filters.Filter)
  • meshi.util.mathTools.Jama.SingularValueDecomposition (implements java.io.Serializable)
  • meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParameters (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions, meshi.energy.Parameters)
    • meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi0
    • meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi1
    • meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi2
    • meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi3
    • meshi.energy.simpleEnergyTerms.compositeTorsions.smoothRotamerLibrary.SmoothRotamerLibraryParametersChi4
  • meshi.energy.solvate.SolvateDistanceAttribute (implements meshi.util.MeshiAttribute)
    • meshi.energy.solvate.SolvateDistanceAttributeBetweenPolars
    • meshi.energy.solvate.SolvateDistanceAttributeNonPolarPolar
    • meshi.energy.solvate.SolvateDistanceAttributePolarNonPolar
    • meshi.energy.solvate.SolvateDistanceAttributeWithAhydrogen
    • meshi.energy.solvate.SolvateDistanceAttributeWithNonPolar
  • meshi.energy.solvate.SolvateDistanceAttributeCreator
  • meshi.energy.solvate.SolvateParametersList (implements meshi.energy.Parameters)
  • meshi.energy.solvateRot1.SolvateRot1DistanceAttribute (implements meshi.util.MeshiAttribute)
  • meshi.energy.solvateRot1.SolvateRot1ParametersList (implements meshi.energy.Parameters)
  • SortableMeshiList
    • meshi.util.histogram.Histogram
  • meshi.util.mathTools.Spline1D
  • meshi.util.mathTools.Spline2D
  • meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomial (implements meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions)
  • meshi.energy.simpleEnergyTerms.compositeTorsions.SplinedPolynomialsLoader
  • meshi.util.string.StringFilter (implements meshi.util.filters.Filter)
    • meshi.util.string.StringFilterEndsWith
    • meshi.util.string.StringFilterEquals
    • meshi.util.string.StringFilterGrep
    • meshi.util.string.StringFilterStartsWith
  • meshi.util.string.StringList.IsString (implements meshi.util.filters.Filter)
  • meshi.util.string.StringParser
  • meshi.sequences.aligner.StructureBasedMatrix (implements meshi.sequences.aligner.CellScorer)
  • meshi.energy.pairwiseNonBondedTerms.atomicPairwisePMFSumma.SummaAttribute (implements meshi.util.MeshiAttribute)
  • meshi.optimizers.TemperatureGenerator
  • meshi.util.Terminator
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • meshi.optimizers.LineSearchException
      • meshi.util.MeshiInitException
      • meshi.optimizers.NoConvergenceException
      • meshi.geometry.putH.NotEnoughBoundAtomsException
      • meshi.optimizers.OptimizerException
      • meshi.util.overlap.RmsException
      • java.lang.RuntimeException
        • java.lang.IllegalStateException
          • meshi.energy.hydrogenBond.SynchronizedUpdateException
        • meshi.util.MeshiException
        • meshi.applications.prediction.PredictionSequenceAlignment.TemplateAlignmentException
        • meshi.sequences.ResidueTypeException
      • meshi.PDB.UnknownAtomTypeException
      • meshi.util.UpdateableException
  • meshi.symmetryComplex.topologyMap.Topology (implements meshi.util.KeyWords)
  • meshi.geometry.Torsion (implements meshi.util.Updateable)
    • meshi.geometry.QuickAndDirtyTorsion
  • meshi.geometry.TorsionList.FilterChi1 (implements meshi.util.filters.Filter)
  • meshi.geometry.TorsionList.FilterChi2 (implements meshi.util.filters.Filter)
  • meshi.geometry.TorsionList.FilterChi3 (implements meshi.util.filters.Filter)
  • meshi.geometry.TorsionList.FilterChi4 (implements meshi.util.filters.Filter)
  • meshi.geometry.TorsionList.FilterOOP (implements meshi.util.filters.Filter)
  • meshi.geometry.TorsionList.FilterPhi (implements meshi.util.filters.Filter)
  • meshi.geometry.TorsionList.FilterPsi (implements meshi.util.filters.Filter)
  • meshi.geometry.TorsionList.FilterSideChain (implements meshi.util.filters.Filter)
  • meshi.geometry.TorsionPair (implements meshi.util.Updateable)
  • meshi.energy.TotalEnergy
  • meshi.energy.TotalEnergy.EnergyComparator (implements java.util.Comparator<T>)
  • meshi.energy.TotalEnergy.FreeAtom (implements meshi.util.filters.Filter)
  • meshi.energy.TotalEnergy.IsEnergy (implements meshi.util.filters.Filter)
  • meshi.energy.TotalEnergy.SortedAtoms
  • meshi.util.Utils (implements meshi.util.KeyWords, meshi.parameters.MeshiPotential)
  • meshi.util.Utils.DefaultExceptionHandler (implements meshi.util.ExceptionHandler)
  • meshi.util.Utils.DoNothingExceptionHandler (implements meshi.util.ExceptionHandler)
  • meshi.geometry.ViewAt
  • meshi.applications.prediction.homology.gui.WeightsForEnergyTermsLayout (implements java.awt.LayoutManager)
  • java.io.Writer (implements java.lang.Appendable, java.io.Closeable, java.io.Flushable)
    • java.io.PrintWriter
      • meshi.util.file.MeshiWriter

Interface Hierarchy

• meshi.util.Attributable
• meshi.sequences.aligner.CellScorer
• meshi.util.Classes
• meshi.util.CommandListGenerator
• meshi.energy.simpleEnergyTerms.compositeTorsions.CompositeTorsionsDefinitions
• meshi.energy.solvate.hydrogenBonds.DahiyatImplementationConstants
• meshi.util.ExceptionHandler
• meshi.util.filters.Filter
• meshi.util.KeyWords
• meshi.util.Logger
• meshi.symmetryComplex.transformations.Matrix
• meshi.util.MeshiAttribute
• meshi.parameters.MeshiPotential
• meshi.energy.Parameters
• meshi.molecularElements.ResidueCreator
• meshi.util.rotamericTools.Rot1Arrays
• aligner.SubstitutionMatrix
• meshi.util.Updateable
• meshi.util.Verbose

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • HomologyModeling.LoopMode
    • meshi.geometry.DistanceMode
    • meshi.optimizers.Optimizer.OptimizerStatus
    • meshi.parameters.AddAtomsFlag
    • meshi.parameters.AtomType
    • meshi.parameters.BBatom
    • meshi.parameters.Element
    • meshi.parameters.ResidueMode
    • meshi.parameters.ResidueType
    • meshi.parameters.SecondaryStructure (implements meshi.util.MeshiAttribute)
    • meshi.applications.prediction.AbitSmarterLoopBuilder.Loop.End
    • meshi.energy.solvate.SolvateDistanceType
    • meshi.energy.solvate.SolvateEnergy.SuperType
    • meshi.energy.templateEnergy.TemplateEnergyCreator.Template
    • meshi.molecularElements.atoms.AtomStatus