Hierarchy For All Packages

Package Hierarchies:

org.simtk.geometry3d, org.simtk.gui, org.simtk.molecularstructure, org.simtk.molecularstructure.atom, org.simtk.molecularstructure.nucleicacid, org.simtk.molecularstructure.protein, org.simtk.mvc, org.simtk.pdb, org.simtk.rnaml, org.simtk.util

Class Hierarchy

• java.lang.Object
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.Vector<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • org.simtk.molecularstructure.atom.AtomSet
        • org.simtk.molecularstructure.nucleicacid.Hairpin
  • java.util.AbstractMap<K,V> (implements java.util.Map<K,V>)
    • java.util.HashMap<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      • org.simtk.geometry3d.Hash3D<V>
  • org.simtk.geometry3d.Angle.Range
  • org.simtk.geometry3d.Angle.Units
  • org.simtk.molecularstructure.atom.AtomClass (implements org.simtk.molecularstructure.atom.Atom)
  • org.simtk.molecularstructure.atom.AtomPosition
  • org.simtk.molecularstructure.atom.ChemicalElementClass (implements org.simtk.molecularstructure.atom.ChemicalElement)
  • org.simtk.util.ColorName
  • org.simtk.util.CommandLineInterface
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Container
      • javax.swing.JComponent (implements java.io.Serializable)
        • javax.swing.JLabel (implements javax.accessibility.Accessible, javax.swing.SwingConstants)
          • org.simtk.pdb.JLinkLabel
          • org.simtk.gui.Throbber
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • org.simtk.gui.ProgressPanel (implements java.awt.event.ActionListener, org.simtk.gui.ProgressDialog)
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • org.simtk.pdb.MoleculeAcquisitionMethodDialog (implements java.awt.event.ActionListener, java.util.Observer)
            • org.simtk.gui.ProgressDialogClass (implements org.simtk.gui.ProgressDialog)
            • org.simtk.gui.UndoableDialog (implements java.awt.event.ActionListener)
  • org.simtk.geometry3d.Cylinder
    • org.simtk.geometry3d.SemiCylinder
  • org.simtk.util.DoubleRing
  • javax.swing.filechooser.FileFilter
    • org.simtk.pdb.FileNameFilter
    • org.simtk.util.MyJFileFilter
  • org.simtk.molecularstructure.FunctionalGroup
  • java.io.InputStream (implements java.io.Closeable)
    • java.io.FilterInputStream
      • org.simtk.util.UncompressInputStream
  • org.simtk.geometry3d.Line3D
  • org.simtk.geometry3d.MassBodyClass (implements org.simtk.geometry3d.MassBody)
  • org.simtk.geometry3d.MathMatrixClass (implements org.simtk.geometry3d.MutableMathMatrix)
    • org.simtk.geometry3d.HomogeneousTransformClass (implements org.simtk.geometry3d.MutableHomogeneousTransform)
    • org.simtk.geometry3d.JamaMatrix
    • org.simtk.geometry3d.Matrix3DClass (implements org.simtk.geometry3d.MutableMatrix3D)
  • org.simtk.geometry3d.MathVectorClass (implements org.simtk.geometry3d.MutableMathVector)
    • org.simtk.geometry3d.Vector2DClass (implements org.simtk.geometry3d.MutableVector2D)
    • org.simtk.geometry3d.Vector3DClass (implements org.simtk.geometry3d.MutableVector3D)
      • org.simtk.geometry3d.Vector3DFloatArrayWrapper
  • org.simtk.molecularstructure.MolecularClass (implements org.simtk.molecularstructure.Molecular)
    • org.simtk.molecularstructure.MoleculeClass (implements org.simtk.molecularstructure.Molecule)
      • org.simtk.molecularstructure.BiopolymerClass (implements org.simtk.molecularstructure.Biopolymer)
        • org.simtk.molecularstructure.nucleicacid.NucleicAcid
          • org.simtk.molecularstructure.nucleicacid.DNA
          • org.simtk.molecularstructure.nucleicacid.RNA
        • org.simtk.molecularstructure.protein.PDBProteinClass (implements org.simtk.molecularstructure.protein.Protein)
    • org.simtk.molecularstructure.MoleculeCollection
    • org.simtk.molecularstructure.ResidueClass (implements org.simtk.molecularstructure.Residue)
  • java.lang.Number (implements java.io.Serializable)
    • org.simtk.geometry3d.Angle
  • java.util.Observable
    • org.simtk.mvc.MoleculeMVCModel (implements org.simtk.mvc.MVCModel)
    • org.simtk.gui.ParameterSetModel
    • org.simtk.mvc.SimpleObservable (implements org.simtk.mvc.ObservableInterface)
  • org.simtk.geometry3d.Plane3D
  • org.simtk.molecularstructure.ResidueBackbone (implements org.simtk.molecularstructure.Chemical)
  • org.simtk.molecularstructure.ResidueTypeClass (implements org.simtk.molecularstructure.ResidueType)
    • org.simtk.molecularstructure.protein.AminoAcid
      • org.simtk.molecularstructure.protein.Alanine
      • org.simtk.molecularstructure.protein.Arginine
      • org.simtk.molecularstructure.protein.Asparagine
      • org.simtk.molecularstructure.protein.Aspartate
      • org.simtk.molecularstructure.protein.Cysteine
      • org.simtk.molecularstructure.protein.Glutamate
      • org.simtk.molecularstructure.protein.Glutamine
      • org.simtk.molecularstructure.protein.Glycine
      • org.simtk.molecularstructure.protein.Histidine
      • org.simtk.molecularstructure.protein.Isoleucine
      • org.simtk.molecularstructure.protein.Leucine
      • org.simtk.molecularstructure.protein.Lysine
      • org.simtk.molecularstructure.protein.Methionine
      • org.simtk.molecularstructure.protein.Phenylalanine
      • org.simtk.molecularstructure.protein.Proline
      • org.simtk.molecularstructure.protein.Serine
      • org.simtk.molecularstructure.protein.Threonine
      • org.simtk.molecularstructure.protein.Tryptophan
      • org.simtk.molecularstructure.protein.Tyrosine
      • org.simtk.molecularstructure.protein.UnknownAminoAcid
      • org.simtk.molecularstructure.protein.Valine
    • org.simtk.molecularstructure.nucleicacid.Nucleotide
      • org.simtk.molecularstructure.nucleicacid.Purine
        • org.simtk.molecularstructure.nucleicacid.Adenylate
        • org.simtk.molecularstructure.nucleicacid.Guanylate
        • org.simtk.molecularstructure.nucleicacid.Inositate
      • org.simtk.molecularstructure.nucleicacid.Pyrimidine
        • org.simtk.molecularstructure.nucleicacid.Cytidylate
        • org.simtk.molecularstructure.nucleicacid.Thymidylate
        • org.simtk.molecularstructure.nucleicacid.Uridylate
  • org.simtk.rnaml.RnamlDocument
  • org.simtk.rnaml.RnamlExportDocument
  • org.simtk.molecularstructure.SecondaryStructureClass (implements org.simtk.molecularstructure.SecondaryStructure)
    • org.simtk.molecularstructure.nucleicacid.BasePair (implements java.lang.Iterable<T>)
    • org.simtk.molecularstructure.nucleicacid.BaseStack
    • org.simtk.molecularstructure.nucleicacid.BaseTriple
    • org.simtk.molecularstructure.protein.BetaStrand
    • org.simtk.molecularstructure.nucleicacid.Duplex
    • org.simtk.molecularstructure.protein.Helix
    • org.simtk.molecularstructure.nucleicacid.Pseudoknot
  • org.simtk.util.SelectionBroadcaster
  • org.simtk.molecularstructure.SequenceAlignment
  • org.simtk.util.Stopwatch
  • org.simtk.geometry3d.Superposition
  • org.simtk.geometry3d.TestSuperposition
  • java.lang.Thread (implements java.lang.Runnable)
    • org.simtk.pdb.LoadPdbUrlProcess
    • org.simtk.gui.ProgressManager (implements org.simtk.mvc.ObservableInterface)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • org.simtk.molecularstructure.InsufficientAtomsException
      • org.simtk.geometry3d.InsufficientPointsException
      • java.lang.RuntimeException
        • org.simtk.geometry3d.MatrixSizeMismatchException
        • org.simtk.util.ProgrammerLogicProblem
        • org.simtk.geometry3d.VectorSizeException
  • org.simtk.gui.UndoRedoMechanism
  • org.simtk.pdb.WebPDB

Interface Hierarchy

• org.simtk.molecularstructure.Chemical
  • org.simtk.molecularstructure.atom.Atom (also extends org.simtk.molecularstructure.atom.ChemicalElement, org.simtk.geometry3d.MassBody)
  • org.simtk.molecularstructure.Biopolymer
    • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule, org.simtk.molecularstructure.protein.Protein)
    • org.simtk.molecularstructure.protein.Protein
      • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule)
  • org.simtk.molecularstructure.atom.ChemicalElement
    • org.simtk.molecularstructure.atom.Atom (also extends org.simtk.geometry3d.MassBody)
  • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule, org.simtk.molecularstructure.protein.Protein)
  • org.simtk.molecularstructure.Molecular (also extends org.simtk.geometry3d.MassBody)
    • org.simtk.molecularstructure.Biopolymer
      • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule, org.simtk.molecularstructure.protein.Protein)
      • org.simtk.molecularstructure.protein.Protein
        • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule)
    • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule, org.simtk.molecularstructure.protein.Protein)
    • org.simtk.molecularstructure.Molecule
      • org.simtk.molecularstructure.Biopolymer
        • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule, org.simtk.molecularstructure.protein.Protein)
        • org.simtk.molecularstructure.protein.Protein
          • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule)
      • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.protein.Protein)
      • org.simtk.molecularstructure.protein.Protein
        • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule)
    • org.simtk.molecularstructure.protein.Protein
      • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule)
    • org.simtk.molecularstructure.Residue (also extends org.simtk.molecularstructure.ResidueType)
  • org.simtk.molecularstructure.Molecule
    • org.simtk.molecularstructure.Biopolymer
      • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule, org.simtk.molecularstructure.protein.Protein)
      • org.simtk.molecularstructure.protein.Protein
        • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule)
    • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.protein.Protein)
    • org.simtk.molecularstructure.protein.Protein
      • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule)
  • org.simtk.molecularstructure.protein.Protein
    • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule)
  • org.simtk.molecularstructure.Residue (also extends org.simtk.molecularstructure.Molecular, org.simtk.molecularstructure.ResidueType)
• java.lang.Iterable<T>
  • org.simtk.geometry3d.MathVector
    • org.simtk.geometry3d.MutableMathVector
      • org.simtk.geometry3d.MutableVector2D (also extends org.simtk.geometry3d.Vector2D)
      • org.simtk.geometry3d.MutableVector3D (also extends org.simtk.geometry3d.Vector3D)
    • org.simtk.geometry3d.MutableVector2D (also extends org.simtk.geometry3d.MutableMathVector, org.simtk.geometry3d.Vector2D)
    • org.simtk.geometry3d.MutableVector3D (also extends org.simtk.geometry3d.MutableMathVector, org.simtk.geometry3d.Vector3D)
    • org.simtk.geometry3d.Vector2D (also extends org.simtk.geometry3d.Location)
      • org.simtk.geometry3d.MutableVector2D (also extends org.simtk.geometry3d.MutableMathVector)
    • org.simtk.geometry3d.Vector3D (also extends org.simtk.geometry3d.Location)
      • org.simtk.geometry3d.MutableVector3D (also extends org.simtk.geometry3d.MutableMathVector)
  • org.simtk.geometry3d.MutableMathVector
    • org.simtk.geometry3d.MutableVector2D (also extends org.simtk.geometry3d.Vector2D)
    • org.simtk.geometry3d.MutableVector3D (also extends org.simtk.geometry3d.Vector3D)
  • org.simtk.geometry3d.MutableVector2D (also extends org.simtk.geometry3d.MutableMathVector, org.simtk.geometry3d.Vector2D)
  • org.simtk.geometry3d.MutableVector3D (also extends org.simtk.geometry3d.MutableMathVector, org.simtk.geometry3d.Vector3D)
  • org.simtk.geometry3d.Vector2D (also extends org.simtk.geometry3d.Location, org.simtk.geometry3d.MathVector)
    • org.simtk.geometry3d.MutableVector2D (also extends org.simtk.geometry3d.MutableMathVector)
  • org.simtk.geometry3d.Vector3D (also extends org.simtk.geometry3d.Location, org.simtk.geometry3d.MathVector)
    • org.simtk.geometry3d.MutableVector3D (also extends org.simtk.geometry3d.MutableMathVector)
• org.simtk.util.LineCommand
• org.simtk.geometry3d.Location
  • org.simtk.geometry3d.MutableVector2D (also extends org.simtk.geometry3d.MutableMathVector, org.simtk.geometry3d.Vector2D)
  • org.simtk.geometry3d.MutableVector3D (also extends org.simtk.geometry3d.MutableMathVector, org.simtk.geometry3d.Vector3D)
  • org.simtk.geometry3d.Vector2D (also extends org.simtk.geometry3d.MathVector)
    • org.simtk.geometry3d.MutableVector2D (also extends org.simtk.geometry3d.MutableMathVector)
  • org.simtk.geometry3d.Vector3D (also extends org.simtk.geometry3d.MathVector)
    • org.simtk.geometry3d.MutableVector3D (also extends org.simtk.geometry3d.MutableMathVector)
• org.simtk.geometry3d.MassBody
  • org.simtk.molecularstructure.atom.Atom (also extends org.simtk.molecularstructure.atom.ChemicalElement)
  • org.simtk.molecularstructure.Biopolymer
    • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule, org.simtk.molecularstructure.protein.Protein)
    • org.simtk.molecularstructure.protein.Protein
      • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule)
  • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule, org.simtk.molecularstructure.protein.Protein)
  • org.simtk.molecularstructure.Molecular (also extends org.simtk.molecularstructure.Chemical)
    • org.simtk.molecularstructure.Biopolymer
      • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule, org.simtk.molecularstructure.protein.Protein)
      • org.simtk.molecularstructure.protein.Protein
        • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule)
    • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule, org.simtk.molecularstructure.protein.Protein)
    • org.simtk.molecularstructure.Molecule
      • org.simtk.molecularstructure.Biopolymer
        • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule, org.simtk.molecularstructure.protein.Protein)
        • org.simtk.molecularstructure.protein.Protein
          • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule)
      • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.protein.Protein)
      • org.simtk.molecularstructure.protein.Protein
        • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule)
    • org.simtk.molecularstructure.protein.Protein
      • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule)
    • org.simtk.molecularstructure.Residue (also extends org.simtk.molecularstructure.ResidueType)
  • org.simtk.molecularstructure.Molecule
    • org.simtk.molecularstructure.Biopolymer
      • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule, org.simtk.molecularstructure.protein.Protein)
      • org.simtk.molecularstructure.protein.Protein
        • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule)
    • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.protein.Protein)
    • org.simtk.molecularstructure.protein.Protein
      • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule)
  • org.simtk.molecularstructure.protein.Protein
    • org.simtk.molecularstructure.protein.LocatedProtein (also extends org.simtk.molecularstructure.Molecule)
  • org.simtk.molecularstructure.Residue (also extends org.simtk.molecularstructure.Molecular, org.simtk.molecularstructure.ResidueType)
• org.simtk.geometry3d.MathMatrix
  • org.simtk.geometry3d.HomogeneousTransform
    • org.simtk.geometry3d.MutableHomogeneousTransform (also extends org.simtk.geometry3d.MutableMathMatrix)
  • org.simtk.geometry3d.Matrix3D
    • org.simtk.geometry3d.MutableMatrix3D (also extends org.simtk.geometry3d.MutableMathMatrix)
  • org.simtk.geometry3d.MutableHomogeneousTransform (also extends org.simtk.geometry3d.HomogeneousTransform, org.simtk.geometry3d.MutableMathMatrix)
  • org.simtk.geometry3d.MutableMathMatrix
    • org.simtk.geometry3d.MutableHomogeneousTransform (also extends org.simtk.geometry3d.HomogeneousTransform)
    • org.simtk.geometry3d.MutableMatrix3D (also extends org.simtk.geometry3d.Matrix3D)
  • org.simtk.geometry3d.MutableMatrix3D (also extends org.simtk.geometry3d.Matrix3D, org.simtk.geometry3d.MutableMathMatrix)
• org.simtk.gui.MonitoredProcess
• org.simtk.mvc.ObservableInterface
  • org.simtk.mvc.MVCModel
• java.util.Observer
  • org.simtk.mvc.MVCView
• org.simtk.gui.ProgressDialog
• org.simtk.molecularstructure.ResidueType
  • org.simtk.molecularstructure.Residue (also extends org.simtk.molecularstructure.Molecular)
• org.simtk.molecularstructure.SecondaryStructure
• org.simtk.util.Selectable
• org.simtk.util.SelectionListener

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • org.simtk.molecularstructure.SecondaryStructureClass.SourceType
    • org.simtk.molecularstructure.nucleicacid.BasePair.EdgeType
    • org.simtk.molecularstructure.nucleicacid.BasePair.BondOrientation