Hierarchy For All Packages

Package Hierarchies:

conformation, contrib, core, core.pbc, energy, esraMath, forcefield, io, io.args, io.g96, io.g96.in, io.g96.out, io.mol2, io.pdb, io.vmd, io.xplor, programs, stuff

Class Hierarchy

• class java.lang.Object
  • class conformation.AlkaneDihedrals
  • class forcefield.Angles
  • class io.args.ArgumentChecker
  • class io.args.ArgumentComparer
  • class io.args.ArgumentDescription
  • class io.args.ArgumentGetter
  • class io.args.ArgumentParser
  • class io.args.ArgumentTypeSpec
  • class io.args.ArgumentValueSpec
  • class junit.framework.Assert
    • class junit.framework.TestCase (implements junit.framework.Test)
      • class conformation.AlkaneDihedralsTest
      • class esraMath.BLA_test
      • class forcefield.BondsTest
      • class conformation.DsspTest
      • class energy.FDPoissonBoltzmannTest
      • class esraMath.FitTest
      • class esraMath.GeometryTest
      • class io.mol2.InMol2Test
      • class io.g96.in.InTopoG96Test
      • class conformation.RingConformationTest
  • class core.AtomSpecifier
  • class esraMath.BLA
  • class forcefield.BondAngleType
  • class forcefield.Bonds
  • class forcefield.BondType
  • class energy.Bornradii_STILL
  • class contrib.CRC
  • class forcefield.DenseExclusions
  • class forcefield.Dihedrals
  • class forcefield.DihedralType
  • class conformation.Dssp
  • class energy.Energy
    • class energy.Energy_Angle (implements energy.InteractionsEnergy, java.lang.Runnable)
    • class energy.Energy_Bond (implements energy.InteractionsEnergy, java.lang.Runnable)
    • class energy.Energy_Dihedral (implements energy.InteractionsEnergy, java.lang.Runnable)
    • class energy.Energy_GBorn (implements energy.InteractionsEnergy, java.lang.Runnable)
    • class energy.Energy_ImpDihedral (implements energy.InteractionsEnergy, java.lang.Runnable)
  • class energy.FD_WriteGrid
  • class energy.FDPoissonBoltzmann
    • class energy.FDPoissonBoltzmann_Boundary
    • class energy.FDPoissonBoltzmann_ChargeGrid
    • class energy.FDPoissonBoltzmann_EpsGrid
  • class energy.FDPoissonBoltzmann_ICCG
    • class energy.FDPoissonBoltzmann_ICCG_NPBC
  • class energy.FDPoissonBoltzmann_Parameters
  • class esraMath.Fit
  • class io.g96.out.G96BoxFormatter
  • class io.g96.G96Frame
  • class io.g96.out.G96GenericFormatter
  • class io.g96.out.G96PositionFormatter
  • class io.g96.out.G96PositionredFormatter
  • class core.G96SolventTopology
  • class io.g96.out.G96TimestepFormatter
  • class io.g96.out.G96TitleFormatter
  • class esraMath.Geometry
  • class io.g96.out.HBondFormatter
  • class conformation.HydrogenBonds
  • class conformation.HydrogenBonds.HBDefinitions
  • class conformation.HydrogenBonds.HBFrameStats
    • class conformation.HydrogenBonds.HBTrajectoryStats
  • class forcefield.ImpDihedralType
  • class forcefield.ImproperDihedrals
  • class io.g96.in.InBlock
    • class io.g96.in.InCorG96
    • class io.g96.in.InEnergiesG96
  • class io.g96.in.InEnergiesG96.G96Energies
  • class io.mol2.InMol2
  • class io.pdb.InPDB
  • class java.io.InputStream
    • class contrib.CBZip2InputStream (implements contrib.BZip2Constants)
  • class forcefield.InteractionParameters
  • class io.g96.in.InTopoG96
  • class io.g96.in.InTopoG96.Topology
  • class io.g96.in.InTrajG96
  • class forcefield.LJ14HashMap
  • class forcefield.LJType
  • class forcefield.LJTypeHashMap
  • class core.pbc.NearestImage
  • class io.g96.out.OutTopoG96
  • class core.Particles
  • class programs.pb_protligand
  • class core.pbc.PBC
    • class core.pbc.PBC_RectBox
    • class core.pbc.PBC_TruncOct
  • class core.pbc.PBC.ByMoleculeGatherer (implements core.pbc.PBC.Gatherer)
  • class core.pbc.PBC.CoGGatherer (implements core.pbc.PBC.Gatherer)
  • class core.pbc.PBC.G96Gatherer (implements core.pbc.PBC.Gatherer)
  • class core.pbc.PBC.InBoxGatherer (implements core.pbc.PBC.Gatherer)
  • class io.pdb.PDBAtomFormatter
  • class io.pdb.PDBTitleFormatter
  • class energy.PositionUtils
  • class contrib.PrintfFormat
  • class contrib.PrintfFormat.ConversionSpecification
  • class conformation.RingConformation
  • class core.SimSystem
  • class esraMath.Statistics
  • class esraMath.Statistics.Cluster
  • class stuff.StringUtils
  • class io.TrajectoryWriter
    • class io.pdb.OutPDB
    • class io.g96.out.OutPosG96
    • class io.g96.out.OutTrajG96
    • class io.vmd.OutVMDAM
    • class io.xplor.OutXPlor
  • class io.vmd.VMDAMFormatter

Interface Hierarchy

• interface contrib.BZip2Constants
• interface energy.InteractionsEnergy
• interface core.pbc.PBC.Gatherer