Hierarchy For All Packages

Package Hierarchies:

• edu.rit.http,
• edu.rit.io,
• edu.rit.mp,
• edu.rit.mp.buf,
• edu.rit.pj,
• edu.rit.pj.cluster,
• edu.rit.pj.io,
• edu.rit.pj.job,
• edu.rit.pj.reduction,
• edu.rit.pj.replica,
• edu.rit.util,
• ffx,
• ffx.algorithms,
• ffx.algorithms.cli,
• ffx.algorithms.dynamics,
• ffx.algorithms.dynamics.integrators,
• ffx.algorithms.dynamics.thermostats,
• ffx.algorithms.mc,
• ffx.algorithms.misc,
• ffx.algorithms.optimize,
• ffx.algorithms.optimize.anneal,
• ffx.algorithms.optimize.manybody,
• ffx.algorithms.thermodynamics,
• ffx.crystal,
• ffx.numerics,
• ffx.numerics.atomic,
• ffx.numerics.estimator,
• ffx.numerics.fft,
• ffx.numerics.func1d,
• ffx.numerics.integrate,
• ffx.numerics.math,
• ffx.numerics.multipole,
• ffx.numerics.optimization,
• ffx.numerics.special,
• ffx.numerics.spline,
• ffx.numerics.switching,
• ffx.numerics.tornado,
• ffx.openmm,
• ffx.openmm.amoeba,
• ffx.potential,
• ffx.potential.bonded,
• ffx.potential.cli,
• ffx.potential.commands,
• ffx.potential.constraint,
• ffx.potential.extended,
• ffx.potential.nonbonded,
• ffx.potential.nonbonded.implicit,
• ffx.potential.nonbonded.octree,
• ffx.potential.nonbonded.pme,
• ffx.potential.openmm,
• ffx.potential.parameters,
• ffx.potential.parsers,
• ffx.potential.utils,
• ffx.realspace,
• ffx.realspace.cli,
• ffx.realspace.parsers,
• ffx.ui,
• ffx.ui.behaviors,
• ffx.ui.commands,
• ffx.ui.properties,
• ffx.utilities,
• ffx.xray,
• ffx.xray.cli,
• ffx.xray.parsers

Class Hierarchy

• java.lang.Object
  • javax.annotation.processing.AbstractProcessor (implements javax.annotation.processing.Processor)
    • ffx.utilities.PropertyProcessor
  • ffx.numerics.atomic.AdderDoubleArray (implements ffx.numerics.atomic.AtomicDoubleArray)
  • ffx.potential.cli.AlchemicalOptions
  • ffx.potential.nonbonded.pme.AlchemicalParameters
  • ffx.potential.bonded.AminoAcidUtils
  • ffx.potential.ANIEnergy (implements ffx.potential.bonded.LambdaInterface, ffx.numerics.Potential)
  • ffx.algorithms.cli.AnnealOptions
  • edu.rit.util.Arrays
  • ffx.potential.AssemblyState
  • ffx.numerics.atomic.AtomicDoubleArray3D
  • ffx.potential.cli.AtomSelectionOptions
  • edu.rit.pj.cluster.BackendFileReader
  • edu.rit.pj.cluster.BackendFileWriter
  • edu.rit.pj.cluster.BackendInfo
  • ffx.potential.parsers.BARFilter
  • ffx.algorithms.dynamics.Barostat (implements ffx.crystal.CrystalPotential)
  • ffx.algorithms.cli.BarostatOptions
  • org.apache.commons.configuration2.event.BaseEventSource (implements org.apache.commons.configuration2.event.EventSource)
    • org.apache.commons.configuration2.AbstractConfiguration (implements org.apache.commons.configuration2.Configuration)
      • org.apache.commons.configuration2.CompositeConfiguration (implements java.lang.Cloneable)
        • ffx.utilities.FFXContext
  • ffx.potential.parameters.BaseType
    • ffx.potential.parameters.AngleTorsionType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.AngleType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.AtomType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.BioType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.BondType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.ChargeType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.ImproperTorsionType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.MultipoleType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.OutOfPlaneBendType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.PiOrbitalTorsionType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.PolarizeType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.RelativeSolvationType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.SoluteType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.StretchBendType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.StretchTorsionType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.TorsionTorsionType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.TorsionType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.UreyBradleyType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.VDWPairType (implements java.util.Comparator<T>)
    • ffx.potential.parameters.VDWType (implements java.util.Comparator<T>)
  • ffx.numerics.switching.BellCurveSwitch (implements ffx.numerics.switching.UnivariateSwitchingFunction)
  • ffx.algorithms.mc.BoltzmannMC (implements ffx.algorithms.mc.MetropolisMC)
    • ffx.algorithms.mc.MolecularMC
    • ffx.algorithms.thermodynamics.MonteCarloOST
    • ffx.algorithms.optimize.manybody.RotamerMatrixMC
  • ffx.openmm.BondArray
  • ffx.potential.bonded.BondedTerm.BondedComparator (implements java.util.Comparator<T>)
  • ffx.potential.bonded.BondedUtils
  • ffx.numerics.math.BootStrapStatistics
  • ffx.potential.nonbonded.implicit.BornTanhRescaling
  • edu.rit.mp.Buf
    • edu.rit.mp.BooleanBuf
      • edu.rit.mp.buf.BooleanArrayBuf
        • edu.rit.mp.buf.BooleanArrayBuf_1
      • edu.rit.mp.buf.BooleanItemBuf
      • edu.rit.mp.buf.BooleanMatrixBuf
        • edu.rit.mp.buf.BooleanMatrixBuf_1
      • edu.rit.mp.buf.EmptyBooleanBuf
      • edu.rit.mp.buf.SharedBooleanArrayBuf
        • edu.rit.mp.buf.SharedBooleanArrayBuf_1
      • edu.rit.mp.buf.SharedBooleanBuf
    • edu.rit.mp.ByteBuf
      • edu.rit.mp.buf.ByteArrayBuf
        • edu.rit.mp.buf.ByteArrayBuf_1
      • edu.rit.mp.buf.ByteItemBuf
      • edu.rit.mp.buf.ByteMatrixBuf
        • edu.rit.mp.buf.ByteMatrixBuf_1
      • edu.rit.mp.buf.EmptyByteBuf
      • edu.rit.mp.buf.SharedByteArrayBuf
        • edu.rit.mp.buf.SharedByteArrayBuf_1
      • edu.rit.mp.buf.SharedByteBuf
    • edu.rit.mp.CharacterBuf
      • edu.rit.mp.buf.CharacterArrayBuf
        • edu.rit.mp.buf.CharacterArrayBuf_1
      • edu.rit.mp.buf.CharacterItemBuf
      • edu.rit.mp.buf.CharacterMatrixBuf
        • edu.rit.mp.buf.CharacterMatrixBuf_1
      • edu.rit.mp.buf.EmptyCharacterBuf
      • edu.rit.mp.buf.SharedCharacterArrayBuf
        • edu.rit.mp.buf.SharedCharacterArrayBuf_1
      • edu.rit.mp.buf.SharedCharacterBuf
    • edu.rit.mp.DoubleBuf
      • edu.rit.mp.buf.DoubleArrayBuf
        • edu.rit.mp.buf.DoubleArrayBuf_1
      • edu.rit.mp.buf.DoubleItemBuf
      • edu.rit.mp.buf.DoubleMatrixBuf
        • edu.rit.mp.buf.DoubleMatrixBuf_1
      • edu.rit.mp.buf.EmptyDoubleBuf
      • edu.rit.mp.buf.SharedDoubleArrayBuf
        • edu.rit.mp.buf.SharedDoubleArrayBuf_1
      • edu.rit.mp.buf.SharedDoubleBuf
    • edu.rit.mp.FloatBuf
      • edu.rit.mp.buf.EmptyFloatBuf
      • edu.rit.mp.buf.FloatArrayBuf
        • edu.rit.mp.buf.FloatArrayBuf_1
      • edu.rit.mp.buf.FloatItemBuf
      • edu.rit.mp.buf.FloatMatrixBuf
        • edu.rit.mp.buf.FloatMatrixBuf_1
      • edu.rit.mp.buf.SharedFloatArrayBuf
        • edu.rit.mp.buf.SharedFloatArrayBuf_1
      • edu.rit.mp.buf.SharedFloatBuf
    • edu.rit.mp.IntegerBuf
      • edu.rit.mp.buf.EmptyIntegerBuf
      • edu.rit.mp.buf.IntegerArrayBuf
        • edu.rit.mp.buf.IntegerArrayBuf_1
      • edu.rit.mp.buf.IntegerItemBuf
      • edu.rit.mp.buf.IntegerMatrixBuf
        • edu.rit.mp.buf.IntegerMatrixBuf_1
      • edu.rit.mp.buf.SharedIntegerArrayBuf
        • edu.rit.mp.buf.SharedIntegerArrayBuf_1
      • edu.rit.mp.buf.SharedIntegerBuf
    • edu.rit.mp.LongBuf
      • edu.rit.mp.buf.EmptyLongBuf
      • edu.rit.mp.buf.LongArrayBuf
        • edu.rit.mp.buf.LongArrayBuf_1
      • edu.rit.mp.buf.LongItemBuf
      • edu.rit.mp.buf.LongMatrixBuf
        • edu.rit.mp.buf.LongMatrixBuf_1
      • edu.rit.mp.buf.SharedLongArrayBuf
        • edu.rit.mp.buf.SharedLongArrayBuf_1
      • edu.rit.mp.buf.SharedLongBuf
    • edu.rit.mp.ObjectBuf<T>
      • edu.rit.mp.buf.EmptyObjectBuf
      • edu.rit.mp.buf.ObjectArrayBuf<T>
        • edu.rit.mp.buf.ObjectArrayBuf_1<T>
      • edu.rit.mp.buf.ObjectItemBuf<T>
      • edu.rit.mp.buf.ObjectMatrixBuf<T>
        • edu.rit.mp.buf.ObjectMatrixBuf_1<T>
      • edu.rit.mp.buf.SharedObjectArrayBuf<T>
        • edu.rit.mp.buf.SharedObjectArrayBuf_1<T>
      • edu.rit.mp.buf.SharedObjectBuf<T>
    • edu.rit.mp.ShortBuf
      • edu.rit.mp.buf.EmptyShortBuf
      • edu.rit.mp.buf.SharedShortArrayBuf
        • edu.rit.mp.buf.SharedShortArrayBuf_1
      • edu.rit.mp.buf.SharedShortBuf
      • edu.rit.mp.buf.ShortArrayBuf
        • edu.rit.mp.buf.ShortArrayBuf_1
      • edu.rit.mp.buf.ShortItemBuf
      • edu.rit.mp.buf.ShortMatrixBuf
        • edu.rit.mp.buf.ShortMatrixBuf_1
    • edu.rit.mp.Signed16BitIntegerBuf
      • edu.rit.mp.buf.EmptySigned16BitIntegerBuf
      • edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf
        • edu.rit.mp.buf.SharedSigned16BitIntegerArrayBuf_1
      • edu.rit.mp.buf.SharedSigned16BitIntegerBuf
      • edu.rit.mp.buf.Signed16BitIntegerArrayBuf
        • edu.rit.mp.buf.Signed16BitIntegerArrayBuf_1
      • edu.rit.mp.buf.Signed16BitIntegerItemBuf
      • edu.rit.mp.buf.Signed16BitIntegerMatrixBuf
        • edu.rit.mp.buf.Signed16BitIntegerMatrixBuf_1
    • edu.rit.mp.Signed8BitIntegerBuf
      • edu.rit.mp.buf.EmptySigned8BitIntegerBuf
      • edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf
        • edu.rit.mp.buf.SharedSigned8BitIntegerArrayBuf_1
      • edu.rit.mp.buf.SharedSigned8BitIntegerBuf
      • edu.rit.mp.buf.Signed8BitIntegerArrayBuf
        • edu.rit.mp.buf.Signed8BitIntegerArrayBuf_1
      • edu.rit.mp.buf.Signed8BitIntegerItemBuf
      • edu.rit.mp.buf.Signed8BitIntegerMatrixBuf
        • edu.rit.mp.buf.Signed8BitIntegerMatrixBuf_1
    • edu.rit.mp.Unsigned16BitIntegerBuf
      • edu.rit.mp.buf.EmptyUnsigned16BitIntegerBuf
      • edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf
        • edu.rit.mp.buf.SharedUnsigned16BitIntegerArrayBuf_1
      • edu.rit.mp.buf.SharedUnsigned16BitIntegerBuf
      • edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf
        • edu.rit.mp.buf.Unsigned16BitIntegerArrayBuf_1
      • edu.rit.mp.buf.Unsigned16BitIntegerItemBuf
      • edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf
        • edu.rit.mp.buf.Unsigned16BitIntegerMatrixBuf_1
    • edu.rit.mp.Unsigned8BitIntegerBuf
      • edu.rit.mp.buf.EmptyUnsigned8BitIntegerBuf
      • edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf
        • edu.rit.mp.buf.SharedUnsigned8BitIntegerArrayBuf_1
      • edu.rit.mp.buf.SharedUnsigned8BitIntegerBuf
      • edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf
        • edu.rit.mp.buf.Unsigned8BitIntegerArrayBuf_1
      • edu.rit.mp.buf.Unsigned8BitIntegerItemBuf
      • edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf
        • edu.rit.mp.buf.Unsigned8BitIntegerMatrixBuf_1
  • edu.rit.util.ByteSequence
  • ffx.utilities.ByteSwap
  • ffx.potential.constraint.CcmaConstraint (implements ffx.numerics.Constraint)
  • ffx.realspace.parsers.CCP4MapFilter (implements ffx.realspace.parsers.RealSpaceFileFilter)
  • ffx.xray.parsers.CCP4MapWriter
  • ffx.potential.nonbonded.implicit.ChandlerCavitation
  • edu.rit.mp.Channel
  • edu.rit.mp.ChannelGroup
  • ffx.xray.parsers.CIFFilter (implements ffx.xray.parsers.DiffractionFileFilter)
  • java.lang.ClassLoader
    • edu.rit.pj.cluster.BackendClassLoader
  • ffx.potential.utils.Clustering
  • ffx.potential.utils.Clustering.Conformation (implements org.apache.commons.math3.ml.clustering.Clusterable)
  • ffx.xray.parsers.CNSFilter (implements ffx.xray.parsers.DiffractionFileFilter)
  • ffx.xray.parsers.CNSMapWriter
  • edu.rit.pj.Comm
  • edu.rit.pj.cluster.CommPattern
  • edu.rit.pj.CommRequest
  • edu.rit.pj.CommStatus
  • ffx.numerics.fft.Complex
  • ffx.numerics.fft.Complex2D
  • ffx.numerics.fft.Complex3D
  • ffx.numerics.fft.Complex3DParallel
  • ffx.numerics.math.ComplexNumber
  • java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
    • java.awt.Canvas (implements javax.accessibility.Accessible)
      • org.jogamp.java3d.Canvas3D
        • ffx.ui.GraphicsCanvas (implements java.awt.event.ActionListener)
    • java.awt.Container
      • javax.swing.JComponent (implements java.io.Serializable)
        • javax.swing.JMenuBar (implements javax.accessibility.Accessible, javax.swing.MenuElement)
          • ffx.ui.MainMenu
        • javax.swing.JPanel (implements javax.accessibility.Accessible)
          • ffx.ui.GraphicsPanel
          • ffx.ui.KeywordPanel (implements java.awt.event.ActionListener)
          • ffx.ui.MainPanel (implements java.awt.event.ActionListener, javax.swing.event.ChangeListener)
          • ffx.ui.ModelingPanel (implements java.awt.event.ActionListener, java.awt.event.MouseListener)
        • javax.swing.JSplitPane (implements javax.accessibility.Accessible)
          • ffx.ui.GraphicsSplitPane (implements java.awt.event.MouseListener, java.awt.event.MouseMotionListener)
        • javax.swing.JTree (implements javax.accessibility.Accessible, javax.swing.Scrollable)
          • ffx.ui.Hierarchy (implements javax.swing.event.TreeModelListener, javax.swing.event.TreeSelectionListener)
      • java.awt.Window (implements javax.accessibility.Accessible)
        • java.awt.Dialog
          • javax.swing.JDialog (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • ffx.ui.GraphicsPrefs (implements java.awt.event.ActionListener)
        • java.awt.Frame (implements java.awt.MenuContainer)
          • javax.swing.JFrame (implements javax.accessibility.Accessible, javax.swing.RootPaneContainer, javax.swing.WindowConstants)
            • ffx.ui.KeyFileEditor
            • ffx.Main
        • ffx.ui.GraphicsFullScreen (implements java.awt.event.KeyListener)
  • ffx.numerics.switching.CompositeSwitch (implements ffx.numerics.switching.UnivariateSwitchingFunction)
  • ffx.potential.nonbonded.COMRestraint (implements ffx.potential.bonded.LambdaInterface)
  • edu.rit.pj.cluster.Configuration
  • ffx.algorithms.optimize.ConformationScan
  • ffx.utilities.Console (implements javax.swing.event.CaretListener, java.awt.event.ComponentListener, java.awt.event.FocusListener, groovy.lang.GroovyObject, javax.swing.event.HyperlinkListener)
    • ffx.ui.ModelingShell (implements ffx.algorithms.AlgorithmListener)
  • edu.rit.pj.cluster.Constants
  • ffx.utilities.Constants
  • ffx.numerics.switching.ConstantSwitch (implements ffx.numerics.switching.UnivariateSwitchingFunction)
  • ffx.openmm.Context
    • ffx.potential.openmm.OpenMMContext
  • ffx.potential.utils.ConvexHullOps
  • ffx.crystal.Crystal
    • ffx.crystal.NCSCrystal
    • ffx.crystal.ReplicatesCrystal
  • ffx.xray.CrystalReciprocalSpace
  • ffx.xray.CrystalStats
  • ffx.xray.cli.DataRefinementOptions
    • ffx.realspace.cli.RealSpaceOptions
    • ffx.xray.cli.XrayOptions
  • javax.swing.tree.DefaultMutableTreeNode (implements java.lang.Cloneable, javax.swing.tree.MutableTreeNode, java.io.Serializable)
    • ffx.potential.bonded.MSNode (implements ffx.potential.bonded.ROLS)
      • ffx.potential.bonded.Atom (implements java.lang.Comparable<T>)
      • ffx.potential.bonded.BondedTerm (implements ffx.potential.bonded.BondedEnergy, java.lang.Comparable<T>)
        • ffx.potential.bonded.Angle
        • ffx.potential.bonded.AngleTorsion (implements ffx.potential.bonded.LambdaInterface)
        • ffx.potential.bonded.Bond
        • ffx.potential.bonded.ImproperTorsion
        • ffx.potential.bonded.OutOfPlaneBend
        • ffx.potential.bonded.PiOrbitalTorsion (implements ffx.potential.bonded.LambdaInterface)
        • ffx.potential.bonded.RestrainDistance (implements ffx.potential.bonded.LambdaInterface)
        • ffx.potential.nonbonded.RestrainPosition (implements ffx.potential.bonded.LambdaInterface)
        • ffx.potential.bonded.RestraintTorsion (implements ffx.potential.bonded.LambdaInterface)
        • ffx.potential.bonded.StretchBend (implements java.lang.Comparable<T>)
        • ffx.potential.bonded.StretchTorsion (implements ffx.potential.bonded.LambdaInterface)
        • ffx.potential.bonded.Torsion (implements ffx.potential.bonded.LambdaInterface)
        • ffx.potential.bonded.TorsionTorsion (implements ffx.potential.bonded.LambdaInterface)
        • ffx.potential.bonded.UreyBradley
      • ffx.potential.bonded.Joint
      • ffx.potential.bonded.MSGroup
        • ffx.potential.MolecularAssembly
          • ffx.ui.FFXSystem
        • ffx.potential.bonded.Molecule
        • ffx.potential.bonded.Polymer
        • ffx.potential.bonded.Residue (implements java.lang.Comparable<T>)
          • ffx.potential.bonded.MultiResidue
      • ffx.potential.bonded.MSRoot
      • ffx.potential.bonded.ROLSP (implements ffx.potential.bonded.ROLS, java.lang.Runnable)
  • ffx.xray.DiffractionData (implements ffx.xray.DataContainer)
  • ffx.xray.parsers.DiffractionFile
  • ffx.xray.DiffractionRefinementData
  • ffx.utilities.DirectoryUtils
  • ffx.algorithms.optimize.manybody.DistanceMatrix
  • ffx.algorithms.optimize.manybody.DistanceMatrix.NeighborDistances
  • ffx.potential.parsers.DistanceMatrixFilter
  • ffx.numerics.math.Double3
  • ffx.openmm.DoubleArray
  • ffx.openmm.DoubleArray3D
  • ffx.numerics.math.DoubleMath
  • edu.rit.io.DoubleMatrixFile
  • edu.rit.io.DoubleMatrixFile.Reader
  • edu.rit.io.DoubleMatrixFile.Writer
  • ffx.numerics.integrate.DoublesDataSet (implements ffx.numerics.integrate.DataSet)
  • ffx.utilities.DownloadUtils
  • ffx.ui.commands.DTDResolver (implements org.xml.sax.EntityResolver)
  • ffx.potential.DualTopologyEnergy (implements ffx.crystal.CrystalPotential, ffx.potential.bonded.LambdaInterface)
  • ffx.algorithms.cli.DynamicsOptions
  • ffx.potential.parsers.DYNFilter
  • ffx.algorithms.optimize.manybody.EliminatedRotamers
  • ffx.algorithms.optimize.manybody.EnergyExpansion
  • ffx.numerics.special.Erf
  • ffx.numerics.estimator.EstimateBootstrapper
  • ffx.potential.parsers.ESVFilter
  • ffx.potential.nonbonded.pme.EwaldParameters
  • ffx.algorithms.optimize.anneal.ExpAnnealSchedule (implements ffx.algorithms.optimize.anneal.AnnealingSchedule)
  • ffx.potential.extended.ExtendedSystem (implements ffx.numerics.Potential)
  • ffx.ui.commands.FFXClient
  • ffx.utilities.FFXCommand
    • ffx.potential.cli.PotentialCommand
      • ffx.potential.commands.Energy
  • ffx.ui.FFXExec (implements java.lang.Runnable)
  • ffx.ui.properties.FFXLocale
  • ffx.ui.commands.FFXServer (implements java.lang.Runnable)
  • ffx.utilities.FFXTest
    • ffx.algorithms.misc.AlgorithmsTest
    • ffx.potential.utils.PotentialTest
  • ffx.numerics.tornado.FFXTornado
  • javax.swing.filechooser.FileFilter
    • ffx.potential.parsers.ARCFileFilter
    • ffx.potential.parsers.CoordinateFileFilter
    • ffx.potential.parsers.DistanceMatrixFileFilter
    • ffx.potential.parsers.DYNFileFilter
    • ffx.potential.parsers.ESVFileFilter
    • ffx.potential.parsers.FFXFileFilter
    • ffx.potential.parsers.ForceFieldFileFilter
    • ffx.potential.parsers.InducedFileFilter
    • ffx.potential.parsers.INTFileFilter
    • ffx.potential.parsers.KeyFileFilter
    • ffx.xray.parsers.MTZFileFilter
    • ffx.potential.parsers.PDBFileFilter
    • ffx.potential.parsers.PDBMLFileFilter
    • ffx.potential.parsers.XPHFileFilter
    • ffx.potential.parsers.XYZFileFilter
  • edu.rit.io.Files
  • ffx.utilities.FileUtils
  • ffx.potential.FiniteDifferenceUtils
  • ffx.potential.openmm.FixedChargeAlchemicalForces
  • ffx.algorithms.optimize.anneal.FlatEndAnnealSchedule (implements ffx.algorithms.optimize.anneal.AnnealingSchedule)
  • ffx.numerics.math.Float3
  • ffx.numerics.math.FloatMath
  • ffx.openmm.Force
    • ffx.openmm.AndersenThermostat
    • ffx.openmm.CMMotionRemover
    • ffx.openmm.CustomAngleForce
      • ffx.potential.openmm.AngleForce
    • ffx.openmm.CustomBondForce
      • ffx.potential.openmm.BondForce
      • ffx.potential.openmm.RestrainBondsForce
    • ffx.openmm.CustomCentroidBondForce
      • ffx.potential.openmm.RestrainGroupsForce
    • ffx.openmm.CustomCompoundBondForce
      • ffx.potential.openmm.AngleTorsionForce
      • ffx.potential.openmm.InPlaneAngleForce
      • ffx.potential.openmm.OutOfPlaneBendForce
      • ffx.potential.openmm.PiOrbitalTorsionForce
      • ffx.potential.openmm.StretchBendForce
      • ffx.potential.openmm.StretchTorsionForce
    • ffx.openmm.CustomExternalForce
      • ffx.potential.openmm.RestrainPositionsForce
    • ffx.openmm.CustomGBForce
      • ffx.potential.openmm.FixedChargeGBForce
    • ffx.openmm.CustomNonbondedForce
    • ffx.openmm.amoeba.GeneralizedKirkwoodForce
      • ffx.potential.openmm.AmoebaGeneralizedKirkwoodForce
    • ffx.openmm.amoeba.GKCavitationForce
      • ffx.potential.openmm.AmoebaGKCavitationForce
    • ffx.openmm.HarmonicBondForce
      • ffx.potential.openmm.UreyBradleyForce
    • ffx.openmm.MonteCarloBarostat
    • ffx.openmm.amoeba.MultipoleForce
      • ffx.potential.openmm.AmoebaMultipoleForce
    • ffx.openmm.NonbondedForce
      • ffx.potential.openmm.FixedChargeNonbondedForce
    • ffx.openmm.PeriodicTorsionForce
      • ffx.potential.openmm.ImproperTorsionForce
      • ffx.potential.openmm.RestrainTorsionsForce
      • ffx.potential.openmm.TorsionForce
    • ffx.openmm.amoeba.TorsionTorsionForce
      • ffx.potential.openmm.AmoebaTorsionTorsionForce
    • ffx.openmm.amoeba.VdwForce
      • ffx.potential.openmm.AmoebaVdwForce
    • ffx.openmm.amoeba.WcaDispersionForce
      • ffx.potential.openmm.AmoebaWcaDispersionForce
  • ffx.potential.parameters.ForceField
  • ffx.potential.ForceFieldEnergy (implements ffx.crystal.CrystalPotential, ffx.potential.bonded.LambdaInterface)
    • ffx.potential.openmm.OpenMMEnergy
  • ffx.potential.parsers.ForceFieldFilter
  • java.util.logging.Formatter
    • java.util.logging.SimpleFormatter
      • ffx.ui.LogFormatter
  • edu.rit.pj.cluster.FrontendFileReader
  • edu.rit.pj.cluster.FrontendFileWriter
  • ffx.numerics.integrate.FunctionDataCurve (implements ffx.numerics.integrate.DataSet)
    • ffx.numerics.integrate.CompositeCurve
    • ffx.numerics.integrate.CosineWave
    • ffx.numerics.integrate.PolynomialCurve
    • ffx.numerics.integrate.SinWave
  • ffx.potential.nonbonded.implicit.GaussVol
  • ffx.potential.nonbonded.GeneralizedKirkwood (implements ffx.potential.bonded.LambdaInterface)
  • ffx.algorithms.misc.GenerateRotamers
  • ffx.potential.utils.GetProteinFeatures
  • ffx.numerics.multipole.GKEnergyGlobal
  • ffx.numerics.multipole.GKEnergyGlobalSIMD
  • ffx.numerics.multipole.GKEnergyQI
  • ffx.numerics.multipole.GKEnergyQISIMD
  • ffx.numerics.multipole.GKSource
  • ffx.numerics.multipole.GKSourceSIMD
  • ffx.potential.cli.GradientOptions
  • ffx.potential.utils.GradientUtils
  • groovy.lang.GroovyObjectSupport (implements groovy.lang.GroovyObject)
    • groovy.lang.Script
      • ffx.utilities.FFXScript
        • ffx.algorithms.cli.AlgorithmsScript
        • ffx.potential.cli.PotentialScript
  • java.util.logging.Handler
    • ffx.ui.LogHandler
  • ffx.HeadlessMain
  • edu.rit.util.Hex
  • ffx.numerics.math.HilbertCurveTransforms
  • ffx.algorithms.thermodynamics.HistogramData
  • ffx.crystal.HKL
  • edu.rit.http.HttpRequest
  • edu.rit.http.HttpResponse
  • edu.rit.http.HttpServer
  • ffx.utilities.Hybrid36
  • ffx.potential.parsers.InducedFilter
  • java.io.InputStream (implements java.io.Closeable)
    • edu.rit.pj.cluster.BackendFileInputStream
    • java.io.FilterInputStream
      • edu.rit.io.DataInputStream
  • edu.rit.util.Instance
  • ffx.openmm.IntArray
  • ffx.numerics.integrate.Integrate1DNumeric
  • ffx.numerics.integrate.Integration
  • ffx.algorithms.dynamics.integrators.Integrator
    • ffx.algorithms.dynamics.integrators.BetterBeeman
    • ffx.algorithms.dynamics.integrators.Respa
    • ffx.algorithms.dynamics.integrators.Stochastic
    • ffx.algorithms.dynamics.integrators.VelocityVerlet
  • ffx.openmm.Integrator
    • ffx.openmm.CustomIntegrator
      • ffx.potential.openmm.CustomMTSIntegrator
      • ffx.potential.openmm.CustomMTSLangevinIntegrator
    • ffx.openmm.LangevinMiddleIntegrator
      • ffx.openmm.LangevinIntegrator
    • ffx.openmm.VerletIntegrator
  • ffx.openmm.IntSet
  • edu.rit.mp.IORequest
  • edu.rit.pj.job.Job (implements java.io.Externalizable, java.lang.Runnable)
  • edu.rit.pj.cluster.JobBackend (implements edu.rit.pj.cluster.JobBackendRef, java.lang.Runnable)
  • edu.rit.pj.cluster.JobFrontend (implements edu.rit.pj.cluster.JobFrontendRef, java.lang.Runnable)
  • edu.rit.pj.job.JobGenerator (implements java.lang.Iterable<T>)
  • edu.rit.pj.cluster.JobInfo
  • edu.rit.pj.cluster.JobScheduler (implements edu.rit.pj.cluster.JobSchedulerRef)
  • ffx.potential.parsers.KeyFilter
  • ffx.utilities.Keyword
  • ffx.ui.KeywordComponent (implements java.awt.event.ActionListener, javax.swing.event.ChangeListener, javax.swing.event.DocumentListener, java.awt.event.MouseListener)
  • ffx.algorithms.thermodynamics.LambdaData
  • ffx.algorithms.mc.LambdaMove (implements ffx.algorithms.mc.MCMove)
  • ffx.algorithms.cli.LambdaParticleOptions
  • ffx.numerics.optimization.LBFGS
  • ffx.algorithms.optimize.anneal.LinearAnnealSchedule (implements ffx.algorithms.optimize.anneal.AnnealingSchedule)
  • ffx.numerics.switching.LinearDerivativeSwitch (implements ffx.numerics.switching.UnivariateSwitchingFunction)
  • ffx.numerics.optimization.LineSearch
  • edu.rit.pj.Lock
  • edu.rit.util.LongRange (implements java.io.Externalizable)
  • ffx.potential.utils.Loop
  • ffx.potential.utils.LoopClosure
  • ffx.algorithms.optimize.manybody.ManyBodyCell
  • ffx.algorithms.cli.ManyBodyOptions
  • edu.rit.util.Mathe
  • ffx.numerics.math.MatrixMath
  • ffx.numerics.estimator.MBARFilter
  • ffx.algorithms.mc.MCLoop (implements ffx.algorithms.mc.MonteCarloListener)
  • ffx.algorithms.mc.MDMove (implements ffx.algorithms.mc.MCMove)
  • edu.rit.pj.cluster.Message (implements java.io.Externalizable)
    • edu.rit.pj.cluster.JobBackendMessage (implements java.io.Externalizable)
    • edu.rit.pj.cluster.JobFrontendMessage (implements java.io.Externalizable)
    • edu.rit.pj.cluster.JobSchedulerMessage (implements java.io.Externalizable)
  • ffx.openmm.MinimizationReporter
  • ffx.algorithms.optimize.Minimize (implements ffx.numerics.optimization.OptimizationListener, ffx.algorithms.Terminatable)
    • ffx.algorithms.optimize.CrystalMinimize (implements ffx.numerics.optimization.OptimizationListener, ffx.algorithms.Terminatable)
    • ffx.algorithms.optimize.MinimizeOpenMM
  • ffx.algorithms.cli.MinimizeOptions
  • ffx.numerics.fft.MixedRadixFactor
    • ffx.numerics.fft.MixedRadixFactor2
    • ffx.numerics.fft.MixedRadixFactor3
    • ffx.numerics.fft.MixedRadixFactor4
    • ffx.numerics.fft.MixedRadixFactor5
    • ffx.numerics.fft.MixedRadixFactor6
    • ffx.numerics.fft.MixedRadixFactor7
    • ffx.numerics.fft.MixedRadixFactorPrime
  • ffx.numerics.special.ModifiedBessel
  • ffx.algorithms.dynamics.MolecularDynamics (implements java.lang.Runnable, ffx.algorithms.Terminatable)
    • ffx.algorithms.dynamics.MolecularDynamicsOpenMM
  • ffx.xray.parsers.MTZFilter (implements ffx.xray.parsers.DiffractionFileFilter)
  • ffx.xray.parsers.MTZWriter
  • ffx.numerics.atomic.MultiDoubleArray (implements ffx.numerics.atomic.AtomicDoubleArray)
  • ffx.algorithms.cli.MultiDynamicsOptions
  • ffx.numerics.switching.MultiplicativeSwitch (implements ffx.numerics.switching.UnivariateSwitchingFunction)
  • ffx.numerics.multipole.MultipoleTensor
    • ffx.numerics.multipole.CoulombTensorGlobal
      • ffx.numerics.multipole.AmoebaPlusDampTensorGlobal
      • ffx.numerics.multipole.AmoebaPlusOverlapTensorGlobal
      • ffx.numerics.multipole.CombinedTensorGlobal
      • ffx.numerics.multipole.EwaldTensorGlobal
      • ffx.numerics.multipole.GKTensorGlobal
      • ffx.numerics.multipole.TholeTensorGlobal
    • ffx.numerics.multipole.CoulombTensorQI
      • ffx.numerics.multipole.EwaldTensorQI
      • ffx.numerics.multipole.GKTensorQI
      • ffx.numerics.multipole.TholeTensorQI
  • ffx.numerics.multipole.MultipoleTensorSIMD
    • ffx.numerics.multipole.CoulombTensorGlobalSIMD
      • ffx.numerics.multipole.EwaldTensorGlobalSIMD
      • ffx.numerics.multipole.GKTensorGlobalSIMD
      • ffx.numerics.multipole.TholeTensorGlobalSIMD
    • ffx.numerics.multipole.CoulombTensorQISIMD
      • ffx.numerics.multipole.EwaldTensorQISIMD
      • ffx.numerics.multipole.GKTensorQISIMD
      • ffx.numerics.multipole.TholeTensorQISIMD
  • ffx.numerics.multipole.MultipoleUtilities
  • ffx.numerics.estimator.MultistateBennettAcceptanceRatio.HarmonicOscillatorsTestCase
  • ffx.potential.bonded.NamingUtils
  • ffx.potential.nonbonded.NCSRestraint (implements ffx.potential.bonded.LambdaInterface)
  • ffx.potential.nonbonded.implicit.NeckIntegral
  • ffx.potential.nonbonded.NeighborList.AtomIndex (implements java.lang.Comparable<T>)
  • ffx.potential.nonbonded.NeighborList.Cell
  • ffx.xray.NeutronFormFactor (implements ffx.xray.FormFactor)
  • ffx.potential.nonbonded.NonbondedCutoff
  • ffx.algorithms.dynamics.NonEquilbriumDynamics
  • edu.rit.pj.cluster.NonPjJobFrontend (implements edu.rit.pj.cluster.JobFrontendRef, java.lang.Runnable)
  • ffx.potential.bonded.NucleicAcidUtils
  • java.lang.Number (implements java.io.Serializable)
    • edu.rit.pj.replica.ReplicatedByte
    • edu.rit.pj.replica.ReplicatedCharacter
    • edu.rit.pj.replica.ReplicatedDouble
    • edu.rit.pj.replica.ReplicatedFloat
    • edu.rit.pj.replica.ReplicatedInteger
    • edu.rit.pj.replica.ReplicatedLong
    • edu.rit.pj.replica.ReplicatedShort
    • edu.rit.pj.reduction.SharedByte
    • edu.rit.pj.reduction.SharedCharacter
    • edu.rit.pj.reduction.SharedDouble
    • edu.rit.pj.reduction.SharedFloat
    • edu.rit.pj.reduction.SharedInteger
    • edu.rit.pj.reduction.SharedLong
    • edu.rit.pj.reduction.SharedShort
  • ffx.potential.nonbonded.octree.Octree
  • ffx.potential.nonbonded.octree.OctreeCell
  • ffx.potential.nonbonded.octree.OctreePoint
    • ffx.potential.nonbonded.octree.OctreeParticle
  • edu.rit.pj.reduction.Op
    • edu.rit.pj.reduction.BooleanOp
    • edu.rit.pj.reduction.ByteOp
    • edu.rit.pj.reduction.CharacterOp
    • edu.rit.pj.reduction.DoubleOp
    • edu.rit.pj.reduction.FloatOp
    • edu.rit.pj.reduction.IntegerOp
    • edu.rit.pj.reduction.LongOp
    • edu.rit.pj.reduction.ObjectOp<T>
    • edu.rit.pj.reduction.ShortOp
  • ffx.potential.openmm.OpenMMIntegrator
  • ffx.potential.parsers.OpenMMXmlFilter
  • ffx.algorithms.thermodynamics.OrthogonalSpaceTempering (implements ffx.crystal.CrystalPotential, ffx.potential.bonded.LambdaInterface)
  • ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.Histogram
  • ffx.algorithms.thermodynamics.OrthogonalSpaceTempering.OptimizationParameters
  • ffx.algorithms.cli.OSTOptions
  • ffx.ui.OSXAdapter (implements com.apple.mrj.MRJAboutHandler, com.apple.mrj.MRJOpenDocumentHandler, com.apple.mrj.MRJPrefsHandler, com.apple.mrj.MRJQuitHandler)
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • edu.rit.pj.cluster.BackendFileOutputStream
    • java.io.FilterOutputStream
      • edu.rit.io.DataOutputStream
      • edu.rit.io.LineBufferedOutputStream
      • java.io.PrintStream (implements java.lang.Appendable, java.io.Closeable)
        • ffx.utilities.StringOutputStream
  • edu.rit.util.Packing
  • edu.rit.pj.ParallelConstruct
    • edu.rit.pj.BarrierAction
    • edu.rit.pj.ParallelForLoop
      • edu.rit.pj.IntegerForLoop
        • ffx.potential.nonbonded.ReciprocalSpace.BSplineRegion.BSplineLoop
        • ffx.potential.nonbonded.RowLoop
        • ffx.potential.nonbonded.SliceLoop
        • ffx.potential.nonbonded.SpatialDensityLoop
      • edu.rit.pj.IntegerStrideForLoop
      • edu.rit.pj.LongForLoop
      • edu.rit.pj.LongStrideForLoop
    • edu.rit.pj.ParallelIteration<T>
    • edu.rit.pj.ParallelRegion
      • ffx.potential.nonbonded.implicit.BornGradRegion
      • ffx.potential.nonbonded.implicit.BornRadiiRegion
      • ffx.xray.BulkSolventList
      • ffx.potential.nonbonded.implicit.ConnollyRegion
      • ffx.potential.nonbonded.pme.DirectRegion
      • ffx.potential.nonbonded.implicit.DispersionRegion
      • ffx.algorithms.optimize.manybody.DistanceRegion
      • ffx.algorithms.optimize.manybody.EnergyRegion
      • ffx.potential.nonbonded.pme.ExpandInducedDipolesRegion
      • ffx.potential.nonbonded.implicit.GKEnergyRegion
      • ffx.algorithms.optimize.manybody.GoldsteinPairRegion
      • ffx.potential.nonbonded.implicit.HydrophobicPMFRegion
      • ffx.potential.nonbonded.pme.InducedDipoleFieldReduceRegion
      • ffx.potential.nonbonded.pme.InducedDipoleFieldRegion
      • ffx.potential.nonbonded.implicit.InducedGKFieldRegion
      • ffx.potential.nonbonded.implicit.InitializationRegion
      • ffx.potential.nonbonded.pme.InitializationRegion
      • edu.rit.pj.KillRegion
      • ffx.potential.nonbonded.NeighborList
      • ffx.potential.nonbonded.pme.OPTRegion
      • ffx.potential.nonbonded.pme.PermanentFieldRegion (implements ffx.potential.nonbonded.MaskingInterface)
      • ffx.potential.nonbonded.implicit.PermanentGKFieldRegion
      • ffx.potential.nonbonded.pme.PolarizationEnergyRegion
      • ffx.potential.nonbonded.pme.RealSpaceEnergyRegion (implements ffx.potential.nonbonded.MaskingInterface)
      • ffx.potential.nonbonded.pme.ReciprocalEnergyRegion
      • ffx.potential.nonbonded.ReciprocalSpace.BSplineRegion
      • ffx.potential.nonbonded.pme.ReduceRegion
      • ffx.potential.nonbonded.RowRegion
        • ffx.xray.BulkSolventRowRegion
      • ffx.potential.nonbonded.SliceRegion
        • ffx.xray.BulkSolventSliceRegion
      • ffx.potential.nonbonded.pme.SORRegion
      • ffx.potential.nonbonded.SpatialDensityRegion
        • ffx.xray.BulkSolventDensityRegion
      • ffx.potential.nonbonded.implicit.SurfaceAreaRegion
    • edu.rit.pj.ParallelSection
  • edu.rit.pj.ParallelTeam
  • ffx.potential.nonbonded.ParticleMeshEwald (implements ffx.potential.bonded.LambdaInterface)
  • ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactors
    • ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactorsESV
    • ffx.potential.nonbonded.ParticleMeshEwald.LambdaFactorsOST
  • ffx.numerics.fft.PassData
  • ffx.potential.nonbonded.pme.PCGSolver
  • ffx.potential.parsers.PDBFilter.Mutation
  • ffx.potential.parsers.PDBMLFilter (implements org.xml.sax.ErrorHandler)
  • ffx.algorithms.optimize.PhMinimize (implements ffx.numerics.optimization.OptimizationListener, ffx.algorithms.Terminatable)
  • ffx.algorithms.dynamics.PhReplicaExchange (implements ffx.algorithms.Terminatable)
  • ffx.numerics.atomic.PJDoubleArray (implements ffx.numerics.atomic.AtomicDoubleArray)
  • edu.rit.pj.PJProperties
  • ffx.openmm.Platform
  • ffx.potential.nonbonded.pme.PMETimings
  • ffx.numerics.multipole.PolarizableMultipole
  • ffx.numerics.multipole.PolarizableMultipoleSIMD
  • ffx.potential.bonded.PolymerUtils
  • ffx.utilities.PortUtils
  • ffx.potential.utils.PotentialsFileOpener (implements ffx.potential.parsers.FileOpener)
  • ffx.potential.utils.PotentialsUtils (implements ffx.potential.utils.PotentialsFunctions)
    • ffx.algorithms.AlgorithmUtils (implements ffx.algorithms.AlgorithmFunctions)
      • ffx.ui.UIUtils (implements ffx.algorithms.AlgorithmFunctions)
  • ffx.numerics.switching.PowerSwitch (implements ffx.numerics.switching.UnivariateSwitchingFunction)
  • edu.rit.util.PrintStreamLogger (implements edu.rit.util.Logger)
  • edu.rit.pj.cluster.ProcessInfo
  • ffx.potential.utils.ProgressiveAlignmentOfCrystals
  • edu.rit.pj.cluster.Proxy
    • edu.rit.pj.cluster.JobBackendProxy (implements edu.rit.pj.cluster.JobBackendRef)
    • edu.rit.pj.cluster.JobFrontendProxy (implements edu.rit.pj.cluster.JobFrontendRef)
    • edu.rit.pj.cluster.JobSchedulerProxy (implements edu.rit.pj.cluster.JobSchedulerRef)
  • ffx.numerics.multipole.QIFrame
  • ffx.numerics.multipole.QIFrameSIMD
  • ffx.potential.QuadTopologyEnergy (implements ffx.crystal.CrystalPotential, ffx.potential.bonded.LambdaInterface)
  • ffx.numerics.func1d.QuasiLinearThetaMap (implements ffx.numerics.func1d.UnivariateDiffFunction)
  • edu.rit.util.Random (implements java.io.Serializable)
    • edu.rit.util.DefaultRandom
    • edu.rit.util.Mcg1Random
  • edu.rit.util.RandomSample
  • edu.rit.util.RandomSubset (implements java.util.Iterator<E>)
  • ffx.algorithms.cli.RandomUnitCellOptions
  • edu.rit.util.Range (implements java.io.Externalizable)
  • ffx.algorithms.dynamics.integrators.Rattle
  • ffx.numerics.fft.Real
  • ffx.numerics.fft.Real3D
  • ffx.numerics.fft.Real3DParallel
  • ffx.realspace.RealSpaceData (implements ffx.xray.DataContainer)
  • ffx.realspace.RealSpaceEnergy (implements ffx.crystal.CrystalPotential, ffx.potential.bonded.LambdaInterface)
  • ffx.realspace.parsers.RealSpaceFile
  • ffx.potential.nonbonded.pme.RealSpaceNeighborParameters
  • ffx.realspace.RealSpaceRefinementData
  • ffx.potential.nonbonded.ReciprocalSpace
  • edu.rit.pj.reduction.ReduceArrays
  • ffx.xray.RefinementEnergy (implements ffx.algorithms.AlgorithmListener, ffx.crystal.CrystalPotential, ffx.potential.bonded.LambdaInterface)
  • ffx.xray.RefinementMinimize (implements ffx.numerics.optimization.OptimizationListener, ffx.algorithms.Terminatable)
  • ffx.xray.RefinementModel
  • ffx.crystal.ReflectionList
  • ffx.crystal.ReflectionSpline
  • ffx.potential.bonded.RelativeSolvation
  • ffx.potential.bonded.RendererCache
  • ffx.algorithms.cli.RepExOptions
  • ffx.algorithms.thermodynamics.RepExOST
  • ffx.algorithms.cli.RepexOSTOptions
  • ffx.algorithms.dynamics.ReplicaExchange (implements ffx.algorithms.Terminatable)
  • edu.rit.pj.replica.ReplicatedBoolean
  • edu.rit.pj.replica.ReplicatedObject<T>
  • ffx.potential.bonded.ResidueState
  • ffx.crystal.Resolution
  • edu.rit.pj.cluster.ResourceCache
  • ffx.utilities.Resources
  • ffx.potential.nonbonded.RestrainGroups
  • ffx.algorithms.mc.RosenbluthCBMC (implements ffx.algorithms.mc.MonteCarloListener)
  • ffx.algorithms.mc.RosenbluthChi0Move (implements ffx.algorithms.mc.MCMove)
  • ffx.algorithms.mc.RosenbluthChiAllMove (implements ffx.algorithms.mc.MCMove)
  • ffx.algorithms.mc.RosenbluthOBMC (implements ffx.algorithms.mc.MonteCarloListener)
  • ffx.potential.bonded.Rotamer
  • ffx.potential.bonded.RotamerLibrary
  • ffx.potential.bonded.RotamerLibrary.RotamerGuess
  • ffx.algorithms.optimize.manybody.RotamerMatrixMove (implements ffx.algorithms.mc.MCMove)
  • ffx.algorithms.optimize.RotamerOptimization (implements ffx.algorithms.Terminatable)
  • edu.rit.pj.job.Runner
  • ffx.numerics.math.RunningStatistics
  • ffx.potential.cli.SaveOptions
  • ffx.numerics.math.ScalarMath
  • ffx.xray.ScaleBulkEnergy (implements ffx.numerics.OptimizationInterface)
  • ffx.xray.ScaleBulkMinimize (implements ffx.numerics.optimization.OptimizationListener, ffx.algorithms.Terminatable)
  • ffx.potential.nonbonded.pme.ScaleParameters
  • org.jogamp.java3d.SceneGraphObject
    • org.jogamp.java3d.Node
      • org.jogamp.java3d.Group
        • ffx.ui.GraphicsAxis (implements ffx.ui.behaviors.MouseBehaviorCallback)
      • org.jogamp.java3d.Leaf
        • org.jogamp.java3d.Behavior
          • ffx.ui.GraphicsEvents
          • ffx.ui.behaviors.MouseBehavior
            • ffx.ui.behaviors.MouseOrbit
            • ffx.ui.behaviors.MouseProperties
            • ffx.ui.behaviors.MouseRotate
            • ffx.ui.behaviors.MouseSelection
            • ffx.ui.behaviors.MouseTranslate
            • ffx.ui.behaviors.MouseZoom
          • ffx.ui.behaviors.PickMouseBehavior
            • ffx.ui.GraphicsPicking
            • ffx.ui.behaviors.PickOrbitBehavior (implements ffx.ui.behaviors.MouseBehaviorCallback)
            • ffx.ui.behaviors.PickPropertiesBehavior (implements ffx.ui.behaviors.MouseBehaviorCallback)
            • ffx.ui.behaviors.PickRotateBehavior (implements ffx.ui.behaviors.MouseBehaviorCallback)
            • ffx.ui.behaviors.PickSelectionBehavior (implements ffx.ui.behaviors.MouseBehaviorCallback)
            • ffx.ui.behaviors.PickTranslateBehavior (implements ffx.ui.behaviors.MouseBehaviorCallback)
            • ffx.ui.behaviors.PickZoomBehavior (implements ffx.ui.behaviors.MouseBehaviorCallback)
          • ffx.potential.Renderer
          • org.jogamp.java3d.utils.behaviors.vp.ViewPlatformBehavior
            • org.jogamp.java3d.utils.behaviors.vp.ViewPlatformAWTBehavior (implements java.awt.event.KeyListener, java.awt.event.MouseListener, java.awt.event.MouseMotionListener, java.awt.event.MouseWheelListener)
              • org.jogamp.java3d.utils.behaviors.vp.OrbitBehavior
                • ffx.ui.behaviors.GlobalBehavior
  • ffx.potential.nonbonded.ScfPredictor
  • ffx.potential.nonbonded.pme.SCFPredictorParameters
  • edu.rit.pj.Schedule
    • edu.rit.pj.IntegerSchedule
      • ffx.xray.GradientSchedule
      • ffx.potential.nonbonded.PairwiseSchedule
      • ffx.xray.RowSchedule
      • ffx.xray.SliceSchedule
      • ffx.potential.nonbonded.SpatialDensitySchedule
    • edu.rit.pj.LongSchedule
  • edu.rit.util.Searching
  • edu.rit.util.Searching.Byte
  • edu.rit.util.Searching.Character
  • edu.rit.util.Searching.Double
  • edu.rit.util.Searching.Float
  • edu.rit.util.Searching.Integer
  • edu.rit.util.Searching.Long
  • edu.rit.util.Searching.Object<T>
  • edu.rit.util.Searching.Short
  • ffx.ui.Selection
  • ffx.algorithms.thermodynamics.SendSynchronous
  • ffx.numerics.estimator.SequentialEstimator (implements ffx.numerics.estimator.StatisticalEstimator)
    • ffx.numerics.estimator.BennettAcceptanceRatio (implements ffx.numerics.estimator.BootstrappableEstimator)
    • ffx.numerics.estimator.MultistateBennettAcceptanceRatio (implements ffx.numerics.estimator.BootstrappableEstimator, ffx.numerics.OptimizationInterface)
    • ffx.numerics.estimator.Zwanzig (implements ffx.numerics.estimator.BootstrappableEstimator)
  • ffx.potential.constraint.SettleConstraint (implements ffx.numerics.Constraint)
  • ffx.potential.constraint.ShakeChargeConstraint (implements ffx.numerics.Constraint)
  • edu.rit.pj.reduction.SharedBoolean
  • edu.rit.pj.reduction.SharedBooleanArray
  • edu.rit.pj.reduction.SharedByteArray
  • edu.rit.pj.reduction.SharedCharacterArray
  • edu.rit.pj.reduction.SharedDoubleArray
  • edu.rit.pj.reduction.SharedFloatArray
  • edu.rit.pj.reduction.SharedIntegerArray
  • edu.rit.pj.reduction.SharedIntegerMatrix
  • edu.rit.pj.reduction.SharedLongArray
  • edu.rit.pj.reduction.SharedLongMatrix
  • edu.rit.pj.reduction.SharedObject<T>
  • edu.rit.pj.reduction.SharedObjectArray<T>
  • edu.rit.pj.reduction.SharedShortArray
  • ffx.xray.SigmaAEnergy (implements ffx.numerics.OptimizationInterface)
  • ffx.xray.SigmaAMinimize (implements ffx.numerics.optimization.OptimizationListener, ffx.algorithms.Terminatable)
  • ffx.algorithms.optimize.anneal.SimulatedAnnealing (implements java.lang.Runnable, ffx.algorithms.Terminatable)
  • ffx.ui.commands.SimulationDefinition (implements java.io.Serializable)
  • ffx.ui.SimulationLoader (implements java.awt.event.ActionListener)
  • ffx.ui.commands.SimulationMessage (implements java.io.Serializable)
  • ffx.ui.commands.SimulationUpdate (implements java.io.Serializable)
  • ffx.xray.SolventBinaryFormFactor (implements ffx.xray.FormFactor)
  • ffx.xray.SolventGaussFormFactor (implements ffx.xray.FormFactor)
  • ffx.xray.SolventPolyFormFactor (implements ffx.xray.FormFactor)
  • edu.rit.util.Sorting
  • edu.rit.util.Sorting.Byte
  • edu.rit.util.Sorting.Character
  • edu.rit.util.Sorting.Double
  • edu.rit.util.Sorting.Float
  • edu.rit.util.Sorting.Integer
  • edu.rit.util.Sorting.Long
  • edu.rit.util.Sorting.Object<T>
  • edu.rit.util.Sorting.Short
  • ffx.crystal.SpaceGroup
  • ffx.crystal.SpaceGroupConversions
  • ffx.crystal.SpaceGroupDefinitions
  • ffx.crystal.SpaceGroupInfo
  • ffx.xray.SplineEnergy (implements ffx.numerics.OptimizationInterface)
  • ffx.xray.SplineMinimize (implements ffx.numerics.optimization.OptimizationListener, ffx.algorithms.Terminatable)
  • ffx.numerics.switching.SquaredTrigSwitch (implements ffx.numerics.switching.UnivariateSwitchingFunction)
  • ffx.numerics.math.SquareRoot
  • ffx.numerics.math.SSETest
  • ffx.openmm.State
    • ffx.potential.openmm.OpenMMState
  • edu.rit.mp.Status
  • edu.rit.io.Stdio
  • edu.rit.pj.io.StreamFile
  • ffx.openmm.StringArray
  • ffx.utilities.StringUtils
  • ffx.potential.utils.StructureMetrics
  • ffx.potential.bonded.SturmMethod
  • ffx.numerics.math.SummaryStatistics
  • ffx.potential.utils.Superpose
  • ffx.ui.SwingWorker
  • ffx.crystal.SymOp
  • ffx.openmm.System
    • ffx.potential.openmm.OpenMMSystem
  • ffx.potential.parsers.SystemFilter
    • ffx.potential.parsers.CIFFilter
    • ffx.potential.parsers.INTFilter
    • ffx.potential.parsers.MergeFilter
    • ffx.potential.parsers.PDBFilter
    • ffx.ui.commands.SimulationFilter
    • ffx.potential.parsers.XPHFilter
    • ffx.potential.parsers.XYZFilter
  • ffx.potential.SystemState
  • ffx.algorithms.cli.ThermodynamicsOptions
  • ffx.algorithms.dynamics.thermostats.Thermostat
    • ffx.algorithms.dynamics.thermostats.Adiabatic
    • ffx.algorithms.dynamics.thermostats.Berendsen
    • ffx.algorithms.dynamics.thermostats.Bussi
  • java.lang.Thread (implements java.lang.Runnable)
    • edu.rit.util.TimerThread
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • ffx.potential.bonded.BondedUtils.MissingAtomTypeException
      • ffx.potential.bonded.BondedUtils.MissingHeavyAtomException
      • java.io.IOException
        • edu.rit.mp.ChannelClosedException
        • edu.rit.mp.ChannelGroupClosedException
        • edu.rit.io.InvalidMatrixFileException
        • edu.rit.pj.cluster.JobSchedulerException
      • edu.rit.pj.MultipleParallelException
      • java.lang.RuntimeException
        • java.lang.ArithmeticException
          • ffx.potential.utils.EnergyException
  • edu.rit.util.Timer
  • ffx.potential.cli.TimerOptions
  • ffx.utilities.TinkerUtils
  • ffx.algorithms.optimize.TitrationManyBody
  • ffx.potential.parameters.TitrationUtils
  • ffx.potential.cli.TopologyOptions
  • ffx.numerics.fft.TornadoDFT
  • ffx.potential.nonbonded.pme.Torque
  • ffx.algorithms.optimize.TorsionSearch
  • ffx.ui.Trajectory (implements java.awt.event.ActionListener)
  • ffx.numerics.spline.TriCubicSpline
  • ffx.ui.UIFileCloser (implements java.lang.Runnable)
  • ffx.ui.UIFileOpener (implements ffx.potential.parsers.FileOpener)
  • ffx.numerics.spline.UniformBSpline
  • ffx.numerics.switching.UnivariateFunctionFactory
  • ffx.potential.Utilities
  • ffx.potential.nonbonded.VanDerWaals (implements ffx.potential.bonded.LambdaInterface, ffx.potential.nonbonded.MaskingInterface)
    • ffx.potential.nonbonded.VanDerWaalsTornado
  • ffx.potential.nonbonded.VanDerWaals.LambdaFactors
    • ffx.potential.nonbonded.VanDerWaals.LambdaFactorsOST
  • ffx.potential.nonbonded.VanDerWaalsForm
  • ffx.openmm.Vec3Array
  • edu.rit.pj.Version
  • ffx.algorithms.dynamics.WeightedEnsembleManager
  • edu.rit.pj.WorkerConstruct
    • edu.rit.pj.WorkerForLoop
      • edu.rit.pj.WorkerIntegerForLoop
      • edu.rit.pj.WorkerIntegerStrideForLoop
      • edu.rit.pj.WorkerLongForLoop
      • edu.rit.pj.WorkerLongStrideForLoop
    • edu.rit.pj.WorkerIteration<T>
    • edu.rit.pj.WorkerRegion
      • ffx.algorithms.optimize.manybody.FourBodyEnergyRegion
      • ffx.algorithms.optimize.manybody.SelfEnergyRegion
      • ffx.algorithms.optimize.manybody.ThreeBodyEnergyRegion
      • ffx.algorithms.optimize.manybody.TwoBodyEnergyRegion
  • edu.rit.pj.WorkerTeam
    • edu.rit.pj.HybridTeam
  • ffx.potential.cli.WriteoutOptions
  • jakarta.xml.bind.annotation.adapters.XmlAdapter<ValueType,BoundType>
    • ffx.utilities.DoubleXMLAdapter
    • ffx.utilities.HistogramXmlAdapter
  • ffx.xray.XRayEnergy (implements ffx.crystal.CrystalPotential, ffx.potential.bonded.LambdaInterface)
  • ffx.xray.XRayFormFactor (implements ffx.xray.FormFactor)
  • ffx.potential.XtalEnergy (implements ffx.numerics.Potential)

Interface Hierarchy

• ffx.algorithms.AlgorithmListener
• ffx.potential.bonded.AminoAcidUtils.SideChainType
• ffx.algorithms.optimize.anneal.AnnealingSchedule
• ffx.numerics.atomic.AtomicDoubleArray
• ffx.potential.bonded.BondedEnergy
• edu.rit.mp.ConnectListener
• ffx.numerics.Constraint
• ffx.xray.DataContainer
• ffx.numerics.integrate.DataSet
• ffx.xray.parsers.DiffractionFileFilter
• ffx.xray.FormFactor
• edu.rit.pj.cluster.JobBackendRef
• edu.rit.pj.cluster.JobFrontendRef
• edu.rit.pj.cluster.JobSchedulerRef
• ffx.potential.bonded.LambdaInterface
• edu.rit.util.Logger
• ffx.potential.nonbonded.MaskingInterface
• ffx.algorithms.mc.MCMove
• ffx.algorithms.mc.MetropolisMC
• ffx.algorithms.mc.MonteCarloListener
• ffx.ui.behaviors.MouseBehaviorCallback
• ffx.xray.parsers.MTZWriter.MTZType
• ffx.numerics.OptimizationInterface
  • ffx.numerics.Potential
    • ffx.crystal.CrystalPotential
• ffx.numerics.optimization.OptimizationListener
• ffx.ui.behaviors.PickingCallback
• ffx.potential.utils.PotentialsFunctions
  • ffx.algorithms.AlgorithmFunctions
• ffx.realspace.parsers.RealSpaceFileFilter
• ffx.potential.bonded.ROLS
• java.lang.Runnable
  • ffx.potential.parsers.FileOpener
• ffx.xray.SplineEnergy.Type
• ffx.numerics.estimator.StatisticalEstimator
  • ffx.numerics.estimator.BootstrappableEstimator
• ffx.algorithms.Terminatable
• edu.rit.util.TimerTask
• ffx.numerics.func1d.UnivariateDiffFunction
  • ffx.numerics.switching.UnivariateSwitchingFunction

Annotation Interface Hierarchy

• ffx.utilities.FFXProperties (implements java.lang.annotation.Annotation)
• ffx.utilities.FFXProperty (implements java.lang.annotation.Annotation)

Enum Class Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.lang.constant.Constable, java.io.Serializable)
    • ffx.potential.nonbonded.pme.AlchemicalParameters.AlchemicalMode
    • ffx.potential.bonded.AminoAcidUtils.AA
    • ffx.potential.bonded.AminoAcidUtils.AIB (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.ALA (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.AminoAcid1
    • ffx.potential.bonded.AminoAcidUtils.AminoAcid3
    • ffx.potential.bonded.AminoAcidUtils.AminoAcidBackboneAtoms
    • ffx.potential.bonded.AminoAcidUtils.ARG (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.ASD (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.ASH (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.ASN (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.ASP (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.CYD (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.CYS (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.CYX (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.GLD (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.GLH (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.GLN (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.GLU (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.GLY
    • ffx.potential.bonded.AminoAcidUtils.GlycineBackboneAtoms
    • ffx.potential.bonded.AminoAcidUtils.HID (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.HIE (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.HIS (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.ILE (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.LEU (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.LYD (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.LYS (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.MET (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.ORN (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.PCA (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.PHE (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.PRO (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.ProlineBackboneAtoms
    • ffx.potential.bonded.AminoAcidUtils.ResiduePosition
    • ffx.potential.bonded.AminoAcidUtils.SER (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.THR (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.TRP (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.TYD (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.TYR (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.bonded.AminoAcidUtils.VAL (implements ffx.potential.bonded.AminoAcidUtils.SideChainType)
    • ffx.potential.parameters.AngleType.AngleFunction
    • ffx.potential.parameters.AngleType.AngleMode
    • ffx.crystal.ASULimit
    • ffx.potential.bonded.Atom.Descriptions
    • ffx.potential.bonded.Atom.ElementSymbol
    • ffx.potential.bonded.Atom.Resolution
    • ffx.numerics.atomic.AtomicDoubleArray.AtomicDoubleArrayImpl
    • edu.rit.pj.cluster.BackendInfo.State
    • ffx.potential.parameters.BondType.BondFunction
    • ffx.numerics.multipole.CoordinateSystem
    • ffx.xray.CrystalReciprocalSpace.GridMethod
    • ffx.xray.CrystalReciprocalSpace.SolventModel
    • ffx.crystal.CrystalSystem
    • ffx.numerics.fft.DataLayout1D
    • ffx.numerics.fft.DataLayout2D
    • ffx.numerics.fft.DataLayout3D
    • ffx.potential.parameters.ForceField.ELEC_FORM
    • ffx.potential.parameters.ForceField.ForceFieldName
    • ffx.potential.parameters.ForceField.ForceFieldType
    • ffx.potential.nonbonded.GeneralizedKirkwood.NonPolarModel
    • ffx.numerics.multipole.GKMultipoleOrder
    • ffx.numerics.multipole.GKTensorMode
    • ffx.ui.GraphicsCanvas.ImageFormat
    • ffx.ui.GraphicsCanvas.LeftButtonMode
    • ffx.ui.GraphicsCanvas.MouseMode
    • ffx.ui.GraphicsPicking.PickLevel
    • edu.rit.http.HttpResponse.Status
    • ffx.numerics.integrate.Integrate1DNumeric.IntegrationSide
    • ffx.numerics.integrate.Integrate1DNumeric.IntegrationType
    • ffx.algorithms.dynamics.integrators.IntegratorEnum
    • edu.rit.pj.cluster.JobInfo.State
    • ffx.ui.KeywordComponent.SwingRepresentation
    • ffx.potential.nonbonded.pme.LambdaMode
    • ffx.crystal.LatticeSystem
    • ffx.crystal.LaueSystem
    • ffx.numerics.optimization.LineSearch.LineSearchResult
    • ffx.algorithms.dynamics.MDEngine
    • ffx.algorithms.dynamics.MDVerbosity
    • ffx.algorithms.dynamics.MDWriteAction
    • ffx.algorithms.optimize.Minimize.MinimizationEngine
    • ffx.potential.MolecularAssembly.FractionalMode
    • ffx.potential.parameters.MultipoleType.MultipoleFrameDefinition
    • ffx.numerics.estimator.MultistateBennettAcceptanceRatio.SeedType
    • ffx.potential.bonded.NamingUtils.HetAtoms
    • ffx.potential.bonded.NucleicAcidUtils.NA
    • ffx.potential.bonded.NucleicAcidUtils.NucleicAcid1
    • ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3
    • ffx.numerics.multipole.Operator
    • ffx.potential.parsers.PDBFilter.PDBFileStandard
    • ffx.potential.Platform
    • ffx.potential.nonbonded.pme.Polarization
    • ffx.numerics.Potential.STATE
    • ffx.numerics.Potential.VARIABLE_TYPE
    • edu.rit.pj.cluster.ProcessInfo.State
    • ffx.utilities.PropertyGroup
    • ffx.potential.nonbonded.ReciprocalSpace.GridMethod
    • ffx.xray.RefinementMinimize.RefinementMode
    • ffx.potential.bonded.RelativeSolvation.SolvationLibrary
    • ffx.potential.bonded.RendererCache.ColorModel
    • ffx.potential.bonded.RendererCache.ViewModel
    • ffx.potential.bonded.Residue.ResidueType
    • ffx.potential.bonded.Residue.SSType
    • ffx.potential.bonded.ROLSP.PARALLELMETHOD
    • ffx.algorithms.mc.RosenbluthChiAllMove.MODE
    • ffx.potential.bonded.RotamerLibrary.NucleicAcidLibrary
    • ffx.potential.bonded.RotamerLibrary.NucleicSugarPucker
    • ffx.potential.bonded.RotamerLibrary.ProteinLibrary
    • ffx.algorithms.optimize.RotamerOptimization.Algorithm
    • ffx.algorithms.optimize.RotamerOptimization.Direction
    • ffx.algorithms.optimize.RotamerOptimization.DistanceMethod
    • ffx.potential.nonbonded.pme.SCFAlgorithm
    • ffx.potential.nonbonded.pme.SCFPredictor
    • ffx.potential.nonbonded.ScfPredictor.PredictorMode
    • ffx.algorithms.optimize.anneal.SimulatedAnnealing.Schedules
    • ffx.potential.parameters.SoluteType.SOLUTE_RADII_TYPE
    • ffx.potential.parsers.SystemFilter.Versioning
    • ffx.algorithms.cli.ThermodynamicsOptions.ThermodynamicsAlgorithm
    • ffx.algorithms.dynamics.thermostats.ThermostatEnum
    • ffx.potential.parameters.TitrationUtils.CysStates
    • ffx.potential.parameters.TitrationUtils.CysteineAtomNames
    • ffx.potential.parameters.TitrationUtils.HisStates
    • ffx.potential.parameters.TitrationUtils.HistidineAtomNames
    • ffx.potential.parameters.TitrationUtils.LysineAtomNames
    • ffx.potential.parameters.TitrationUtils.LysStates
    • ffx.potential.parameters.TitrationUtils.Titration
    • ffx.potential.parameters.TorsionType.TorsionMode
    • ffx.potential.Utilities.FileType
    • ffx.potential.Utilities.PolymerType
    • ffx.potential.parameters.VDWType.EPSILON_RULE
    • ffx.potential.parameters.VDWType.RADIUS_RULE
    • ffx.potential.parameters.VDWType.RADIUS_SIZE
    • ffx.potential.parameters.VDWType.RADIUS_TYPE
    • ffx.potential.parameters.VDWType.VDW_TYPE
    • ffx.potential.parameters.VDWType.VDWMode
    • ffx.algorithms.dynamics.WeightedEnsembleManager.OneDimMetric
    • ffx.numerics.estimator.Zwanzig.Directionality

Record Class Hierarchy

• java.lang.Object
  • java.lang.Record
    • ffx.utilities.DoubleIndexPair (implements java.lang.Comparable<T>)
    • ffx.utilities.IndexIndexPair (implements java.lang.Comparable<T>)
    • ffx.utilities.ObjectPair<T,S> (implements java.lang.Comparable<T>)
    • ffx.numerics.fft.PassConstants
    • ffx.potential.UnmodifiableState