Serialized Form

Package edu.duke.cs.osprey.astar
- Class edu.duke.cs.osprey.astar.AStarProgress
  
  class AStarProgress extends Object implements Serializable
  
  serialVersionUID:
  
  767988861537797830L
  - Serialized Fields
    
    deepestLevel
    
    int deepestLevel
    
    goalScore
    
    double goalScore
    
    gscore
    
    double gscore
    
    hscore
    
    double hscore
    
    level
    
    int level
    
    msRunning
    
    int msRunning
    
    numLeafNodes
    
    int numLeafNodes
    
    numLevels
    
    int numLevels
    
    numNodesExpanded
    
    long numNodesExpanded
    
    numNodesInQueue
    
    long numNodesInQueue
    
    numNodesQueuedThisReport
    
    long numNodesQueuedThisReport
    
    stopwatch
    
    Stopwatch stopwatch
- Class edu.duke.cs.osprey.astar.AStarTree
  
  class AStarTree extends Object implements Serializable
  
  serialVersionUID:
  
  2311735341816014431L
  - Serialized Fields
    
    numExpanded
    
    int numExpanded
    
    numPruned
    
    int numPruned
    
    pq
    
    PriorityQueue<T extends AStarNode> pq
- Class edu.duke.cs.osprey.astar.ConfTree
  
  class ConfTree extends AStarTree<T extends AStarNode> implements Serializable
  
  serialVersionUID:
  
  -2776047349227703884L
  - Serialized Fields
    
    childConf
    
    int[] childConf
    
    definedPos
    
    int[] definedPos
    
    definedRCs
    
    int[] definedRCs
    
    emat
    
    EnergyMatrix emat
    
    epicMat
    
    EPICMatrix epicMat
    
    minPartialConfs
    
    boolean minPartialConfs
    
    mutSpace
    
    GMECMutSpace mutSpace
    
    newEPICMat
    
    NewEPICMatrix newEPICMat
    
    nodeFactory
    
    AStarNode.Factory<T extends AStarNode> nodeFactory
    
    numDefined
    
    int numDefined
    
    numPos
    
    int numPos
    
    numUndefined
    
    int numUndefined
    
    rcTuple
    
    RCTuple rcTuple
    
    traditionalScore
    
    boolean traditionalScore
    
    undefinedPos
    
    int[] undefinedPos
    
    unprunedRCsAtPos
    
    int[][] unprunedRCsAtPos
    
    useDynamicAStar
    
    boolean useDynamicAStar
    
    useRefinement
    
    boolean useRefinement
- Class edu.duke.cs.osprey.astar.FullAStarNode
  
  class FullAStarNode extends Object implements Serializable
  
  serialVersionUID:
  
  -537132381411057989L
  - Serialized Fields
    
    gscore
    
    double gscore
    
    hscore
    
    double hscore
    
    nodeAssignments
    
    int[] nodeAssignments
    
    score
    
    double score
    
    scoreNeedsRefinement
    
    boolean scoreNeedsRefinement
    
    UB
    
    double UB
    
    UBConf
    
    int[] UBConf
- Class edu.duke.cs.osprey.astar.FullAStarNode.Factory
  
  class Factory extends Object implements Serializable
  
  serialVersionUID:
  
  -6909420740336320965L
  - Serialized Fields
    
    numPos
    
    int numPos
- Class edu.duke.cs.osprey.astar.SlimAStarNode
  
  class SlimAStarNode extends Object implements Serializable
  
  serialVersionUID:
  
  -8612409900432350474L
  - Serialized Fields
    
    gscore
    
    double gscore
    
    hscore
    
    double hscore
    
    level
    
    short level
    
    link
    
    SlimAStarNode.Link link
    
    numPos
    
    short numPos
- Class edu.duke.cs.osprey.astar.SlimAStarNode.Factory
  
  class Factory extends Object implements Serializable
  
  serialVersionUID:
  
  4759571366344935185L
  - Serialized Fields
    
    numPos
    
    int numPos
- Class edu.duke.cs.osprey.astar.SlimAStarNode.Link
  
  class Link extends Object implements Serializable
  
  serialVersionUID:
  
  -6371596109692467264L
  - Serialized Fields
    
    parent
    
    SlimAStarNode.Link parent
    
    pos
    
    short pos
    
    rc
    
    short rc
Package edu.duke.cs.osprey.astar.comets
- Class edu.duke.cs.osprey.astar.comets.COMETSNode
  
  class COMETSNode extends FullAStarNode implements Serializable
  - Serialized Fields
    
    pruneMat
    
    PruningMatrix[] pruneMat
    
    stateTrees
    
    ConfTree<FullAStarNode>[] stateTrees
    
    stateUB
    
    double[] stateUB
- Class edu.duke.cs.osprey.astar.comets.COMETSTree
  
  class COMETSTree extends AStarTree<FullAStarNode> implements Serializable
  - Serialized Fields
    
    AATypeOptions
    
    ArrayList<ArrayList<String>> AATypeOptions
    
    constraints
    
    LME[] constraints
    
    mutable2StatePosNums
    
    ArrayList<ArrayList<Integer>> mutable2StatePosNums
    
    numMaxMut
    
    int numMaxMut
    
    numSeqsReturned
    
    int numSeqsReturned
    
    numStates
    
    int numStates
    
    numTreeLevels
    
    int numTreeLevels
    
    objFcn
    
    LME objFcn
    
    outputGMECStructs
    
    boolean outputGMECStructs
    
    stateGMECsForPruning
    
    int stateGMECsForPruning
    
    stateNumPos
    
    int[] stateNumPos
    
    stateSP
    
    SearchProblem[] stateSP
    
    wtSeq
    
    String[] wtSeq
- Class edu.duke.cs.osprey.astar.comets.LME
  
  class LME extends Object implements Serializable
  - Serialized Fields
    
    coeffs
    
    double[] coeffs
    
    constTerm
    
    double constTerm
- Class edu.duke.cs.osprey.astar.comets.NewCOMETSTree
  
  class NewCOMETSTree extends AStarTree<COMETSNode> implements Serializable
  - Serialized Fields
    
    AATypeOptions
    
    ArrayList<ArrayList<String>> AATypeOptions
    
    confECalc
    
    ConfEnergyCalculator[] confECalc
    
    confSpaces
    
    SimpleConfSpace[] confSpaces
    
    constraints
    
    LME[] constraints
    
    mutable2StatePosNums
    
    ArrayList<ArrayList<Integer>> mutable2StatePosNums
    
    numMaxMut
    
    int numMaxMut
    
    numSeqsReturned
    
    int numSeqsReturned
    
    numStates
    
    int numStates
    
    numTreeLevels
    
    int numTreeLevels
    
    objFcn
    
    LME objFcn
    
    outputGMECStructs
    
    boolean outputGMECStructs
    
    precompMats
    
    PrecomputedMatrices[] precompMats
    
    stateGMECsForPruning
    
    int stateGMECsForPruning
    
    stateNumPos
    
    int[] stateNumPos
    
    wtSeq
    
    String[] wtSeq
- Class edu.duke.cs.osprey.astar.comets.UpdatedPruningMatrix
  
  class UpdatedPruningMatrix extends PruningMatrix implements Serializable
  - Serialized Fields
    
    parent
    
    PruningMatrix parent
    
    prunedPairUpdates
    
    ArrayList<ArrayList<TreeMap<Integer,TreeSet<Integer>>>> prunedPairUpdates
    
    prunedRCUpdates
    
    ArrayList<TreeSet<Integer>> prunedRCUpdates

Package edu.duke.cs.osprey.bbfree

Class edu.duke.cs.osprey.bbfree.BBFreeBlock

class BBFreeBlock extends Object implements Serializable

Serialized Fields

curFreeDOFVals
```
double[] curFreeDOFVals
```
deriv1
```
double[][] deriv1
```
deriv2
```
double[][][] deriv2
```
deriv3
```
double[][][][] deriv3
```
deriv4
```
double[][][][][] deriv4
```

freeDOFCenter

cern.colt.matrix.DoubleMatrix1D freeDOFCenter

freeDOFMatrix

cern.colt.matrix.DoubleMatrix2D freeDOFMatrix

freeDOFs
```
ArrayList<BBFreeDOF> freeDOFs
```
freeDOFVoxel
```
double[][] freeDOFVoxel
```
fullDOFCenter
```
double[] fullDOFCenter
```
fullDOFPolys
```
double[][] fullDOFPolys
```

jacDerivs

ArrayList<ArrayList<edu.duke.cs.osprey.bbfree.BBFreeBlock.JacDerivEntry>> jacDerivs

pepPlanes
```
PepPlaneLinModel[] pepPlanes
```
residues
```
List<Residue> residues
```
wderiv2
```
double[][][] wderiv2
```
wderiv3
```
double[][][][] wderiv3
```
wderiv4
```
double[][][][][] wderiv4
```

Class edu.duke.cs.osprey.bbfree.BBFreeDOF

class BBFreeDOF extends DegreeOfFreedom implements Serializable
- Serialized Fields
  - block
    
    BBFreeBlock block
  - coeffs
    
    cern.colt.matrix.DoubleMatrix1D coeffs
  - indexInBlock
    
    int indexInBlock
Class edu.duke.cs.osprey.bbfree.PepPlaneLinModel

class PepPlaneLinModel extends Object implements Serializable
- Serialized Fields
  - CCoeffs
    
    cern.colt.matrix.DoubleMatrix1D CCoeffs
  - HCoeffs
    
    cern.colt.matrix.DoubleMatrix1D HCoeffs
  - OCoeffs
    
    cern.colt.matrix.DoubleMatrix1D OCoeffs

Package edu.duke.cs.osprey.coffee
- Exception edu.duke.cs.osprey.coffee.ClusterMember.TimeoutException
  
  class TimeoutException extends RuntimeException implements Serializable
Package edu.duke.cs.osprey.confspace
- Class edu.duke.cs.osprey.confspace.AbstractPosMatrix
  
  class AbstractPosMatrix extends Object implements Serializable
  - Serialized Fields
    
    numPairs
    
    int numPairs
    
    numPos
    
    int numPos
- Class edu.duke.cs.osprey.confspace.AbstractTupleMatrix
  
  class AbstractTupleMatrix extends Object implements Serializable
  
  serialVersionUID:
  
  1654821458320722522L
  - Serialized Fields
    
    defaultHigherInteraction
    
    T defaultHigherInteraction
    
    higherTerms
    
    ArrayList<HigherTupleFinder<T>> higherTerms
    
    Deprecated.
    
    use tuple trees instead, they're much faster
    
    numConfAtPos
    
    int[] numConfAtPos
    
    numOneBodyTerms
    
    int numOneBodyTerms
    
    numPairwiseTerms
    
    int numPairwiseTerms
    
    numPos
    
    int numPos
    
    oneBodyOffsets
    
    int[] oneBodyOffsets
    
    pairwiseOffsets
    
    int[] pairwiseOffsets
    
    pruningInterval
    
    double pruningInterval
    
    tupleTrees
    
    TupleTree<T>[] tupleTrees
- Class edu.duke.cs.osprey.confspace.CATSStrandFlex
  
  class CATSStrandFlex extends StrandFlex implements Serializable
  - Serialized Fields
    
    block
    
    BBFreeBlock block
- Class edu.duke.cs.osprey.confspace.ConfDB.Key
  
  class Key extends Object implements Serializable
  - Serialized Fields
    
    rtIndices
    
    int[] rtIndices
    
    table
    
    String table
- Class edu.duke.cs.osprey.confspace.ConfSearch.EnergiedConf
  
  class EnergiedConf extends ConfSearch.ScoredConf implements Serializable
  - Serialized Fields
    
    energy
    
    double energy
- Class edu.duke.cs.osprey.confspace.ConfSearch.ScoredConf
  
  class ScoredConf extends Object implements Serializable
  - Serialized Fields
    
    assignments
    
    int[] assignments
    
    score
    
    double score
- Exception edu.duke.cs.osprey.confspace.ConfSearch.Splitter.OutOfOrderException
  
  class OutOfOrderException extends RuntimeException implements Serializable
- Class edu.duke.cs.osprey.confspace.ConfSpace
  
  class ConfSpace extends Object implements Serializable
  
  serialVersionUID:
  
  6414329117813457771L
  - Serialized Fields
    
    confDOFs
    
    ArrayList<DegreeOfFreedom> confDOFs
    
    flexibleRes
    
    ArrayList<String> flexibleRes
    
    m
    
    Molecule m
    
    mutDOFs
    
    ArrayList<ResidueTypeDOF> mutDOFs
    
    numPos
    
    int numPos
    
    posFlex
    
    ArrayList<PositionConfSpace> posFlex
    
    useEllipses
    
    boolean useEllipses
- Class edu.duke.cs.osprey.confspace.DEEPerStrandFlex
  
  class DEEPerStrandFlex extends StrandFlex implements Serializable
  - Serialized Fields
    
    dset
    
    DEEPerSettings dset
    
    perts
    
    ArrayList<Perturbation> perts
- Class edu.duke.cs.osprey.confspace.HigherTupleFinder
  
  class HigherTupleFinder extends Object implements Serializable
  - Serialized Fields
    
    defaultInteraction
    
    T defaultInteraction
    
    higher
    
    ArrayList<TreeMap<Integer,HigherTupleFinder<T>>> higher
    
    interactingPos
    
    ArrayList<Integer> interactingPos
    
    interactions
    
    ArrayList<TreeMap<Integer,T>> interactions
- Class edu.duke.cs.osprey.confspace.ParametricMolecule
  
  class ParametricMolecule extends Object implements Serializable
  - Serialized Fields
    
    dofBounds
    
    ObjectiveFunction.DofBounds dofBounds
    
    Bounds on the degrees of freedom
    
    dofs
    
    List<DegreeOfFreedom> dofs
    
    Degrees of freedom.
    
    mol
    
    Molecule mol
    
    The molecule manipulated by the degrees of freedom.
- Class edu.duke.cs.osprey.confspace.PositionConfSpace
  
  class PositionConfSpace extends Object implements Serializable
  
  serialVersionUID:
  
  2705824580246579508L
  - Serialized Fields
    
    designIndex
    
    int designIndex
    
    ellipsoidalDOFs
    
    ArrayList<EllipseCoordDOF> ellipsoidalDOFs
    
    RCs
    
    ArrayList<RC> RCs
    
    res
    
    Residue res
    
    wtRCs
    
    ArrayList<RC> wtRCs
- Class edu.duke.cs.osprey.confspace.PosMatrixGeneric
  
  class PosMatrixGeneric extends AbstractPosMatrix<T> implements Serializable
  - Serialized Fields
    
    vals
    
    T[] vals
- Class edu.duke.cs.osprey.confspace.RC
  
  class RC extends Object implements Serializable
  - Serialized Fields
    
    AAType
    
    String AAType
    
    DOFmax
    
    ArrayList<Double> DOFmax
    
    DOFmin
    
    ArrayList<Double> DOFmin
    
    DOFs
    
    ArrayList<DegreeOfFreedom> DOFs
    
    RCIndex
    
    int RCIndex
    
    rotNum
    
    int rotNum
    
    template
    
    ResidueTemplate template
- Class edu.duke.cs.osprey.confspace.RCTuple
  
  class RCTuple extends Object implements Serializable
  
  serialVersionUID:
  
  3773470316855163174L
  - Serialized Fields
    
    pos
    
    ArrayList<Integer> pos
    
    RCs
    
    ArrayList<Integer> RCs
- Class edu.duke.cs.osprey.confspace.SearchProblem
  
  class SearchProblem extends Object implements Serializable
  
  serialVersionUID:
  
  2590525329048496524L
  - Serialized Fields
    
    addResEntropy
    
    boolean addResEntropy
    
    allowedAAs
    
    ArrayList<ArrayList<String>> allowedAAs
    
    competitorPruneMat
    
    PruningMatrix competitorPruneMat
    
    confSpace
    
    ConfSpace confSpace
    
    contSCFlex
    
    boolean contSCFlex
    
    deeperSettings
    
    DEEPerSettings deeperSettings
    
    emat
    
    EnergyMatrix emat
    
    epicMat
    
    EPICMatrix epicMat
    
    epicSettings
    
    EPICSettings epicSettings
    
    flexRes
    
    ArrayList<String> flexRes
    
    fullConfE
    
    EnergyFunction fullConfE
    
    gCalc
    
    VoxelGCalculator gCalc
    
    luteSettings
    
    LUTESettings luteSettings
    
    name
    
    String name
    
    numEmatThreads
    
    int numEmatThreads
    
    plugMat
    
    PolytopeMatrix plugMat
    
    pruneMat
    
    PruningMatrix pruneMat
    
    shellResidues
    
    ArrayList<Residue> shellResidues
    
    tupExpEMat
    
    EnergyMatrix tupExpEMat
    
    useEPIC
    
    boolean useEPIC
    
    useERef
    
    boolean useERef
    
    useTupExpForSearch
    
    boolean useTupExpForSearch
    
    useVoxelG
    
    boolean useVoxelG
- Class edu.duke.cs.osprey.confspace.SeqSpace
  
  class SeqSpace extends Object implements Serializable
  
  serialVersionUID:
  
  -7309869148482636562L
  - Serialized Fields
    
    positions
    
    List<SeqSpace.Position> positions
    
    positionsByResNum
    
    Map<String,SeqSpace.Position> positionsByResNum
- Class edu.duke.cs.osprey.confspace.SeqSpace.Position
  
  class Position extends Object implements Serializable
  
  serialVersionUID:
  
  -8317027786742083135L
  - Serialized Fields
    
    index
    
    int index
    
    mutations
    
    List<SeqSpace.ResType> mutations
    
    resNum
    
    String resNum
    
    resTypes
    
    List<SeqSpace.ResType> resTypes
    
    resTypesByName
    
    Map<String,SeqSpace.ResType> resTypesByName
    
    seqSpace
    
    SeqSpace seqSpace
    
    wildType
    
    SeqSpace.ResType wildType
- Class edu.duke.cs.osprey.confspace.SeqSpace.ResType
  
  class ResType extends Object implements Serializable
  
  serialVersionUID:
  
  1628630395970846143L
  - Serialized Fields
    
    index
    
    int index
    
    name
    
    String name
    
    pos
    
    SeqSpace.Position pos
- Class edu.duke.cs.osprey.confspace.SimpleConfSpace
  
  class SimpleConfSpace extends Object implements Serializable
  - Serialized Fields
    
    immutablePositions
    
    List<SimpleConfSpace.Position> immutablePositions
    
    The subset of design positions with no mutations
    
    molTemplate
    
    Molecule molTemplate
    
    mutablePositions
    
    List<SimpleConfSpace.Position> mutablePositions
    
    The subset of design positions with allowed mutations
    
    mutAlignmentCache
    
    MutAlignmentCache mutAlignmentCache
    
    numResConfsByPos
    
    int[] numResConfsByPos
    
    positions
    
    List<SimpleConfSpace.Position> positions
    
    The design positions
    
    positionsByResNum
    
    Map<String,SimpleConfSpace.Position> positionsByResNum
    
    The design positions, indexed by residue number
    
    seqSpace
    
    SeqSpace seqSpace
    
    The sequence space for this conformation space
    
    shellDist
    
    double shellDist
    
    Distance from flexible residues (in Angstroms) within which to include shell residues
    
    shellResNumbers
    
    Set<String> shellResNumbers
    
    The residue numbers of the shell residues
    
    strandFlex
    
    Map<Strand,List<StrandFlex>> strandFlex
    
    The flexibility of each strand
    
    strands
    
    List<Strand> strands
    
    The strands
- Exception edu.duke.cs.osprey.confspace.SimpleConfSpace.NonMutablePositionException
  
  class NonMutablePositionException extends IllegalStateException implements Serializable
- Class edu.duke.cs.osprey.confspace.SimpleConfSpace.Position
  
  class Position extends Object implements Serializable
  - Serialized Fields
    
    index
    
    int index
    
    index in the positions list
    
    mindex
    
    int mindex
    
    index in the mutable positions list, or -1 if not there
    
    resConfs
    
    List<SimpleConfSpace.ResidueConf> resConfs
    
    resFlex
    
    Strand.ResidueFlex resFlex
    
    resNum
    
    String resNum
    
    resTypes
    
    List<String> resTypes
    
    seqPos
    
    SeqSpace.Position seqPos
    
    strand
    
    Strand strand
- Class edu.duke.cs.osprey.confspace.SimpleConfSpace.ResidueConf
  
  class ResidueConf extends Object implements Serializable
  - Serialized Fields
    
    dofBounds
    
    HashMap<String,double[]> dofBounds
    
    index
    
    int index
    
    postTemplateModifier
    
    SimpleConfSpace.ResidueConf.PostTemplateModifier postTemplateModifier
    
    rotamerIndex
    
    Integer rotamerIndex
    
    template
    
    ResidueTemplate template
    
    type
    
    SimpleConfSpace.ResidueConf.Type type
- Class edu.duke.cs.osprey.confspace.Strand
  
  class Strand extends Object implements Serializable
  - Serialized Fields
    
    flexibility
    
    Strand.Flexibility flexibility
    
    Flexibility parameters for this strand
    
    mol
    
    Molecule mol
    
    The molecule this strand represents
    
    nonTemplateResNames
    
    Set<String> nonTemplateResNames
    
    Names of residues that couldn't be matched to templates
    
    templateLib
    
    ResidueTemplateLibrary templateLib
    
    The template library used to pick templates for this strand
- Class edu.duke.cs.osprey.confspace.Strand.Flexibility
  
  class Flexibility extends Object implements Serializable
  - Serialized Fields
    
    residues
    
    Map<String,Strand.ResidueFlex> residues
- Class edu.duke.cs.osprey.confspace.Strand.ResidueFlex
  
  class ResidueFlex extends Object implements Serializable
  - Serialized Fields
    
    addWildTypeRotamers
    
    boolean addWildTypeRotamers
    
    resTypes
    
    Set<String> resTypes
    
    voxelShape
    
    VoxelShape voxelShape
    
    wildType
    
    String wildType
- Class edu.duke.cs.osprey.confspace.StrandFlex
  
  class StrandFlex extends Object implements Serializable
- Class edu.duke.cs.osprey.confspace.StrandFlex.None
  
  class None extends StrandFlex implements Serializable
- Class edu.duke.cs.osprey.confspace.StrandFlex.TranslateRotate
  
  class TranslateRotate extends StrandFlex implements Serializable
  - Serialized Fields
    
    maxRotDegrees
    
    double maxRotDegrees
    
    maxTranslation
    
    double maxTranslation
- Class edu.duke.cs.osprey.confspace.TupleMatrixBoolean
  
  class TupleMatrixBoolean extends AbstractTupleMatrix<Boolean> implements Serializable
  
  serialVersionUID:
  
  -1286639255089978027L
  - Serialized Fields
    
    oneBody
    
    BitSet oneBody
    
    pairwise
    
    BitSet pairwise
- Class edu.duke.cs.osprey.confspace.TupleMatrixDouble
  
  class TupleMatrixDouble extends AbstractTupleMatrix<Double> implements Serializable
  
  serialVersionUID:
  
  -1286639255089978027L
  - Serialized Fields
    
    oneBody
    
    double[] oneBody
    
    pairwise
    
    double[] pairwise
- Class edu.duke.cs.osprey.confspace.TupleMatrixGeneric
  
  class TupleMatrixGeneric extends AbstractTupleMatrix<T> implements Serializable
  
  serialVersionUID:
  
  845854459137269739L
  - Serialized Fields
    
    oneBody
    
    ArrayList<T> oneBody
    
    pairwise
    
    ArrayList<T> pairwise
- Exception edu.duke.cs.osprey.confspace.TuplesIndex.NoSuchTupleException
  
  class NoSuchTupleException extends RuntimeException implements Serializable
- Class edu.duke.cs.osprey.confspace.TupleTree
  
  class TupleTree extends Object implements Serializable
  
  serialVersionUID:
  
  -8048566743262701431L
  - Serialized Fields
    
    baseTuple
    
    RCTuple baseTuple
    
    a common tuple prefix shared by all tuples in this tree useful for implementing a pairwise matrix of tuple trees, for e.g. AbstractTupleMatrix
    
    root
    
    TupleTree<T>.edu.duke.cs.osprey.confspace.TupleTree.Node root
- Class edu.duke.cs.osprey.confspace.VoxelShape
  
  class VoxelShape extends Object implements Serializable
- Class edu.duke.cs.osprey.confspace.VoxelShape.Point
  
  class Point extends VoxelShape implements Serializable
- Class edu.duke.cs.osprey.confspace.VoxelShape.Rect
  
  class Rect extends VoxelShape implements Serializable
  - Serialized Fields
    
    halfWidth
    
    double halfWidth
Package edu.duke.cs.osprey.control
- Class edu.duke.cs.osprey.control.ParamSet
  
  class ParamSet extends Object implements Serializable
  
  serialVersionUID:
  
  4364963601242324780L
  - Serialized Fields
    
    defaultParams
    
    Map<String,edu.duke.cs.osprey.control.ParamSet.Entry> defaultParams
    
    isVerbose
    
    boolean isVerbose
    
    params
    
    Map<String,edu.duke.cs.osprey.control.ParamSet.Entry> params
    
    wildcardDefaults
    
    Map<String,edu.duke.cs.osprey.control.ParamSet.Entry> wildcardDefaults
Package edu.duke.cs.osprey.dof
- Class edu.duke.cs.osprey.dof.DegreeOfFreedom
  
  class DegreeOfFreedom extends Object implements Serializable
  
  serialVersionUID:
  
  3348198591978172994L
  - Serialized Fields
    
    curVal
    
    double curVal
- Class edu.duke.cs.osprey.dof.EllipseCoordDOF
  
  class EllipseCoordDOF extends DegreeOfFreedom implements Serializable
  - Serialized Fields
    
    A
    
    cern.colt.matrix.DoubleMatrix2D A
    
    c
    
    cern.colt.matrix.DoubleMatrix1D c
    
    curVal
    
    double curVal
    
    dihedrals
    
    ArrayList<DegreeOfFreedom> dihedrals
    
    et
    
    EllipseTransform et
    
    index
    
    int index
    
    initSet
    
    boolean initSet
    
    initVals
    
    double[] initVals
    
    isRadius
    
    boolean isRadius
- Class edu.duke.cs.osprey.dof.FreeDihedral
  
  class FreeDihedral extends DegreeOfFreedom implements Serializable
  
  serialVersionUID:
  
  8005789766951509654L
  - Serialized Fields
    
    curVal
    
    double curVal
    
    dihedralCoords
    
    double[][] dihedralCoords
    
    dihedralNum
    
    int dihedralNum
    
    res
    
    Residue res
- Class edu.duke.cs.osprey.dof.MoveableStrand
  
  class MoveableStrand extends Object implements Serializable
  - Serialized Fields
    
    curAngles
    
    double[] curAngles
    
    curRotMatrix
    
    RotationMatrix curRotMatrix
    
    curTrans
    
    double[] curTrans
    
    initCenter
    
    double[] initCenter
    
    res
    
    ArrayList<Residue> res
    
    rotations
    
    StrandRotation[] rotations
    
    translations
    
    StrandTranslation[] translations
- Class edu.duke.cs.osprey.dof.ProlinePucker
  
  class ProlinePucker extends DegreeOfFreedom implements Serializable
  
  serialVersionUID:
  
  -5326286110623671996L
  - Serialized Fields
    
    basePucker
    
    ProlinePucker.Direction basePucker
    
    curPucker
    
    ProlinePucker.Direction curPucker
    
    puckerProblem
    
    ConfProblem puckerProblem
    
    res
    
    Residue res
    
    templateLib
    
    ResidueTemplateLibrary templateLib
- Class edu.duke.cs.osprey.dof.ResidueTypeDOF
  
  class ResidueTypeDOF extends DegreeOfFreedom implements Serializable
  
  serialVersionUID:
  
  4285811771185813789L
  - Serialization Methods
    
    readObject
    
    private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException
    
    Throws:
    
    ClassNotFoundException
    
    IOException
  - Serialized Fields
    
    idealizeSidechainAfterMutation
    
    boolean idealizeSidechainAfterMutation
    
    res
    
    Residue res
- Class edu.duke.cs.osprey.dof.StrandRotation
  
  class StrandRotation extends DegreeOfFreedom implements Serializable
  - Serialized Fields
    
    angleNum
    
    int angleNum
    
    strand
    
    MoveableStrand strand
- Class edu.duke.cs.osprey.dof.StrandTranslation
  
  class StrandTranslation extends DegreeOfFreedom implements Serializable
  - Serialized Fields
    
    coordNum
    
    int coordNum
    
    strand
    
    MoveableStrand strand
Package edu.duke.cs.osprey.dof.deeper
- Class edu.duke.cs.osprey.dof.deeper.DEEPerSettings
  
  class DEEPerSettings extends Object implements Serializable
  
  serialVersionUID:
  
  1L
  - Serialized Fields
    
    doPerturbations
    
    boolean doPerturbations
    
    doRamaCheck
    
    boolean doRamaCheck
    
    flexibleRes
    
    ArrayList<String> flexibleRes
    
    maxBackrubParam
    
    double maxBackrubParam
    
    maxShearParam
    
    double maxShearParam
    
    onlyStarting
    
    boolean onlyStarting
    
    PDBFile
    
    String PDBFile
    
    pertFileName
    
    String pertFileName
    
    perts
    
    PertSet perts
    
    selectLCAs
    
    boolean selectLCAs
    
    selectPerturbations
    
    boolean selectPerturbations
    
    startingPertFile
    
    String startingPertFile
    
    templateLib
    
    ResidueTemplateLibrary templateLib
- Class edu.duke.cs.osprey.dof.deeper.PertSet
  
  class PertSet extends Object implements Serializable
  - Serialized Fields
    
    additionalInfo
    
    ArrayList<ArrayList<String>> additionalInfo
    
    pertIntervals
    
    ArrayList<ArrayList<double[]>> pertIntervals
    
    pertStates
    
    ArrayList<ArrayList<ArrayList<int[]>>> pertStates
    
    pertTypes
    
    ArrayList<String> pertTypes
    
    resNums
    
    ArrayList<ArrayList<String>> resNums
- Class edu.duke.cs.osprey.dof.deeper.ResBBState
  
  class ResBBState extends Object implements Serializable
  - Serialized Fields
    
    CBCoord
    
    double[] CBCoord
    
    coords
    
    HashMap<String,double[]> coords
Package edu.duke.cs.osprey.dof.deeper.perts
- Class edu.duke.cs.osprey.dof.deeper.perts.Backrub
  
  class Backrub extends Perturbation implements Serializable
- Class edu.duke.cs.osprey.dof.deeper.perts.LoopClosureAdjustment
  
  class LoopClosureAdjustment extends Perturbation implements Serializable
  - Serialized Fields
    
    problems
    
    ArrayList<ConfProblem> problems
    
    solnCache
    
    HashMap<String,RigidBodyMotion[][]> solnCache
- Class edu.duke.cs.osprey.dof.deeper.perts.PartialStructureSwitch
  
  class PartialStructureSwitch extends Perturbation implements Serializable
  - Serialized Fields
    
    altResConfs
    
    ArrayList<ArrayList<ResBBState>> altResConfs
- Class edu.duke.cs.osprey.dof.deeper.perts.Perturbation
  
  class Perturbation extends DegreeOfFreedom implements Serializable
  - Serialized Fields
    
    block
    
    PerturbationBlock block
    
    curParamVal
    
    double curParamVal
    
    indexInBlock
    
    int indexInBlock
    
    resDirectlyAffected
    
    ArrayList<Residue> resDirectlyAffected
- Class edu.duke.cs.osprey.dof.deeper.perts.PerturbationBlock
  
  class PerturbationBlock extends Object implements Serializable
  - Serialized Fields
    
    allResidues
    
    ArrayList<Residue> allResidues
    
    dependentResidues
    
    ArrayList<ArrayList<Residue>> dependentResidues
    
    perts
    
    ArrayList<Perturbation> perts
    
    prePertBBStates
    
    ArrayList<LinkedHashMap<Residue,ResBBState>> prePertBBStates
    
    successors
    
    ArrayList<ArrayList<Perturbation>> successors
- Class edu.duke.cs.osprey.dof.deeper.perts.Shear
  
  class Shear extends Perturbation implements Serializable
- Class edu.duke.cs.osprey.dof.deeper.perts.SturmSolver
  
  class SturmSolver extends Object implements Serializable
  - Serialized Fields
    
    MAX_ITER_SECANT
    
    int MAX_ITER_SECANT
    
    MAX_ORDER
    
    int MAX_ORDER
    
    MAXIT
    
    int MAXIT
    
    MAXPOW
    
    int MAXPOW
    
    PRINT_LEVEL
    
    int PRINT_LEVEL
    
    RELERROR
    
    double RELERROR
    
    SMALL_ENOUGH
    
    double SMALL_ENOUGH
- Class edu.duke.cs.osprey.dof.deeper.perts.TripeptideClosure
  
  class TripeptideClosure extends Object implements Serializable
  - Serialized Fields
    
    aa13_max_sqr
    
    double aa13_max_sqr
    
    aa13_min_sqr
    
    double aa13_min_sqr
    
    alpha
    
    double[] alpha
    
    b_a1a3
    
    double[] b_a1a3
    
    b_a1n1
    
    double[] b_a1n1
    
    b_a3c3
    
    double[] b_a3c3
    
    b_ang0
    
    double[] b_ang0
    
    C0
    
    double[][] C0
    
    C1
    
    double[][] C1
    
    C2
    
    double[][] C2
    
    cos_alpha
    
    double[] cos_alpha
    
    cos_delta
    
    double[] cos_delta
    
    cos_eta
    
    double[] cos_eta
    
    cos_theta
    
    double[] cos_theta
    
    cos_xi
    
    double[] cos_xi
    
    deg_pol
    
    int deg_pol
    
    deg2rad
    
    double deg2rad
    
    delta
    
    double[] delta
    
    eta
    
    double[] eta
    
    len_aa
    
    double[] len_aa
    
    len_ac
    
    double[] len_ac
    
    len_na
    
    double[] len_na
    
    len0
    
    double[] len0
    
    max_soln
    
    int max_soln
    
    n_soln
    
    int n_soln
    
    pi
    
    double pi
    
    print_level
    
    int print_level
    
    Q
    
    double[][] Q
    
    R
    
    double[][] R
    
    r_a1a3
    
    double[] r_a1a3
    
    r_a1n1
    
    double[] r_a1n1
    
    r_a3c3
    
    double[] r_a3c3
    
    rad2deg
    
    double rad2deg
    
    sin_alpha
    
    double[] sin_alpha
    
    sin_delta
    
    double[] sin_delta
    
    sin_eta
    
    double[] sin_eta
    
    sin_theta
    
    double[] sin_theta
    
    sin_xi
    
    double[] sin_xi
    
    sturm
    
    SturmSolver sturm
    
    t_ang0
    
    double[] t_ang0
    
    theta
    
    double[] theta
    
    two_pi
    
    double two_pi
    
    xi
    
    double[] xi
Package edu.duke.cs.osprey.ematrix
- Class edu.duke.cs.osprey.ematrix.DofMatrix
  
  class DofMatrix extends TupleMatrixGeneric<cern.colt.matrix.DoubleMatrix1D> implements Serializable
  
  serialVersionUID:
  
  7381812984847056950L
- Class edu.duke.cs.osprey.ematrix.EnergyMatrix
  
  class EnergyMatrix extends TupleMatrixDouble implements Serializable
  
  serialVersionUID:
  
  6503270845014990929L
  - Serialized Fields
    
    constTerm
    
    double constTerm
    
    eRefMat
    
    ReferenceEnergies eRefMat
- Class edu.duke.cs.osprey.ematrix.LazyEnergyMatrix
  
  class LazyEnergyMatrix extends EnergyMatrix implements Serializable
  
  serialVersionUID:
  
  -6363593602037378135L
  - Serialized Fields
    
    ecalc
    
    SimpleEnergyCalculator ecalc
    
    nullVal
    
    double nullVal
- Class edu.duke.cs.osprey.ematrix.NegatedEnergyMatrix
  
  class NegatedEnergyMatrix extends ProxyEnergyMatrix implements Serializable
- Class edu.duke.cs.osprey.ematrix.ProxyEnergyMatrix
  
  class ProxyEnergyMatrix extends EnergyMatrix implements Serializable
  - Serialized Fields
    
    target
    
    EnergyMatrix target
- Class edu.duke.cs.osprey.ematrix.ReferenceEnergies
  
  class ReferenceEnergies extends Object implements Serializable
  - Serialized Fields
    
    cSpace
    
    ConfSpace cSpace
    
    eRefMatrix
    
    ArrayList<TreeMap<String,Double>> eRefMatrix
- Class edu.duke.cs.osprey.ematrix.SimpleReferenceEnergies
  
  class SimpleReferenceEnergies extends Object implements Serializable
  - Serialized Fields
    
    energies
    
    Map<String,Double> energies
- Class edu.duke.cs.osprey.ematrix.UpdatingEnergyMatrix
  
  class UpdatingEnergyMatrix extends ProxyEnergyMatrix implements Serializable
  - Serialized Fields
    
    corrections
    
    UpdatingEnergyMatrix.TupleTrie corrections
    
    numPos
    
    int numPos
    
    sourceECalc
    
    ConfEnergyCalculator sourceECalc
Package edu.duke.cs.osprey.ematrix.epic
- Class edu.duke.cs.osprey.ematrix.epic.EPICEnergyFunction
  
  class EPICEnergyFunction extends Object implements Serializable
  
  serialVersionUID:
  
  -6797584391009212938L
  - Serialized Fields
    
    curDOFVals
    
    cern.colt.matrix.DoubleMatrix1D curDOFVals
    
    includeMinE
    
    boolean includeMinE
    
    termDOFs
    
    ArrayList<ArrayList<Integer>> termDOFs
    
    terms
    
    ArrayList<EPoly> terms
    
    useSharedMolec
    
    boolean useSharedMolec
- Class edu.duke.cs.osprey.ematrix.epic.EPICMatrix
  
  class EPICMatrix extends TupleMatrixGeneric<EPoly> implements Serializable
  - Serialized Fields
    
    confSpace
    
    ConfSpace confSpace
- Class edu.duke.cs.osprey.ematrix.epic.EPICSettings
  
  class EPICSettings extends Object implements Serializable
  - Serialized Fields
    
    EPICGoalResid
    
    double EPICGoalResid
    
    EPICThresh1
    
    double EPICThresh1
    
    EPICThresh2
    
    double EPICThresh2
    
    minPartialConfs
    
    boolean minPartialConfs
    
    quadOnly
    
    boolean quadOnly
    
    useEPIC
    
    boolean useEPIC
    
    useEPICPruning
    
    boolean useEPICPruning
    
    usePC
    
    boolean usePC
    
    useSAPE
    
    boolean useSAPE
- Class edu.duke.cs.osprey.ematrix.epic.EPoly
  
  class EPoly extends Object implements Serializable
  - Serialized Fields
    
    baseSAPE
    
    double baseSAPE
    
    center
    
    cern.colt.matrix.DoubleMatrix1D center
    
    coeffs
    
    double[] coeffs
    
    DOFmax
    
    cern.colt.matrix.DoubleMatrix1D DOFmax
    
    DOFmin
    
    cern.colt.matrix.DoubleMatrix1D DOFmin
    
    DOFNames
    
    ArrayList<String> DOFNames
    
    fitDescription
    
    String fitDescription
    
    minE
    
    double minE
    
    numDOFs
    
    int numDOFs
    
    order
    
    int order
    
    sapeTerm
    
    SAPE sapeTerm
- Class edu.duke.cs.osprey.ematrix.epic.EPolyPC
  
  class EPolyPC extends EPoly implements Serializable
  - Serialized Fields
    
    axisCoeffs
    
    cern.colt.matrix.DoubleMatrix2D axisCoeffs
    
    fullOrder
    
    int fullOrder
    
    invAxisCoeffs
    
    cern.colt.matrix.DoubleMatrix2D invAxisCoeffs
    
    isPC
    
    boolean[] isPC
    
    PCOrder
    
    int PCOrder
- Class edu.duke.cs.osprey.ematrix.epic.FitParams
  
  class FitParams extends Object implements Serializable
  - Serialized Fields
    
    includeConst
    
    boolean includeConst
    
    numDims
    
    int numDims
    
    numPCParams
    
    int numPCParams
    
    order
    
    int order
    
    PCFac
    
    double PCFac
    
    PCOrder
    
    int PCOrder
    
    SAPECutoff
    
    double SAPECutoff
- Class edu.duke.cs.osprey.ematrix.epic.NewEPICMatrix
  
  class NewEPICMatrix extends TupleMatrixGeneric<EPoly> implements Serializable
  - Serialized Fields
    
    confSpace
    
    SimpleConfSpace confSpace
- Class edu.duke.cs.osprey.ematrix.epic.SAPE
  
  class SAPE extends Object implements Serializable
  - Serialized Fields
    
    atomPairList
    
    ArrayList<ArrayList<int[]>> atomPairList
    
    ffParams
    
    ForcefieldParams ffParams
    
    interactingRes
    
    ArrayList<int[]> interactingRes
    
    mofStandalone
    
    MoleculeModifierAndScorer mofStandalone
    
    sharedMolecEnergyFunction
    
    EnergyFunction sharedMolecEnergyFunction
Package edu.duke.cs.osprey.energy
- Class edu.duke.cs.osprey.energy.MultiTermEnergyFunction
  
  class MultiTermEnergyFunction extends Object implements Serializable
  
  serialVersionUID:
  
  -3516267414126293331L
  - Serialized Fields
    
    coeffs
    
    ArrayList<Double> coeffs
    
    indexes
    
    ArrayList<Integer> indexes
    
    partialE
    
    ArrayList<Double> partialE
    
    preCompE
    
    double preCompE
    
    terms
    
    ArrayList<EnergyFunction> terms
- Class edu.duke.cs.osprey.energy.ParallelEnergyFunction
  
  class ParallelEnergyFunction extends Object implements Serializable
  
  serialVersionUID:
  
  -2789380428939629566L
  - Serialized Fields
    
    coeffs
    
    ArrayList<Double> coeffs
    
    terms
    
    ArrayList<EnergyFunction> terms
- Class edu.duke.cs.osprey.energy.PoissonBoltzmannEnergy
  
  class PoissonBoltzmannEnergy extends Object implements Serializable
  - Serialized Fields
    
    m
    
    Molecule m
- Class edu.duke.cs.osprey.energy.ScaledEnergyFunction
  
  class ScaledEnergyFunction extends Object implements Serializable
  
  serialVersionUID:
  
  -1352051347168314110L
  - Serialized Fields
    
    c
    
    double c
    
    efunc
    
    EnergyFunction efunc
Package edu.duke.cs.osprey.energy.approximation
- Class edu.duke.cs.osprey.energy.approximation.ApproximatedObjectiveFunction
  
  class ApproximatedObjectiveFunction extends Object implements Serializable
  - Serialized Fields
    
    approximator
    
    ApproximatedObjectiveFunction.Approximator approximator
    
    f
    
    ObjectiveFunction f
    
    x
    
    cern.colt.matrix.DoubleMatrix1D x
Package edu.duke.cs.osprey.energy.forcefield
- Class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy
  
  class BigForcefieldEnergy extends Object implements Serializable
  
  serialVersionUID:
  
  5242606861996508290L
  - Serialized Fields
    
    atomFlags
    
    IntBuffer atomFlags
    
    atomOffsets
    
    int[] atomOffsets
    
    bufferType
    
    BufferTools.Type bufferType
    
    coords
    
    DoubleBuffer coords
    
    fullSubset
    
    BigForcefieldEnergy.Subset fullSubset
    
    groups
    
    edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.Groups groups
    
    groupsSequenceNumber
    
    int groupsSequenceNumber
    
    interactions
    
    ForcefieldInteractions interactions
    
    pinfo
    
    BigForcefieldEnergy.ParamInfo pinfo
    
    precomputed
    
    DoubleBuffer precomputed
    
    subsetCache
    
    Map<Residue,BigForcefieldEnergy.Subset> subsetCache
- Class edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.Subset
  
  class Subset extends Object implements Serializable
  
  serialVersionUID:
  
  -2038116438543332018L
  - Serialized Fields
    
    groupPairs
    
    List<edu.duke.cs.osprey.energy.forcefield.BigForcefieldEnergy.GroupPair> groupPairs
    
    internalSolvEnergy
    
    double internalSolvEnergy
    
    makeTable
    
    boolean makeTable
    
    num14Pairs
    
    int num14Pairs
    
    numPairs
    
    int numPairs
    
    sequenceNumber
    
    int sequenceNumber
    
    subsetTable
    
    IntBuffer subsetTable
- Class edu.duke.cs.osprey.energy.forcefield.CoordsAndCharges
  
  class CoordsAndCharges extends Object implements Serializable
  
  serialVersionUID:
  
  3611517841418160913L
  - Serialized Fields
    
    data
    
    double[] data
    
    res1
    
    Residue res1
    
    res1Start
    
    int res1Start
    
    res2
    
    Residue res2
    
    res2Start
    
    int res2Start
- Class edu.duke.cs.osprey.energy.forcefield.EEF1
  
  class EEF1 extends Object implements Serializable
  
  serialVersionUID:
  
  -4783417295676415124L
  - Serialized Fields
    
    atEEF1Vol
    
    double[] atEEF1Vol
    
    atTypeEEF1names
    
    String[] atTypeEEF1names
    
    dCpiRef
    
    double[] dCpiRef
    
    dGiFree
    
    double[] dGiFree
    
    dGiRef
    
    double[] dGiRef
    
    dHiRef
    
    double[] dHiRef
    
    groupEEF1names
    
    String[] groupEEF1names
    
    lambdai
    
    double[] lambdai
    
    numAtTypesEEF1
    
    int numAtTypesEEF1
    
    vdWri
    
    double[] vdWri
- Class edu.duke.cs.osprey.energy.forcefield.ForcefieldEnergy
  
  class ForcefieldEnergy extends Object implements Serializable
  
  serialVersionUID:
  
  944833567342112297L
  - Serialized Fields
    
    constCoulomb
    
    double constCoulomb
    
    coordsAndCharges
    
    CoordsAndCharges coordsAndCharges
    
    D2R
    
    double D2R
    
    halfNonBondedTerms
    
    double[] halfNonBondedTerms
    
    internalSolvEnergy
    
    double internalSolvEnergy
    
    isInternal
    
    boolean isInternal
    
    nonBondedTerms
    
    double[] nonBondedTerms
    
    numberHalfNonBonded
    
    int numberHalfNonBonded
    
    numberNonBonded
    
    int numberNonBonded
    
    numberSolvated
    
    int numberSolvated
    
    params
    
    ForcefieldParams params
    
    R2D
    
    double R2D
    
    res1
    
    Residue res1
    
    res2
    
    Residue res2
    
    solvationTerms
    
    double[] solvationTerms
    
    solvCutoff
    
    double solvCutoff
- Class edu.duke.cs.osprey.energy.forcefield.ForcefieldInteractions
  
  class ForcefieldInteractions extends ArrayList<ForcefieldInteractions.AtomGroup[]> implements Serializable
  
  serialVersionUID:
  
  -2052346528544825763L
  - Serialized Fields
    
    groupsById
    
    Map<Integer,ForcefieldInteractions.AtomGroup> groupsById
    
    Deprecated.
- Class edu.duke.cs.osprey.energy.forcefield.ForcefieldParams
  
  class ForcefieldParams extends Object implements Serializable
  
  serialVersionUID:
  
  3124964506851762586L
  - Serialized Fields
    
    angleAtomType1
    
    int[] angleAtomType1
    
    angleAtomType2
    
    int[] angleAtomType2
    
    angleAtomType3
    
    int[] angleAtomType3
    
    angleEBA
    
    double[] angleEBA
    
    angleHFC
    
    double[] angleHFC
    
    atomAtomicMasses
    
    double[] atomAtomicMasses
    
    atomNamesMap
    
    Map<String,AtomSymbolAndMass> atomNamesMap
    
    atomTypeNames
    
    String[] atomTypeNames
    
    atomTypeX
    
    int atomTypeX
    
    bondAtomType1
    
    int[] bondAtomType1
    
    bondAtomType2
    
    int[] bondAtomType2
    
    bondEBL
    
    double[] bondEBL
    
    bondHFC
    
    double[] bondHFC
    
    bondLengthByName
    
    Map<String,BondLengthParameter> bondLengthByName
    
    dielectric
    
    double dielectric
    
    dihedAtomType1
    
    int[] dihedAtomType1
    
    dihedAtomType2
    
    int[] dihedAtomType2
    
    dihedAtomType3
    
    int[] dihedAtomType3
    
    dihedAtomType4
    
    int[] dihedAtomType4
    
    dihedPhase
    
    double[] dihedPhase
    
    dihedPN
    
    double[] dihedPN
    
    dihedTerm1
    
    double[] dihedTerm1
    
    distDepDielect
    
    boolean distDepDielect
    
    eef1parms
    
    EEF1 eef1parms
    
    equivAtoms
    
    int[][] equivAtoms
    
    forcefld
    
    ForcefieldParams.Forcefield forcefld
    
    hElect
    
    boolean hElect
    
    hVDW
    
    boolean hVDW
    
    impDihedAtomType1
    
    int[] impDihedAtomType1
    
    impDihedAtomType2
    
    int[] impDihedAtomType2
    
    impDihedAtomType3
    
    int[] impDihedAtomType3
    
    impDihedAtomType4
    
    int[] impDihedAtomType4
    
    impDihedPhase
    
    double[] impDihedPhase
    
    impDihedPN
    
    double[] impDihedPN
    
    impDihedTerm1
    
    double[] impDihedTerm1
    
    noMatchInt
    
    int noMatchInt
    
    numGeneralDihedParams
    
    int numGeneralDihedParams
    
    parameters
    
    ForcefieldFileParser parameters
    
    shellDistCutoff
    
    double shellDistCutoff
    
    Deprecated.
    
    for new code, use SimpleConfSpace.Builder.setShellDistance(double) instead
    
    solvationForcefield
    
    ForcefieldParams.SolvationForcefield solvationForcefield
    
    solvScale
    
    double solvScale
    
    vanDerWaalsMap
    
    Map<String,VanDerWaalsRadius> vanDerWaalsMap
    
    vdwAtomType1
    
    int[] vdwAtomType1
    
    vdwE
    
    double[] vdwE
    
    vdwMultiplier
    
    double vdwMultiplier
    
    vdwR
    
    double[] vdwR
- Class edu.duke.cs.osprey.energy.forcefield.GpuForcefieldEnergy
  
  class GpuForcefieldEnergy extends Object implements Serializable
  
  serialVersionUID:
  
  -9142317985561910731L
  - Serialized Fields
    
    cudaStream
    
    GpuStream cudaStream
    
    cudaStreamPool
    
    GpuStreamPool cudaStreamPool
    
    efuncCache
    
    Map<Residue,GpuForcefieldEnergy> efuncCache
    
    ffenergy
    
    BigForcefieldEnergy ffenergy
    
    ffsubset
    
    BigForcefieldEnergy.Subset ffsubset
    
    kernelBuilder
    
    edu.duke.cs.osprey.energy.forcefield.GpuForcefieldEnergy.KernelBuilder kernelBuilder
    
    openclQueue
    
    GpuQueue openclQueue
    
    openclQueuePool
    
    GpuQueuePool openclQueuePool
- Class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy
  
  class ResidueForcefieldEnergy extends Object implements Serializable
  
  serialVersionUID:
  
  -4768384219061898745L
  - Serialized Fields
    
    coulombFactor
    
    double coulombFactor
    
    inters
    
    ResidueInteractions inters
    
    isBroken
    
    boolean isBroken
    
    residues
    
    Residues residues
    
    resPairCache
    
    ResPairCache resPairCache
    
    resPairs
    
    ResPairCache.ResPair[] resPairs
    
    scaledCoulombFactor
    
    double scaledCoulombFactor
- Class edu.duke.cs.osprey.energy.forcefield.ResidueForcefieldEnergy.Vdw
  
  class Vdw extends ResidueForcefieldEnergy implements Serializable
- Class edu.duke.cs.osprey.energy.forcefield.ResPairEnergy
  
  class ResPairEnergy extends Object implements Serializable
  - Serialized Fields
    
    ffEnergy
    
    ForcefieldEnergy ffEnergy
    
    ffParams
    
    ForcefieldParams ffParams
    
    res1
    
    Residue res1
    
    res2
    
    Residue res2
    
    templ1
    
    ResidueTemplate templ1
    
    templ2
    
    ResidueTemplate templ2
- Class edu.duke.cs.osprey.energy.forcefield.SingleResEnergy
  
  class SingleResEnergy extends Object implements Serializable
  - Serialized Fields
    
    ffEnergy
    
    ForcefieldEnergy ffEnergy
    
    ffParams
    
    ForcefieldParams ffParams
    
    res
    
    Residue res
    
    templ
    
    ResidueTemplate templ
- Class edu.duke.cs.osprey.energy.forcefield.SparseFFEnergy
  
  class SparseFFEnergy extends Object implements Serializable
  - Serialized Fields
    
    ffEnergy
    
    ForcefieldEnergy ffEnergy
    
    ffParams
    
    ForcefieldParams ffParams
    
    res1
    
    Residue res1
    
    res2
    
    Residue res2
    
    templ1
    
    ResidueTemplate templ1
    
    templ2
    
    ResidueTemplate templ2
Package edu.duke.cs.osprey.ewakstar
- Exception edu.duke.cs.osprey.ewakstar.EWAKStar.InitException
  
  class InitException extends RuntimeException implements Serializable
- Exception edu.duke.cs.osprey.ewakstar.EwakstarDoer.Builder.InitException
  
  class InitException extends RuntimeException implements Serializable
- Exception edu.duke.cs.osprey.ewakstar.EwakstarDoer.State.InitException
  
  class InitException extends RuntimeException implements Serializable
- Exception edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.WithConfTable.UnsupportedException
  
  class UnsupportedException extends RuntimeException implements Serializable
- Exception edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.WithExternalMemory.UnsupportedException
  
  class UnsupportedException extends RuntimeException implements Serializable
- Class edu.duke.cs.osprey.ewakstar.EWAKStarScoreWriter.Writers
  
  class Writers extends ArrayList<EWAKStarScoreWriter> implements Serializable
  
  serialVersionUID:
  
  1239885431627352405L
Package edu.duke.cs.osprey.externalMemory
- Exception edu.duke.cs.osprey.externalMemory.AssignmentsSerializer.WrongEncodingException
  
  class WrongEncodingException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -7973280483158957646L
- Exception edu.duke.cs.osprey.externalMemory.AssignmentsSerializer.WrongNumberOfAssignmentsException
  
  class WrongNumberOfAssignmentsException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -2877773001328314147L
- Exception edu.duke.cs.osprey.externalMemory.ExternalMemory.InternalMemoryLimitNotSetException
  
  class InternalMemoryLimitNotSetException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  1672062453287951982L
Package edu.duke.cs.osprey.gmec
- Exception edu.duke.cs.osprey.gmec.Comets.State.InitException
  
  class InitException extends RuntimeException implements Serializable
- Class edu.duke.cs.osprey.gmec.PruningSettings
  
  class PruningSettings extends Object implements Serializable
  - Serialized Fields
    
    algOption
    
    int algOption
    
    boundsThresh
    
    double boundsThresh
    
    stericThresh
    
    double stericThresh
    
    typedep
    
    boolean typedep
    
    useFlags
    
    boolean useFlags
    
    useTriples
    
    boolean useTriples
Package edu.duke.cs.osprey.gpu
- Error edu.duke.cs.osprey.gpu.BufferTools.OutOfDirectMemoryError
  
  class OutOfDirectMemoryError extends VirtualMachineError implements Serializable

Package edu.duke.cs.osprey.gpu.cuda.kernels

Class edu.duke.cs.osprey.gpu.cuda.kernels.ResidueForcefieldEnergyCuda

class ResidueForcefieldEnergyCuda extends Kernel implements Serializable

serialVersionUID:: 4015880661919715967L

Serialized Fields

allIndices
```
CUBuffer<IntBuffer> allIndices
```
coords
```
CUBuffer<DoubleBuffer> coords
```
data
```
CUBuffer<ByteBuffer> data
```
energy
```
CUBuffer<DoubleBuffer> energy
```
ffparams
```
ForcefieldParams ffparams
```
func
```
Kernel.Function func
```
inters
```
ResidueInteractions inters
```
isBroken
```
boolean isBroken
```
residues
```
Residues residues
```
resPairs
```
ResPairCache.ResPair[] resPairs
```
streams
```
GpuStreamPool streams
```

subsets

Map<Residue,edu.duke.cs.osprey.gpu.cuda.kernels.ResidueForcefieldEnergyCuda.Subset> subsets

Package edu.duke.cs.osprey.gpu.opencl
- Exception edu.duke.cs.osprey.gpu.opencl.GpuInitException
  
  class GpuInitException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  -7618850500199218177L
Package edu.duke.cs.osprey.ibis
- Class edu.duke.cs.osprey.ibis.IBISKStarTupleExpander
  
  class IBISKStarTupleExpander extends BasicPruningTupleExpander implements Serializable
  - Serialized Fields
    
    baseMatrix
    
    EnergyMatrix baseMatrix
    
    basePruneMat
    
    PruningMatrix basePruneMat
    
    curIntegPos
    
    int curIntegPos
    
    RCsforAA
    
    ArrayList<ArrayList<Integer>> RCsforAA
Package edu.duke.cs.osprey.kstar
- Class edu.duke.cs.osprey.kstar.KAStarConfTree
  
  class KAStarConfTree extends ConfTree<FullAStarNode> implements Serializable
  - Serialized Fields
    
    energyLB
    
    boolean energyLB
    
    panPmat
    
    PruningMatrix panPmat
    
    panUprunedRCsAtPos
    
    ArrayList<ArrayList<Integer>> panUprunedRCsAtPos
    
    reducedPmat
    
    PruningMatrix reducedPmat
    
    sp
    
    KSSearchProblem sp
- Class edu.duke.cs.osprey.kstar.KSConf
  
  class KSConf extends Object implements Serializable
  - Serialized Fields
    
    conf
    
    ArrayList<Integer> conf
    
    energy
    
    double energy
    
    energyBound
    
    double energyBound
- Class edu.duke.cs.osprey.kstar.KSConf.KSConfMinEComparator
  
  class KSConfMinEComparator extends Object implements Serializable
- Class edu.duke.cs.osprey.kstar.KSConfigFileParser
  
  class KSConfigFileParser extends ConfigFileParser implements Serializable
  
  serialVersionUID:
  
  3653519769830569960L
- Class edu.duke.cs.osprey.kstar.KSConfQ
  
  class KSConfQ extends Thread implements Serializable
  - Serialized Fields
    
    confSearch
    
    ConfSearch confSearch
    
    confsExhausted
    
    boolean confsExhausted
    
    lock
    
    String lock
    
    minCapacity
    
    int minCapacity
    
    pf
    
    PFAbstract pf
    
    q
    
    LinkedHashSet<ArrayList<Integer>> q
    
    qCap
    
    int qCap
    
    tail
    
    ArrayList<Integer> tail
- Class edu.duke.cs.osprey.kstar.KSPStarCalculator
  
  class KSPStarCalculator extends Thread implements Serializable
  - Serialized Fields
    
    confSearch
    
    ConfSearch confSearch
    
    confsExhausted
    
    boolean confsExhausted
    
    enumerated
    
    BigInteger enumerated
    
    lastBoltzmannWeight
    
    BigDecimal lastBoltzmannWeight
    
    lastEnergyBound
    
    double lastEnergyBound
    
    lock
    
    String lock
    
    pf
    
    PFAbstract pf
    
    pruned
    
    BigInteger pruned
    
    totalPF
    
    BigDecimal totalPF
- Class edu.duke.cs.osprey.kstar.KSQPrimeCalculator
  
  class KSQPrimeCalculator extends KSPStarCalculator implements Serializable
  - Serialized Fields
    
    unPruned
    
    BigInteger unPruned
- Class edu.duke.cs.osprey.kstar.KSSearchProblem
  
  class KSSearchProblem extends SearchProblem implements Serializable
  
  serialVersionUID:
  
  -6946555904198558059L
  - Serialized Fields
    
    allowedAAs
    
    ArrayList<ArrayList<String>> allowedAAs
    
    flexibleRes
    
    ArrayList<String> flexibleRes
    
    inverseMat
    
    InvertedPruningMatrix inverseMat
    
    params
    
    ParamSet params
    
    posNums
    
    ArrayList<Integer> posNums
    
    reducedAllowedAAs
    
    ArrayList<ArrayList<String>> reducedAllowedAAs
    
    reducedMat
    
    ReducedPruningMatrix reducedMat
- Exception edu.duke.cs.osprey.kstar.KStar.InitException
  
  class InitException extends RuntimeException implements Serializable
- Class edu.duke.cs.osprey.kstar.KStarScoreWriter.Writers
  
  class Writers extends ArrayList<KStarScoreWriter> implements Serializable
  
  serialVersionUID:
  
  1239885431627352405L
- Exception edu.duke.cs.osprey.kstar.MSKStar.State.InitException
  
  class InitException extends RuntimeException implements Serializable
- Exception edu.duke.cs.osprey.kstar.SequenceAnalyzer.NoSuchConfSpaceException
  
  class NoSuchConfSpaceException extends NoSuchElementException implements Serializable
Package edu.duke.cs.osprey.kstar.emat
- Class edu.duke.cs.osprey.kstar.emat.ReducedEnergyMatrix
  
  class ReducedEnergyMatrix extends EnergyMatrix implements Serializable
  - Serialized Fields
    
    sp
    
    KSSearchProblem sp

Package edu.duke.cs.osprey.kstar.pfunc

Exception edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.WithExternalMemory.UnsupportedException

class UnsupportedException extends RuntimeException implements Serializable

Class edu.duke.cs.osprey.kstar.pfunc.PFAbstract

class PFAbstract extends Object implements Serializable

Serialized Fields

absolutePos
```
ArrayList<Integer> absolutePos
```
cfp
```
KSConfigFileParser cfp
```
checkPointPath
```
String checkPointPath
```
doingPhase2
```
boolean doingPhase2
```
e
```
ExpFunction e
```
E0
```
double E0
```
eAppx
```
PFAbstract.EApproxReached eAppx
```
effectiveEpsilon
```
double effectiveEpsilon
```
EPSILON_NEVER_POSSIBLE
```
double EPSILON_NEVER_POSSIBLE
```
EPSILON_PHASE_2
```
double EPSILON_PHASE_2
```
Et
```
double Et
```
HOTs
```
ArrayList<ArrayList<Integer>> HOTs
```
isContinuous
```
boolean isContinuous
```
isFullyDefined
```
boolean isFullyDefined
```
numberFormat
```
DecimalFormat numberFormat
```
panSP
```
KSSearchProblem panSP
```
partialQLB
```
BigDecimal partialQLB
```
printedHeader
```
boolean printedHeader
```
processedConfs
```
BigInteger processedConfs
```
processedConfsDuringInterval
```
BigInteger processedConfsDuringInterval
```

processedConfsSet

HashSet<ArrayList<Integer>> processedConfsSet

processingConfs
```
BigInteger processingConfs
```
prunedConfs
```
BigInteger prunedConfs
```
pStar
```
BigDecimal pStar
```
qPrime
```
BigDecimal qPrime
```
qStar
```
BigDecimal qStar
```
reducedSP
```
KSSearchProblem reducedSP
```
reducedSPName
```
String reducedSPName
```
runState
```
PFAbstract.RunState runState
```
sequence
```
ArrayList<String> sequence
```
startTime
```
long startTime
```
strand
```
int strand
```
topConfsPQ
```
PriorityQueue<KSConf> topConfsPQ
```
unPrunedConfs
```
BigInteger unPrunedConfs
```

Package edu.duke.cs.osprey.kstar.pfunc.impl
- Class edu.duke.cs.osprey.kstar.pfunc.impl.PFAdapter
  
  class PFAdapter extends PFAbstract implements Serializable
  
  serialVersionUID:
  
  -4339776095146902581L
  - Serialized Fields
    
    pfImpl
    
    String pfImpl
    
    pfunc
    
    PartitionFunction pfunc
- Class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel0
  
  class PFParallel0 extends PFParallel1 implements Serializable
- Class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel1
  
  class PFParallel1 extends PFTraditional implements Serializable
  - Serialized Fields
    
    confsQ
    
    KSConfQ confsQ
    
    initSleepTime
    
    long initSleepTime
    
    pStarCalculator
    
    KSPStarCalculator pStarCalculator
    
    qPrimeCalculator
    
    KSQPrimeCalculator qPrimeCalculator
- Class edu.duke.cs.osprey.kstar.pfunc.impl.PFParallel2
  
  class PFParallel2 extends PFParallel1 implements Serializable
  - Serialized Fields
    
    indexes
    
    ArrayList<Integer> indexes
    
    partialQConfs
    
    ArrayList<KSConf> partialQConfs
    
    sps
    
    ArrayList<KSSearchProblem> sps
- Class edu.duke.cs.osprey.kstar.pfunc.impl.PFTraditional
  
  class PFTraditional extends PFAbstract implements Serializable
  - Serialized Fields
    
    confSearch
    
    ConfSearch confSearch
- Class edu.duke.cs.osprey.kstar.pfunc.impl.PFUB
  
  class PFUB extends PFTraditional implements Serializable
  - Serialized Fields
    
    enumeratedConfs
    
    BigInteger enumeratedConfs
Package edu.duke.cs.osprey.kstar.pruning
- Class edu.duke.cs.osprey.kstar.pruning.InvertedPruningMatrix
  
  class InvertedPruningMatrix extends ReducedPruningMatrix implements Serializable
- Class edu.duke.cs.osprey.kstar.pruning.ReducedPruningMatrix
  
  class ReducedPruningMatrix extends PruningMatrix implements Serializable
  - Serialized Fields
    
    sp
    
    KSSearchProblem sp
    
    upm
    
    UpdatedPruningMatrix upm
- Class edu.duke.cs.osprey.kstar.pruning.UnprunedPruningMatrix
  
  class UnprunedPruningMatrix extends ReducedPruningMatrix implements Serializable
Package edu.duke.cs.osprey.lute
- Exception edu.duke.cs.osprey.lute.ConfSampler.NoMoreSamplesException
  
  class NoMoreSamplesException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  3248938824507606370L
Package edu.duke.cs.osprey.markstar
- Exception edu.duke.cs.osprey.markstar.MARKStar.InitException
  
  class InitException extends RuntimeException implements Serializable
- Class edu.duke.cs.osprey.markstar.MARKStarProgress
  
  class MARKStarProgress extends AStarProgress implements Serializable
  
  serialVersionUID:
  
  767988861537797830L
  - Serialized Fields
    
    curEpsilon
    
    double curEpsilon
    
    deepestLevel
    
    int deepestLevel
    
    goalScore
    
    double goalScore
    
    gscore
    
    double gscore
    
    hscore
    
    double hscore
    
    level
    
    int level
    
    msRunning
    
    int msRunning
    
    numLeafNodes
    
    int numLeafNodes
    
    numLevels
    
    int numLevels
    
    numNodesExpanded
    
    long numNodesExpanded
    
    numNodesInQueue
    
    long numNodesInQueue
    
    numNodesQueuedThisReport
    
    long numNodesQueuedThisReport
    
    numPartialMinimizations
    
    int numPartialMinimizations
    
    stopwatch
    
    Stopwatch stopwatch
Package edu.duke.cs.osprey.minimization
- Class edu.duke.cs.osprey.minimization.GenCoord
  
  class GenCoord extends Object implements Serializable
  - Serialized Fields
    
    coeffs
    
    double[] coeffs
    
    type
    
    int type
- Class edu.duke.cs.osprey.minimization.IdealSeparableReference
  
  class IdealSeparableReference extends MoleculeModifierAndScorer implements Serializable
  - Serialized Fields
    
    baseValForDOF
    
    double[] baseValForDOF
    
    centerE
    
    double centerE
    
    fullCurDOFVals
    
    cern.colt.matrix.DoubleMatrix1D fullCurDOFVals
- Class edu.duke.cs.osprey.minimization.MoleculeModifierAndScorer
  
  class MoleculeModifierAndScorer extends Object implements Serializable
  
  serialVersionUID:
  
  3898313221157632380L
  - Serialized Fields
    
    constraints
    
    cern.colt.matrix.DoubleMatrix1D[] constraints
    
    curDOFVals
    
    cern.colt.matrix.DoubleMatrix1D curDOFVals
    
    DOFs
    
    ArrayList<DegreeOfFreedom> DOFs
    
    efunc
    
    EnergyFunction efunc
    
    molec
    
    Molecule molec
    
    partialEFuncs
    
    List<EnergyFunction> partialEFuncs
- Class edu.duke.cs.osprey.minimization.MoleculeObjectiveFunction
  
  class MoleculeObjectiveFunction extends Object implements Serializable
  
  serialVersionUID:
  
  -5301575611582359731L
  - Serialized Fields
    
    curDOFVals
    
    cern.colt.matrix.DoubleMatrix1D curDOFVals
    
    efunc
    
    EnergyFunction efunc
    
    efuncsByDof
    
    List<EnergyFunction> efuncsByDof
    
    pmol
    
    ParametricMolecule pmol
- Class edu.duke.cs.osprey.minimization.ObjectiveFunction.DofBounds
  
  class DofBounds extends Object implements Serializable
  - Serialized Fields
    
    bounds
    
    cern.colt.matrix.DoubleMatrix1D[] bounds
- Class edu.duke.cs.osprey.minimization.ObjectiveFunction.OneDof
  
  class OneDof extends Object implements Serializable
  - Serialized Fields
    
    d
    
    int d
    
    f
    
    ObjectiveFunction f
    
    xdmax
    
    double xdmax
    
    xdmin
    
    double xdmin
Package edu.duke.cs.osprey.multistatekstar
- Class edu.duke.cs.osprey.multistatekstar.MSSearchProblem
  
  class MSSearchProblem extends SearchProblem implements Serializable
  - Serialized Fields
    
    numAssignedPos
    
    int numAssignedPos
    
    settings
    
    MSSearchSettings settings
- Class edu.duke.cs.osprey.multistatekstar.MSSearchSettings
  
  class MSSearchSettings extends Object implements Serializable
  - Serialized Fields
    
    AATypeOptions
    
    ArrayList<ArrayList<String>> AATypeOptions
    
    energyLBs
    
    boolean energyLBs
    
    mutRes
    
    ArrayList<String> mutRes
    
    pruningWindow
    
    double pruningWindow
    
    stericThreshold
    
    double stericThreshold
- Class edu.duke.cs.osprey.multistatekstar.MultiSequenceConfTree
  
  class MultiSequenceConfTree extends ConfTree<FullAStarNode> implements Serializable
  - Serialized Fields
    
    allowedPos
    
    Integer[] allowedPos
    
    energyLBs
    
    boolean energyLBs
    
    pmat
    
    PruningMatrix pmat
    
    search
    
    MSSearchProblem search
- Class edu.duke.cs.osprey.multistatekstar.PruningMatrixInverted
  
  class PruningMatrixInverted extends PruningMatrix implements Serializable
  - Serialized Fields
    
    other
    
    PruningMatrix other
    
    search
    
    MSSearchProblem search
- Class edu.duke.cs.osprey.multistatekstar.PruningMatrixNull
  
  class PruningMatrixNull extends PruningMatrix implements Serializable
  - Serialized Fields
    
    other
    
    PruningMatrix other
- Class edu.duke.cs.osprey.multistatekstar.ResidueTermini
  
  class ResidueTermini extends Object implements Serializable
  - Serialized Fields
    
    lBound
    
    String lBound
    
    state
    
    int state
    
    uBound
    
    String uBound
Package edu.duke.cs.osprey.parallelism
- Class edu.duke.cs.osprey.parallelism.Cluster.Task
  
  class Task extends Object implements Serializable
  - Serialized Fields
    
    id
    
    long id
    
    instanceId
    
    int instanceId
- Exception edu.duke.cs.osprey.parallelism.Generator.GeneratorFailedException
  
  class GeneratorFailedException extends RuntimeException implements Serializable
- Exception edu.duke.cs.osprey.parallelism.TaskExecutor.TaskException
  
  class TaskException extends RuntimeException implements Serializable
  
  serialVersionUID:
  
  8523925290195831558L
  - Serialized Fields
    
    listener
    
    TaskExecutor.TaskListener<?> listener
    
    task
    
    TaskExecutor.Task<?> task
Package edu.duke.cs.osprey.paste
- Exception edu.duke.cs.osprey.paste.Paste.InitException
  
  class InitException extends RuntimeException implements Serializable
- Exception edu.duke.cs.osprey.paste.PastePartitionFunction.WithConfTable.UnsupportedException
  
  class UnsupportedException extends RuntimeException implements Serializable
- Exception edu.duke.cs.osprey.paste.PastePartitionFunction.WithExternalMemory.UnsupportedException
  
  class UnsupportedException extends RuntimeException implements Serializable
- Class edu.duke.cs.osprey.paste.PasteScoreWriter.Writers
  
  class Writers extends ArrayList<PasteScoreWriter> implements Serializable
  
  serialVersionUID:
  
  1239885431627352405L
Package edu.duke.cs.osprey.plug
- Class edu.duke.cs.osprey.plug.PolytopeMatrix
  
  class PolytopeMatrix extends TupleMatrixGeneric<RCTuplePolytope> implements Serializable
  - Serialized Fields
    
    cSpace
    
    ConfSpace cSpace
- Class edu.duke.cs.osprey.plug.RCTuplePolytope
  
  class RCTuplePolytope extends Object implements Serializable
  - Serialized Fields
    
    atomPairNames
    
    ArrayList<String> atomPairNames
    
    constr
    
    ArrayList<org.apache.commons.math3.optim.linear.LinearConstraint> constr
    
    DOFs
    
    ArrayList<DegreeOfFreedom> DOFs
Package edu.duke.cs.osprey.pruning
- Class edu.duke.cs.osprey.pruning.InvertedPruningMatrix
  
  class InvertedPruningMatrix extends PruningMatrix implements Serializable
  
  serialVersionUID:
  
  1993173402264691539L
  - Serialized Fields
    
    pmat
    
    PruningMatrix pmat
- Class edu.duke.cs.osprey.pruning.PruningMatrix
  
  class PruningMatrix extends TupleMatrixBoolean implements Serializable
  
  serialVersionUID:
  
  1212622649775905467L
Package edu.duke.cs.osprey.restypes
- Class edu.duke.cs.osprey.restypes.InterResBondingTemplate
  
  class InterResBondingTemplate extends Object implements Serializable
- Class edu.duke.cs.osprey.restypes.InterResBondingTemplate.CysteineBondingTemplate
  
  class CysteineBondingTemplate extends InterResBondingTemplate.PeptideBondingTemplate implements Serializable
- Class edu.duke.cs.osprey.restypes.InterResBondingTemplate.NoBondingTemplate
  
  class NoBondingTemplate extends InterResBondingTemplate implements Serializable
- Class edu.duke.cs.osprey.restypes.InterResBondingTemplate.NucleotideBondingTemplate
  
  class NucleotideBondingTemplate extends InterResBondingTemplate implements Serializable
- Class edu.duke.cs.osprey.restypes.InterResBondingTemplate.PeptideBondingTemplate
  
  class PeptideBondingTemplate extends InterResBondingTemplate implements Serializable
- Class edu.duke.cs.osprey.restypes.InterResBondingTemplate.SpecifiedBondingAtomsTemplate
  
  class SpecifiedBondingAtomsTemplate extends InterResBondingTemplate implements Serializable
  - Serialized Fields
    
    bondingAtomNames
    
    List<String> bondingAtomNames
- Class edu.duke.cs.osprey.restypes.ResidueEntropies
  
  class ResidueEntropies extends Object implements Serializable
  - Serialized Fields
    
    values
    
    HashMap<String,Double> values
- Class edu.duke.cs.osprey.restypes.ResidueTemplate
  
  class ResidueTemplate extends Object implements Serializable
  
  serialVersionUID:
  
  4568917747972477569L
  - Serialized Fields
    
    CAEquivalent
    
    String CAEquivalent
    
    dihedral4Atoms
    
    int[][] dihedral4Atoms
    
    dihedralMovingAtoms
    
    ArrayList<ArrayList<Integer>> dihedralMovingAtoms
    
    interResBonding
    
    InterResBondingTemplate interResBonding
    
    name
    
    String name
    
    The three letter code, e.g. ARG
    
    numberOfPhiPsiBins
    
    int numberOfPhiPsiBins
    
    numDihedrals
    
    int numDihedrals
    
    numRotamers
    
    int[][] numRotamers
    
    phiPsiResolution
    
    double phiPsiResolution
    
    rotamericDihedrals
    
    double[][][][] rotamericDihedrals
    
    templateRes
    
    Residue templateRes
- Class edu.duke.cs.osprey.restypes.ResidueTemplateLibrary
  
  class ResidueTemplateLibrary extends Object implements Serializable
  - Serialized Fields
    
    ffparams
    
    ForcefieldParams ffparams
    
    residueEntropies
    
    ResidueEntropies residueEntropies
    
    templates
    
    ArrayList<ResidueTemplate> templates
    
    totalNumRotamers
    
    int totalNumRotamers
    
    wildTypeTemplates
    
    Map<String,ResidueTemplate> wildTypeTemplates
- Class edu.duke.cs.osprey.restypes.RotamerLibraryReader
  
  class RotamerLibraryReader extends Object implements Serializable
Package edu.duke.cs.osprey.sofea
- Class edu.duke.cs.osprey.sofea.ZMatrix
  
  class ZMatrix extends TupleMatrixGeneric<BigExp> implements Serializable
  - Serialized Fields
    
    bcalc
    
    BoltzmannCalculator bcalc
Package edu.duke.cs.osprey.structure
- Class edu.duke.cs.osprey.structure.Atom
  
  class Atom extends Object implements Serializable
  - Serialized Fields
    
    BFactor
    
    double BFactor
    
    bonds
    
    ArrayList<Atom> bonds
    
    charge
    
    double charge
    
    elementNumber
    
    int elementNumber
    
    elementType
    
    String elementType
    
    forceFieldType
    
    String forceFieldType
    
    indexInRes
    
    int indexInRes
    
    mass
    
    double mass
    
    modelAtomNumber
    
    int modelAtomNumber
    
    name
    
    String name
    
    radius
    
    double radius
    
    res
    
    Residue res
    
    type
    
    int type
- Class edu.duke.cs.osprey.structure.ConfProblem
  
  class ConfProblem extends Object implements Serializable
  - Serialized Fields
    
    brokenResidue
    
    Residue brokenResidue
    
    problemDOF
    
    DegreeOfFreedom problemDOF
- Class edu.duke.cs.osprey.structure.Molecule
  
  class Molecule extends Object implements Serializable
  
  serialVersionUID:
  
  -2709516483892891323L
  - Serialized Fields
    
    alternates
    
    Map<Integer,ArrayList<Residue>> alternates
    
    name
    
    String name
    
    residues
    
    Residues residues
- Class edu.duke.cs.osprey.structure.Residue
  
  class Residue extends Object implements Serializable
  
  serialVersionUID:
  
  -6188262155881479376L
  - Serialized Fields
    
    atoms
    
    ArrayList<Atom> atoms
    
    Information about the individual atoms. When assigning the template we will copy this from the template.
    
    confProblems
    
    ArrayList<ConfProblem> confProblems
    
    coords
    
    double[] coords
    
    coordinates of all the atoms: x1, y1, z1, x2, ...
    
    fullName
    
    String fullName
    
    indexInMolecule
    
    int indexInMolecule
    
    Index of this residue in the molecule it's in
    
    interResBondsMarked
    
    boolean interResBondsMarked
    
    intraResBondsMarked
    
    boolean intraResBondsMarked
    
    molec
    
    Molecule molec
    
    The molecule the residue's in
    
    pucker
    
    ProlinePucker pucker
    
    resNum
    
    String resNum
    
    secondaryStruct
    
    Residue.SecondaryStructure secondaryStruct
    
    template
    
    ResidueTemplate template
    
    Gives the name of the residue like "GLU" or "H2O" or whatever and any information about bonds, force-field, rotatable dihedrals, and rotamers Only assignment using Residue.assignTemplate(ResidueTemplateLibrary), which will reorder atoms to match template.
- Class edu.duke.cs.osprey.structure.Residues
  
  class Residues extends ArrayList<Residue> implements Serializable
  
  serialVersionUID:
  
  4950265664624559802L
  - Serialized Fields
    
    indicesByNum
    
    Map<String,Integer> indicesByNum
Package edu.duke.cs.osprey.tools
- Class edu.duke.cs.osprey.tools.BigExp
  
  class BigExp extends Object implements Serializable
  - Serialized Fields
    
    exp
    
    int exp
    
    fp
    
    double fp
- Class edu.duke.cs.osprey.tools.EllipseTransform
  
  class EllipseTransform extends Object implements Serializable
  - Serialized Fields
    
    A
    
    cern.colt.matrix.DoubleMatrix2D A
    
    c
    
    cern.colt.matrix.DoubleMatrix1D c
- Class edu.duke.cs.osprey.tools.ExpFunction
  
  class ExpFunction extends Object implements Serializable
  - Serialized Fields
    
    mathContext
    
    MathContext mathContext
    
    maxPrecision
    
    int maxPrecision
- Class edu.duke.cs.osprey.tools.FileTools.FilePathRoot
  
  class FilePathRoot extends FileTools.PathRoot implements Serializable
  
  serialVersionUID:
  
  882642923777325590L
  - Serialized Fields
    
    rootFile
    
    File rootFile
- Class edu.duke.cs.osprey.tools.FileTools.PathRoot
  
  class PathRoot extends Object implements Serializable
  
  serialVersionUID:
  
  2265693476401349502L
  - Serialized Fields
    
    type
    
    String type
- Class edu.duke.cs.osprey.tools.FileTools.ResourcePathRoot
  
  class ResourcePathRoot extends FileTools.PathRoot implements Serializable
  
  serialVersionUID:
  
  6035021994505586535L
  - Serialized Fields
    
    rootPath
    
    String rootPath
- Class edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal
  
  class MagicBigDecimal extends BigDecimal implements Serializable
  - Serialized Fields
    
    doubleValue
    
    double doubleValue
- Exception edu.duke.cs.osprey.tools.MathTools.MagicBigDecimal.DontDoRawMathWithMagicException
  
  class DontDoRawMathWithMagicException extends UnsupportedOperationException implements Serializable
- Class edu.duke.cs.osprey.tools.MinVolEllipse
  
  class MinVolEllipse extends Object implements Serializable
  - Serialized Fields
    
    A
    
    cern.colt.matrix.DoubleMatrix2D A
    
    c
    
    cern.colt.matrix.DoubleMatrix1D c
    
    nc
    
    cern.colt.matrix.DoubleMatrix1D nc
- Exception edu.duke.cs.osprey.tools.ObjectIO.BadFileException
  
  class BadFileException extends Exception implements Serializable
  
  serialVersionUID:
  
  -9191066141220686516L
- Exception edu.duke.cs.osprey.tools.ObjectIO.CantWriteException
  
  class CantWriteException extends Exception implements Serializable
  
  serialVersionUID:
  
  8152920955998224621L
- Class edu.duke.cs.osprey.tools.RotationMatrix
  
  class RotationMatrix extends Object implements Serializable
  
  serialVersionUID:
  
  2915420374293280379L
  - Serialized Fields
    
    matrix
    
    double[][] matrix
- Class edu.duke.cs.osprey.tools.Stopwatch
  
  class Stopwatch extends Object implements Serializable
  - Serialized Fields
    
    isRunning
    
    boolean isRunning
    
    startTime
    
    long startTime
    
    timeNs
    
    long timeNs
- Exception edu.duke.cs.osprey.tools.TomlParseException
  
  class TomlParseException extends RuntimeException implements Serializable
  - Serialized Fields
    
    pos
    
    org.tomlj.TomlPosition pos
- Error edu.duke.cs.osprey.tools.UnpossibleError
  
  class UnpossibleError extends Error implements Serializable
Package edu.duke.cs.osprey.tupexp
- Class edu.duke.cs.osprey.tupexp.BasicEPICTupleExpander
  
  class BasicEPICTupleExpander extends TupleExpander implements Serializable
  - Serialized Fields
    
    epicMat
    
    NewEPICMatrix epicMat
    
    pruneMat
    
    PruningMatrix pruneMat
- Class edu.duke.cs.osprey.tupexp.BasicPruningTupleExpander
  
  class BasicPruningTupleExpander extends TupleExpander implements Serializable
  - Serialized Fields
    
    plugMat
    
    PolytopeMatrix plugMat
    
    pruneMat
    
    PruningMatrix pruneMat
- Class edu.duke.cs.osprey.tupexp.ConfETupleExpander
  
  class ConfETupleExpander extends TupleExpander implements Serializable
  - Serialized Fields
    
    fullPLUGPruning
    
    boolean fullPLUGPruning
    
    sp
    
    SearchProblem sp
    
    worstELBDiff
    
    double worstELBDiff
- Class edu.duke.cs.osprey.tupexp.LUTESettings
  
  class LUTESettings extends Object implements Serializable
  - Serialized Fields
    
    goalResid
    
    double goalResid
    
    useLUTE
    
    boolean useLUTE
    
    useRelWt
    
    boolean useRelWt
    
    useThreshWt
    
    boolean useThreshWt
- Class edu.duke.cs.osprey.tupexp.NewConfETupleExpander
  
  class NewConfETupleExpander extends TupleExpander implements Serializable
  - Serialized Fields
    
    confECalc
    
    ConfEnergyCalculator confECalc
    
    pruneMat
    
    PruningMatrix pruneMat
- Class edu.duke.cs.osprey.tupexp.TESampleSet
  
  class TESampleSet extends Object implements Serializable
  - Serialized Fields
    
    curFitVals
    
    ArrayList<Double> curFitVals
    
    numTuplesDone
    
    int numTuplesDone
    
    sampleResids
    
    ArrayList<Double> sampleResids
    
    samples
    
    ArrayList<int[]> samples
    
    te
    
    TupleExpander te
    
    totalResid
    
    double totalResid
    
    trueVals
    
    ArrayList<Double> trueVals
    
    tupleNumSamples
    
    ArrayList<Integer> tupleNumSamples
    
    tupleResids
    
    ArrayList<Double> tupleResids
    
    tuplesDone
    
    boolean[] tuplesDone
    
    worstResid
    
    double worstResid
- Class edu.duke.cs.osprey.tupexp.TupleExpander
  
  class TupleExpander extends Object implements Serializable
  - Serialized Fields
    
    assignmentSets
    
    ArrayList<ArrayList<ArrayList<Integer>>> assignmentSets
    
    canCheckPartialPruning
    
    boolean canCheckPartialPruning
    
    constTerm
    
    double constTerm
    
    CVSamples
    
    TESampleSet CVSamples
    
    ezPruneCount
    
    int ezPruneCount
    
    fof
    
    edu.duke.cs.osprey.tupexp.FittingObjFcn fof
    
    numAllowed
    
    int[] numAllowed
    
    numPos
    
    int numPos
    
    numSampsPerTuple
    
    int numSampsPerTuple
    
    pruningInterval
    
    double pruningInterval
    
    trainingSamples
    
    TESampleSet trainingSamples
    
    tuples
    
    ArrayList<RCTuple> tuples
    
    tupleTerms
    
    double[] tupleTerms
- Class edu.duke.cs.osprey.tupexp.TupleIndexMatrix
  
  class TupleIndexMatrix extends TupleMatrixGeneric<Integer> implements Serializable

Serialized Form

Package edu.duke.cs.osprey.astar

Class edu.duke.cs.osprey.astar.AStarProgress

Serialized Fields

deepestLevel

goalScore

gscore

hscore

level

msRunning

numLeafNodes

numLevels

numNodesExpanded

numNodesInQueue

numNodesQueuedThisReport

stopwatch

Class edu.duke.cs.osprey.astar.AStarTree

Serialized Fields

numExpanded

numPruned

pq

Class edu.duke.cs.osprey.astar.ConfTree

Serialized Fields

childConf

definedPos

definedRCs

emat

epicMat

minPartialConfs

mutSpace

newEPICMat

nodeFactory

numDefined

numPos

numUndefined

rcTuple

traditionalScore

undefinedPos

unprunedRCsAtPos

useDynamicAStar

useRefinement

Class edu.duke.cs.osprey.astar.FullAStarNode

Serialized Fields

gscore

hscore

nodeAssignments

score

scoreNeedsRefinement

UB

UBConf

Class edu.duke.cs.osprey.astar.FullAStarNode.Factory

Serialized Fields

numPos

Class edu.duke.cs.osprey.astar.SlimAStarNode

Serialized Fields

gscore

hscore

level

link

numPos

Class edu.duke.cs.osprey.astar.SlimAStarNode.Factory

Serialized Fields

numPos

Class edu.duke.cs.osprey.astar.SlimAStarNode.Link

Serialized Fields

parent

pos

rc

Package edu.duke.cs.osprey.astar.comets

Class edu.duke.cs.osprey.astar.comets.COMETSNode

Serialized Fields

pruneMat

stateTrees

stateUB

Class edu.duke.cs.osprey.astar.comets.COMETSTree

Serialized Fields

AATypeOptions

constraints

mutable2StatePosNums

numMaxMut