Package edu.duke.cs.osprey.kstar.pruning

Class UnprunedPruningMatrix

java.lang.Object

edu.duke.cs.osprey.confspace.AbstractTupleMatrix<Boolean>

edu.duke.cs.osprey.confspace.TupleMatrixBoolean

edu.duke.cs.osprey.pruning.PruningMatrix

edu.duke.cs.osprey.kstar.pruning.ReducedPruningMatrix

edu.duke.cs.osprey.kstar.pruning.UnprunedPruningMatrix

All Implemented Interfaces:

TupleMatrix<Boolean>, Serializable

public class UnprunedPruningMatrix
extends ReducedPruningMatrix

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class edu.duke.cs.osprey.pruning.PruningMatrix

PruningMatrix.IteratorCommand, PruningMatrix.PairConsumer, PruningMatrix.SingleConsumer, PruningMatrix.TripleConsumer

Field Summary

Fields inherited from class edu.duke.cs.osprey.kstar.pruning.ReducedPruningMatrix

sp, upm

Constructor Summary

Constructors

Constructor	Description
UnprunedPruningMatrix(KSSearchProblem sp, UpdatedPruningMatrix upm, double pruningInterval)

Method Summary

Modifier and Type	Method	Description
HigherTupleFinder<Boolean>	getHigherOrderTerms(int res1, int index1, int res2, int index2)
Boolean	getOneBody(int res, int index)
Boolean	getPairwise(int res1, int index1, int res2, int index2)

Methods inherited from class edu.duke.cs.osprey.kstar.pruning.ReducedPruningMatrix

countUpdates, getNumConfAtPos, getNumPos, getUpdatedPruningMatrix

Methods inherited from class edu.duke.cs.osprey.pruning.PruningMatrix

calcUnprunedConfsLowerBound, calcUnprunedConfsUpperBound, countPrunedPairs, countPrunedRCs, countPrunedTriples, countUnprunedSingles, forEachUnprunedPair, forEachUnprunedPairAt, forEachUnprunedSingle, forEachUnprunedSingleAt, forEachUnprunedTriple, forEachUnprunedTripleAt, getTuple, isPairPruned, isPruned, isPrunedHigherOrder, isQuadruplePruned, isQuintuplePruned, isSinglePruned, isTriplePruned, markAsPruned, prunedRCsAtPos, prunedRCsAtPos, prunePair, prunePairsFromSingle, prunePairsFromSingles, pruneSingle, pruneTriple, unprunedRCsAtPos, unprunedRCsAtPos, unprunedRCTuplesAtPos

Methods inherited from class edu.duke.cs.osprey.confspace.TupleMatrixBoolean

allocate, setOneBody, setOneBody, setPairwise, setPairwise, toString

Methods inherited from class edu.duke.cs.osprey.confspace.AbstractTupleMatrix

equals, equals, fill, fill, getDefaultHigherInteraction, getHigherOrderTuples, getNumConfAtPos, getNumOneBody, getNumPairwise, getOneBodyIndex, getOrMakeHigherOrderTuples, getPairwiseIndex, getPairwiseIndex, getPruningInterval, hasHigherOrderTermFor, hasHigherOrderTerms, hasHigherOrderTuples, matches, setHigherOrder, setHigherOrderTerms, setPruningInterval, setTupleValue, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface edu.duke.cs.osprey.confspace.TupleMatrix

forEachHigherOrderTupleIn, forEachHigherOrderTupleIn, forEachHigherOrderTupleIn, getOneBody, getPairwise, setOneBody, setPairwise, setTuple

Constructor Details

UnprunedPruningMatrix

public UnprunedPruningMatrix(KSSearchProblem sp,
 UpdatedPruningMatrix upm,
 double pruningInterval)

Method Details

getOneBody

public Boolean getOneBody(int res,
 int index)

Specified by:

getOneBody in interface TupleMatrix<Boolean>

Overrides:

getOneBody in class ReducedPruningMatrix

getPairwise

public Boolean getPairwise(int res1,
 int index1,
 int res2,
 int index2)

Specified by:

getPairwise in interface TupleMatrix<Boolean>

Overrides:

getPairwise in class ReducedPruningMatrix

getHigherOrderTerms

public HigherTupleFinder<Boolean> getHigherOrderTerms(int res1,
 int index1,
 int res2,
 int index2)

Specified by:

getHigherOrderTerms in interface TupleMatrix<Boolean>

Overrides:

getHigherOrderTerms in class ReducedPruningMatrix