Package edu.duke.cs.osprey.multistatekstar

Class MultiSequenceConfTree

java.lang.Object

edu.duke.cs.osprey.astar.AStarTree<T>

edu.duke.cs.osprey.astar.ConfTree<FullAStarNode>

edu.duke.cs.osprey.multistatekstar.MultiSequenceConfTree

All Implemented Interfaces:

ConfSearch, Serializable

public class MultiSequenceConfTree
extends ConfTree<FullAStarNode>

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface edu.duke.cs.osprey.confspace.ConfSearch

ConfSearch.EnergiedConf, ConfSearch.MultiSplitter, ConfSearch.ScoredConf, ConfSearch.Splitter

Field Summary

Fields

Modifier and Type	Field	Description
boolean	energyLBs

Fields inherited from class edu.duke.cs.osprey.astar.ConfTree

childConf, definedPos, definedRCs, emat, epicMat, minPartialConfs, newEPICMat, numDefined, numPos, numUndefined, rcTuple, traditionalScore, undefinedPos, unprunedRCsAtPos, useDynamicAStar, useRefinement

Fields inherited from class edu.duke.cs.osprey.astar.AStarTree

numExpanded, numPruned

Constructor Summary

Constructors

Constructor	Description
MultiSequenceConfTree(MSSearchProblem search, EnergyMatrix emat, PruningMatrix pmat)

Method Summary

Modifier and Type	Method	Description
BigInteger	getNumConformations()	Get the total number of conformations in the conformation space.
protected Integer[]	getPosNums(boolean defined)
protected double	higherOrderContrib(int pos1, int rc1, int pos2, int rc2, RCTuple definedTuple)
protected void	init()
protected boolean	posComesBefore(int pos1, int pos2, RCTuple definedTuple)
protected double	RCContribution(int pos1, int rc1, RCTuple definedTuple)
protected double	scoreConfDifferential(FullAStarNode parentNode, int childPos, int childRc)
protected double	scoreNode(int[] partialConf)
protected void	splitPositions(FullAStarNode node)

Methods inherited from class edu.duke.cs.osprey.astar.ConfTree

assertSplitPositions, getChildren, isFullyAssigned, makeFull, makeFull, makeFull, makeFull, nextLevelToExpand, refineScore, rootNode, scoreNode, scoreNodeDifferential

Methods inherited from class edu.duke.cs.osprey.astar.AStarTree

canPruneNode, curBestScore, getQueue, initQueue, nextConf, nextConfs, nextLeafNodes, outputNode

Methods inherited from class java.lang.Object

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

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

nextConfs

Field Details

energyLBs

public boolean energyLBs

Constructor Details

MultiSequenceConfTree

public MultiSequenceConfTree(MSSearchProblem search,
 EnergyMatrix emat,
 PruningMatrix pmat)

Method Details

getPosNums

protected Integer[] getPosNums(boolean defined)

init

protected void init()

getNumConformations

public BigInteger getNumConformations()

Description copied from interface: ConfSearch

Get the total number of conformations in the conformation space. This can be an astronomically large number.

Specified by:

getNumConformations in interface ConfSearch

Overrides:

getNumConformations in class ConfTree<FullAStarNode>

splitPositions

protected void splitPositions(FullAStarNode node)

Overrides:

splitPositions in class ConfTree<FullAStarNode>

scoreNode

protected double scoreNode(int[] partialConf)

RCContribution

protected double RCContribution(int pos1,
 int rc1,
 RCTuple definedTuple)

higherOrderContrib

protected double higherOrderContrib(int pos1,
 int rc1,
 int pos2,
 int rc2,
 RCTuple definedTuple)

posComesBefore

protected boolean posComesBefore(int pos1,
 int pos2,
 RCTuple definedTuple)

scoreConfDifferential

protected double scoreConfDifferential(FullAStarNode parentNode,
 int childPos,
 int childRc)

Overrides:

scoreConfDifferential in class ConfTree<FullAStarNode>