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

Class COMETSTree

java.lang.Object

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

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

All Implemented Interfaces:

ConfSearch, Serializable

public class COMETSTree
extends AStarTree<FullAStarNode>

Tree for constrained optimization of multistate energies by tree search

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

numExpanded, numPruned

Constructor Summary

Constructors

Constructor	Description
COMETSTree(int numTreeLevels, LME objFcn, LME[] constraints, ArrayList<ArrayList<String>> AATypeOptions, int numMaxMut, String[] wtSeq, int numStates, SearchProblem[] stateSP, ArrayList<ArrayList<Integer>> mutable2StatePosNums, boolean outputGMECStructs)

Method Summary

Modifier and Type	Method	Description
boolean	canPruneNode(FullAStarNode node)
ArrayList<FullAStarNode>	getChildren(FullAStarNode curNode)
boolean	isFullyAssigned(FullAStarNode node)
ConfSearch.ScoredConf	outputNode(FullAStarNode node)
FullAStarNode	rootNode()
String	seqAsString(int[] seqNodeAssignments)

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

curBestScore, getQueue, initQueue, nextConf, nextConfs, nextLeafNodes, refineScore

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

getNumConformations, nextConfs

Constructor Details

COMETSTree

public COMETSTree(int numTreeLevels,
 LME objFcn,
 LME[] constraints,
 ArrayList<ArrayList<String>> AATypeOptions,
 int numMaxMut,
 String[] wtSeq,
 int numStates,
 SearchProblem[] stateSP,
 ArrayList<ArrayList<Integer>> mutable2StatePosNums,
 boolean outputGMECStructs)

Method Details

getChildren

public ArrayList<FullAStarNode> getChildren(FullAStarNode curNode)

Specified by:

getChildren in class AStarTree<FullAStarNode>

rootNode

public FullAStarNode rootNode()

Specified by:

rootNode in class AStarTree<FullAStarNode>

canPruneNode

public boolean canPruneNode(FullAStarNode node)

Overrides:

canPruneNode in class AStarTree<FullAStarNode>

isFullyAssigned

public boolean isFullyAssigned(FullAStarNode node)

Specified by:

isFullyAssigned in class AStarTree<FullAStarNode>

outputNode

public ConfSearch.ScoredConf outputNode(FullAStarNode node)

Overrides:

outputNode in class AStarTree<FullAStarNode>

seqAsString

public String seqAsString(int[] seqNodeAssignments)