Package edu.duke.cs.osprey.astar.conf

Class ConfAStarTree.Builder

java.lang.Object

edu.duke.cs.osprey.astar.conf.ConfAStarTree.Builder

Enclosing class:

ConfAStarTree

public static class ConfAStarTree.Builder
extends Object

Constructor Summary

Constructors

Constructor	Description
Builder(EnergyMatrix emat, RCs rcs)
Builder(EnergyMatrix emat, ConfSpace confSpace)
Builder(EnergyMatrix emat, SimpleConfSpace confSpace)
Builder(EnergyMatrix emat, PruningMatrix pmat)

Method Summary

Modifier and Type	Method	Description
ConfAStarTree	build()
ConfAStarTree.Builder	setCustom(AStarOrder order, AStarScorer gscorer, AStarScorer hscorer)
ConfAStarTree.Builder	setLUTE(LUTEConfEnergyCalculator luteEcalc)	Uses estimation functions that are compatible with LUTE conformation energies
ConfAStarTree.Builder	setMaxNumNodes(int val)
ConfAStarTree.Builder	setMaxNumNodes(Long val)
ConfAStarTree.Builder	setMPLP()	Creates an A* search using a newer estimation function based on Max Product Linear Programming (MPLP).
ConfAStarTree.Builder	setMPLP(ConfAStarTree.MPLPBuilder builder)
ConfAStarTree.Builder	setPruner(AStarPruner val)
ConfAStarTree.Builder	setShowProgress(boolean val)
ConfAStarTree.Builder	setTraditional()	Uses the traditional estimation function to guide the tree search.
ConfAStarTree.Builder	setTraditionalOpt(MathTools.Optimizer optimizer)	Just like setTraditional, but allow maximization or minimization
ConfAStarTree.Builder	useExternalMemory()	Use external memory (eg, disk, SSD, NAS) when large A* searches cannot fit in internal memory (eg, RAM).

Methods inherited from class java.lang.Object

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

Constructor Details

Builder

public Builder(EnergyMatrix emat,
 SimpleConfSpace confSpace)

Builder

public Builder(EnergyMatrix emat,
 ConfSpace confSpace)

Builder

public Builder(EnergyMatrix emat,
 PruningMatrix pmat)

Builder

public Builder(EnergyMatrix emat,
 RCs rcs)

Method Details

setCustom

public ConfAStarTree.Builder setCustom(AStarOrder order,
 AStarScorer gscorer,
 AStarScorer hscorer)

setTraditional

public ConfAStarTree.Builder setTraditional()

Uses the traditional estimation function to guide the tree search.

setTraditionalOpt

public ConfAStarTree.Builder setTraditionalOpt(MathTools.Optimizer optimizer)

Just like setTraditional, but allow maximization or minimization

setMPLP

public ConfAStarTree.Builder setMPLP()

Creates an A* search using a newer estimation function based on Max Product Linear Programming (MPLP). For large designs, this A* implementation can be dramatically faster than the traditional one, and often require much less memory too.

setMPLP

public ConfAStarTree.Builder setMPLP(ConfAStarTree.MPLPBuilder builder)

setLUTE

public ConfAStarTree.Builder setLUTE(LUTEConfEnergyCalculator luteEcalc)

Uses estimation functions that are compatible with LUTE conformation energies

useExternalMemory

public ConfAStarTree.Builder useExternalMemory()

Use external memory (eg, disk, SSD, NAS) when large A* searches cannot fit in internal memory (eg, RAM). Use ExternalMemory.setInternalLimit(int) to set the amount of fixed internal memory and ExternalMemory.setTempDir(java.lang.String) to set the file path for external memory.

setShowProgress

public ConfAStarTree.Builder setShowProgress(boolean val)

setPruner

public ConfAStarTree.Builder setPruner(AStarPruner val)

setMaxNumNodes

public ConfAStarTree.Builder setMaxNumNodes(Long val)

setMaxNumNodes

public ConfAStarTree.Builder setMaxNumNodes(int val)

build

public ConfAStarTree build()