Package edu.duke.cs.osprey.lute

Class LUTEPfunc

java.lang.Object

edu.duke.cs.osprey.lute.LUTEPfunc

All Implemented Interfaces:

PartitionFunction, PartitionFunction.WithConfDB

public class LUTEPfunc
extends Object
implements PartitionFunction.WithConfDB

Since LUTE energies are assumed to be correct, we don't have to deal with minimization and bounding, so it's vastly easier to estimate partition functions.

Nested Class Summary

Nested classes/interfaces inherited from interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction

PartitionFunction.ConfListener, PartitionFunction.Result, PartitionFunction.Status, PartitionFunction.Values, PartitionFunction.WithConfDB, PartitionFunction.WithExternalMemory

Field Summary

Fields

Modifier and Type	Field	Description
final LUTEConfEnergyCalculator	ecalc

Fields inherited from interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction

decimalPrecision

Constructor Summary

Constructors

Constructor	Description
LUTEPfunc(LUTEConfEnergyCalculator ecalc, ConfAStarTree astar, BigInteger numConfsBeforePruning)

Method Summary

Modifier and Type	Method	Description
void	compute(int maxNumConfs)
int	getNumConfsEvaluated()
int	getParallelism()
PartitionFunction.Status	getStatus()
PartitionFunction.Values	getValues()
void	init(double epsilon)	Initializes the partition function for calculation.
void	setConfDB(ConfDB confDB, ConfDB.Key key)
void	setConfListener(PartitionFunction.ConfListener val)
void	setReportProgress(boolean val)
void	setStabilityThreshold(BigDecimal val)	Sets the stability threshold for this PartitionFunction, if supported

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.kstar.pfunc.PartitionFunction

compute, compute, makeResult, putTaskContexts, setInstanceId

Methods inherited from interface edu.duke.cs.osprey.kstar.pfunc.PartitionFunction.WithConfDB

setConfDB, setConfDB

Field Details

ecalc

public final LUTEConfEnergyCalculator ecalc

Constructor Details

LUTEPfunc

public LUTEPfunc(LUTEConfEnergyCalculator ecalc,
 ConfAStarTree astar,
 BigInteger numConfsBeforePruning)

Method Details

setReportProgress

public void setReportProgress(boolean val)

Specified by:

setReportProgress in interface PartitionFunction

setConfListener

public void setConfListener(PartitionFunction.ConfListener val)

Specified by:

setConfListener in interface PartitionFunction

setConfDB

public void setConfDB(ConfDB confDB,
 ConfDB.Key key)

Specified by:

setConfDB in interface PartitionFunction.WithConfDB

init

public void init(double epsilon)

Description copied from interface: PartitionFunction

Initializes the partition function for calculation.

Specified by:

init in interface PartitionFunction

Parameters:

epsilon - The accuracy with which to estimate the partition function.

setStabilityThreshold

public void setStabilityThreshold(BigDecimal val)

Description copied from interface: PartitionFunction

Sets the stability threshold for this PartitionFunction, if supported

Specified by:

setStabilityThreshold in interface PartitionFunction

Parameters:

val - If the partition function upper bound value falls below this threshold, the sequence is considered unstable.

getStatus

public PartitionFunction.Status getStatus()

Specified by:

getStatus in interface PartitionFunction

getValues

public PartitionFunction.Values getValues()

Specified by:

getValues in interface PartitionFunction

getParallelism

public int getParallelism()

Specified by:

getParallelism in interface PartitionFunction

getNumConfsEvaluated

public int getNumConfsEvaluated()

Specified by:

getNumConfsEvaluated in interface PartitionFunction

compute

public void compute(int maxNumConfs)

Specified by:

compute in interface PartitionFunction