Package edu.duke.cs.osprey.multistatekstar

Class PartitionFunctionDiscreteUppperBound

java.lang.Object

edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction

edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized

edu.duke.cs.osprey.multistatekstar.PartitionFunctionDiscrete

edu.duke.cs.osprey.multistatekstar.PartitionFunctionDiscreteUppperBound

All Implemented Interfaces:

PartitionFunction

public class PartitionFunctionDiscreteUppperBound
extends PartitionFunctionDiscrete

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 inherited from class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized

invmat, MAX_VALUE, maxNumTopConfs, MIN_VALUE, numActiveThreads, qstarScoreWeights, topConfs

Fields inherited from class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction

boltzmann, confListener, confSearchFactory, ecalc, emat, energyConfs, isReportingProgress, numConfsEvaluated, numConfsToScore, pmat, qprimeUnevaluated, qprimeUnscored, scoreConfs, status, stopwatch, targetEpsilon, values

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

decimalPrecision

Constructor Summary

Constructors

Constructor	Description
PartitionFunctionDiscreteUppperBound(EnergyMatrix emat, PruningMatrix pmat, PruningMatrix invmat, ConfSearchFactory confSearchFactory, GMECConfEnergyCalculator.Async ecalc)

Method Summary

Modifier and Type	Method	Description
void	compute(int maxNumConfs)
void	compute(BigDecimal targetScoreWeights)
protected double	getEffectiveEpsilon()

Methods inherited from class edu.duke.cs.osprey.multistatekstar.PartitionFunctionDiscrete

init, updateQprime

Methods inherited from class edu.duke.cs.osprey.multistatekstar.PartitionFunctionMinimized

cleanup, saveConf, saveEConfs, setStatus, updateQprime, writeTopConfs

Methods inherited from class edu.duke.cs.osprey.kstar.pfunc.ParallelConfPartitionFunction

calcWeightSumUpperBound, compute, getNumConfsEvaluated, getParallelism, getStatus, getValues, setConfListener, setReportProgress

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, makeResult, putTaskContexts, setInstanceId, setStabilityThreshold

Constructor Details

PartitionFunctionDiscreteUppperBound

public PartitionFunctionDiscreteUppperBound(EnergyMatrix emat,
 PruningMatrix pmat,
 PruningMatrix invmat,
 ConfSearchFactory confSearchFactory,
 GMECConfEnergyCalculator.Async ecalc)

Method Details

compute

public void compute(int maxNumConfs)

Specified by:

compute in interface PartitionFunction

Overrides:

compute in class PartitionFunctionDiscrete

compute

public void compute(BigDecimal targetScoreWeights)

Overrides:

compute in class PartitionFunctionDiscrete

getEffectiveEpsilon

protected double getEffectiveEpsilon()

Overrides:

getEffectiveEpsilon in class PartitionFunctionDiscrete