Package edu.duke.cs.osprey.ewakstar

Interface EWAKStarPartitionFunction

All Known Subinterfaces:

EWAKStarPartitionFunction.WithConfTable, EWAKStarPartitionFunction.WithExternalMemory

All Known Implementing Classes:

EWAKStarGradientDescentPfunc

public interface EWAKStarPartitionFunction

based on PartitionFunction.java, author: lowegard

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static interface	EWAKStarPartitionFunction.ConfListener
static class	EWAKStarPartitionFunction.Result
static enum	EWAKStarPartitionFunction.Status
static class	EWAKStarPartitionFunction.Values
static interface	EWAKStarPartitionFunction.WithConfTable
static interface	EWAKStarPartitionFunction.WithExternalMemory

Field Summary

Fields

Modifier and Type	Field	Description
static final MathContext	decimalPrecision

Method Summary

Modifier and Type	Method	Description
default void	compute()
void	compute(int maxNumConfs)
ArrayList<EnergyCalculator.EnergiedParametricMolecule>	getEpMols()
int	getNumConfsEvaluated()
int	getParallelism()
HashMap<Double,ConfSearch.ScoredConf>	getSConfs()
EWAKStarPartitionFunction.Status	getStatus()
EWAKStarPartitionFunction.Values	getValues()
void	init(ConfSearch scoreConfs, ConfSearch energyConfs, BigInteger numConfsBeforePruning, double targetEpsilon, double targetEnergy, int highestNumConfs, boolean printPDBs)	Initializes the partition function for calculation.
default EWAKStarPartitionFunction.Result	makeResult()
void	setConfListener(EWAKStarPartitionFunction.ConfListener val)
void	setReportProgress(boolean val)
default void	setStabilityThreshold(BigDecimal stabilityThreshold)	Sets the stability threshold for this PartitionFunction, if supported

Field Details

decimalPrecision

static final MathContext decimalPrecision

Method Details

setReportProgress

void setReportProgress(boolean val)

setConfListener

void setConfListener(EWAKStarPartitionFunction.ConfListener val)

init

void init(ConfSearch scoreConfs,
 ConfSearch energyConfs,
 BigInteger numConfsBeforePruning,
 double targetEpsilon,
 double targetEnergy,
 int highestNumConfs,
 boolean printPDBs)

Initializes the partition function for calculation.

Parameters:

scoreConfs - The A* tree of conformations to enumerate (which may have been pruned)

energyConfs - The A* tree of conformations to enumerate (which may have been pruned)

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

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

numConfsBeforePruning - The total number of conformations in the conformation space for this search, including any conformations removed by pruned tuples.

highestNumConfs - The maximum number of conformations allowed for a partition function calculation.

printPDBs - Boolean value for printing PDB files

setStabilityThreshold

default void setStabilityThreshold(BigDecimal stabilityThreshold)

Sets the stability threshold for this PartitionFunction, if supported

Parameters:

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

getStatus

EWAKStarPartitionFunction.Status getStatus()

getEpMols

ArrayList<EnergyCalculator.EnergiedParametricMolecule> getEpMols()

getSConfs

HashMap<Double,ConfSearch.ScoredConf> getSConfs()

getValues

EWAKStarPartitionFunction.Values getValues()

getParallelism

int getParallelism()

getNumConfsEvaluated

int getNumConfsEvaluated()

compute

void compute(int maxNumConfs)

compute

default void compute()

makeResult

default EWAKStarPartitionFunction.Result makeResult()