Package edu.duke.cs.osprey.paste

Interface PastePartitionFunction

All Known Subinterfaces:

PastePartitionFunction.WithConfTable, PastePartitionFunction.WithExternalMemory

All Known Implementing Classes:

PasteGradientDescentPfunc

public interface PastePartitionFunction

based on PartitionFunction.java, author: lowegard

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static interface	PastePartitionFunction.ConfListener
static class	PastePartitionFunction.Result
static enum	PastePartitionFunction.Status
static class	PastePartitionFunction.Values
static interface	PastePartitionFunction.WithConfTable
static interface	PastePartitionFunction.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, int numPDBs)
ArrayList<EnergyCalculator.EnergiedParametricMolecule>	getEpMols()
int	getNumConfsEvaluated()
int	getParallelism()
HashMap<Double,ConfSearch.ScoredConf>	getSConfs()
PastePartitionFunction.Status	getStatus()
PastePartitionFunction.Values	getValues()
void	init(ConfSearch scoreConfs, ConfSearch energyConfs, BigInteger numConfsBeforePruning, double targetEpsilon, double targetEnergy, PastePartitionFunction.Result wtResult, boolean useWindowCriterion)	Initializes the partition function for calculation.
default PastePartitionFunction.Result	makeResult()
void	setConfListener(PastePartitionFunction.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(PastePartitionFunction.ConfListener val)

init

void init(ConfSearch scoreConfs,
 ConfSearch energyConfs,
 BigInteger numConfsBeforePruning,
 double targetEpsilon,
 double targetEnergy,
 PastePartitionFunction.Result wtResult,
 boolean useWindowCriterion)

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.

useWindowCriterion - True if you want to stop calculating when the lower/upper bounds do not overlap with the WT lower/upper bounds, otherwise false (you then calculate to epsilon)

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

PastePartitionFunction.Status getStatus()

getEpMols

ArrayList<EnergyCalculator.EnergiedParametricMolecule> getEpMols()

getSConfs

HashMap<Double,ConfSearch.ScoredConf> getSConfs()

getValues

PastePartitionFunction.Values getValues()

getParallelism

int getParallelism()

getNumConfsEvaluated

int getNumConfsEvaluated()

compute

void compute(int maxNumConfs,
 int numPDBs)

compute

default void compute()

makeResult

default PastePartitionFunction.Result makeResult()