Package edu.duke.cs.osprey.ewakstar

Class EWAKStarGradientDescentPfunc

java.lang.Object

edu.duke.cs.osprey.ewakstar.EWAKStarGradientDescentPfunc

All Implemented Interfaces:

EWAKStarPartitionFunction, EWAKStarPartitionFunction.WithConfTable, EWAKStarPartitionFunction.WithExternalMemory

public class EWAKStarGradientDescentPfunc
extends Object
implements EWAKStarPartitionFunction.WithConfTable, EWAKStarPartitionFunction.WithExternalMemory

This partition function calculator estimates the partition function value by alternating between two operations: 1. compute lower energy bounds on conformations to refine the pfunc upper bound and: 2. compute upper energy bounds on conformations to refine the pfunc lower bound This implementation will always do operation 1 first, then operation 2 to get off the initial "flat spot" the pfunc surface. After that, this implementation is an attempt at a gradient-descent type partition function calculator. At each step, the operation that maximizes the drop in delta (according to slope sampling heuristics) is chosen. This implementation should also perform much better whe operation 2 is not orders of magnitude slower than operation 1 (when e.g. we're reading energies out of a cache).

Nested Class Summary

Nested classes/interfaces inherited from interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction

EWAKStarPartitionFunction.ConfListener, EWAKStarPartitionFunction.Result, EWAKStarPartitionFunction.Status, EWAKStarPartitionFunction.Values, EWAKStarPartitionFunction.WithConfTable, EWAKStarPartitionFunction.WithExternalMemory

Nested classes/interfaces inherited from interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.WithConfTable

EWAKStarPartitionFunction.WithConfTable.UnsupportedException

Nested classes/interfaces inherited from interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction.WithExternalMemory

EWAKStarPartitionFunction.WithExternalMemory.UnsupportedException

Field Summary

Fields

Modifier and Type	Field	Description
final ConfEnergyCalculator	ecalc

Fields inherited from interface edu.duke.cs.osprey.ewakstar.EWAKStarPartitionFunction

decimalPrecision

Constructor Summary

Constructors

Constructor	Description
EWAKStarGradientDescentPfunc(ConfEnergyCalculator ecalc)

Method Summary

Modifier and Type	Method	Description
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.
void	setConfListener(EWAKStarPartitionFunction.ConfListener val)
void	setConfTable(ConfDB.ConfTable val)
void	setReportProgress(boolean val)
void	setStabilityThreshold(BigDecimal val)	Sets the stability threshold for this PartitionFunction, if supported
void	setUseExternalMemory(boolean val, RCs rcs)
void	traceTo(PfuncSurface val)

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.ewakstar.EWAKStarPartitionFunction

compute, makeResult

Field Details

ecalc

public final ConfEnergyCalculator ecalc

Constructor Details

EWAKStarGradientDescentPfunc

public EWAKStarGradientDescentPfunc(ConfEnergyCalculator ecalc)

Method Details

setReportProgress

public void setReportProgress(boolean val)

Specified by:

setReportProgress in interface EWAKStarPartitionFunction

setConfListener

public void setConfListener(EWAKStarPartitionFunction.ConfListener val)

Specified by:

setConfListener in interface EWAKStarPartitionFunction

getStatus

public EWAKStarPartitionFunction.Status getStatus()

Specified by:

getStatus in interface EWAKStarPartitionFunction

getEpMols

public ArrayList<EnergyCalculator.EnergiedParametricMolecule> getEpMols()

Specified by:

getEpMols in interface EWAKStarPartitionFunction

getSConfs

public HashMap<Double,ConfSearch.ScoredConf> getSConfs()

Specified by:

getSConfs in interface EWAKStarPartitionFunction

getValues

public EWAKStarPartitionFunction.Values getValues()

Specified by:

getValues in interface EWAKStarPartitionFunction

getNumConfsEvaluated

public int getNumConfsEvaluated()

Specified by:

getNumConfsEvaluated in interface EWAKStarPartitionFunction

getParallelism

public int getParallelism()

Specified by:

getParallelism in interface EWAKStarPartitionFunction

setConfTable

public void setConfTable(ConfDB.ConfTable val)

Specified by:

setConfTable in interface EWAKStarPartitionFunction.WithConfTable

setUseExternalMemory

public void setUseExternalMemory(boolean val,
 RCs rcs)

Specified by:

setUseExternalMemory in interface EWAKStarPartitionFunction.WithExternalMemory

traceTo

public void traceTo(PfuncSurface val)

init

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

Description copied from interface: EWAKStarPartitionFunction

Initializes the partition function for calculation.

Specified by:

init in interface EWAKStarPartitionFunction

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)

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

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

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

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

printPDBs - Boolean value for printing PDB files

setStabilityThreshold

public void setStabilityThreshold(BigDecimal val)

Description copied from interface: EWAKStarPartitionFunction

Sets the stability threshold for this PartitionFunction, if supported

Specified by:

setStabilityThreshold in interface EWAKStarPartitionFunction

Parameters:

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

compute

public void compute(int maxNumConfs)

Specified by:

compute in interface EWAKStarPartitionFunction