Package edu.duke.cs.osprey.sofea

Class SequenceLMFE

java.lang.Object

edu.duke.cs.osprey.sofea.SequenceLMFE

All Implemented Interfaces:

Sofea.Criterion

public class SequenceLMFE
extends Object
implements Sofea.Criterion

Finished SOFEA computation when the state free energies for a single sequence reach a desired precision.

Nested Class Summary

Nested classes/interfaces inherited from interface edu.duke.cs.osprey.sofea.Sofea.Criterion

Sofea.Criterion.Filter, Sofea.Criterion.Satisfied

Field Summary

Fields

Modifier and Type	Field	Description
final MultiStateConfSpace.LMFE	lmfe	The multi-state objective function.
final double	minFreeEnergyWidth	The best desired precision for a state free energy.
final Sequence	seq	The sequence.

Constructor Summary

Constructors

Constructor	Description
SequenceLMFE(Sequence seq, MultiStateConfSpace.LMFE lmfe, double minFreeEnergyWidth)

Method Summary

Modifier and Type	Method	Description
Sofea.Criterion.Filter	filterNode(MultiStateConfSpace.State state, int[] conf, BoltzmannCalculator bcalc)
MathTools.DoubleBounds	getGBounds(SeqDB seqdb, MultiStateConfSpace.State state)
MathTools.DoubleBounds	getGBounds(SeqDB seqdb, MultiStateConfSpace.State state, MathContext mathContext)
MathTools.BigDecimalBounds	getZBounds(SeqDB seqdb, MultiStateConfSpace.State state)
Sofea.Criterion.Satisfied	isSatisfied(SeqDB seqdb, FringeDB fringedbLower, FringeDB fringedbUpper, long pass1Step, long pass2Step, BoltzmannCalculator bcalc)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

seq

public final Sequence seq

The sequence.

lmfe

public final MultiStateConfSpace.LMFE lmfe

The multi-state objective function.

minFreeEnergyWidth

public final double minFreeEnergyWidth

The best desired precision for a state free energy.

Constructor Details

SequenceLMFE

public SequenceLMFE(Sequence seq,
 MultiStateConfSpace.LMFE lmfe,
 double minFreeEnergyWidth)

Method Details

filterNode

public Sofea.Criterion.Filter filterNode(MultiStateConfSpace.State state,
 int[] conf,
 BoltzmannCalculator bcalc)

Specified by:

filterNode in interface Sofea.Criterion

isSatisfied

public Sofea.Criterion.Satisfied isSatisfied(SeqDB seqdb,
 FringeDB fringedbLower,
 FringeDB fringedbUpper,
 long pass1Step,
 long pass2Step,
 BoltzmannCalculator bcalc)

Specified by:

isSatisfied in interface Sofea.Criterion

getZBounds

public MathTools.BigDecimalBounds getZBounds(SeqDB seqdb,
 MultiStateConfSpace.State state)

getGBounds

public MathTools.DoubleBounds getGBounds(SeqDB seqdb,
 MultiStateConfSpace.State state,
 MathContext mathContext)

getGBounds

public MathTools.DoubleBounds getGBounds(SeqDB seqdb,
 MultiStateConfSpace.State state)