Package edu.duke.cs.osprey.sofea
Class SequenceLMFE
java.lang.Object
edu.duke.cs.osprey.sofea.SequenceLMFE
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Sofea.Criterion
Finished SOFEA computation when the state free energies for a single sequence
reach a desired precision.
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Nested Class Summary
Nested classes/interfaces inherited from interface edu.duke.cs.osprey.sofea.Sofea.Criterion
Sofea.Criterion.Filter, Sofea.Criterion.Satisfied -
Field Summary
FieldsModifier and TypeFieldDescriptionfinal MultiStateConfSpace.LMFEThe multi-state objective function.final doubleThe best desired precision for a state free energy.final SequenceThe sequence. -
Constructor Summary
ConstructorsConstructorDescriptionSequenceLMFE(Sequence seq, MultiStateConfSpace.LMFE lmfe, double minFreeEnergyWidth) -
Method Summary
Modifier and TypeMethodDescriptionfilterNode(MultiStateConfSpace.State state, int[] conf, BoltzmannCalculator bcalc) getGBounds(SeqDB seqdb, MultiStateConfSpace.State state) getGBounds(SeqDB seqdb, MultiStateConfSpace.State state, MathContext mathContext) getZBounds(SeqDB seqdb, MultiStateConfSpace.State state) isSatisfied(SeqDB seqdb, FringeDB fringedbLower, FringeDB fringedbUpper, long pass1Step, long pass2Step, BoltzmannCalculator bcalc)
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Field Details
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seq
The sequence. -
lmfe
The multi-state objective function. -
minFreeEnergyWidth
public final double minFreeEnergyWidthThe best desired precision for a state free energy.
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Constructor Details
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SequenceLMFE
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Method Details
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filterNode
public Sofea.Criterion.Filter filterNode(MultiStateConfSpace.State state, int[] conf, BoltzmannCalculator bcalc) - Specified by:
filterNodein interfaceSofea.Criterion
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isSatisfied
public Sofea.Criterion.Satisfied isSatisfied(SeqDB seqdb, FringeDB fringedbLower, FringeDB fringedbUpper, long pass1Step, long pass2Step, BoltzmannCalculator bcalc) - Specified by:
isSatisfiedin interfaceSofea.Criterion
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getZBounds
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getGBounds
public MathTools.DoubleBounds getGBounds(SeqDB seqdb, MultiStateConfSpace.State state, MathContext mathContext) -
getGBounds
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