Package edu.duke.cs.osprey.kstar

Class BBKStar

java.lang.Object

edu.duke.cs.osprey.kstar.BBKStar

public class BBKStar
extends Object

Implementation of the BBK* algorithm to predict protein sequence mutations that improve binding affinity by computing provably accurate Boltzmann-weighted ensembles .

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static interface	BBKStar.ConfSearchFactory
class	BBKStar.ConfSpaceInfo
class	BBKStar.MultiSequenceNode
static enum	BBKStar.PfuncsStatus
static class	BBKStar.Settings
class	BBKStar.SingleSequenceNode

Field Summary

Fields

Modifier and Type	Field	Description
final BBKStar.Settings	bbkstarSettings	Optional and overridable settings for BBK*
final BBKStar.ConfSpaceInfo	complex	A configuration space containing both the protein and ligand strands
final KStar.Settings	kstarSettings	Optional and overridable settings for BBK*, shared with K*
final BBKStar.ConfSpaceInfo	ligand	A configuration space containing just the ligand strand
final BBKStar.ConfSpaceInfo	protein	A configuration space containing just the protein strand

Constructor Summary

Constructors

Constructor	Description
BBKStar(ConfSpaceIteration protein, ConfSpaceIteration ligand, ConfSpaceIteration complex, KStar.Settings kstarSettings, BBKStar.Settings bbkstarSettings)

Method Summary

Modifier and Type	Method	Description
Iterable<BBKStar.ConfSpaceInfo>	confSpaceInfos()
BBKStar.ConfSpaceInfo	getConfSpaceInfo(SimpleConfSpace confSpace)
List<KStar.ScoredSequence>	run()
List<KStar.ScoredSequence>	run(TaskExecutor tasks)

Methods inherited from class java.lang.Object

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

Field Details

protein

public final BBKStar.ConfSpaceInfo protein

A configuration space containing just the protein strand

ligand

public final BBKStar.ConfSpaceInfo ligand

A configuration space containing just the ligand strand

complex

public final BBKStar.ConfSpaceInfo complex

A configuration space containing both the protein and ligand strands

kstarSettings

public final KStar.Settings kstarSettings

Optional and overridable settings for BBK*, shared with K*

bbkstarSettings

public final BBKStar.Settings bbkstarSettings

Optional and overridable settings for BBK*

Constructor Details

BBKStar

public BBKStar(ConfSpaceIteration protein,
 ConfSpaceIteration ligand,
 ConfSpaceIteration complex,
 KStar.Settings kstarSettings,
 BBKStar.Settings bbkstarSettings)

Method Details

confSpaceInfos

public Iterable<BBKStar.ConfSpaceInfo> confSpaceInfos()

getConfSpaceInfo

public BBKStar.ConfSpaceInfo getConfSpaceInfo(SimpleConfSpace confSpace)

run

public List<KStar.ScoredSequence> run()

run

public List<KStar.ScoredSequence> run(TaskExecutor tasks)