Package edu.duke.cs.osprey.confspace.compiled

Enum Class PosInterDist

java.lang.Object

java.lang.Enum<PosInterDist>

edu.duke.cs.osprey.confspace.compiled.PosInterDist

All Implemented Interfaces:

Serializable, Comparable<PosInterDist>, Constable

public enum PosInterDist
extends Enum<PosInterDist>

Defines how position interactions should be distributed among conformation fragments.

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Enum

Enum.EnumDesc<E extends Enum<E>>

Enum Constant Summary

Enum Constants

Enum Constant	Description
DesmetEtAl1992	Uses the traditional distribution introduced in the original DEE paper: Namely, pos-static and pos interactions are placed on "single" conf fragments.
TighterBounds	A newer distribution that yields tighter lower bounds on conformation energy.

Method Summary

Modifier and Type	Method	Description
static List<PosInter>	all(ConfSpace confSpace, int[] conf)
static List<PosInter>	all(ConfSpace confSpace, SimpleReferenceEnergies eref, int[] conf)	Include all interactions, except ones between unassigned positions.
static List<PosInter>	dynamic(ConfSpace confSpace, int[] conf)
static List<PosInter>	dynamic(ConfSpace confSpace, SimpleReferenceEnergies eref, int[] conf)	Include all dynamic interactions, except ones between unassigned positions.
abstract List<PosInter>	pair(ConfSpace confSpace, SimpleReferenceEnergies eref, int posi1, int confi1, int posi2, int confi2)
abstract List<PosInter>	single(ConfSpace confSpace, SimpleReferenceEnergies eref, int posi1, int confi1)
static List<PosInter>	staticStatic()	Include interactions between static regions (unaffected by motions and mutations) in the input molecules.
abstract List<PosInter>	tripleCorrection(ConfSpace confSpace, SimpleReferenceEnergies eref, int posi1, int confi1, int posi2, int confi2, int posi3, int confi3)	Interactions of a tuple of three positions, but weighted to prevent over-counting when all possible triples are used simultaneously.
static PosInterDist	valueOf(String name)	Returns the enum constant of this class with the specified name.
static PosInterDist[]	values()	Returns an array containing the constants of this enum class, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, describeConstable, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Details

DesmetEtAl1992

public static final PosInterDist DesmetEtAl1992

Uses the traditional distribution introduced in the original DEE paper: Namely, pos-static and pos interactions are placed on "single" conf fragments. And pos-pos interactions are placed on "pair" conf fragments.

TighterBounds

public static final PosInterDist TighterBounds

A newer distribution that yields tighter lower bounds on conformation energy. No interactions are placed on "single" conf fragments. Instead, the pos-static and pos interactions are distributed evenly among the "pair" conf fragments involving that position, without double-counting. This re-distribution allows minimizing "pair" conf fragments in the presence of the fixed atoms, which generally results in less optimistic lower bounds for "pair" energies.

Method Details

values

public static PosInterDist[] values()

Returns an array containing the constants of this enum class, in the order they are declared.

Returns:

an array containing the constants of this enum class, in the order they are declared

valueOf

public static PosInterDist valueOf(String name)

Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)

Parameters:

name - the name of the enum constant to be returned.

Returns:

the enum constant with the specified name

Throws:

IllegalArgumentException - if this enum class has no constant with the specified name

NullPointerException - if the argument is null

staticStatic

public static List<PosInter> staticStatic()

Include interactions between static regions (unaffected by motions and mutations) in the input molecules. Doesn't depend on the distribution.

all

public static List<PosInter> all(ConfSpace confSpace,
 SimpleReferenceEnergies eref,
 int[] conf)

Include all interactions, except ones between unassigned positions. Doesn't depend on the distribution.

all

public static List<PosInter> all(ConfSpace confSpace,
 int[] conf)

dynamic

public static List<PosInter> dynamic(ConfSpace confSpace,
 SimpleReferenceEnergies eref,
 int[] conf)

Include all dynamic interactions, except ones between unassigned positions. ie all except the static-static interactions. Doesn't depend on the distribution.

dynamic

public static List<PosInter> dynamic(ConfSpace confSpace,
 int[] conf)

single

public abstract List<PosInter> single(ConfSpace confSpace,
 SimpleReferenceEnergies eref,
 int posi1,
 int confi1)

pair

public abstract List<PosInter> pair(ConfSpace confSpace,
 SimpleReferenceEnergies eref,
 int posi1,
 int confi1,
 int posi2,
 int confi2)

tripleCorrection

public abstract List<PosInter> tripleCorrection(ConfSpace confSpace,
 SimpleReferenceEnergies eref,
 int posi1,
 int confi1,
 int posi2,
 int confi2,
 int posi3,
 int confi3)

Interactions of a tuple of three positions, but weighted to prevent over-counting when all possible triples are used simultaneously.