statalign.model.ext.plugins.structalign
Class RotationProposal

java.lang.Object
  statalign.model.ext.plugins.structalign.RotationProposal

public class RotationProposal
extends java.lang.Object

Field Summary

double

sd

Constructor Summary

RotationProposal(StructAlign s)

Method Summary

Transformation[]	calculateAllOptimal(int a, int b, int window)
double	libraryLogDensity(int index, Transformation candidate)
Transformation	propose(int index) propose from a library mixture distribution
Transformation[]	selectBest(Transformation[] library, double percent)

Methods inherited from class java.lang.Object

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

Field Detail

sd

public double sd

Constructor Detail

RotationProposal

public RotationProposal(StructAlign s)

Method Detail

calculateAllOptimal

public Transformation[] calculateAllOptimal(int a,
                                            int b,
                                            int window)

selectBest

public Transformation[] selectBest(Transformation[] library,
                                   double percent)

Parameters:

-

library - - a set of optimal Transformations between protein fragments

Returns:

- the @percent of optimal Transformations with the lowest RMSD

propose

public Transformation propose(int index)

propose from a library mixture distribution

libraryLogDensity

public double libraryLogDensity(int index,
                                Transformation candidate)

Parameters:

index - - index indicating the set of Transformations on which mixture components are centered

candidate - - a candidate Transformation whose density is to be evaluated

Returns:

the log density of @candidate according to the library mixture distribution