Package ffx.algorithms.optimize.manybody

Class DistanceRegion

java.lang.Object

edu.rit.pj.ParallelConstruct

edu.rit.pj.ParallelRegion

ffx.algorithms.optimize.manybody.DistanceRegion

public class DistanceRegion
extends ParallelRegion

Compute the minimum distance between each pair of residues for all rotamer permutations.

Field Summary

Fields

Modifier and Type	Field	Description
protected AlgorithmListener	algorithmListener	AlgorithmListener who should receive updates as the optimization runs.

Constructor Summary

Constructors

Constructor	Description
DistanceRegion(int nt, int nResidues, Crystal crystal, int[][][] lists, IntegerSchedule schedule)

Method Summary

Modifier and Type	Method	Description
void	init(DistanceMatrix dM, MolecularAssembly molecularAssembly, Residue[] allResiduesArray, AlgorithmListener algorithmListener, DistanceMatrix.NeighborDistances[][] distanceMatrix)
void	run()	Execute parallel code.

Methods inherited from class edu.rit.pj.ParallelRegion

barrier, barrier, critical, critical, criticalNonexclusive, criticalNonexclusive, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, execute, finish, start

Methods inherited from class edu.rit.pj.ParallelConstruct

getThreadCount, getThreadIndex, isExecutingInParallel, region, team

Methods inherited from class java.lang.Object

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

Field Details

algorithmListener

protected AlgorithmListener algorithmListener

AlgorithmListener who should receive updates as the optimization runs.

Constructor Details

DistanceRegion

public DistanceRegion(int nt,
 int nResidues,
 Crystal crystal,
 int[][][] lists,
 IntegerSchedule schedule)

Method Details

init

public void init(DistanceMatrix dM,
 MolecularAssembly molecularAssembly,
 Residue[] allResiduesArray,
 AlgorithmListener algorithmListener,
 DistanceMatrix.NeighborDistances[][] distanceMatrix)

run

public void run()

Description copied from class: ParallelRegion

Execute parallel code. All threads of the parallel team call the run() method concurrently.

The run() method must be implemented in a subclass.

Specified by:

run in class ParallelRegion