Package ffx.algorithms.commands

Class Anneal

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.Anneal

public class Anneal
extends AlgorithmsCommand

The Anneal script.
Usage:
ffxc Anneal [options] <filename>

Field Summary

Fields inherited from class ffx.algorithms.cli.AlgorithmsCommand

activeAssembly, algorithmFunctions, algorithmListener, baseDir

Fields inherited from class ffx.utilities.FFXCommand

args, binding, color, help, logger, parseResult, version

Constructor Summary

Constructors

Constructor	Description
Anneal()	Anneal Constructor.
Anneal(FFXBinding binding)	Anneal Constructor.
Anneal(String[] args)	Anneal constructor that sets the command line arguments.

Method Summary

Modifier and Type	Method	Description
boolean	destroyPotentials()	Reclaims resources associated with all Potential objects associated with this script.
SimulatedAnnealing	getAnnealing()	Get the SimulatedAnnealing object.
List<Potential>	getPotentials()	Returns a List of all Potential objects associated with this script.
Anneal	run()	Execute this Command.

Methods inherited from class ffx.algorithms.cli.AlgorithmsCommand

getActiveAssemblies, getActiveAssembly, getPotentialsFromAssemblies, init, saveDirFile, setBaseDir, updateTitle

Methods inherited from class ffx.utilities.FFXCommand

getCommand, helpString, listCommands, setBinding

Methods inherited from class java.lang.Object

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

Constructor Details

Anneal

public Anneal()

Anneal Constructor.

Anneal

public Anneal(FFXBinding binding)

Anneal Constructor.

Parameters:

binding - The Binding to use.

Anneal

public Anneal(String[] args)

Anneal constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

run

public Anneal run()

Execute this Command.

Overrides:

run in class FFXCommand

Returns:

The current FFXCommand.

getAnnealing

public SimulatedAnnealing getAnnealing()

Get the SimulatedAnnealing object.

Returns:

The SimulatedAnnealing instance.

getPotentials

public List<Potential> getPotentials()

Returns a List of all Potential objects associated with this script.

Overrides:

getPotentials in class AlgorithmsCommand

Returns:

All Potentials. Sometimes empty, never null.

destroyPotentials

public boolean destroyPotentials()

Reclaims resources associated with all Potential objects associated with this script.

Overrides:

destroyPotentials in class AlgorithmsCommand

Returns:

If all Potentials had resources reclaimed.