Package ffx.algorithms.commands

Class SuperposeCrystals

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.SuperposeCrystals

public class SuperposeCrystals
extends AlgorithmsCommand

Field Summary

Fields

Modifier and Type	Field	Description
RunningStatistics	runningStatistics
final StringBuilder	symOpsA
final StringBuilder	symOpsB

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
SuperposeCrystals()
SuperposeCrystals(FFXBinding binding)
SuperposeCrystals(String[] args)

Method Summary

Modifier and Type	Method	Description
List<Potential>	getPotentials()	Returns a List of all Potential objects associated with this script.
SuperposeCrystals	run()	Execute this Command.

Methods inherited from class ffx.algorithms.cli.AlgorithmsCommand

destroyPotentials, 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

Field Details

runningStatistics

public RunningStatistics runningStatistics

symOpsA

public final StringBuilder symOpsA

symOpsB

public final StringBuilder symOpsB

Constructor Details

SuperposeCrystals

public SuperposeCrystals()

SuperposeCrystals

public SuperposeCrystals(FFXBinding binding)

SuperposeCrystals

public SuperposeCrystals(String[] args)

Method Details

run

public SuperposeCrystals run()

Description copied from class: FFXCommand

Execute this Command.

Overrides:

run in class FFXCommand

Returns:

The current FFXCommand.

getPotentials

public List<Potential> getPotentials()

Description copied from class: AlgorithmsCommand

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

Overrides:

getPotentials in class AlgorithmsCommand

Returns:

All Potentials. Sometimes empty, never null.