Package ffx.xray.commands.test

Class Alchemical

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.xray.commands.test.Alchemical

public class Alchemical
extends AlgorithmsCommand

The Alchemical Changes script.
Usage:
ffxc xray.Alchemical [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, parseResult, version

Constructor Summary

Constructors

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

Method Summary

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

Constructor Details

Alchemical

public Alchemical()

Alchemical constructor.

Alchemical

public Alchemical(String[] args)

Alchemical constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Alchemical

public Alchemical(FFXBinding binding)

Alchemical constructor.

Parameters:

binding - The Binding to use.

Method Details

run

public Alchemical 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.