Package ffx.xray.commands

Class GenZ

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.xray.commands.GenZ

public class GenZ
extends AlgorithmsCommand

The GenZ script for calculating free energy changes.
Usage:
ffxc xray.GenZ [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
GenZ()	GenZ Constructor.
GenZ(FFXBinding binding)	GenZ Constructor.
GenZ(String[] args)	GenZ 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.
GenZ	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

GenZ

public GenZ()

GenZ Constructor.

GenZ

public GenZ(String[] args)

GenZ constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

GenZ

public GenZ(FFXBinding binding)

GenZ Constructor.

Parameters:

binding - The Binding to use.

Method Details

run

public GenZ run()

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.