Package ffx.algorithms.commands

Class BAR

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.BAR

public class BAR
extends AlgorithmsCommand

The BAR script finds the free energy difference across a lambda window. It presently assumes that the number of files composing the first end of the window equals the number of files composing the other end.
Usage:
ffxc BAR [options] <structures1> <structures2>

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
BAR()	BAR Constructor.
BAR(FFXBinding binding)	BAR Constructor.
BAR(String[] args)	BAR 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.
FreeEnergyDifferenceReporter	getReporter()	Obtain the Free Energy Difference reporter for this class.
BAR	run()	Execute this Command.
void	setProperties(org.apache.commons.configuration2.Configuration additionalProps)	Sets an optional Configuration with additional properties.

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

BAR

public BAR()

BAR Constructor.

BAR

public BAR(FFXBinding binding)

BAR Constructor.

Parameters:

binding - The Binding to use.

BAR

public BAR(String[] args)

BAR constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

setProperties

public void setProperties(org.apache.commons.configuration2.Configuration additionalProps)

Sets an optional Configuration with additional properties.

Parameters:

additionalProps - Additional properties configuration.

run

public BAR run()

Execute this Command.

Overrides:

run in class FFXCommand

Returns:

The current FFXCommand.

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.

getReporter

public FreeEnergyDifferenceReporter getReporter()

Obtain the Free Energy Difference reporter for this class.

Returns:

The Free Energy Difference reporter.