Package ffx.algorithms.commands

Class MBAR

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.MBAR

public class MBAR
extends AlgorithmsCommand

Perform MBAR calculation or necessary energy evaluations. See PhEnergy for CpHMD energy evaluations.
Usage:
ffxc test.MBAR [options] <path>

Field Summary

Fields

Modifier and Type	Field	Description
MultistateBennettAcceptanceRatio	mbar

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
MBAR()	MBAR Constructor.
MBAR(FFXBinding binding)	MBAR Constructor.
MBAR(String[] args)	MBAR 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.
MBAR	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

mbar

public MultistateBennettAcceptanceRatio mbar

Constructor Details

MBAR

public MBAR()

MBAR Constructor.

MBAR

public MBAR(FFXBinding binding)

MBAR Constructor.

Parameters:

binding - The Groovy Binding to use.

MBAR

public MBAR(String[] args)

MBAR constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

run

public MBAR 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.