Package ffx.algorithms.commands

Class AnalyzeNEQ

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.AnalyzeNEQ

public class AnalyzeNEQ
extends AlgorithmsCommand

Performs analysis of Non-equilibrium work simulations. Takes directory paths to the forward and reverse work logs and uses them to create BAR files and calculate the BAR free energy difference.
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
AnalyzeNEQ()	AnalyzeNEQ Constructor.
AnalyzeNEQ(FFXBinding binding)	AnalyzeNEQ Constructor.
AnalyzeNEQ(String[] args)	AnalyzeNEQ 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.
AnalyzeNEQ	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

AnalyzeNEQ

public AnalyzeNEQ()

AnalyzeNEQ Constructor.

AnalyzeNEQ

public AnalyzeNEQ(FFXBinding binding)

AnalyzeNEQ Constructor.

Parameters:

binding - The Binding to use.

AnalyzeNEQ

public AnalyzeNEQ(String[] args)

AnalyzeNEQ constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

run

public AnalyzeNEQ 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.