Package ffx.potential.commands.test

Class ReorderAtoms

java.lang.Object

ffx.utilities.FFXCommand

ffx.potential.cli.PotentialCommand

ffx.potential.commands.test.ReorderAtoms

public class ReorderAtoms
extends PotentialCommand

The ReorderAtoms script sorts the atoms within an XYZ file based on atomic weight. Usage: ffxc test.ReorderAtoms <filename>

Field Summary

Fields inherited from class ffx.potential.cli.PotentialCommand

activeAssembly, baseDir, potentialFunctions

Fields inherited from class ffx.utilities.FFXCommand

args, binding, color, help, logger, parseResult, version

Constructor Summary

Constructors

Constructor	Description
ReorderAtoms()	Constructor.
ReorderAtoms(FFXBinding binding)	Constructor using Binding.
ReorderAtoms(String[] args)	Constructor using args.

Method Summary

Modifier and Type	Method	Description
ReorderAtoms	run()	Execute this Command.

Methods inherited from class ffx.potential.cli.PotentialCommand

createOutputFile, destroyPotentials, getActiveAssemblies, getActiveAssembly, getActiveAssembly, getBaseDirString, getPotentials, getPotentialsFromAssemblies, init, parseFilePath, saveByExtension, saveByExtension, saveByOriginalExtension, saveByOriginalExtension, setActiveAssembly

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

ReorderAtoms

public ReorderAtoms()

Constructor.

ReorderAtoms

public ReorderAtoms(FFXBinding binding)

Constructor using Binding.

ReorderAtoms

public ReorderAtoms(String[] args)

Constructor using args.

Method Details

run

public ReorderAtoms run()

Description copied from class: FFXCommand

Execute this Command.

Overrides:

run in class FFXCommand

Returns:

The current FFXCommand.