Package ffx.algorithms.commands

Class Superpose

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.Superpose

public class Superpose
extends AlgorithmsCommand

The Superpose script superposes molecules in an arc/multiple model pdb file (all versus all or one versus all) or in two pdb/xyz files. TODO: Create a Superpose Unit Test.
Usage:
ffxc Superpose [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
Superpose()	Superpose Constructor.
Superpose(FFXBinding binding)	Superpose Constructor.
Superpose(String[] args)	Superpose 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.
Superpose	run()	Execute the script.

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

Superpose

public Superpose()

Superpose Constructor.

Superpose

public Superpose(FFXBinding binding)

Superpose Constructor.

Parameters:

binding - Groovy to use.

Superpose

public Superpose(String[] args)

Superpose constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

run

public Superpose run()

Execute the script.

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.