Package ffx.xray.commands

Class Deuterate

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.xray.commands.Deuterate

public class Deuterate
extends AlgorithmsCommand

Deuterate changes exchangeable hydrogen atoms to deuterium atoms for a PDB file.
Usage:
ffxc xray.Deuterate <pdbfile1>

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
Deuterate()	Deuterate constructor.
Deuterate(FFXBinding binding)	Deuterate constructor.
Deuterate(String[] args)	Deuterate 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.
Deuterate	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

Deuterate

public Deuterate()

Deuterate constructor.

Deuterate

public Deuterate(String[] args)

Deuterate constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Deuterate

public Deuterate(FFXBinding binding)

Deuterate constructor.

Parameters:

binding - The Binding to use.

Method Details

run

public Deuterate 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.