Package ffx.xray.commands

Class EditPDB

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.xray.commands.EditPDB

public class EditPDB
extends AlgorithmsCommand

EditPDB edits a PDB model for use in experimental refinement.
Usage:
ffxc xray.EditPDB <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
EditPDB()	Deuterate constructor.
EditPDB(FFXBinding binding)	Deuterate constructor.
EditPDB(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.
EditPDB	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

EditPDB

public EditPDB()

Deuterate constructor.

EditPDB

public EditPDB(String[] args)

Deuterate constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

EditPDB

public EditPDB(FFXBinding binding)

Deuterate constructor.

Parameters:

binding - The Binding to use.

Method Details

run

public EditPDB 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.