Package ffx.algorithms.commands

Class MutatePDB

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.MutatePDB

public class MutatePDB
extends AlgorithmsCommand

The MutatePDB script mutates residue(s) of a PDB file.
Usage:
ffxc MutatePDB [options] <pdb>

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
MutatePDB()	MutatePDB Constructor.
MutatePDB(FFXBinding binding)	MutatePDB Constructor.
MutatePDB(String[] args)	MutatePDB 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.
MutatePDB	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

MutatePDB

public MutatePDB()

MutatePDB Constructor.

MutatePDB

public MutatePDB(FFXBinding binding)

MutatePDB Constructor.

Parameters:

binding - The Binding to use.

MutatePDB

public MutatePDB(String[] args)

MutatePDB constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

run

public MutatePDB run()

Execute the script.

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.