Package ffx.algorithms.commands

Class TorsionScan

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.TorsionScan

public class TorsionScan
extends AlgorithmsCommand

The TorsionSearch command enumerates conformations of a molecule using torsional scans around rotatable bonds.

Author:

Aaron J. Nessler, Matthew J. Speranza, Michael J. Schnieders
Usage:
ffxc TorsionSearch <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
TorsionScan()
TorsionScan(FFXBinding binding)
TorsionScan(String[] args)

Method Summary

Modifier and Type	Method	Description
List<Potential>	getPotentials()	Returns a List of all Potential objects associated with this script.
TorsionScan	run()	Execute this Command.

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

TorsionScan

public TorsionScan()

TorsionScan

public TorsionScan(FFXBinding binding)

TorsionScan

public TorsionScan(String[] args)

Method Details

run

public TorsionScan run()

Description copied from class: FFXCommand

Execute this Command.

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.