Package ffx.potential.commands

Class MoveIntoUnitCell

java.lang.Object

ffx.utilities.FFXCommand

ffx.potential.cli.PotentialCommand

ffx.potential.commands.MoveIntoUnitCell

public class MoveIntoUnitCell
extends PotentialCommand

Move the center of mass of each molecule into the unit cell. Usage: ffxc MoveIntoUnitCell <filename>

Field Summary

Fields

Modifier and Type	Field	Description
protected MolecularAssembly[]	molecularAssemblies	Save a reference to the MolecularAssembly instances to destroy their potentials.
double[][]	origCoordinates	Original Cartesian coordinates before moving into the unit cell.
double[][]	unitCellCoordinates	Cartesian coordinates after moving into the unit cell.

Fields inherited from class ffx.potential.cli.PotentialCommand

activeAssembly, baseDir, potentialFunctions

Fields inherited from class ffx.utilities.FFXCommand

args, binding, color, help, logger, parseResult, version

Constructor Summary

Constructors

Constructor	Description
MoveIntoUnitCell()
MoveIntoUnitCell(FFXBinding binding)
MoveIntoUnitCell(String[] args)

Method Summary

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

Methods inherited from class ffx.potential.cli.PotentialCommand

createOutputFile, destroyPotentials, getActiveAssemblies, getActiveAssembly, getActiveAssembly, getBaseDirString, getPotentialsFromAssemblies, init, parseFilePath, saveByExtension, saveByExtension, saveByOriginalExtension, saveByOriginalExtension, setActiveAssembly

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

Field Details

molecularAssemblies

protected MolecularAssembly[] molecularAssemblies

Save a reference to the MolecularAssembly instances to destroy their potentials.

origCoordinates

public double[][] origCoordinates

Original Cartesian coordinates before moving into the unit cell.

unitCellCoordinates

public double[][] unitCellCoordinates

Cartesian coordinates after moving into the unit cell.

Constructor Details

MoveIntoUnitCell

public MoveIntoUnitCell()

MoveIntoUnitCell

public MoveIntoUnitCell(FFXBinding binding)

MoveIntoUnitCell

public MoveIntoUnitCell(String[] args)

Method Details

run

public MoveIntoUnitCell 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: PotentialCommand

Returns a List of all Potential objects associated with this command. Should be written to tolerate nulls, as many tests run help() and exit without instantiating their Potentials.

Overrides:

getPotentials in class PotentialCommand

Returns:

All Potentials. Sometimes empty, never null.