Package ffx.algorithms.commands

Class GenZ

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.GenZ

public class GenZ
extends AlgorithmsCommand

The ReductionPartition script performs a discrete optimization using a many-body expansion and elimination expressions.
Usage:
ffxc ManyBody [options] <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
GenZ()	ManyBody Constructor.
GenZ(FFXBinding binding)	ManyBody Constructor.
GenZ(String[] args)	GenZ constructor that sets the command line arguments.

Method Summary

Modifier and Type	Method	Description
double[][]	getPopulationArray()	The population for each rotamer of each residue.
ForceFieldEnergy	getPotential()	Returns the potential energy of the active assembly.
GenZ	run()	Execute this Command.

Methods inherited from class ffx.algorithms.cli.AlgorithmsCommand

destroyPotentials, getActiveAssemblies, getActiveAssembly, getPotentials, 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

GenZ

public GenZ()

ManyBody Constructor.

GenZ

public GenZ(FFXBinding binding)

ManyBody Constructor.

Parameters:

binding - The Binding to use.

GenZ

public GenZ(String[] args)

GenZ constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

run

public GenZ run()

Execute this Command.

Overrides:

run in class FFXCommand

Returns:

The current FFXCommand.

getPopulationArray

public double[][] getPopulationArray()

The population for each rotamer of each residue.

Returns:

The population array.

getPotential

public ForceFieldEnergy getPotential()

Returns the potential energy of the active assembly. Used during testing assertions.

Returns:

potentialEnergy Potential energy of the active assembly.