Class Cluster

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.Cluster

public class Cluster
extends AlgorithmsCommand

The Cluster script clusters structures utilizing RMSD.

The Iterative Hierarchical Clustering method was contributed by Yuya Kinoshita, Koki Nishimura and Masatoshi Karashima from Takeda Pharmaceuticals.

Author:

Aaron J. Nessler, Mallory R. Tollefson, Michael J. Schnieders
Usage:
ffxc Cluster [options] <filename>

Field Summary

Fields inherited from class AlgorithmsCommand

activeAssembly, algorithmFunctions, algorithmListener, baseDir

Fields inherited from class FFXCommand

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

Constructor Summary

Constructors

Constructor	Description
Cluster()	Cluster constructor.
Cluster(FFXBinding binding)	Cluster constructor.
Cluster(String[] args)	Cluster constructor that sets the command line arguments.

Method Summary

Modifier and Type	Method	Description
List<org.apache.commons.math3.ml.clustering.CentroidCluster<Clustering.Conformation>>	getClusterList()	Return the Clusters.
List<Potential>	getPotentials()	Returns a List of all Potential objects associated with this script.
Cluster	run()	Execute the script.

Methods inherited from class AlgorithmsCommand

destroyPotentials, getActiveAssemblies, getActiveAssembly, getPotentialsFromAssemblies, init, saveDirFile, setBaseDir, updateTitle

Methods inherited from class FFXCommand

getCommand, helpString, listCommands, setBinding

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

Cluster

public Cluster()

Cluster constructor.

Cluster

public Cluster(FFXBinding binding)

Cluster constructor.

Parameters:

binding - The Binding to use.

Cluster

public Cluster(String[] args)

Cluster constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

getClusterList

public List<org.apache.commons.math3.ml.clustering.CentroidCluster<Clustering.Conformation>> getClusterList()

Return the Clusters.

Returns:

Returns the generated clusters.

run

public Cluster 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.