Package ffx.algorithms.commands
Class Cluster
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.algorithms.commands.Cluster
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>
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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
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Constructor Summary
ConstructorsConstructorDescriptionCluster()
Cluster constructor.Cluster
(FFXBinding binding) Cluster constructor.Cluster constructor that sets the command line arguments. -
Method Summary
Modifier and TypeMethodDescriptionList
<org.apache.commons.math3.ml.clustering.CentroidCluster<Clustering.Conformation>> Return the Clusters.Returns a List of all Potential objects associated with this script.run()
Execute the script.Methods inherited from class ffx.algorithms.cli.AlgorithmsCommand
destroyPotentials, getActiveAssemblies, getActiveAssembly, init, saveDirFile, setActiveAssembly, setBaseDir, updateTitle
Methods inherited from class ffx.utilities.FFXCommand
getCommand, helpString, listCommands, setBinding
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Constructor Details
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Cluster
public Cluster()Cluster constructor. -
Cluster
Cluster constructor.- Parameters:
binding
- The Binding to use.
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Cluster
Cluster constructor that sets the command line arguments.- Parameters:
args
- Command line arguments.
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Method Details
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getClusterList
public List<org.apache.commons.math3.ml.clustering.CentroidCluster<Clustering.Conformation>> getClusterList()Return the Clusters.- Returns:
- Returns the generated clusters.
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run
Execute the script.- Overrides:
run
in classFFXCommand
- Returns:
- The current FFXCommand.
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getPotentials
Returns a List of all Potential objects associated with this script.- Overrides:
getPotentials
in classAlgorithmsCommand
- Returns:
- All Potentials. Sometimes empty, never null.
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