Class 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>
  • 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.