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>

  • 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.