Package ffx.xray.commands

Class Dynamics

java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.xray.commands.Dynamics
All Implemented Interfaces:
AlgorithmListener
public class Dynamics extends AlgorithmsCommand implements AlgorithmListener
The X-ray Dynamics script.
Usage:
ffxc xray.Dynamics [options] <filename>

  • Constructor Details

    • Dynamics

      public Dynamics()
      Dynamics constructor.

    • Dynamics

      public Dynamics(String[] args)
      Dynamics constructor that sets the command line arguments.
      Parameters:
      args - Command line arguments.

    • Dynamics

      public Dynamics(FFXBinding binding)
      Dynamics constructor.
      Parameters:
      binding - The Binding to use.

  • Method Details

    • run

      public Dynamics run()
      Description copied from class: FFXCommand
      Execute this Command.
      Overrides:
      run in class FFXCommand
      Returns:
      The current FFXCommand.

    • getPotentials

      public List<Potential> getPotentials()
      Description copied from class: AlgorithmsCommand
      Returns a List of all Potential objects associated with this script.
      Overrides:
      getPotentials in class AlgorithmsCommand
      Returns:
      All Potentials. Sometimes empty, never null.

    • destroyPotentials

      public boolean destroyPotentials()
      Description copied from class: AlgorithmsCommand
      Reclaims resources associated with all Potential objects associated with this script.
      Overrides:
      destroyPotentials in class AlgorithmsCommand
      Returns:
      If all Potentials had resources reclaimed.

    • algorithmUpdate

      public boolean algorithmUpdate(MolecularAssembly active)
      Description copied from interface: AlgorithmListener
      After a successful step or interval of an algorithm, this method of the listener will be called.
      Specified by:
      algorithmUpdate in interface AlgorithmListener
      Parameters:
      active - The system the algorithm is operating on.
      Returns:
      A return of true indicates the algorithm continues.