Class BAR


public class BAR extends AlgorithmsCommand
The BAR script finds the free energy difference across a lambda window. It presently assumes that the number of files composing the first end of the window equals the number of files composing the other end.
Usage:
ffxc BAR [options] <structures1> <structures2>
  • Constructor Details

    • BAR

      public BAR()
      BAR Constructor.
    • BAR

      public BAR(FFXBinding binding)
      BAR Constructor.
      Parameters:
      binding - The Binding to use.
    • BAR

      public BAR(String[] args)
      BAR constructor that sets the command line arguments.
      Parameters:
      args - Command line arguments.
  • Method Details

    • setProperties

      public void setProperties(org.apache.commons.configuration2.Configuration additionalProps)
      Sets an optional Configuration with additional properties.
      Parameters:
      additionalProps - Additional properties configuration.
    • run

      public BAR run()
      Execute this Command.
      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.
    • getReporter

      public FreeEnergyDifferenceReporter getReporter()
      Obtain the Free Energy Difference reporter for this class.
      Returns:
      The Free Energy Difference reporter.