Package ffx.algorithms.commands
Class BAR
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.algorithms.commands.BAR
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>
Usage:
ffxc BAR [options] <structures1> <structures2>
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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
ConstructorsConstructorDescriptionBAR()
BAR Constructor.BAR
(FFXBinding binding) BAR Constructor.BAR constructor that sets the command line arguments. -
Method Summary
Modifier and TypeMethodDescriptionReturns a List of all Potential objects associated with this script.Obtain the Free Energy Difference reporter for this class.run()
Execute this Command.void
setProperties
(org.apache.commons.configuration2.Configuration additionalProps) Sets an optional Configuration with additional properties.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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BAR
public BAR()BAR Constructor. -
BAR
BAR Constructor.- Parameters:
binding
- The Binding to use.
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BAR
BAR constructor that sets the command line arguments.- Parameters:
args
- Command line arguments.
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Method Details
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setProperties
public void setProperties(org.apache.commons.configuration2.Configuration additionalProps) Sets an optional Configuration with additional properties.- Parameters:
additionalProps
- Additional properties configuration.
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run
Execute this Command.- 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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getReporter
Obtain the Free Energy Difference reporter for this class.- Returns:
- The Free Energy Difference reporter.
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