Package ffx.algorithms.commands
Class AnalyzeNEQ
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.algorithms.commands.AnalyzeNEQ
Performs analysis of Non-equilibrium work simulations. Takes directory paths to the forward and reverse work logs and
uses them to create BAR files and calculate the BAR free energy difference.
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
ConstructorsConstructorDescriptionAnalyzeNEQ Constructor.AnalyzeNEQ
(FFXBinding binding) AnalyzeNEQ Constructor.AnalyzeNEQ
(String[] args) AnalyzeNEQ constructor that sets the command line arguments. -
Method Summary
Modifier and TypeMethodDescriptionReturns a List of all Potential objects associated with this script.run()
Execute this Command.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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AnalyzeNEQ
public AnalyzeNEQ()AnalyzeNEQ Constructor. -
AnalyzeNEQ
AnalyzeNEQ Constructor.- Parameters:
binding
- The Binding to use.
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AnalyzeNEQ
AnalyzeNEQ constructor that sets the command line arguments.- Parameters:
args
- Command line arguments.
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Method Details
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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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