Package ffx.algorithms.commands
Class MBAR
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.algorithms.commands.MBAR
Perform MBAR calculation or necessary energy evaluations. See PhEnergy for CpHMD energy evaluations.
Usage:
ffxc test.MBAR [options] <path>
Usage:
ffxc test.MBAR [options] <path>
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Field Summary
FieldsFields 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
ConstructorsConstructorDescriptionMBAR()
MBAR Constructor.MBAR
(FFXBinding binding) MBAR Constructor.MBAR 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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Field Details
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mbar
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Constructor Details
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MBAR
public MBAR()MBAR Constructor. -
MBAR
MBAR Constructor.- Parameters:
binding
- The Groovy Binding to use.
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MBAR
MBAR 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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