Package ffx.xray.commands
Class GenZ
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.xray.commands.GenZ
The GenZ script for calculating free energy changes.
Usage:
ffxc xray.GenZ [options] <filename>
Usage:
ffxc xray.GenZ [options] <filename>
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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
ConstructorsConstructorDescriptionGenZ()
GenZ Constructor.GenZ
(FFXBinding binding) GenZ Constructor.GenZ 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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GenZ
public GenZ()GenZ Constructor. -
GenZ
GenZ constructor that sets the command line arguments.- Parameters:
args
- Command line arguments.
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GenZ
GenZ Constructor.- Parameters:
binding
- The Binding to use.
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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
Description copied from class:AlgorithmsCommand
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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