Package ffx.algorithms.commands
Class Superpose
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.algorithms.commands.Superpose
The Superpose script superposes molecules in an arc/multiple model pdb file (all versus all or one versus all) or in two pdb/xyz files.
TODO: Create a Superpose Unit Test.
Usage:
ffxc Superpose [options] <filename>
Usage:
ffxc Superpose [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
ConstructorsConstructorDescriptionSuperpose Constructor.Superpose
(FFXBinding binding) Superpose Constructor.Superpose constructor that sets the command line arguments. -
Method Summary
Modifier and TypeMethodDescriptionReturns a List of all Potential objects associated with this script.run()
Execute the script.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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Superpose
public Superpose()Superpose Constructor. -
Superpose
Superpose Constructor.- Parameters:
binding
- Groovy to use.
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Superpose
Superpose constructor that sets the command line arguments.- Parameters:
args
- Command line arguments.
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Method Details
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run
Execute the script.- 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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