Package ffx.algorithms.commands
Class MutatePDB
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.algorithms.commands.MutatePDB
The MutatePDB script mutates residue(s) of a PDB file.
Usage:
ffxc MutatePDB [options] <pdb>
Usage:
ffxc MutatePDB [options] <pdb>
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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
ConstructorsConstructorDescriptionMutatePDB Constructor.MutatePDB
(FFXBinding binding) MutatePDB Constructor.MutatePDB 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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MutatePDB
public MutatePDB()MutatePDB Constructor. -
MutatePDB
MutatePDB Constructor.- Parameters:
binding
- The Binding to use.
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MutatePDB
MutatePDB 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
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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