Package ffx.algorithms.commands.test
Class PhDynamics
java.lang.Object
ffx.utilities.FFXCommand
ffx.algorithms.cli.AlgorithmsCommand
ffx.algorithms.commands.test.PhDynamics
The PhDynamics command implements constant pH molecular dynamics.
Usage:
ffxc PhDynamics [options] <filename> [file2...]
Usage:
ffxc PhDynamics [options] <filename> [file2...]
-
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
-
Constructor Summary
ConstructorsConstructorDescriptionPhDynamics Constructor.PhDynamics
(FFXBinding binding) PhDynamics Constructor.PhDynamics
(String[] args) PhDynamics 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.static void
Sort archive files by pH with string parsingMethods 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
-
Field Details
-
molecularDynamics
-
-
Constructor Details
-
PhDynamics
public PhDynamics()PhDynamics Constructor. -
PhDynamics
PhDynamics Constructor.- Parameters:
binding
- The Binding to use.
-
PhDynamics
PhDynamics constructor that sets the command line arguments.- Parameters:
args
- Command line arguments.
-
-
Method Details
-
getMolecularDynamics
-
getPotentialObject
-
run
Execute this Command.- Overrides:
run
in classFFXCommand
- Returns:
- The current FFXCommand.
-
getPotentials
Returns a List of all Potential objects associated with this script.- Overrides:
getPotentials
in classAlgorithmsCommand
- Returns:
- All Potentials. Sometimes empty, never null.
-
sortMyArc
Sort archive files by pH with string parsing
-