Package ffx.algorithms.commands

Class PhDynamics

java.lang.Object

ffx.utilities.FFXCommand

ffx.algorithms.cli.AlgorithmsCommand

ffx.algorithms.commands.PhDynamics

public class PhDynamics
extends AlgorithmsCommand

The PhDynamics command implements constant pH molecular dynamics.
Usage:
ffxc PhDynamics [options] <filename> [file2...]

Field Summary

Fields

Modifier and Type	Field	Description
MolecularDynamics	molecularDynamics

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

Constructor Summary

Constructors

Constructor	Description
PhDynamics()	PhDynamics Constructor.
PhDynamics(FFXBinding binding)	PhDynamics Constructor.
PhDynamics(String[] args)	PhDynamics constructor that sets the command line arguments.

Method Summary

Modifier and Type	Method	Description
MolecularDynamics	getMolecularDynamics()
Potential	getPotentialObject()
List<Potential>	getPotentials()	Returns a List of all Potential objects associated with this script.
PhDynamics	run()	Execute this Command.
static void	sortMyArc(File structureFile, int nReplicas, double pH, int myRank)	Sort archive files by pH with string parsing

Methods inherited from class ffx.algorithms.cli.AlgorithmsCommand

destroyPotentials, getActiveAssemblies, getActiveAssembly, getPotentialsFromAssemblies, init, saveDirFile, setBaseDir, updateTitle

Methods inherited from class ffx.utilities.FFXCommand

getCommand, helpString, listCommands, setBinding

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

molecularDynamics

public MolecularDynamics molecularDynamics

Constructor Details

PhDynamics

public PhDynamics()

PhDynamics Constructor.

PhDynamics

public PhDynamics(FFXBinding binding)

PhDynamics Constructor.

Parameters:

binding - The Binding to use.

PhDynamics

public PhDynamics(String[] args)

PhDynamics constructor that sets the command line arguments.

Parameters:

args - Command line arguments.

Method Details

getMolecularDynamics

public MolecularDynamics getMolecularDynamics()

getPotentialObject

public Potential getPotentialObject()

run

public PhDynamics run()

Execute this Command.

Overrides:

run in class FFXCommand

Returns:

The current FFXCommand.

getPotentials

public List<Potential> getPotentials()

Returns a List of all Potential objects associated with this script.

Overrides:

getPotentials in class AlgorithmsCommand

Returns:

All Potentials. Sometimes empty, never null.

sortMyArc

public static void sortMyArc(File structureFile,
 int nReplicas,
 double pH,
 int myRank)

Sort archive files by pH with string parsing