Uses of Interface
ffx.algorithms.AlgorithmListener

Packages that use AlgorithmListener

Package	Description
ffx.algorithms	The Algorithms package has support for local and global optimization, molecular dynamics simulations, and calculation of free energy differences.
ffx.algorithms.cli	The Algorithms CLI package defines options for PicoCLI command line scripts.
ffx.algorithms.dynamics	The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and via OpenMM.
ffx.algorithms.mc	The MC package implements a variety of Monte Carlo moves for optimization and simulation algorithms.
ffx.algorithms.misc	The Misc package contains a few miscellaneous algorithms.
ffx.algorithms.optimize	The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.
ffx.algorithms.optimize.anneal
ffx.algorithms.optimize.manybody
ffx.algorithms.thermodynamics	The Thermodynamics package computes free energy differences using Orthogonal Space Tempering (OST) sampling via pure Java or OpenMM (via Monte Carlo OST).
ffx.ui	The UI package provides views and controllers for manipulating molecular systems.
ffx.xray	The X-ray package implements support for X-ray and Neutron refinement.

Uses of AlgorithmListener in ffx.algorithms

Methods in ffx.algorithms that return AlgorithmListener

Modifier and Type	Method	Description
default AlgorithmListener	AlgorithmFunctions.getDefaultListener()	Returns a default Listener if available (null by default).

Uses of AlgorithmListener in ffx.algorithms.cli

Fields in ffx.algorithms.cli declared as AlgorithmListener

Modifier and Type	Field	Description
AlgorithmListener	AlgorithmsScript.algorithmListener	An instance of the AlgorithmListener interface.

Methods in ffx.algorithms.cli with parameters of type AlgorithmListener

Modifier and Type	Method	Description
MolecularDynamics	OSTOptions.assembleMolecularDynamics(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, AlgorithmListener algorithmListener)	Assembles a MolecularDynamics wrapped around a Potential.
void	OSTOptions.beginMDOST(OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, WriteoutOptions writeoutOptions, ThermodynamicsOptions thermodynamicsOptions, File dynFile, AlgorithmListener algorithmListener)	Begins MD-OST sampling from an assembled OST.
OrthogonalSpaceTempering	OSTOptions.constructOST(CrystalPotential crystalPotential, File lambdaRestartFile, File histogramRestartFile, MolecularAssembly firstAssembly, org.apache.commons.configuration2.Configuration addedProperties, DynamicsOptions dynamicsOptions, ThermodynamicsOptions thermodynamicsOptions, LambdaParticleOptions lambdaParticleOptions, AlgorithmListener algorithmListener, boolean async)	constructOST.
SimulatedAnnealing	AnnealOptions.createAnnealer(DynamicsOptions dynamicsOptions, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener)	Creates a SimulatedAnnealing object.
SimulatedAnnealing	AnnealOptions.createAnnealer(DynamicsOptions dynamicsOptions, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener, File dynFile)	Creates a SimulatedAnnealing object.
MolecularDynamics	DynamicsOptions.getDynamics(WriteoutOptions writeoutOptions, Potential potential, MolecularAssembly activeAssembly, AlgorithmListener algorithmListener)	Initialize a MolecularDynamics from the parsed options.
MolecularDynamics	DynamicsOptions.getDynamics(WriteoutOptions writeoutOptions, Potential potential, MolecularAssembly activeAssembly, AlgorithmListener algorithmListener, MDEngine requestedEngine)	Initialize a MolecularDynamics from the parsed options.
MolecularDynamics	ThermodynamicsOptions.runFixedAlchemy(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, WriteoutOptions writeoutOptions, File dyn, AlgorithmListener algorithmListener)	Run an alchemical free energy window.
MolecularDynamics	ThermodynamicsOptions.runNEQ(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, WriteoutOptions writeoutOptions, File dyn, AlgorithmListener algorithmListener)	Run a non-equilibrium alchemical free energy simulation.
MonteCarloOST	OSTOptions.setupMCOST(OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularAssembly[] molecularAssemblies, DynamicsOptions dynamicsOptions, ThermodynamicsOptions thermodynamicsOptions, boolean verbose, File dynRestart, AlgorithmListener algorithmListener)	setupMCOST.

Uses of AlgorithmListener in ffx.algorithms.dynamics

Fields in ffx.algorithms.dynamics declared as AlgorithmListener

Modifier and Type	Field	Description
protected final AlgorithmListener	MolecularDynamics.algorithmListener	An Algorithm Listener to send updates to the GUI.

Methods in ffx.algorithms.dynamics with parameters of type AlgorithmListener

Modifier and Type	Method	Description
static MolecularDynamics	MolecularDynamics.dynamicsFactory(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, ThermostatEnum requestedThermostat, IntegratorEnum requestedIntegrator)	Method that determines whether a dynamics is done by the java implementation native to ffx or the OpenMM implementation
static MolecularDynamics	MolecularDynamics.dynamicsFactory(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, ThermostatEnum requestedThermostat, IntegratorEnum requestedIntegrator, MDEngine engine)	dynamicsFactory.

Constructors in ffx.algorithms.dynamics with parameters of type AlgorithmListener

Modifier	Constructor	Description
	MolecularDynamics(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, ThermostatEnum requestedThermostat, IntegratorEnum requestedIntegrator)	Constructor for MolecularDynamics.
	MolecularDynamicsOpenMM(MolecularAssembly assembly, Potential potential, AlgorithmListener listener, ThermostatEnum thermostat, IntegratorEnum integrator)	Constructs an MolecularDynamicsOpenMM object, to perform molecular dynamics using native OpenMM routines, avoiding the cost of communicating coordinates, gradients, and energies back and forth across the PCI bus.
	ReplicaExchange(MolecularDynamics molecularDynamics, AlgorithmListener listener, double temperature, double exponent, boolean monteCarlo)	ReplicaExchange constructor.

Uses of AlgorithmListener in ffx.algorithms.mc

Constructors in ffx.algorithms.mc with parameters of type AlgorithmListener

Modifier	Constructor	Description
	MDMove(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, DynamicsOptions dynamics, long stepsPerCycle, File dynRestartFile)	Constructor for MDMove.

Uses of AlgorithmListener in ffx.algorithms.misc

Constructors in ffx.algorithms.misc with parameters of type AlgorithmListener

Modifier	Constructor	Description
	GenerateRotamers(MolecularAssembly molecularAssembly, Potential potential, Residue residue, File file, int nChi, AlgorithmListener listener)	Intended to create rotamer sets for nonstandard amino acids.
	GenerateRotamers(MolecularAssembly molecularAssembly, Potential potential, Residue residue, File file, int nChi, AlgorithmListener listener, RotamerLibrary library)	Intended to create rotamer sets for nonstandard amino acids.

Uses of AlgorithmListener in ffx.algorithms.optimize

Fields in ffx.algorithms.optimize declared as AlgorithmListener

Modifier and Type	Field	Description
protected final AlgorithmListener	Minimize.algorithmListener	The AlgorithmListener to update the UI.
protected final AlgorithmListener	PhMinimize.algorithmListener	The AlgorithmListener to update the UI.
protected final AlgorithmListener	RotamerOptimization.algorithmListener	AlgorithmListener who should receive updates as the optimization runs.

Methods in ffx.algorithms.optimize with parameters of type AlgorithmListener

Modifier and Type	Method	Description
static Minimize	Minimize.minimizeFactory(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, Minimize.MinimizationEngine engine)	dynamicsFactory.

Constructors in ffx.algorithms.optimize with parameters of type AlgorithmListener

Modifier	Constructor	Description
	CrystalMinimize(MolecularAssembly molecularAssembly, XtalEnergy xtalEnergy, AlgorithmListener algorithmListener)	Constructor for CrystalMinimize.
	Minimize(MolecularAssembly molecularAssembly, AlgorithmListener algorithmListener)	Constructor for Minimize.
	Minimize(MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener)	Constructor for Minimize.
	MinimizeOpenMM(MolecularAssembly molecularAssembly, OpenMMEnergy openMMEnergy, AlgorithmListener algorithmListener)	MinimizeOpenMM constructor.
	PhMinimize(MolecularAssembly molecularAssembly, AlgorithmListener algorithmListener, ExtendedSystem esvSystem)	Constructor for Minimize.
	PhMinimize(MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener, ExtendedSystem esvSystem)	Constructor for Minimize.
	RotamerOptimization(MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener)	RotamerOptimization constructor.

Uses of AlgorithmListener in ffx.algorithms.optimize.anneal

Constructors in ffx.algorithms.optimize.anneal with parameters of type AlgorithmListener

Modifier	Constructor	Description
	SimulatedAnnealing(MolecularAssembly molecularAssembly, Potential potentialEnergy, AlgorithmListener algorithmListener, ThermostatEnum requestedThermostat, IntegratorEnum requestedIntegrator, AnnealingSchedule annealingSchedule, long mdSteps, double timeStep, boolean reInitVelocity, File dynFile)	Constructor for SimulatedAnnealing.

Uses of AlgorithmListener in ffx.algorithms.optimize.manybody

Fields in ffx.algorithms.optimize.manybody declared as AlgorithmListener

Modifier and Type	Field	Description
protected AlgorithmListener	DistanceRegion.algorithmListener	AlgorithmListener who should receive updates as the optimization runs.

Methods in ffx.algorithms.optimize.manybody with parameters of type AlgorithmListener

Modifier and Type	Method	Description
void	DistanceRegion.init(DistanceMatrix dM, MolecularAssembly molecularAssembly, Residue[] allResiduesArray, AlgorithmListener algorithmListener, DistanceMatrix.NeighborDistances[][] distanceMatrix)

Constructors in ffx.algorithms.optimize.manybody with parameters of type AlgorithmListener

Modifier	Constructor	Description
	DistanceMatrix(MolecularAssembly molecularAssembly, AlgorithmListener algorithmListener, Residue[] allResiduesArray, List<Residue> allResiduesList, RotamerOptimization.DistanceMethod distanceMethod, double distance, double twoBodyCutoffDist, double threeBodyCutoffDist)
	EnergyExpansion(RotamerOptimization rO, DistanceMatrix dM, EliminatedRotamers eR, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener, List<Residue> allResiduesList, int[][] resNeighbors, boolean threeBodyTerm, boolean decomposeOriginal, boolean usingBoxOptimization, boolean verbose, boolean pruneClashes, boolean prunePairClashes, boolean master)

Uses of AlgorithmListener in ffx.algorithms.thermodynamics

Fields in ffx.algorithms.thermodynamics declared as AlgorithmListener

Modifier and Type	Field	Description
protected final AlgorithmListener	OrthogonalSpaceTempering.algorithmListener	The AlgorithmListener is called each time a count is added.

Constructors in ffx.algorithms.thermodynamics with parameters of type AlgorithmListener

Modifier	Constructor	Description
	MonteCarloOST(Potential potentialEnergy, OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularAssembly molecularAssembly, org.apache.commons.configuration2.CompositeConfiguration properties, AlgorithmListener listener, DynamicsOptions dynamics, boolean verbose, int cycleLength, File dynRestartFile)	Constructor for MonteCarloOST.
	OrthogonalSpaceTempering(LambdaInterface lambdaInterface, CrystalPotential potential, HistogramData histogramData, LambdaData lambdaData, org.apache.commons.configuration2.CompositeConfiguration properties, DynamicsOptions dynamicsOptions, LambdaParticleOptions lambdaParticleOptions, AlgorithmListener algorithmListener)	OST Constructor.

Uses of AlgorithmListener in ffx.ui

Classes in ffx.ui that implement AlgorithmListener

Modifier and Type	Class	Description
class	ModelingShell	The ModelingShell is used to script Multiscale Modeling Routines via the Groovy scripting language.

Methods in ffx.ui that return AlgorithmListener

Modifier and Type	Method	Description
AlgorithmListener	UIUtils.getDefaultListener()

Uses of AlgorithmListener in ffx.xray

Classes in ffx.xray that implement AlgorithmListener

Modifier and Type	Class	Description
class	RefinementEnergy	Combine the X-ray target and chemical potential energy using the CrystalPotential interface

Constructors in ffx.xray with parameters of type AlgorithmListener

Modifier	Constructor	Description
	RefinementMinimize(DataContainer data, RefinementMinimize.RefinementMode refinementMode, AlgorithmListener listener)	constructor for refinement