Uses of Interface
ffx.algorithms.AlgorithmListener
Package
Description
The Algorithms package has support for local and global optimization, molecular dynamics
simulations, and calculation of free energy differences.
The Algorithms CLI package defines options for PicoCLI command line scripts.
The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and
via OpenMM.
The MC package implements a variety of Monte Carlo moves for optimization and simulation
algorithms.
The Misc package contains a few miscellaneous algorithms.
The Optimize package contains local and global optimization algorithms using pure Java and OpenMM
code paths.
The Thermodynamics package computes free energy differences using Orthogonal Space Tempering
(OST) sampling via pure Java or OpenMM (via Monte Carlo OST).
The UI package provides views and controllers for manipulating molecular systems.
The X-ray package implements support for X-ray and Neutron refinement.
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Uses of AlgorithmListener in ffx.algorithms
Modifier and TypeMethodDescriptiondefault AlgorithmListener
AlgorithmFunctions.getDefaultListener()
Returns a default Listener if available (null by default). -
Uses of AlgorithmListener in ffx.algorithms.cli
Modifier and TypeFieldDescriptionAlgorithmsScript.algorithmListener
An instance of the AlgorithmListener interface.Modifier and TypeMethodDescriptionOSTOptions.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.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.AnnealOptions.createAnnealer
(DynamicsOptions dynamicsOptions, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener) Creates a SimulatedAnnealing object.AnnealOptions.createAnnealer
(DynamicsOptions dynamicsOptions, MolecularAssembly molecularAssembly, Potential potential, AlgorithmListener algorithmListener, File dynFile) Creates a SimulatedAnnealing object.DynamicsOptions.getDynamics
(WriteoutOptions writeoutOptions, Potential potential, MolecularAssembly activeAssembly, AlgorithmListener algorithmListener) Initialize a MolecularDynamics from the parsed options.DynamicsOptions.getDynamics
(WriteoutOptions writeoutOptions, Potential potential, MolecularAssembly activeAssembly, AlgorithmListener algorithmListener, MDEngine requestedEngine) Initialize a MolecularDynamics from the parsed options.ThermodynamicsOptions.runFixedAlchemy
(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, WriteoutOptions writeoutOptions, File dyn, AlgorithmListener algorithmListener) Run an alchemical free energy window.OSTOptions.setupMCOST
(OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularAssembly[] molecularAssemblies, DynamicsOptions dynamicsOptions, ThermodynamicsOptions thermodynamicsOptions, boolean verbose, File dynRestart, AlgorithmListener algorithmListener) setupMCOST. -
Uses of AlgorithmListener in ffx.algorithms.dynamics
Modifier and TypeFieldDescriptionprotected final AlgorithmListener
MolecularDynamics.algorithmListener
An Algorithm Listener to send updates to the GUI.Modifier and TypeMethodDescriptionstatic 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 implementationstatic MolecularDynamics
MolecularDynamics.dynamicsFactory
(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, ThermostatEnum requestedThermostat, IntegratorEnum requestedIntegrator, MDEngine engine) dynamicsFactory.ModifierConstructorDescriptionMolecularDynamics
(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
ModifierConstructorDescriptionMDMove
(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, DynamicsOptions dynamics, long stepsPerCycle, File dynRestartFile) Constructor for MDMove. -
Uses of AlgorithmListener in ffx.algorithms.misc
ModifierConstructorDescriptionGenerateRotamers
(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
Modifier and TypeFieldDescriptionprotected 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.Modifier and TypeMethodDescriptionstatic Minimize
Minimize.minimizeFactory
(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, Minimize.MinimizationEngine engine) dynamicsFactory.ModifierConstructorDescriptionCrystalMinimize
(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) 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
ModifierConstructorDescriptionSimulatedAnnealing
(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
Modifier and TypeFieldDescriptionprotected AlgorithmListener
DistanceRegion.algorithmListener
AlgorithmListener who should receive updates as the optimization runs.Modifier and TypeMethodDescriptionvoid
DistanceRegion.init
(DistanceMatrix dM, MolecularAssembly molecularAssembly, Residue[] allResiduesArray, AlgorithmListener algorithmListener, double[][][][] distanceMatrix) ModifierConstructorDescriptionDistanceMatrix
(MolecularAssembly molecularAssembly, AlgorithmListener algorithmListener, Residue[] allResiduesArray, List<Residue> allResiduesList, RotamerOptimization.DistanceMethod distanceMethod, double distance, double twoBodyCutoffDist, double threeBodyCutoffDist, boolean lazyMatrix) 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
Modifier and TypeFieldDescriptionprotected final AlgorithmListener
OrthogonalSpaceTempering.algorithmListener
The AlgorithmListener is called each time a count is added.ModifierConstructorDescriptionMonteCarloOST
(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
Modifier and TypeClassDescriptionclass
The ModelingShell is used to script Multiscale Modeling Routines via the Groovy scripting language. -
Uses of AlgorithmListener in ffx.xray
Modifier and TypeClassDescriptionclass
Combine the X-ray target and chemical potential energy using theCrystalPotential
interfaceModifierConstructorDescriptionRefinementMinimize
(DataContainer data, RefinementMinimize.RefinementMode refinementMode, AlgorithmListener listener) constructor for refinement