Uses of Class
ffx.potential.MolecularAssembly
Packages that use MolecularAssembly
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 Integrators package implements integrators for molecular dynamics simulations.
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 Potential package implements molecular mechanics force fields with shared memory Parallel
Java and via OpenMM.
The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions,
etc.
The Potential CLI package defines reusable options for PicoCLI command line scripts.
The Extended package is progress toward support for constant pH molecular dynamics using extended
system variables (i.e. lambda dynamics on protonation).
The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and
Particle Mesh Ewald electrostastics.
The Parsers package handles reading/writing files to/from the internal data structure.
The Utils package implements core functionality needed for using the Potential package, such as
opening and closing structure files, basic force field energy evaluations, etc.
The Real Space package implements real space structure refinement.
The Real Space CLI package defines options for PicoCLI command line scripts.
The Parsers package reads and writes CCP4 map files.
The UI package provides views and controllers for manipulating molecular systems.
The Commands package implements a Client/Server interface between Force Field X and simulations.
The X-ray package implements support for X-ray and Neutron refinement.
The X-ray CLI package defines options for PicoCLI command line scripts.
The Parsers package reads CNS files and reads/writes MTZ files.
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Uses of MolecularAssembly in ffx.algorithms
Methods in ffx.algorithms with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionboolean
AlgorithmListener.algorithmUpdate
(MolecularAssembly active) After a successful step or interval of an algorithm, this method of the listener will be called.void
AlgorithmFunctions.md
(MolecularAssembly assembly, int nStep, double timeStep, double printInterval, double saveInterval, double temperature, boolean initVelocities, File dyn) Runs molecular dynamics on an assembly.void
AlgorithmUtils.md
(MolecularAssembly assembly, int nStep, double timeStep, double printInterval, double saveInterval, double temperature, boolean initVelocities, File dyn) Runs molecular dynamics on an assembly.AlgorithmFunctions.minimize
(MolecularAssembly assembly, double eps) Relax the coordinates of a MolecularAssembly and minimize its potential energyAlgorithmUtils.minimize
(MolecularAssembly assembly, double eps) Relax the coordinates of a MolecularAssembly and minimize its potential energy -
Uses of MolecularAssembly in ffx.algorithms.cli
Fields in ffx.algorithms.cli declared as MolecularAssemblyModifier and TypeFieldDescriptionAlgorithmsScript.activeAssembly
An active MolecularAssembly passed into the current context or loaded by the Script from a file argument.Methods in ffx.algorithms.cli that return MolecularAssemblyModifier and TypeMethodDescriptionAlgorithmsScript.getActiveAssemblies
(String filename) If a filename is supplied, open it and return the MolecularAssemblies.AlgorithmsScript.getActiveAssembly
(String filename) If a filename is supplied, open it and return the MolecularAssembly.MultiDynamicsOptions.openFile
(AlgorithmFunctions algorithmFunctions, TopologyOptions topologyOptions, int threadsPer, String toOpen, int topNum, AlchemicalOptions alchemicalOptions, File structureFile, int rank) Opens a file and processes it.Methods in ffx.algorithms.cli with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionOSTOptions.applyAllOSTOptions
(OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularAssembly firstAssembly, DynamicsOptions dynamicsOptions, BarostatOptions barostatOptions) Applies relevant options to an OST, and returns either the OST object or something that wraps the OST (such as a Barostat).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.BarostatOptions.checkNPT
(MolecularAssembly molecularAssembly, CrystalPotential crystalPotential) If pressure has been set > 0, creates a Barostat around a CrystalPotential, else returns the original, unmodified CrystalPotential.ManyBodyOptions.collectResidues
(MolecularAssembly activeAssembly) Collect residues based on residue selection flags.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.BarostatOptions.createBarostat
(MolecularAssembly assembly, CrystalPotential crystalPotential) Creates a Barostat around a CrystalPotential.void
MultiDynamicsOptions.distribute
(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, AlgorithmFunctions algorithmFunctions, int rank, int worldSize) If residues selected for distributing initial configurations, performs many-body optimization for this distribution.void
MultiDynamicsOptions.distribute
(MolecularAssembly[] molecularAssemblies, Potential[] potentials, CrystalPotential crystalPotential, AlgorithmFunctions algorithmFunctions, int rank, int worldSize) If residues selected for distributing initial configurations, performs many-body optimization for this distribution.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.void
ManyBodyOptions.initRotamerOptimization
(RotamerOptimization rotamerOptimization, MolecularAssembly activeAssembly) initRotamerOptimization.void
RandomUnitCellOptions.randomize
(MolecularAssembly assembly) Randomize the unit cell for a MolecularAssembly.ThermodynamicsOptions.runFixedAlchemy
(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, WriteoutOptions writeoutOptions, File dyn, AlgorithmListener algorithmListener) Run an alchemical free energy window.ThermodynamicsOptions.runNEQ
(MolecularAssembly[] molecularAssemblies, CrystalPotential crystalPotential, DynamicsOptions dynamicsOptions, WriteoutOptions writeoutOptions, File dyn, AlgorithmListener algorithmListener) Run a non-equilibrium alchemical free energy simulation.void
AlgorithmsScript.setActiveAssembly
(MolecularAssembly molecularAssembly) Set the Active Assembly.OSTOptions.setupMCOST
(OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularAssembly[] molecularAssemblies, DynamicsOptions dynamicsOptions, ThermodynamicsOptions thermodynamicsOptions, boolean verbose, File dynRestart, AlgorithmListener algorithmListener) setupMCOST. -
Uses of MolecularAssembly in ffx.algorithms.dynamics
Fields in ffx.algorithms.dynamics declared as MolecularAssemblyModifier and TypeFieldDescriptionprotected MolecularAssembly[]
MolecularDynamics.molecularAssembly
MolecularAssembly to run dynamics on.Methods in ffx.algorithms.dynamics that return MolecularAssemblyModifier and TypeMethodDescriptionMolecularDynamics.getAssemblyArray()
Returns the MolecularAssembly array.Methods in ffx.algorithms.dynamics with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionvoid
MolecularDynamics.addAssembly
(MolecularAssembly assembly) Adds a MolecularAssembly to be tracked by this MolecularDynamics.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 implementationstatic 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 MolecularAssemblyModifierConstructorDescriptionBarostat
(MolecularAssembly molecularAssembly, CrystalPotential potential) Initialize the Barostat.Barostat
(MolecularAssembly molecularAssembly, CrystalPotential potential, double temperature) Initialize the Barostat.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. -
Uses of MolecularAssembly in ffx.algorithms.dynamics.integrators
Methods in ffx.algorithms.dynamics.integrators with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionvoid
Rattle.postForce1
(MolecularAssembly molAss, double dt) postForce1.Constructors in ffx.algorithms.dynamics.integrators with parameters of type MolecularAssemblyModifierConstructorDescriptionRattle
(int nVariables, MolecularAssembly molAss, double[] v) Constructor for Rattle. -
Uses of MolecularAssembly in ffx.algorithms.mc
Methods in ffx.algorithms.mc that return MolecularAssemblyModifier and TypeMethodDescriptionMolecularMC.getMolecularAssembly()
Returns the associated MolecularAssembly.Constructors in ffx.algorithms.mc with parameters of type MolecularAssemblyModifierConstructorDescriptionMDMove
(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, DynamicsOptions dynamics, long stepsPerCycle, File dynRestartFile) Constructor for MDMove.MolecularMC
(MolecularAssembly molecularAssembly) Constructs a DefaultMC instance with a molecular assembly and its PotentialEnergy.MolecularMC
(MolecularAssembly molecularAssembly, Potential potential) Constructs a DefaultMC instance with a molecular assembly and a specific Potential.RosenbluthCBMC
(MolecularAssembly molecularAssembly, ForceFieldEnergy ffe, Thermostat thermostat, List<Residue> targets, int mcFrequency, int trialSetSize, boolean writeSnapshots) RRMC constructor.RosenbluthOBMC
(MolecularAssembly molecularAssembly, ForceFieldEnergy forceFieldEnergy, Thermostat thermostat, List<Residue> targets, int mcFrequency, int trialSetSize) RRMC constructor.RosenbluthOBMC
(MolecularAssembly molecularAssembly, ForceFieldEnergy forceFieldEnergy, Thermostat thermostat, List<Residue> targets, int mcFrequency, int trialSetSize, boolean writeSnapshots) Constructor for RosenbluthOBMC. -
Uses of MolecularAssembly in ffx.algorithms.misc
Constructors in ffx.algorithms.misc with parameters of type MolecularAssemblyModifierConstructorDescriptionGenerateRotamers
(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 MolecularAssembly in ffx.algorithms.optimize
Fields in ffx.algorithms.optimize declared as MolecularAssemblyModifier and TypeFieldDescriptionprotected final MolecularAssembly
Minimize.molecularAssembly
The MolecularAssembly being operated on.protected final MolecularAssembly
PhMinimize.molecularAssembly
The MolecularAssembly being operated on.protected final MolecularAssembly
RotamerOptimization.molecularAssembly
MolecularAssembly to perform rotamer optimization on.Methods in ffx.algorithms.optimize that return MolecularAssemblyModifier and TypeMethodDescriptionTitrationManyBody.getProtonatedAssemblies()
TitrationManyBody.getProtonatedAssembly()
Methods in ffx.algorithms.optimize with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionstatic Minimize.MinimizationEngine
Minimize.defaultEngine
(MolecularAssembly molecularAssembly, Potential potentialEnergy) static Minimize
Minimize.minimizeFactory
(MolecularAssembly assembly, Potential potentialEnergy, AlgorithmListener listener, Minimize.MinimizationEngine engine) dynamicsFactory.double
RotamerOptimization.rotamerOptimization
(MolecularAssembly molecularAssembly, Residue[] residues, int i, double lowEnergy, int[] optimum) A brute-force global optimization over side-chain rotamers using a recursive algorithm.Constructors in ffx.algorithms.optimize with parameters of type MolecularAssemblyModifierConstructorDescriptionConformationScan
(MolecularAssembly molecularAssembly, Molecule[] systemOne, Molecule[] systemTwo, double minimizeEps, int minimizeMaxIterations, boolean staticTorsionScan, boolean excludeExtraHydrogen, boolean minimize) 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) MinimizeOpenMM constructor.MinimizeOpenMM
(MolecularAssembly molecularAssembly, OpenMMEnergy openMMEnergy) MinimizeOpenMM constructor.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.TorsionSearch
(MolecularAssembly molecularAssembly, Molecule molecule, int nTorsionsPerBond, int returnedStates) -
Uses of MolecularAssembly in ffx.algorithms.optimize.anneal
Constructors in ffx.algorithms.optimize.anneal with parameters of type MolecularAssemblyModifierConstructorDescriptionSimulatedAnnealing
(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 MolecularAssembly in ffx.algorithms.optimize.manybody
Methods in ffx.algorithms.optimize.manybody with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionvoid
DistanceRegion.init
(DistanceMatrix dM, MolecularAssembly molecularAssembly, Residue[] allResiduesArray, AlgorithmListener algorithmListener, DistanceMatrix.NeighborDistances[][] distanceMatrix) Constructors in ffx.algorithms.optimize.manybody with parameters of type MolecularAssemblyModifierConstructorDescriptionDistanceMatrix
(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 MolecularAssembly in ffx.algorithms.thermodynamics
Fields in ffx.algorithms.thermodynamics declared as MolecularAssemblyModifier and TypeFieldDescriptionprotected MolecularAssembly
OrthogonalSpaceTempering.molecularAssembly
The MolecularAssembly being simulated.Methods in ffx.algorithms.thermodynamics with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionvoid
OrthogonalSpaceTempering.setMolecularAssembly
(MolecularAssembly molecularAssembly) void
OrthogonalSpaceTempering.OptimizationParameters.setOptimization
(boolean doOptimization, MolecularAssembly molecularAssembly) setOptimization.Constructors in ffx.algorithms.thermodynamics with parameters of type MolecularAssemblyModifierConstructorDescriptionMonteCarloOST
(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. -
Uses of MolecularAssembly in ffx.potential
Fields in ffx.potential declared as MolecularAssemblyModifier and TypeFieldDescriptionprotected final MolecularAssembly
ForceFieldEnergy.molecularAssembly
The MolecularAssembly associated with this force field energy.Methods in ffx.potential that return MolecularAssemblyModifier and TypeMethodDescriptionAssemblyState.getMolecularAssembly()
Returns the MolecularAssembly associated with this AssemblyState.Methods in ffx.potential with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionstatic void
Utilities.biochemistry
(MolecularAssembly molecularAssembly, List<Atom> atoms) This routine sub-divides a system into groups of ions, water, hetero molecules, and polynucleotides/polypeptides.static ForceFieldEnergy
ForceFieldEnergy.energyFactory
(MolecularAssembly assembly) Static factory method to create a ForceFieldEnergy, possibly via FFX or OpenMM implementations.static ForceFieldEnergy
ForceFieldEnergy.energyFactory
(MolecularAssembly assembly, int numThreads) Static factory method to create a ForceFieldEnergy, possibly via FFX or OpenMM implementations.static double
Utilities.RMSCoordDev
(MolecularAssembly m1, MolecularAssembly m2) Finds the RMS deviation between the atoms of MolecularAssembly m1 and m2 provided they have the same number of atoms.Constructors in ffx.potential with parameters of type MolecularAssemblyModifierConstructorDescriptionANIEnergy
(MolecularAssembly molecularAssembly) AssemblyState
(MolecularAssembly assembly) Construct a snapshot of a MolecularAssembly.DualTopologyEnergy
(MolecularAssembly topology1, MolecularAssembly topology2, UnivariateSwitchingFunction switchFunction) Constructor for DualTopologyEnergy.protected
ForceFieldEnergy
(MolecularAssembly molecularAssembly) Constructor for ForceFieldEnergy.protected
ForceFieldEnergy
(MolecularAssembly molecularAssembly, int numThreads) Constructor for ForceFieldEnergy.XtalEnergy
(ForceFieldEnergy forceFieldEnergy, MolecularAssembly molecularAssembly) Constructor for XtalEnergy.XtalEnergy
(ForceFieldEnergy forceFieldEnergy, MolecularAssembly molecularAssembly, boolean latticeOnly) Constructor for XtalEnergy. -
Uses of MolecularAssembly in ffx.potential.bonded
Methods in ffx.potential.bonded with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionPolymerUtils.assignAtomTypes
(MolecularAssembly molecularAssembly, PDBFilter.PDBFileStandard fileStandard) Assign force field atoms types to common chemistries using "biotype" records.static void
PolymerUtils.buildDisulfideBonds
(List<Bond> ssBondList, MolecularAssembly molecularAssembly, List<Bond> bondList) Assign parameters to disulfide bonds.static int
PolymerUtils.buildMissingResidues
(int xyzIndex, MolecularAssembly molecularAssembly, Map<Character, String[]> seqres, Map<Character, int[]> dbref) Currently builds missing internal loops based on information in DBREF and SEQRES records.PolymerUtils.locateDisulfideBonds
(List<String> ssbonds, MolecularAssembly molecularAssembly, Map<String, String> pdbToNewResMap) Locate disulfide bonds based on SSBOND records.static void
BondedUtils.numberAtoms
(MolecularAssembly molecularAssembly) Re-number atoms, especially if missing atoms were created.static void
RotamerLibrary.readRotFile
(File rotamerFile, MolecularAssembly assembly) static void
NamingUtils.renameAtomsToPDBStandard
(MolecularAssembly molecularAssembly) Renames Atoms to PDB standard using bonding patterns, atomic numbers, and residue types.static void
PolymerUtils.resolvePolymerLinks
(List<MSNode> molecules, MolecularAssembly molecularAssembly, List<Bond> bondList) Resolves links between polymeric hetero groups; presently only functional for cyclic molecules.SturmMethod.writePDBBackbone
(double[][] r_n, double[][] r_a, double[][] r_c, int stt_res, int end_res, MolecularAssembly molAss, int counter, boolean writeFile) Write out loop coordinates and determine oxygen placement. -
Uses of MolecularAssembly in ffx.potential.cli
Fields in ffx.potential.cli declared as MolecularAssemblyModifier and TypeFieldDescriptionPotentialCommand.activeAssembly
An active MolecularAssembly passed into the current context or loaded by the Script from a file argument.PotentialScript.activeAssembly
An active MolecularAssembly passed into the current context or loaded by the Script from a file argument.Methods in ffx.potential.cli that return MolecularAssemblyModifier and TypeMethodDescriptionPotentialCommand.getActiveAssemblies
(String filename) If a filename is supplied, open it and return the MolecularAssemblies.PotentialScript.getActiveAssemblies
(String filename) If a filename is supplied, open it and return the MolecularAssemblies.PotentialCommand.getActiveAssembly
(String filename) If a filename is supplied, open it and return the MolecularAssembly.PotentialScript.getActiveAssembly
(String filename) If a filename is supplied, open it and return the MolecularAssembly.AlchemicalOptions.openFile
(PotentialsFunctions potentialFunctions, TopologyOptions topologyOptions, int threadsPer, String toOpen, int topNum) Opens a File to a MolecularAssembly for alchemistry.AlchemicalOptions.processFile
(TopologyOptions topologyOptions, MolecularAssembly molecularAssembly, int topNum) Performs processing on a MolecularAssembly for alchemistry.Methods in ffx.potential.cli with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionstatic void
AtomSelectionOptions.actOnAtoms
(MolecularAssembly assembly, String selection, BiConsumer<Atom, Boolean> action, String description) TopologyOptions.assemblePotential
(MolecularAssembly[] assemblies, int threadsAvail, StringBuilder sb) Performs the bulk of the work of setting up a multi-topology system.TopologyOptions.getTopology
(MolecularAssembly[] topologies, UnivariateSwitchingFunction sf, List<Integer> uniqueA, List<Integer> uniqueB, int numParallel, StringBuilder sb) Configure a Dual-, Quad- or Oct- Topology.TopologyOptions.getUniqueAtoms
(MolecularAssembly assembly, String label, String unshared) Collect unique atoms for a dual-topology.TopologyOptions.getUniqueAtomsA
(MolecularAssembly topology) Collect unique atoms for the A dual-topology.TopologyOptions.getUniqueAtomsB
(MolecularAssembly topology) Collect unique atoms for the B dual-topology.void
SaveOptions.preSaveOperations
(MolecularAssembly molecularAssembly) Performs key operations prior to saving to disc, such as application of geometric constraints.AlchemicalOptions.processFile
(TopologyOptions topologyOptions, MolecularAssembly molecularAssembly, int topNum) Performs processing on a MolecularAssembly for alchemistry.WriteoutOptions.saveFile
(String baseFileName, PotentialsFunctions potentialsFunctions, MolecularAssembly molecularAssembly) Saves a single-snapshot file to either .xyz or .pdb, depending on the value of fileType.void
PotentialCommand.setActiveAssembly
(MolecularAssembly molecularAssembly) Set the Active Assembly.void
PotentialScript.setActiveAssembly
(MolecularAssembly molecularAssembly) Set the Active Assembly.void
AtomSelectionOptions.setActiveAtoms
(MolecularAssembly molecularAssembly) Set active atoms for a MolecularAssembly.static void
AlchemicalOptions.setAlchemicalAtoms
(MolecularAssembly assembly, String alchemicalAtoms) Sets the alchemical atoms for a MolecularAssembly.void
AlchemicalOptions.setFirstSystemAlchemistry
(MolecularAssembly topology) Set the alchemical atoms for this molecularAssembly.void
AlchemicalOptions.setFirstSystemUnchargedAtoms
(MolecularAssembly topology) Set uncharged atoms for this molecularAssembly.void
TopologyOptions.setSecondSystemAlchemistry
(MolecularAssembly topology) Set the alchemical atoms for this topology.void
TopologyOptions.setSecondSystemUnchargedAtoms
(MolecularAssembly topology) Set uncharged atoms for this topology.static void
AlchemicalOptions.setUnchargedAtoms
(MolecularAssembly assembly, String unchargedAtoms) Sets the uncharged atoms for a MolecularAssembly. -
Uses of MolecularAssembly in ffx.potential.extended
Constructors in ffx.potential.extended with parameters of type MolecularAssemblyModifierConstructorDescriptionExtendedSystem
(MolecularAssembly mola, double pH, File esvFile) Construct extended system with the provided configuration. -
Uses of MolecularAssembly in ffx.potential.nonbonded
Methods in ffx.potential.nonbonded with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionstatic RestrainPosition[]
RestrainPosition.parseRestrainPositions
(MolecularAssembly molecularAssembly) Constructors in ffx.potential.nonbonded with parameters of type MolecularAssemblyModifierConstructorDescriptionCOMRestraint
(MolecularAssembly molecularAssembly) This COMRestraint is based on the unit cell parameters and symmetry operators of the supplied crystal.RestrainGroups
(MolecularAssembly molecularAssembly) Group Restraint Constructor. -
Uses of MolecularAssembly in ffx.potential.openmm
Methods in ffx.potential.openmm that return MolecularAssemblyModifier and TypeMethodDescriptionOpenMMEnergy.getMolecularAssembly()
Returns the MolecularAssembly instance.Constructors in ffx.potential.openmm with parameters of type MolecularAssemblyModifierConstructorDescriptionOpenMMEnergy
(MolecularAssembly molecularAssembly, Platform requestedPlatform, int nThreads) ForceFieldEnergyOpenMM constructor; offloads heavy-duty computation to an OpenMM Platform while keeping track of information locally. -
Uses of MolecularAssembly in ffx.potential.parsers
Fields in ffx.potential.parsers with type parameters of type MolecularAssemblyModifier and TypeFieldDescriptionprotected List
<MolecularAssembly> SystemFilter.systems
All MolecularAssembly instances defined.Methods in ffx.potential.parsers that return MolecularAssemblyModifier and TypeMethodDescriptionSystemFilter.getActiveMolecularSystem()
Return the MolecularSystem that has been read inFileOpener.getAllAssemblies()
getAllAssemblies.FileOpener.getAssembly()
getAssembly.SystemFilter.getMolecularAssemblyArray()
Get the MolecularAssembly array.Methods in ffx.potential.parsers with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionstatic boolean
XPHFilter.readOnto
(File newFile, MolecularAssembly oldSystem) readOntostatic boolean
XYZFilter.readOnto
(File newFile, MolecularAssembly oldSystem) readOntovoid
PDBFilter.setAltID
(MolecularAssembly molecularAssembly, Character altLoc) Specify the alternate location.boolean
CIFFilter.writeOutputFile
(MolecularAssembly ma) Write an output file.Constructors in ffx.potential.parsers with parameters of type MolecularAssemblyModifierConstructorDescriptionCIFFilter
(File file, MolecularAssembly molecularAssembly, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties, boolean saveCIF) Constructor for CIFFilter on a single file and a single assembly.CIFFilter
(List<File> files, MolecularAssembly molecularAssembly, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties, boolean saveCIF) Constructor for CIFFilter on a multiple files and a single assembly.Constructor for InducedFilter.INTFilter
(File file, MolecularAssembly molecularAssembly, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties) Constructor for INTFilter.INTFilter
(List<File> files, MolecularAssembly molecularAssembly, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties) Constructor for INTFilter.MergeFilter
(MolecularAssembly f, ArrayList<Atom> a, ArrayList<Bond> b) Constructor for MergeFilter.PDBFilter
(File file, MolecularAssembly molecularAssembly, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties) Parse the PDB File from a URL.PDBFilter
(File file, MolecularAssembly molecularAssembly, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties, List<Integer> resNumberList) Constructor for PDBFilter with residue numbers.PDBFilter
(List<File> files, MolecularAssembly molecularAssembly, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties) Constructor for PDBFilter.SystemFilter
(File file, MolecularAssembly molecularAssembly, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties) Constructor for SystemFilter.SystemFilter
(List<File> files, MolecularAssembly molecularAssembly, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties) Constructor for SystemFilter.XPHFilter
(File file, MolecularAssembly system, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties, ExtendedSystem esvSystem) Constructor for XPHFilter.XYZFilter
(File file, MolecularAssembly system, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties) Constructor for XYZFilter.XYZFilter
(List<File> files, MolecularAssembly system, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties) Constructor for XYZFilter.Constructor parameters in ffx.potential.parsers with type arguments of type MolecularAssemblyModifierConstructorDescriptionCIFFilter
(File file, List<MolecularAssembly> molecularAssemblies, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties, boolean saveCIF) Constructor for CIFFilter on a single file and multiple assemblies.PDBFilter
(File file, List<MolecularAssembly> molecularAssemblies, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties) Parse the PDB File from a URL.SystemFilter
(File file, List<MolecularAssembly> molecularAssemblies, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties) Constructor for SystemFilter. -
Uses of MolecularAssembly in ffx.potential.utils
Methods in ffx.potential.utils that return MolecularAssemblyModifier and TypeMethodDescriptiondefault MolecularAssembly
PotentialsFunctions.getActiveAssembly()
Returns either the active assembly from the overlying UI, or the "active" molecular assembly from the last used SystemFilter.PotentialsFileOpener.getAllAssemblies()
getAllAssemblies.PotentialsFileOpener.getAssembly()
getAssembly.default MolecularAssembly
open.default MolecularAssembly[]
Opens an array of files and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads.Return one MolecularAssembly.open.Opens an array of files and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads.Opens a file and returns all created MolecularAssembly objects.Opens an array of files and returns the created MolecularAssembly objects.default MolecularAssembly[]
Opens a file and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads.Opens a file and returns all created MolecularAssembly objects.Opens an array of files and returns the created MolecularAssembly objects.Opens a file and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads.PotentialsUtils.openQuietly
(String filename) Open one filename string without printing all the header material.PotentialsUtils.openWithMutations
(File file, List<PDBFilter.Mutation> mutations) Mutates file on-the-fly as it is being opened.Methods in ffx.potential.utils with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionvoid
PotentialsFunctions.close
(MolecularAssembly assembly) Performs any necessary shutdown operations on a MolecularAssembly, primarily shutting down Parallel Java threads and closing any other open resources.void
PotentialsUtils.close
(MolecularAssembly assembly) Performs any necessary shutdown operations on a MolecularAssembly, primarily shutting down Parallel Java threads and closing any other open resources.void
PotentialsFunctions.closeAll
(MolecularAssembly[] assemblies) Performs any necessary shutdown operations on an array of MolecularAssembly, primarily shutting down Parallel Java threads and closing any other open resources.void
PotentialsUtils.closeAll
(MolecularAssembly[] assemblies) Performs any necessary shutdown operations on an array of MolecularAssembly, primarily shutting down Parallel Java threads and closing any other open resources.PotentialsFunctions.energy
(MolecularAssembly assembly) Evaluates the energy of a MolecularAssembly and returns its ForceFieldEnergy object.PotentialsFunctions.energy
(MolecularAssembly[] molecularAssemblies) Evaluates the energy of each MolecularAssembly and returns their ForceFieldEnergy instances.PotentialsUtils.energy
(MolecularAssembly molecularAssembly) Evaluates the energy of a MolecularAssembly and returns its ForceFieldEnergy object.PotentialsUtils.energy
(MolecularAssembly[] molecularAssemblies) Evaluates the energy of each MolecularAssembly and returns their ForceFieldEnergy instances.double
PotentialsFunctions.returnEnergy
(MolecularAssembly assembly) Returns the energy of a MolecularAssembly in kcal/mol (as a double) and prints the energy evaluationdouble
PotentialsUtils.returnEnergy
(MolecularAssembly assembly) Returns the energy of a MolecularAssembly in kcal/mol (as a double) and prints the energy evaluationvoid
PotentialsFunctions.save
(MolecularAssembly assembly, File file) Saves the current state of a MolecularAssembly to an XYZ file.void
PotentialsUtils.save
(MolecularAssembly assembly, File file) Saves the current state of a MolecularAssembly to an XYZ file.void
PotentialsFunctions.saveAsPDB
(MolecularAssembly[] assemblies, File file) Saves the current state of an array of MolecularAssembly instances to a PDB file.void
PotentialsFunctions.saveAsPDB
(MolecularAssembly assembly, File file) Saves the current state of a MolecularAssembly to a PDB file.void
PotentialsFunctions.saveAsPDB
(MolecularAssembly assembly, File file, boolean writeEnd, boolean append) void
PotentialsUtils.saveAsPDB
(MolecularAssembly[] assemblies, File file) Saves the current state of an array of MolecularAssembly instances to a PDB file.void
PotentialsUtils.saveAsPDB
(MolecularAssembly assembly, File file) Saves the current state of a MolecularAssembly to a PDB file.void
PotentialsUtils.saveAsPDB
(MolecularAssembly assembly, File file, boolean writeEnd, boolean append) void
PotentialsFunctions.saveAsPDBinP1
(MolecularAssembly assembly, File file) Saves the symmetry mates of a MolecularAssembly to PDB files.void
PotentialsUtils.saveAsPDBinP1
(MolecularAssembly assembly, File file) Saves the symmetry mates of a MolecularAssembly to PDB files.void
PotentialsUtils.saveAsPDBinP1
(MolecularAssembly assembly, File file, int[] lmn) void
PotentialsFunctions.saveAsXYZ
(MolecularAssembly assembly, File file) Saves the current state of a MolecularAssembly to an XYZ file.void
PotentialsUtils.saveAsXYZ
(MolecularAssembly assembly, File file) Saves the current state of a MolecularAssembly to an XYZ file.void
PotentialsFunctions.saveAsXYZasReplicates
(MolecularAssembly assembly, File file, int[] replicatesVector) Saves the current state of a MolecularAssembly to an XYZ file as a replicates crystal.void
PotentialsUtils.saveAsXYZasReplicates
(MolecularAssembly assembly, File file, int[] lmn) Saves the current state of a MolecularAssembly to an XYZ file as a replicates crystal.void
PotentialsFunctions.saveAsXYZinP1
(MolecularAssembly assembly, File file) Saves the current state of a MolecularAssembly to an XYZ file as a P1 crystal.void
PotentialsUtils.saveAsXYZinP1
(MolecularAssembly assembly, File file) Saves the current state of a MolecularAssembly to an XYZ file as a P1 crystal.Constructors in ffx.potential.utils with parameters of type MolecularAssemblyModifierConstructorDescriptionLoop
(MolecularAssembly molecularAssembly) Constructor for Loop.Loop
(MolecularAssembly molecularAssembly, int firstResidue, int endResidue) Constructor for Loop. -
Uses of MolecularAssembly in ffx.realspace
Methods in ffx.realspace that return MolecularAssemblyConstructors in ffx.realspace with parameters of type MolecularAssemblyModifierConstructorDescriptionRealSpaceData
(MolecularAssembly[] molecularAssemblies, org.apache.commons.configuration2.CompositeConfiguration properties, ParallelTeam parallelTeam, RealSpaceFile... dataFile) Construct a real space data molecularAssemblies.RealSpaceData
(MolecularAssembly[] molecularAssemblies, org.apache.commons.configuration2.CompositeConfiguration properties, ParallelTeam parallelTeam, DiffractionData diffractionData) Construct a real space data molecularAssemblies, assumes a real space map with a weight of 1.0 using the same name as the molecularAssemblies.RealSpaceData
(MolecularAssembly assembly, org.apache.commons.configuration2.CompositeConfiguration properties, ParallelTeam parallelTeam) Construct a real space data molecularAssemblies, assumes a real space map with a weight of 1.0 using the same name as the molecular molecularAssemblies.RealSpaceData
(MolecularAssembly assembly, org.apache.commons.configuration2.CompositeConfiguration properties, ParallelTeam parallelTeam, RealSpaceFile... datafile) Construct a real space data molecularAssemblies.RealSpaceData
(MolecularAssembly molecularAssembly, org.apache.commons.configuration2.CompositeConfiguration properties, ParallelTeam parallelTeam, DiffractionData diffractionData) Construct a real space data molecularAssemblies, assumes a real space map with a weight of 1.0 using the same name as the molecular molecularAssemblies. -
Uses of MolecularAssembly in ffx.realspace.cli
Methods in ffx.realspace.cli with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionRealSpaceOptions.processData
(List<String> filenames, MolecularAssembly molecularAssembly) Process input to collect Real Space Files.RealSpaceOptions.toRealSpaceEnergy
(List<String> filenames, MolecularAssembly[] molecularAssemblies) Process input from opened molecular assemblies to a RefinementEnergy -
Uses of MolecularAssembly in ffx.realspace.parsers
Constructors in ffx.realspace.parsers with parameters of type MolecularAssemblyModifierConstructorDescriptionRealSpaceFile
(MolecularAssembly assembly) Read in a Real Space density file based on the molecular assembly filename, using a weight of 1.0.RealSpaceFile
(MolecularAssembly[] assembly) Read in a Real Space density file based on the molecular assembly filename, using a weight of 1.0 and neutron value of false.RealSpaceFile
(MolecularAssembly assembly, double weight) Read in a Real Space density file based on the molecular assembly filename, using a weight of 1.0. -
Uses of MolecularAssembly in ffx.ui
Subclasses of MolecularAssembly in ffx.uiModifier and TypeClassDescriptionclass
The FFXSystem class contains extensions to the generic MolecularAssembly class.Methods in ffx.ui that return MolecularAssemblyModifier and TypeMethodDescriptionUIUtils.getActiveAssembly()
UIFileOpener.getAllAssemblies()
Returns all MolecularAssemblys in the user interface hierarchy.UIFileOpener.getAssembly()
Returns the active MolecularAssembly from the user interface hierarchy.Trajectory.getFSystem()
getFSystemMainPanel.openWaitUtils
(String file) UIUtils.openWithMutations
(File file, List<PDBFilter.Mutation> mutations) Mutates file on-the-fly as it is being opened.Methods in ffx.ui with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionboolean
ModelingShell.algorithmUpdate
(MolecularAssembly active) After a successful step or interval of an algorithm, this method of the listener will be called.void
UIUtils.close
(MolecularAssembly assembly) void
UIUtils.closeAll
(MolecularAssembly[] assemblies) UIUtils.energy
(MolecularAssembly molecularAssembly) void
UIUtils.md
(MolecularAssembly assembly, int nStep, double timeStep, double printInterval, double saveInterval, double temperature, boolean initVelocities, File dyn) UIUtils.minimize
(MolecularAssembly assembly, double eps) double
UIUtils.returnEnergy
(MolecularAssembly assembly) void
UIUtils.save
(MolecularAssembly assembly, File file) void
UIUtils.saveAsPDB
(MolecularAssembly[] assemblies, File file) void
UIUtils.saveAsPDB
(MolecularAssembly assembly, File file) void
UIUtils.saveAsPDB
(MolecularAssembly assembly, File file, boolean writeEnd, boolean append) void
UIUtils.saveAsPDBinP1
(MolecularAssembly assembly, File file) void
UIUtils.saveAsXYZ
(MolecularAssembly assembly, File file) void
UIUtils.saveAsXYZinP1
(MolecularAssembly assembly, File file) Constructors in ffx.ui with parameters of type MolecularAssemblyModifierConstructorDescriptionTrajectory
(MolecularAssembly mol, MainPanel f) Constructor for Trajectory. -
Uses of MolecularAssembly in ffx.ui.commands
Constructors in ffx.ui.commands with parameters of type MolecularAssemblyModifierConstructorDescriptionConstructor for SimulationFilter. -
Uses of MolecularAssembly in ffx.xray
Methods in ffx.xray that return MolecularAssemblyModifier and TypeMethodDescriptionDiffractionData.getAssembly()
Getter for the fieldassembly
.DataContainer.getMolecularAssemblies()
getMolecularAssembliesDiffractionData.getMolecularAssemblies()
getMolecularAssembliesMethods in ffx.xray with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionboolean
RefinementEnergy.algorithmUpdate
(MolecularAssembly active) After a successful step or interval of an algorithm, this method of the listener will be called.void
DiffractionData.AverageFc
(MolecularAssembly[] assembly, int index) read in a different assembly to average in structure factorsConstructors in ffx.xray with parameters of type MolecularAssemblyModifierConstructorDescriptionDiffractionData
(MolecularAssembly[] assembly, org.apache.commons.configuration2.CompositeConfiguration properties) construct a diffraction data assembly, assumes an X-ray data set with a weight of 1.0 using the same name as the molecular assemblyDiffractionData
(MolecularAssembly[] assembly, org.apache.commons.configuration2.CompositeConfiguration properties, CrystalReciprocalSpace.SolventModel solventmodel, DiffractionFile... datafile) construct a diffraction data assemblyDiffractionData
(MolecularAssembly[] assembly, org.apache.commons.configuration2.CompositeConfiguration properties, DiffractionFile... datafile) construct a diffraction data assemblyDiffractionData
(MolecularAssembly assembly, org.apache.commons.configuration2.CompositeConfiguration properties) construct a diffraction data assembly, assumes an X-ray data set with a weight of 1.0 using the same name as the molecular assemblyDiffractionData
(MolecularAssembly assembly, org.apache.commons.configuration2.CompositeConfiguration properties, CrystalReciprocalSpace.SolventModel solventmodel) construct a diffraction data assembly, assumes an X-ray data set with a weight of 1.0 using the same name as the molecular assemblyDiffractionData
(MolecularAssembly assembly, org.apache.commons.configuration2.CompositeConfiguration properties, CrystalReciprocalSpace.SolventModel solventmodel, DiffractionFile... datafile) construct a diffraction data assemblyDiffractionData
(MolecularAssembly assembly, org.apache.commons.configuration2.CompositeConfiguration properties, DiffractionFile... datafile) construct a diffraction data assemblyRefinementModel
(MolecularAssembly[] molecularAssemblies) Constructor for RefinementModel.RefinementModel
(MolecularAssembly[] molecularAssemblies, boolean refineMolOcc) Constructor for RefinementModel. -
Uses of MolecularAssembly in ffx.xray.cli
Methods in ffx.xray.cli with parameters of type MolecularAssemblyModifier and TypeMethodDescriptionXrayOptions.getDiffractionData
(List<String> filenames, MolecularAssembly[] assemblies, org.apache.commons.configuration2.CompositeConfiguration properties) Process input from opened molecular assemblies to a DiffractionData.XrayOptions.processData
(List<String> filenames, MolecularAssembly[] systems) Process input to collect Diffraction Files. -
Uses of MolecularAssembly in ffx.xray.parsers
Constructors in ffx.xray.parsers with parameters of type MolecularAssemblyModifierConstructorDescriptionDiffractionFile
(MolecularAssembly assembly) read in a diffraction file based on the molecular assembly fileName, using a weight of 1.0 and neutron value of falseDiffractionFile
(MolecularAssembly[] assembly) read in a diffraction file based on the molecular assembly fileName, using a weight of 1.0 and neutron value of falseDiffractionFile
(MolecularAssembly[] assembly, double weight) Constructor for DiffractionFile.DiffractionFile
(MolecularAssembly[] assembly, double weight, boolean neutron) Constructor for DiffractionFile.DiffractionFile
(MolecularAssembly assembly, double weight) read in a diffraction file based on the molecular assembly fileName, using a neutron value of falseDiffractionFile
(MolecularAssembly assembly, double weight, boolean neutron) read in a diffraction file based on the molecular assembly fileName, using a weight of 1.0 and neutron value of false