Uses of Class
ffx.potential.MolecularAssembly

Packages that use MolecularAssembly

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.commands
ffx.algorithms.dynamics	The Dynamics package implements molecular and stochastic dynamics using a pure Java code path and via OpenMM.
ffx.algorithms.dynamics.integrators	The Integrators package implements integrators for molecular dynamics simulations.
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	The anneal package implements simulated annealing-based optimization, including an interface for annealing schedules and several concrete schedule implementations (linear, exponential, and flat-end) used to control temperature during optimization runs.
ffx.algorithms.optimize.manybody	The manybody package implements many-body rotamer optimization infrastructure, including distance matrices, an energy expansion (self, two-body, three-body, and four-body), Dead-end elimination criteria, Goldstein elimination criteria, and supporting data structures for efficient optimization.
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.potential	The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
ffx.potential.bonded	The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
ffx.potential.cli	The Potential CLI package defines reusable options for PicoCLI command line scripts.
ffx.potential.commands
ffx.potential.extended	The Extended package is progress toward support for constant pH molecular dynamics using extended system variables (i.e. lambda dynamics on protonation).
ffx.potential.nonbonded	The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and Particle Mesh Ewald electrostastics.
ffx.potential.openmm	The openmm package contains utilities to construct and run Force Field X potentials on the OpenMM platform, including system builders, custom forces, alchemical fixed-charge forces, and integrators tailored to FFX simulations.
ffx.potential.parsers	The Parsers package handles reading/writing files to/from the internal data structure.
ffx.potential.terms	The terms package contains analytical potential energy terms and their gradients for bonded interactions (bond, angle, stretch-bend, torsions, impropers, Urey-Bradley) and restraint terms used by Force Field X.
ffx.potential.utils	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.
ffx.realspace	The Real Space package implements real space structure refinement.
ffx.realspace.cli	The Real Space CLI package defines options for PicoCLI command line scripts.
ffx.realspace.parsers	The Parsers package reads and writes CCP4 map files.
ffx.ui	The UI package provides views and controllers for manipulating molecular systems.
ffx.ui.commands	The Commands package implements a Client/Server interface between Force Field X and simulations.
ffx.xray	The X-ray package implements support for X-ray and Neutron refinement.
ffx.xray.cli	The X-ray CLI package defines options for PicoCLI command line scripts.
ffx.xray.parsers	The Parsers package reads CNS files and reads/writes MTZ files.

Uses of MolecularAssembly in ffx.algorithms

Methods in ffx.algorithms with parameters of type MolecularAssembly

Modifier and Type	Method	Description
boolean	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.
Potential	AlgorithmFunctions.minimize(MolecularAssembly assembly, double eps)	Relax the coordinates of a MolecularAssembly and minimize its potential energy
Potential	AlgorithmUtils.minimize(MolecularAssembly assembly, double eps)	Relax the coordinates of a MolecularAssembly and minimize its potential energy

Constructors in ffx.algorithms with parameters of type MolecularAssembly

Modifier	Constructor	Description
	ParallelStateEnergy(int nStates, double[] lambdaValues, MolecularAssembly[] molecularAssemblies, Potential potential, String[][] fullFilePaths, SystemFilter[] openers)	The ParallelEnergy constructor.

Uses of MolecularAssembly in ffx.algorithms.cli

Fields in ffx.algorithms.cli declared as MolecularAssembly

Modifier and Type	Field	Description
MolecularAssembly	AlgorithmsCommand.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 MolecularAssembly

Modifier and Type	Method	Description
MolecularAssembly[]	AlgorithmsCommand.getActiveAssemblies(String filename)	If a filename is supplied, open it and return the MolecularAssemblies.
MolecularAssembly	AlgorithmsCommand.getActiveAssembly(String filename)	If a filename is supplied, open it and return the MolecularAssembly.
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 MolecularAssembly

Modifier and Type	Method	Description
CrystalPotential	OSTOptions.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).
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.
CrystalPotential	BarostatOptions.checkNPT(MolecularAssembly molecularAssembly, CrystalPotential crystalPotential)	If pressure has been set > 0, creates a Barostat around a CrystalPotential, else returns the original, unmodified CrystalPotential.
List<Residue>	ManyBodyOptions.collectResidues(MolecularAssembly activeAssembly)	Collect residues based on residue selection flags.
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.
Barostat	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.
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.
void	ManyBodyOptions.initRotamerOptimization(RotamerOptimization rotamerOptimization, MolecularAssembly activeAssembly)	initRotamerOptimization.
void	RandomUnitCellOptions.randomize(MolecularAssembly assembly)	Randomize the unit cell for a MolecularAssembly.
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.
void	AlgorithmsCommand.setActiveAssembly(MolecularAssembly molecularAssembly)	Set the Active Assembly.
MonteCarloOST	OSTOptions.setupMCOST(OrthogonalSpaceTempering orthogonalSpaceTempering, MolecularAssembly[] molecularAssemblies, DynamicsOptions dynamicsOptions, ThermodynamicsOptions thermodynamicsOptions, boolean verbose, File dynRestart, AlgorithmListener algorithmListener)	setupMCOST.

Uses of MolecularAssembly in ffx.algorithms.commands

Fields in ffx.algorithms.commands declared as MolecularAssembly

Modifier and Type	Field	Description
MolecularAssembly[]	Thermodynamics.topologies

Uses of MolecularAssembly in ffx.algorithms.dynamics

Fields in ffx.algorithms.dynamics declared as MolecularAssembly

Modifier and Type	Field	Description
protected MolecularAssembly[]	MolecularDynamics.molecularAssembly	MolecularAssembly to run dynamics on.

Methods in ffx.algorithms.dynamics that return MolecularAssembly

Modifier and Type	Method	Description
MolecularAssembly[]	MolecularDynamics.getAssemblyArray()	Returns the MolecularAssembly array.

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

Modifier and Type	Method	Description
void	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 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 MolecularAssembly

Modifier	Constructor	Description
	Barostat(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 a 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 MolecularAssembly

Modifier and Type	Method	Description
void	Rattle.postForce1(MolecularAssembly molAss, double dt)	postForce1.

Constructors in ffx.algorithms.dynamics.integrators with parameters of type MolecularAssembly

Modifier	Constructor	Description
	Rattle(int nVariables, MolecularAssembly molAss, double[] v)	Constructor for Rattle.

Uses of MolecularAssembly in ffx.algorithms.mc

Methods in ffx.algorithms.mc that return MolecularAssembly

Modifier and Type	Method	Description
MolecularAssembly	MolecularMC.getMolecularAssembly()	Returns the associated MolecularAssembly.

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

Modifier	Constructor	Description
	MDMove(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 MolecularAssembly

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 MolecularAssembly in ffx.algorithms.optimize

Fields in ffx.algorithms.optimize declared as MolecularAssembly

Modifier and Type	Field	Description
protected final MolecularAssembly	Minimize.molecularAssembly	The MolecularAssembly being operated on.
protected final MolecularAssembly	PhMinimize.molecularAssembly	The MolecularAssembly being operated on.
protected MolecularAssembly	RotamerOptimization.molecularAssembly	MolecularAssembly to perform rotamer optimization on.

Methods in ffx.algorithms.optimize that return MolecularAssembly

Modifier and Type	Method	Description
MolecularAssembly[]	TitrationManyBody.getProtonatedAssemblies()
MolecularAssembly	TitrationManyBody.getProtonatedAssembly()

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

Modifier and Type	Method	Description
static Minimize.MinimizationEngine	Minimize.defaultEngine(MolecularAssembly molecularAssembly, Potential potentialEnergy)
boolean	TitrationManyBody.excludeExcessAtoms(Set<Atom> excludeAtoms, int[] optimalRotamers, MolecularAssembly molecularAssembly, List<Residue> residueList)
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 MolecularAssembly

Modifier	Constructor	Description
	ConformationScan(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 MolecularAssembly

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 MolecularAssembly in ffx.algorithms.optimize.manybody

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

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 MolecularAssembly

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 MolecularAssembly in ffx.algorithms.thermodynamics

Fields in ffx.algorithms.thermodynamics declared as MolecularAssembly

Modifier and Type	Field	Description
protected MolecularAssembly	OrthogonalSpaceTempering.molecularAssembly	The MolecularAssembly being simulated.

Methods in ffx.algorithms.thermodynamics with parameters of type MolecularAssembly

Modifier and Type	Method	Description
void	OrthogonalSpaceTempering.setMolecularAssembly(MolecularAssembly molecularAssembly)
void	OrthogonalSpaceTempering.OptimizationParameters.setOptimization(boolean doOptimization, MolecularAssembly molecularAssembly)	setOptimization.

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

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.

Uses of MolecularAssembly in ffx.potential

Fields in ffx.potential declared as MolecularAssembly

Modifier and Type	Field	Description
protected final MolecularAssembly	ForceFieldEnergy.molecularAssembly	The MolecularAssembly associated with this force field energy.

Methods in ffx.potential that return MolecularAssembly

Modifier and Type	Method	Description
MolecularAssembly	AssemblyState.getMolecularAssembly()	Returns the MolecularAssembly associated with this AssemblyState.
MolecularAssembly	ForceFieldEnergy.getMolecularAssembly()	Get the MolecularAssembly associated with this ForceFieldEnergy.

Methods in ffx.potential with parameters of type MolecularAssembly

Modifier and Type	Method	Description
static 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 DualTopologyEnergy	DualTopologyEnergy.energyFactory(MolecularAssembly molecularAssembly1, MolecularAssembly molecularAssembly2, UnivariateSwitchingFunction switchFunction)	Static factory method to create a DualTopologyEnergy, possibly via FFX or OpenMM implementations.
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 MolecularAssembly

Modifier	Constructor	Description
	ANIEnergy(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 MolecularAssembly

Modifier and Type	Method	Description
static List<Bond>	PolymerUtils.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.
static List<Bond>	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 RestrainPosition[]	RestrainPosition.parseRestrainPositions(MolecularAssembly molecularAssembly)
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.
File	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 MolecularAssembly

Modifier and Type	Field	Description
MolecularAssembly	PotentialCommand.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 MolecularAssembly

Modifier and Type	Method	Description
MolecularAssembly[]	PotentialCommand.getActiveAssemblies(String filename)	If a filename is supplied, open it and return the MolecularAssemblies.
MolecularAssembly	PotentialCommand.getActiveAssembly(String filename)	If a filename is supplied, open it and return the MolecularAssembly.
MolecularAssembly	AlchemicalOptions.openFile(PotentialsFunctions potentialFunctions, TopologyOptions topologyOptions, int threadsPer, String toOpen, int topNum)	Opens a File to a MolecularAssembly for alchemistry.
MolecularAssembly	AlchemicalOptions.processFile(TopologyOptions topologyOptions, MolecularAssembly molecularAssembly, int topNum)	Performs processing on a MolecularAssembly for alchemistry.

Methods in ffx.potential.cli with parameters of type MolecularAssembly

Modifier and Type	Method	Description
static void	AtomSelectionOptions.actOnAtoms(MolecularAssembly assembly, String selection, BiConsumer<Atom,Boolean> action, String description)
static void	AtomSelectionOptions.actOnResidueAtoms(MolecularAssembly assembly, String selection, BiConsumer<Atom,Boolean> action, String description)
Potential	TopologyOptions.assemblePotential(MolecularAssembly[] assemblies, StringBuilder sb)	Performs the bulk of the work of setting up a multi-topology system.
Potential	TopologyOptions.getTopology(MolecularAssembly[] topologies, UnivariateSwitchingFunction sf, List<Integer> uniqueA, List<Integer> uniqueB, int numParallel, StringBuilder sb)	Configure a Dual-, Quad- or Oct- Topology.
static List<Integer>	TopologyOptions.getUniqueAtoms(MolecularAssembly assembly, String label, String unshared)	Collect unique atoms for a dual-topology.
List<Integer>	TopologyOptions.getUniqueAtomsA(MolecularAssembly topology)	Collect unique atoms for the A dual-topology.
List<Integer>	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.
MolecularAssembly	AlchemicalOptions.processFile(TopologyOptions topologyOptions, MolecularAssembly molecularAssembly, int topNum)	Performs processing on a MolecularAssembly for alchemistry.
File	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	AtomSelectionOptions.setActiveAtoms(MolecularAssembly molecularAssembly)	Set active atoms for a MolecularAssembly.
static void	AlchemicalOptions.setAlchemicalAtoms(MolecularAssembly assembly, String alchemicalAtoms, String alchemicalResidues)	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.commands

Fields in ffx.potential.commands declared as MolecularAssembly

Modifier and Type	Field	Description
MolecularAssembly	PhEnergy.mola
protected MolecularAssembly[]	MoveIntoUnitCell.molecularAssemblies	Save a reference to the MolecularAssembly instances to destroy their potentials.

Uses of MolecularAssembly in ffx.potential.extended

Constructors in ffx.potential.extended with parameters of type MolecularAssembly

Modifier	Constructor	Description
	ExtendedSystem(MolecularAssembly mola, double pH, File esvFile)	Construct extended system with the provided configuration.

Uses of MolecularAssembly in ffx.potential.nonbonded

Constructors in ffx.potential.nonbonded with parameters of type MolecularAssembly

Modifier	Constructor	Description
	COMRestraint(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 MolecularAssembly

Modifier and Type	Method	Description
MolecularAssembly	OpenMMDualTopologyEnergy.getMolecularAssembly(int topology)	Get the MolecularAssembly.
MolecularAssembly	OpenMMEnergy.getMolecularAssembly()	Returns the MolecularAssembly instance.

Constructors in ffx.potential.openmm with parameters of type MolecularAssembly

Modifier	Constructor	Description
	OpenMMDualTopologyEnergy(MolecularAssembly topology1, MolecularAssembly topology2, UnivariateSwitchingFunction switchFunction, Platform requestedPlatform)	Constructor for DualTopologyEnergy.
	OpenMMEnergy(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 MolecularAssembly

Modifier and Type	Field	Description
protected List<MolecularAssembly>	SystemFilter.systems	All MolecularAssembly instances defined.

Methods in ffx.potential.parsers that return MolecularAssembly

Modifier and Type	Method	Description
MolecularAssembly	SystemFilter.getActiveMolecularSystem()	Return the MolecularSystem that has been read in
MolecularAssembly[]	FileOpener.getAllAssemblies()	getAllAssemblies.
MolecularAssembly	FileOpener.getAssembly()	getAssembly.
MolecularAssembly[]	SystemFilter.getMolecularAssemblyArray()	Get the MolecularAssembly array.

Methods in ffx.potential.parsers with parameters of type MolecularAssembly

Modifier and Type	Method	Description
static boolean	XPHFilter.readOnto(File newFile, MolecularAssembly oldSystem)	readOnto
static boolean	XYZFilter.readOnto(File newFile, MolecularAssembly oldSystem)	readOnto
void	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 MolecularAssembly

Modifier	Constructor	Description
	CIFFilter(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.
	InducedFilter(MolecularAssembly s, File f)	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 MolecularAssembly

Modifier	Constructor	Description
	CIFFilter(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.terms

Constructors in ffx.potential.terms with parameters of type MolecularAssembly

Modifier	Constructor	Description
	EnergyTermRegion(ParallelTeam parallelTeam, MolecularAssembly molecularAssembly, boolean lambdaTerm)	Constructor for BondedRegion.

Uses of MolecularAssembly in ffx.potential.utils

Methods in ffx.potential.utils that return MolecularAssembly

Modifier and Type	Method	Description
default MolecularAssembly	PotentialsFunctions.getActiveAssembly()	Returns either the active assembly from the overlying UI, or the "active" molecular assembly from the last used SystemFilter.
MolecularAssembly[]	PotentialsFileOpener.getAllAssemblies()	getAllAssemblies.
MolecularAssembly	PotentialsFileOpener.getAssembly()	getAssembly.
default MolecularAssembly	PotentialsFunctions.open(String filename)	open.
default MolecularAssembly[]	PotentialsFunctions.open(String[] files, int nThreads)	Opens an array of files and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads.
MolecularAssembly	PotentialsUtils.open(File file)	Return one MolecularAssembly.
MolecularAssembly	PotentialsUtils.open(String filename)	open.
MolecularAssembly[]	PotentialsUtils.open(String[] files, int nThreads)	Opens an array of files and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads.
MolecularAssembly[]	PotentialsFunctions.openAll(String file)	Opens a file and returns all created MolecularAssembly objects.
MolecularAssembly[]	PotentialsFunctions.openAll(String[] files)	Opens an array of files and returns the created MolecularAssembly objects.
default MolecularAssembly[]	PotentialsFunctions.openAll(String file, int nThreads)	Opens a file and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads.
MolecularAssembly[]	PotentialsUtils.openAll(String file)	Opens a file and returns all created MolecularAssembly objects.
MolecularAssembly[]	PotentialsUtils.openAll(String[] files)	Opens an array of files and returns the created MolecularAssembly objects.
MolecularAssembly[]	PotentialsUtils.openAll(String file, int nThreads)	Opens a file and returns all created MolecularAssembly objects, setting any underlying Potential to use a certain number of threads.
MolecularAssembly	PotentialsUtils.openQuietly(String filename)	Open one filename string without printing all the header material.
MolecularAssembly	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 MolecularAssembly

Modifier and Type	Method	Description
void	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.
ForceFieldEnergy	PotentialsFunctions.energy(MolecularAssembly assembly)	Evaluates the energy of a MolecularAssembly and returns its ForceFieldEnergy object.
ForceFieldEnergy[]	PotentialsFunctions.energy(MolecularAssembly[] molecularAssemblies)	Evaluates the energy of each MolecularAssembly and returns their ForceFieldEnergy instances.
ForceFieldEnergy	PotentialsUtils.energy(MolecularAssembly molecularAssembly)	Evaluates the energy of a MolecularAssembly and returns its ForceFieldEnergy object.
ForceFieldEnergy[]	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 evaluation
double	PotentialsUtils.returnEnergy(MolecularAssembly assembly)	Returns the energy of a MolecularAssembly in kcal/mol (as a double) and prints the energy evaluation
void	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 MolecularAssembly

Modifier	Constructor	Description
	GetProteinFeatures(MolecularAssembly molecularAssembly)
	Loop(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 MolecularAssembly

Modifier and Type	Method	Description
MolecularAssembly[]	RealSpaceData.getMolecularAssemblies()	getMolecularAssemblies

Constructors in ffx.realspace with parameters of type MolecularAssembly

Modifier	Constructor	Description
	RealSpaceData(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 MolecularAssembly

Modifier and Type	Method	Description
List<RealSpaceFile>	RealSpaceOptions.processData(List<String> filenames, MolecularAssembly molecularAssembly)	Process input to collect Real Space Files.
RefinementEnergy	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 MolecularAssembly

Modifier	Constructor	Description
	RealSpaceFile(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.ui

Modifier and Type	Class	Description
class	FFXSystem	The FFXSystem class contains extensions to the generic MolecularAssembly class.

Methods in ffx.ui that return MolecularAssembly

Modifier and Type	Method	Description
MolecularAssembly	UIUtils.getActiveAssembly()
MolecularAssembly[]	UIFileOpener.getAllAssemblies()	Returns all MolecularAssemblys in the user interface hierarchy.
MolecularAssembly	UIFileOpener.getAssembly()	Returns the active MolecularAssembly from the user interface hierarchy.
MolecularAssembly	Trajectory.getFSystem()	getFSystem
MolecularAssembly[]	MainPanel.openWaitUtils(String file)
MolecularAssembly	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 MolecularAssembly

Modifier and Type	Method	Description
boolean	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)
ForceFieldEnergy	UIUtils.energy(MolecularAssembly molecularAssembly)
void	UIUtils.md(MolecularAssembly assembly, int nStep, double timeStep, double printInterval, double saveInterval, double temperature, boolean initVelocities, File dyn)
Potential	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 MolecularAssembly

Modifier	Constructor	Description
	Trajectory(MolecularAssembly mol, MainPanel f)	Constructor for Trajectory.

Uses of MolecularAssembly in ffx.ui.commands

Constructors in ffx.ui.commands with parameters of type MolecularAssembly

Modifier	Constructor	Description
	SimulationFilter(SimulationDefinition sys, MolecularAssembly m)	Constructor for SimulationFilter.

Uses of MolecularAssembly in ffx.xray

Methods in ffx.xray that return MolecularAssembly

Modifier and Type	Method	Description
MolecularAssembly[]	DiffractionData.getAssembly()	Getter for the field assembly.
MolecularAssembly[]	DataContainer.getMolecularAssemblies()	getMolecularAssemblies
MolecularAssembly[]	DiffractionData.getMolecularAssemblies()	getMolecularAssemblies

Methods in ffx.xray with parameters of type MolecularAssembly

Modifier and Type	Method	Description
boolean	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 factors

Constructors in ffx.xray with parameters of type MolecularAssembly

Modifier	Constructor	Description
	DiffractionData(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 assembly
	DiffractionData(MolecularAssembly[] assembly, org.apache.commons.configuration2.CompositeConfiguration properties, CrystalReciprocalSpace.SolventModel solventmodel, DiffractionFile... datafile)	construct a diffraction data assembly
	DiffractionData(MolecularAssembly[] assembly, org.apache.commons.configuration2.CompositeConfiguration properties, DiffractionFile... datafile)	construct a diffraction data assembly
	DiffractionData(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 assembly
	DiffractionData(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 assembly
	DiffractionData(MolecularAssembly assembly, org.apache.commons.configuration2.CompositeConfiguration properties, CrystalReciprocalSpace.SolventModel solventmodel, DiffractionFile... datafile)	construct a diffraction data assembly
	DiffractionData(MolecularAssembly assembly, org.apache.commons.configuration2.CompositeConfiguration properties, DiffractionFile... datafile)	construct a diffraction data assembly
	RefinementModel(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 MolecularAssembly

Modifier and Type	Method	Description
DiffractionData	XrayOptions.getDiffractionData(List<String> filenames, MolecularAssembly[] assemblies, org.apache.commons.configuration2.CompositeConfiguration properties)	Process input from opened molecular assemblies to a DiffractionData.
List<DiffractionFile>	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 MolecularAssembly

Modifier	Constructor	Description
	DiffractionFile(MolecularAssembly assembly)	read in a diffraction file based on the molecular assembly fileName, using a weight of 1.0 and neutron value of false
	DiffractionFile(MolecularAssembly[] assembly)	read in a diffraction file based on the molecular assembly fileName, using a weight of 1.0 and neutron value of false
	DiffractionFile(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 false
	DiffractionFile(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