Uses of Class
ffx.potential.parameters.ForceField

Packages that use ForceField

Package	Description
ffx.algorithms.optimize	The Optimize package contains local and global optimization algorithms using pure Java and OpenMM code paths.
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.nonbonded	The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and Particle Mesh Ewald electrostastics.
ffx.potential.nonbonded.implicit
ffx.potential.nonbonded.pme
ffx.potential.openmm
ffx.potential.parameters	The Parameters package stores force field atom types, bond types, etc, and keywords that define the potential.
ffx.potential.parsers	The Parsers package handles reading/writing files to/from the internal data structure.

Uses of ForceField in ffx.algorithms.optimize

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

Modifier	Constructor	Description
	TitrationManyBody(String filename, ForceField forceField, List<Integer> resNumberList, double pH)

Uses of ForceField in ffx.potential

Fields in ffx.potential declared as ForceField

Modifier and Type	Field	Description
protected ForceField	MolecularAssembly.forceField

Methods in ffx.potential that return ForceField

Modifier and Type	Method	Description
ForceField	MolecularAssembly.getForceField()	Getter for the field forceField.

Methods in ffx.potential with parameters of type ForceField

Modifier and Type	Method	Description
void	MolecularAssembly.finalize(boolean finalizeGroups, ForceField forceField)	Abstract method that should specify how to finalize a MSGroup
void	MolecularAssembly.setForceField(ForceField forceField)	Setter for the field forceField.

Uses of ForceField in ffx.potential.bonded

Methods in ffx.potential.bonded with parameters of type ForceField

Modifier and Type	Method	Description
static void	AminoAcidUtils.assignAminoAcidAtomTypes(Residue residue, Residue previousResidue, Residue nextResidue, ForceField forceField, List<Bond> bondList)	assignAminoAcidAtomTypes.
static void	AminoAcidUtils.assignAminoAcidAtomTypes(List<Residue> residues, ForceField forceField, List<Bond> bondList)	Assign atom types to an amino acid polymer.
void	MSGroup.assignBondedTerms(ForceField forceField)	assignBondedTerms
void	MultiResidue.assignBondedTerms(ForceField forceField)	assignBondedTerms
static void	NucleicAcidUtils.assignNucleicAcidAtomTypes(List<Residue> residues, ForceField forceField, List<Bond> bondList)	Assign atom types for a nucleic acid polymer.
static Residue	AminoAcidUtils.buildAIB(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAIB.
static Residue	AminoAcidUtils.buildAlanine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAlanine.
static Residue	AminoAcidUtils.buildArginine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildArginine.
static Residue	AminoAcidUtils.buildAsparagine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAsparagine.
static Residue	AminoAcidUtils.buildAspartate(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildAspartate.
static Bond	BondedUtils.buildBond(Atom a1, Atom a2, ForceField forceField, List<Bond> bondList)	Build a bond between two atoms.
static Residue	AminoAcidUtils.buildCysteine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildCysteine.
static Residue	AminoAcidUtils.buildCystine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildCystine.
static Residue	AminoAcidUtils.buildDeprotonatedCysteine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildDeprotonatedCysteine.
static Residue	AminoAcidUtils.buildDeprotonatedLysine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildDeprotonatedLysine.
static Residue	AminoAcidUtils.buildDeprotonatedTyrosine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildDeprotonatedTyrosine.
static Residue	AminoAcidUtils.buildGlutamate(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildGlutamate.
static Residue	AminoAcidUtils.buildGlutamine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildGlutamine.
static Residue	AminoAcidUtils.buildGlycine(Residue res, Atom CA, Atom N, Atom C, AminoAcidUtils.ResiduePosition position, ForceField ff, List<Bond> bonds)	buildGlycine.
static Atom	BondedUtils.buildH(MSGroup residue, AminoAcidUtils.SideChainType atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, ForceField forceField, List<Bond> bondList)	Build a hydrogen atom.
static Atom	BondedUtils.buildH(MSGroup residue, String atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, int lookUp, ForceField forceField, List<Bond> bondList)	Build a hydrogen atom.
static Atom	BondedUtils.buildHeavy(MSGroup residue, AminoAcidUtils.SideChainType atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, ForceField forceField, List<Bond> bondList)	Build a heavy atom.
static Atom	BondedUtils.buildHeavy(MSGroup residue, String atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, int lookUp, ForceField forceField)	Build a heavy atom.
static Atom	BondedUtils.buildHeavy(MSGroup residue, String atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, int lookUp, ForceField forceField, List<Bond> bondList)	Build a heavy atom.
static Atom	BondedUtils.buildHeavy(MSGroup residue, String atomName, Atom bondedTo, int key, ForceField forceField, List<Bond> bondList)	Build a heavy atom.
static Residue	AminoAcidUtils.buildHistidine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildHistidine.
static Atom	BondedUtils.buildHydrogenAtom(MSGroup residue, String atomName, Atom ia, double bond, Atom ib, double angle1, Atom ic, double angle2, int chiral, AtomType atomType, ForceField forceField, List<Bond> bondList)	Build a hydrogen atom.
static Residue	AminoAcidUtils.buildIsoleucine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildIsoleucine.
static Residue	AminoAcidUtils.buildLeucine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildLeucine.
static Residue	AminoAcidUtils.buildLysine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildLysine.
static Residue	AminoAcidUtils.buildMethionine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bond)	buildMethionine.
static Residue	AminoAcidUtils.buildNeutralAsparticAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralAsparticAcid.
static Residue	AminoAcidUtils.buildNeutralGlutamicAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralGlutamicAcid.
static Residue	AminoAcidUtils.buildNeutralHistidineD(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralHistidineD.
static Residue	AminoAcidUtils.buildNeutralHistidineE(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildNeutralHistidineE.
static Residue	AminoAcidUtils.buildOrnithine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildOrnithine.
static Residue	AminoAcidUtils.buildPCA(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildPCA.
static Residue	AminoAcidUtils.buildPhenylalanine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildPhenylalanine.
static Residue	AminoAcidUtils.buildProline(Residue res, Atom CA, Atom N, Atom C, AminoAcidUtils.ResiduePosition position, ForceField ff, List<Bond> bonds)	buildProline.
static Residue	AminoAcidUtils.buildSerine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildSerine.
static Residue	AminoAcidUtils.buildThreonine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildThreonine.
static Residue	AminoAcidUtils.buildTryptophan(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bond)	buildTryptophan.
static Residue	AminoAcidUtils.buildTwoProtonAsparticAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildTwoProtonAsparticAcid.
static Residue	AminoAcidUtils.buildTwoProtonGlutamicAcid(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildTwoProtonGlutamicAcid.
static Residue	AminoAcidUtils.buildTyrosine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildTyrosine.
static Residue	AminoAcidUtils.buildValine(Residue res, Atom CA, Atom N, Atom C, ForceField ff, List<Bond> bonds)	buildValine.
Joint	MSGroup.createJoint(Bond bond, MSGroup group1, MSGroup group2, ForceField forceField)	Create a joint between two chemical groups.
Joint	MSGroup.createJoint(MSGroup group1, MSGroup group2, ForceField forceField)	Joiner joins Moieties m1 and m2 and returns the Geometry objects formed in a Joint.
Joint	MultiResidue.createJoint(Bond bond, MSGroup group1, MSGroup group2, ForceField forceField)	Create a joint between two chemical groups.
Joint	MultiResidue.createJoint(MSGroup group1, MSGroup group2, ForceField forceField)	Joiner joins Moieties m1 and m2 and returns the Geometry objects formed in a Joint.
Joint	Polymer.createJoint(Residue residue1, Residue residue2, ForceField forceField)
void	Molecule.finalize(boolean finalizeGeometry, ForceField forceField)	Abstract method that should specify how to finalize a MSGroup
abstract void	MSGroup.finalize(boolean finalizeGroups, ForceField forceField)	Abstract method that should specify how to finalize a MSGroup
void	MultiResidue.finalize(boolean finalizeGeometry, ForceField forceField)	Abstract method that should specify how to finalize a MSGroup
void	Polymer.finalize(boolean finalizeGroups, ForceField forceField)	Abstract method that should specify how to finalize a MSGroup
void	Residue.finalize(boolean finalizeGeometry, ForceField forceField)	Abstract method that should specify how to finalize a MSGroup
static AtomType	BondedUtils.findAtomType(int key, ForceField forceField)	findAtomType.
double	Atom.getCharge(ForceField ff)	Gets the partial atomic charge.
static void	Angle.logNoAngleType(Atom a1, Atom a2, Atom a3, ForceField forceField)	Log that no AngleType exists.
static void	Bond.logNoBondType(Atom a1, Atom a2, ForceField forceField)	Log that no BondType exists.
static void	Torsion.logNoTorsionType(Atom a0, Atom a1, Atom a2, Atom a3, ForceField forceField)	Log that no TorsionType exists.
static OutOfPlaneBend	OutOfPlaneBend.outOfPlaneBendFactory(Angle angle, ForceField forceField)	Attempt to create a new OutOfPlaneBend instance for a given Angle and Force Field.
static PiOrbitalTorsion	PiOrbitalTorsion.piOrbitalTorsionFactory(Bond bond, ForceField forceField)	Attempt to create a new PiOrbitalTorsion based on the supplied bond and forceField.
static StretchTorsion	StretchTorsion.stretchTorsionFactory(Torsion torsion, ForceField forceField)	Attempt to create a new StretchTorsion based on the supplied torsion.
static TorsionTorsion	TorsionTorsion.torsionTorsionFactory(Bond firstBond, Angle angle, Bond lastBond, ForceField forceField)	torsionTorsionFactory.
static UreyBradley	UreyBradley.ureyBradlyFactory(Angle angle, ForceField forceField)	Attempt to create a new UreyBradley for the specified Angle.

Constructors in ffx.potential.bonded with parameters of type ForceField

Modifier	Constructor	Description
	MultiResidue(Residue residue, ForceField forceField)	Constructor for MultiResidue.
	RelativeSolvation(RelativeSolvation.SolvationLibrary solvationLibrary, ForceField forceField)	Constructor for RelativeSolvation.
	Residue(String name, int resNumber, MSNode atoms, Residue.ResidueType residueType, ForceField forceField)	As above, with atoms being a MSNode with this Residue's atoms as child nodes

Uses of ForceField in ffx.potential.nonbonded

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

Modifier	Constructor	Description
	GeneralizedKirkwood(ForceField forceField, Atom[] atoms, ParticleMeshEwald particleMeshEwald, Crystal crystal, ParallelTeam parallelTeam, double gkCutoff)	Constructor for GeneralizedKirkwood.
	NCSRestraint(Atom[] atoms, ForceField forceField, Crystal crystal)	This NCSRestraint is based on the unit cell parameters and symmetry operators of the supplied crystal.
	ParticleMeshEwald(Atom[] atoms, int[] molecule, ForceField forceField, Crystal crystal, NeighborList neighborList, ForceField.ELEC_FORM elecForm, double ewaldCutoff, double gkCutoff, ParallelTeam parallelTeam)	ParticleMeshEwald constructor.
	ReciprocalSpace(ParticleMeshEwald particleMeshEwald, Crystal crystal, ForceField forceField, Atom[] atoms, double aewald, ParallelTeam fftTeam, ParallelTeam parallelTeam)	Reciprocal Space PME contribution.
	ScfPredictor(ScfPredictor.PredictorMode mode, int order, ForceField ff)	Constructor for ScfPredictor.
	VanDerWaals(Atom[] atoms, int[] molecule, boolean[] neuralNetwork, Crystal crystal, ForceField forceField, ParallelTeam parallelTeam, double vdwCutoff, double neighborListCutoff)	The VanDerWaals class constructor.
	VanDerWaalsForm(ForceField forceField)	Constructor for VanDerWaalsForm.
	VanDerWaalsTornado(Atom[] atoms, Crystal crystal, ForceField forceField, double vdwCutoff)	The VanDerWaalsTornado class constructor.

Uses of ForceField in ffx.potential.nonbonded.implicit

Constructors in ffx.potential.nonbonded.implicit with parameters of type ForceField

Modifier	Constructor	Description
	BornRadiiRegion(int nt, int nAtoms, ForceField forceField, boolean neckCorrection, boolean tanhCorrection, boolean perfectHCTScale)	BornRadiiRegion Constructor.
	ChandlerCavitation(Atom[] atoms, ConnollyRegion connollyRegion, ForceField forceField)
	ChandlerCavitation(Atom[] atoms, GaussVol gaussVol, ForceField forceField)
	DispersionRegion(int nt, Atom[] atoms, ForceField forceField)	DispersionRegion constructor.
	GaussVol(Atom[] atoms, ForceField forceField, ParallelTeam parallelTeam)	Creates/Initializes a GaussVol instance.

Uses of ForceField in ffx.potential.nonbonded.pme

Methods in ffx.potential.nonbonded.pme with parameters of type ForceField

Modifier and Type	Method	Description
void	SCFPredictorParameters.init(ForceField forceField)

Constructors in ffx.potential.nonbonded.pme with parameters of type ForceField

Modifier	Constructor	Description
	AlchemicalParameters(ForceField forceField, boolean lambdaTerm, boolean nnTerm, Polarization polarization)
	InducedDipoleFieldRegion(ParallelTeam parallelTeam, ForceField forceField, boolean lambdaTerm)
	InitializationRegion(ParticleMeshEwald particleMeshEwald, int maxThreads, ForceField forceField)
	PCGSolver(int maxThreads, double poleps, ForceField forceField, int nAtoms)	Constructor the PCG solver.
	PermanentFieldRegion(ParallelTeam pt, ForceField forceField, boolean lambdaTerm)
	RealSpaceEnergyRegion(ForceField.ELEC_FORM elecForm, int nt, ForceField forceField, boolean lambdaTerm, double electric)
	ReduceRegion(int threadCount, ForceField forceField)
	ScaleParameters(ForceField.ELEC_FORM elecForm, ForceField forceField)
	SORRegion(int nt, ForceField forceField)

Uses of ForceField in ffx.potential.openmm

Methods in ffx.potential.openmm that return ForceField

Modifier and Type	Method	Description
ForceField	OpenMMSystem.getForceField()	Get the ForceField in use.

Methods in ffx.potential.openmm with parameters of type ForceField

Modifier and Type	Method	Description
static LangevinIntegrator	OpenMMIntegrator.createLangevinIntegrator(double dt, double temperature, ForceField forceField)	Create a Langevin integrator.

Uses of ForceField in ffx.potential.parameters

Methods in ffx.potential.parameters with parameters of type ForceField

Modifier and Type	Method	Description
void	ForceField.append(ForceField patch)	Append a 2nd ForceField "patch" to the current ForceField.
static boolean	MultipoleType.assignMultipole(ForceField.ELEC_FORM elecForm, Atom atom, ForceField forceField, double[] multipole, int i, int[][] axisAtom, MultipoleType.MultipoleFrameDefinition[] frame)	Assign the multipole type.
static SoluteType	SoluteType.getFitSoluteType(ForceField forceField, int type)
static SoluteType	SoluteType.getSoluteType(Atom atom, ForceField forceField, SoluteType.SOLUTE_RADII_TYPE soluteRadiiType)
static MultipoleType	MultipoleType.multipoleTypeFactory(ForceField.ELEC_FORM elecForm, Atom atom, ForceField forceField)	multipoleTypeFactory.
static void	SoluteType.setSoluteRadii(ForceField forceField, Atom[] atoms, SoluteType.SOLUTE_RADII_TYPE soluteRadiiType)

Constructors in ffx.potential.parameters with parameters of type ForceField

Modifier	Constructor	Description
	TitrationUtils(ForceField forceField)
	TitrationUtils(ForceField forceField, double proteinDielectric, boolean tanhCorrection)

Uses of ForceField in ffx.potential.parsers

Fields in ffx.potential.parsers declared as ForceField

Modifier and Type	Field	Description
protected ForceField	SystemFilter.forceField	The molecular mechanics force field being used.

Methods in ffx.potential.parsers that return ForceField

Modifier and Type	Method	Description
ForceField	ForceFieldFilter.parse()	parse

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

Modifier and Type	Method	Description
void	SystemFilter.setForceField(ForceField forceField)	Setter for the field forceField.

Constructors in ffx.potential.parsers with parameters of type ForceField

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(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.
	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.
	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.
	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(File file, List<MolecularAssembly> molecularAssemblies, ForceField forceField, org.apache.commons.configuration2.CompositeConfiguration properties)	Parse the PDB File from a URL.
	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(File file, List<MolecularAssembly> molecularAssemblies, 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.