Uses of Annotation Interface
ffx.utilities.FFXProperty

Packages that use FFXProperty

Package	Description
ffx.crystal	The Crystal package implements space group symmetry and periodic boundary condition support.
ffx.potential	The Potential package implements molecular mechanics force fields with shared memory Parallel Java and via OpenMM.
ffx.potential.nonbonded	The Nonbonded package implements nonbonded molecular mechanics terms such as van der Waals and Particle Mesh Ewald electrostastics.
ffx.potential.nonbonded.pme	The pme package implements polarization and permanent electrostatics using Particle Mesh Ewald (PME).
ffx.potential.parameters	The Parameters package stores force field atom types, bond types, etc, and keywords that define the potential.
ffx.xray.cli	The X-ray CLI package defines options for PicoCLI command line scripts.

Uses of FFXProperty in ffx.crystal

Fields in ffx.crystal with annotations of type FFXProperty

Modifier and Type	Field	Description
double	Crystal.a	Length of the cell edge in the direction of the a basis vector.
double	Crystal.alpha	The interaxial lattice angle between b and c.
double	Crystal.b	Length of the cell edge in the direction of the b basis vector.
double	Crystal.beta	The interaxial lattice angle between a and c.
double	Crystal.c	Length of the cell edge in the direction of the c basis vector.
double	Crystal.gamma	The interaxial lattice angle between a and b.
final SpaceGroup	Crystal.spaceGroup	The space group of the crystal.

Uses of FFXProperty in ffx.potential

Fields in ffx.potential with annotations of type FFXProperty

Modifier and Type	Field	Description
protected boolean	ForceFieldEnergy.lambdaTerm	Indicates use of the Lambda state variable.

Uses of FFXProperty in ffx.potential.nonbonded

Fields in ffx.potential.nonbonded with annotations of type FFXProperty

Modifier and Type	Field	Description
final double	VanDerWaalsForm.delta	Second constant suggested by Halgren for the Buffered-14-7 potential.
double	ParticleMeshEwald.electric	Coulomb constant in units of kcal*Ang/(mol*electron^2)
VDWType.EPSILON_RULE	VanDerWaalsForm.epsilonRule	Epsilon combining rule.
final double	VanDerWaalsForm.gamma	First constant suggested by Halgren for the Buffered-14-7 potential.
final double	GeneralizedKirkwood.gkc	The Generalized Kirkwood cross-term parameter.
VDWType.RADIUS_RULE	VanDerWaalsForm.radiusRule	Radius combining rule.
VDWType.RADIUS_SIZE	VanDerWaalsForm.radiusSize	Radius size in the parameter file (radius or diameter).
VDWType.RADIUS_TYPE	VanDerWaalsForm.radiusType	Radius type in the parameter file (R-Min or Sigma).
protected double	VanDerWaalsForm.scale12	Define scale factors between 1-2 atoms.
protected double	VanDerWaalsForm.scale13	Define scale factors between 1-3 atoms.
protected double	VanDerWaalsForm.scale14	Define scale factors between 1-4 atoms.
VDWType.VDW_TYPE	VanDerWaalsForm.vdwType	van der Waals functional form.

Uses of FFXProperty in ffx.potential.nonbonded.pme

Classes in ffx.potential.nonbonded.pme with annotations of type FFXProperty

Modifier and Type	Class	Description
enum	Polarization

Fields in ffx.potential.nonbonded.pme with annotations of type FFXProperty

Modifier and Type	Field	Description
double	EwaldParameters.aewald
final double	ScaleParameters.d11scale	DIRECT-11-SCALE factor.
final double	ScaleParameters.d12scale	The DIRECT_12_SCALE factor is assumed to be 1.0.
final double	ScaleParameters.d13scale	The DIRECT_13_SCALE factor is assumed to be 1.0.
final double	ScaleParameters.d14scale	The DIRECT_14_SCALE factor is assumed to be 1.0.
final double	ScaleParameters.intra12Scale	An intra-12-scale factor other than 0.0 is not supported and will cause FFX to exit.
final double	ScaleParameters.intra13Scale	An intra-13-scale factor other than 0.0 is not supported and will cause FFX to exit.
final double	ScaleParameters.intra14Scale	Provides a multiplicative scale factor that is applied to polarization interactions between 1-4 connected atoms located in the same polarization group.
final double	ScaleParameters.intra15Scale	An intra-15-scale factor other than 1.0 is not supported and will cause FFX to exit.
final double	ScaleParameters.p12scale	The interaction energy between a permanent multipole and polarizable site that are 1-2 is scaled by p12scale.
final double	ScaleParameters.p13scale	The interaction energy between a permanent multipole and polarizable site that are 1-3 is scaled by p13scale.
final double	ScaleParameters.p14scale	The interaction energy between a permanent multipole and polarizable site that are 1-4 is scaled by p14scale.
final double	ScaleParameters.p15scale	The interaction energy between a permanent multipole and polarizable site that are 1-5 is scaled by p15scale.

Uses of FFXProperty in ffx.potential.parameters

Classes in ffx.potential.parameters with annotations of type FFXProperty

Modifier and Type	Class	Description
final class	AngleTorsionType	The AngleTorsionType class defines one angle-torsion energy type.
final class	AtomType	The AtomType class represents one molecular mechanics atom type.
final class	BioType	The BioType class maps PDB identifiers to atom types.
final class	BondType	The BondType class defines one harmonic bond stretch energy term.
final class	ChargeType	The ChargeType class defines a partial atomic charge type.
class	ForceField	The ForceField class organizes parameters for a molecular mechanics force field.
final class	ImproperTorsionType	The ImproperTorsionType class defines an improper torsion.
final class	MultipoleType	The MultipoleType class defines a multipole in its local frame.
final class	OutOfPlaneBendType	The OutOfPlaneBendType class defines one Allinger style out-of-plane angle bending energy type.
final class	PiOrbitalTorsionType	The PiOrbitalTorsionType class defines a Pi-Orbital Torsion energy term.
final class	PolarizeType	The PolarizeType class defines an isotropic atomic polarizability.
final class	SoluteType	The SoluteType class defines one implicit solvent radius.
final class	StretchBendType	The StretchBendType class defines one out-of-plane angle bending energy type.
final class	StretchTorsionType	The StretchTorsionType class defines one stretch-torsion energy type.
final class	TorsionTorsionType	The TorsionTorsionType class defines a Torsion-Torsion spline.
final class	UreyBradleyType	The UreyBradleyType class defines one harmonic UreyBradley cross term.
final class	VDWPairType	The VDWPairType class defines a van der Waals Pair type.

Fields in ffx.potential.parameters with annotations of type FFXProperty

Modifier and Type	Field	Description
double	AngleType.angleUnit	Convert angle bending energy to kcal/mole.
double	AngleTorsionType.angtorunit	Convert angle-torsion to kcal/mole.
double	BondType.bondUnit	Convert bond stretch energy to kcal/mole.
double	AngleType.cubic	Cubic coefficient in angle bending potential.
double	BondType.cubic	Cubic coefficient in bond stretch potential.
double	OutOfPlaneBendType.cubic	Cubic coefficient in out-of-plane angle bending potential.
double	UreyBradleyType.cubic	Cubic coefficient in bond stretch potential.
double	ImproperTorsionType.impTorUnit	Convert angle bending energy to kcal/mole.
double	OutOfPlaneBendType.opBendUnit	Convert Out-of-Plane bending energy to kcal/mole.
double	AngleType.pentic	Pentic coefficient in angle bending potential.
double	OutOfPlaneBendType.pentic	Quintic coefficient in out-of-plane angle bending potential.
double	PiOrbitalTorsionType.piTorsUnit	Convert Pi-Torsion energy to kcal/mole.
double	AngleType.quartic	Quartic coefficient in angle bending potential.
double	BondType.quartic	Quartic coefficient in bond stretch potential.
double	OutOfPlaneBendType.quartic	Quartic coefficient in out-of-plane angle bending potential.
double	UreyBradleyType.quartic	Quartic coefficient in bond stretch potential.
double	AngleType.sextic	Sextic coefficient in angle bending potential.
double	OutOfPlaneBendType.sextic	Sextic coefficient in out-of-plane angle bending potential.
double	StretchBendType.strbndunit
double	StretchTorsionType.strTorUnit	Unit conversion.
double	TorsionType.torsionUnit	Unit conversion.
double	TorsionTorsionType.torTorUnit	Convert Torsion-Torsion energy to kcal/mole.
double	UreyBradleyType.ureyUnit	Convert Urey-Bradley stretch energy to kcal/mole.

Uses of FFXProperty in ffx.xray.cli

Fields in ffx.xray.cli with annotations of type FFXProperty

Modifier and Type	Field	Description
protected double	DataRefinementOptions.wA	--wA or --dataWeight The weight of the data (wA).