Uses of Interface
ffx.potential.bonded.ROLS

Packages that use ROLS

Package	Description
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.ui	The UI package provides views and controllers for manipulating molecular systems.

Uses of ROLS in ffx.potential

Classes in ffx.potential that implement ROLS

Modifier and Type	Class	Description
class	MolecularAssembly	The MolecularAssembly class is a collection of Polymers, Hetero Molecules, Ions and Water

Uses of ROLS in ffx.potential.bonded

Classes in ffx.potential.bonded that implement ROLS

Modifier and Type	Class	Description
class	Angle	The Angle class represents an angle formed between three linearly bonded atoms.
class	AngleTorsion	The AngleTorsion class represents an angle torsion coupling between four bonded atoms.
class	Atom	The Atom class represents a single atom and defines its alternate conformations and molecular mechanics atom type.
class	Bond	The Bond class represents a covalent bond formed between two atoms.
class	BondedTerm	The BondedTerm class is extended by all Valence Geometry classes (bond, angle, dihedral, torsion, etc.).
class	ImproperTorsion	The ImproperTorsion class represents an Improper Torsion.
class	Joint	The Joint class contains the geometry produced by the FGroup Joiner method.
class	Molecule	The Molecule class is a general container used for simple compounds or in cases where more specialized classes have not been implemented.
class	MSGroup	The MSGroup class has one sub-node containing atoms, and one that contains molecular mechanics/geometry terms.
class	MSNode	The MSNode class forms the basic unit that all data classes extend.
class	MSRoot	The MSRoot class is the root of the Force Field X data structure.
class	MultiResidue	The MultiResidue class allows switching between residues for uses such as sequence optimization.
class	OutOfPlaneBend	The OutOfPlaneBend class represents an Out-Of-Plane Bend.
class	PiOrbitalTorsion	The Pi-Orbital Torsion class.
class	Polymer	The Polymer class encapsulates a peptide or nucleotide chain.
class	Residue	The Residue class represents individual amino acids or nucleic acid bases.
class	RestrainDistance	RestraintBond class.
class	RestraintTorsion
class	ROLSP	The ROLSP class is used for Proof-Of-Concept Parallel Recusive Over Length Scales (ROLS) Methods (currently only on shared memory systems).
class	StretchBend	The StretchBend class represents a Stretch-Bend formed between three linearly bonded atoms.
class	StretchTorsion	The StretchTorsion class represents a coupling between a torsional angle and the three bonds contained in the torsion, as defined in the 2017 AMOEBA nucleic acid force field.
class	Torsion	The Torsion class represents a torsional angle formed between four bonded atoms.
class	TorsionTorsion	The TorsionTorsion class represents two adjacent torsional angles formed by five bonded atoms.
class	UreyBradley	The UreyBradley class.

Uses of ROLS in ffx.potential.nonbonded

Classes in ffx.potential.nonbonded that implement ROLS

Modifier and Type	Class	Description
class	RestrainPosition	Restrain the position of atoms to their initial coordinates.

Uses of ROLS in ffx.ui

Classes in ffx.ui that implement ROLS

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