Uses of Class
ffx.potential.bonded.BondedTerm

Packages that use BondedTerm

Package	Description
ffx.potential.bonded	The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
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.

Uses of BondedTerm in ffx.potential.bonded

Subclasses of BondedTerm in ffx.potential.bonded

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	Bond	The Bond class represents a covalent bond formed between two atoms.
class	ImproperTorsion	The ImproperTorsion class represents an Improper Torsion.
class	OutOfPlaneBend	The OutOfPlaneBend class represents an Out-Of-Plane Bend.
class	PiOrbitalTorsion	The Pi-Orbital Torsion class.
class	RestrainDistance	RestraintDistance class.
class	RestrainPosition	Restrain the position of atoms to their initial coordinates.
class	RestrainTorsion	RestraintTorsion is a class that restrains the torsion angle defined by four atoms.
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.

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

Modifier and Type	Method	Description
static <T extends BondedTerm> void	BondedTerm.removeNeuralNetworkTerms(List<T> list)	This method removes terms from a list that are marked as being part of a neural network.

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

Modifier and Type	Method	Description
int	BondedTerm.BondedComparator.compare(BondedTerm bondedTerm1, BondedTerm bondedTerm2)	Sort using position in the naturalOrder list; fallback to alphabetical.
int	Angle.compareTo(BondedTerm a)
int	Bond.compareTo(BondedTerm b)
int	BondedTerm.compareTo(BondedTerm t)
int	ImproperTorsion.compareTo(BondedTerm o)
int	OutOfPlaneBend.compareTo(BondedTerm o)
int	StretchBend.compareTo(BondedTerm sb)
int	UreyBradley.compareTo(BondedTerm ub)

Uses of BondedTerm in ffx.potential.terms

Methods in ffx.potential.terms that return BondedTerm

Modifier and Type	Method	Description
BondedTerm[]	AnglePotentialEnergy.getBondedTermsArray()	Get an array of BondedTerms in this term.
BondedTerm[]	AngleTorsionPotentialEnergy.getBondedTermsArray()	Get an array of BondedTerms in this term.
BondedTerm[]	BondPotentialEnergy.getBondedTermsArray()	Get an array of BondedTerms in this term.
abstract BondedTerm[]	EnergyTerm.getBondedTermsArray()	Get an array of BondedTerms in this term.
BondedTerm[]	ImproperTorsionPotentialEnergy.getBondedTermsArray()	Get an array of BondedTerms in this term.
BondedTerm[]	OutOfPlaneBendPotentialEnergy.getBondedTermsArray()	Get an array of BondedTerms in this term.
BondedTerm[]	PiOrbitalTorsionPotentialEnergy.getBondedTermsArray()	Get an array of BondedTerms in this term.
BondedTerm[]	RestrainDistancePotentialEnergy.getBondedTermsArray()	Get an array of BondedTerms in this term.
BondedTerm[]	RestrainPositionPotentialEnergy.getBondedTermsArray()	Get an array of BondedTerms in this term.
BondedTerm[]	RestrainTorsionPotentialEnergy.getBondedTermsArray()	Get an array of BondedTerms in this term.
BondedTerm[]	StretchBendPotentialEnergy.getBondedTermsArray()	Get an array of BondedTerms in this term.
BondedTerm[]	StretchTorsionPotentialEnergy.getBondedTermsArray()	Get an array of BondedTerms in this term.
BondedTerm[]	TorsionPotentialEnergy.getBondedTermsArray()	Get an array of BondedTerms in this term.
BondedTerm[]	TorsionTorsionPotentialEnergy.getBondedTermsArray()	Get an array of BondedTerms in this term.
BondedTerm[]	UreyBradleyPotentialEnergy.getBondedTermsArray()	Get an array of BondedTerms in this term.