Uses of Class
ffx.potential.bonded.BondedTerm
Packages that use BondedTerm
Package
Description
The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions,
etc.
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Uses of BondedTerm in ffx.potential.bonded
Subclasses of BondedTerm in ffx.potential.bondedModifier and TypeClassDescriptionclass
The Angle class represents an angle formed between three linearly bonded atoms.class
The AngleTorsion class represents an angle torsion coupling between four bonded atoms.class
The Bond class represents a covalent bond formed between two atoms.class
The ImproperTorsion class represents an Improper Torsion.class
The OutOfPlaneBend class represents an Out-Of-Plane Bend.class
The Pi-Orbital Torsion class.class
RestraintDistance class.class
Restrain the position of atoms to their initial coordinates.class
RestraintTorsion is a class that restrains the torsion angle defined by four atoms.class
The StretchBend class represents a Stretch-Bend formed between three linearly bonded atoms.class
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
The Torsion class represents a torsional angle formed between four bonded atoms.class
The TorsionTorsion class represents two adjacent torsional angles formed by five bonded atoms.class
The UreyBradley class.Methods in ffx.potential.bonded with type parameters of type BondedTermModifier and TypeMethodDescriptionstatic <T extends BondedTerm>
voidBondedTerm.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 BondedTermModifier and TypeMethodDescriptionint
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)