Uses of Class
ffx.potential.bonded.Bond

Packages that use Bond

Package	Description
ffx.potential.bonded	The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
ffx.potential.constraint	The constraint package implements holonomic constraint algorithms used during molecular dynamics and minimization, including CCMA, SETTLE, and SHAKE-style constraints (as well as charge constraints).
ffx.potential.parsers	The Parsers package handles reading/writing files to/from the internal data structure.
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 Bond in ffx.potential.bonded

Fields in ffx.potential.bonded declared as Bond

Modifier and Type	Field	Description
protected Bond[]	BondedTerm.bonds	Bonds that are used to form this term.

Methods in ffx.potential.bonded that return Bond

Modifier and Type	Method	Description
static Bond	BondedUtils.buildBond(Atom a1, Atom a2, ForceField forceField, List<Bond> bondList)	Build a bond between two atoms.
Bond	Atom.getBond(Atom a)	getBond
Bond	BondedTerm.getBond(int index)	Get the constituent Bond specified by index.
Bond	MSGroup.getBond(int index)	Returns the Bond at the supplied index.
Bond	MSGroup.getBond(String id)	Returns the Bond with the given id.
Bond	MultiResidue.getBond(int index)	Returns the Bond at the supplied index.
Bond	MultiResidue.getBond(String id)	Returns the Bond with the given id.
Bond	PiOrbitalTorsion.getMiddleBond()	Get the middle bond that the Pi-Orbital Torsion is formed around.

Methods in ffx.potential.bonded that return types with arguments of type Bond

Modifier and Type	Method	Description
static List<Bond>	PolymerUtils.assignAtomTypes(MolecularAssembly molecularAssembly, PDBFilter.PDBFileStandard fileStandard)	Assign force field atoms types to common chemistries using "biotype" records.
List<Bond>	MSNode.getBondList()	Returns a List of all Bonds below the present MSNode.
List<Bond>	Atom.getBonds()	Gets the list of the Bonds this Atom helps to form
static List<Bond>	PolymerUtils.locateDisulfideBonds(List<String> ssbonds, MolecularAssembly molecularAssembly, Map<String,String> pdbToNewResMap)	Locate disulfide bonds based on SSBOND records.

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

Modifier and Type	Method	Description
Joint	MSGroup.createJoint(Bond bond, MSGroup group1, MSGroup group2, ForceField forceField)	Create a joint between two chemical groups.
Joint	MultiResidue.createJoint(Bond bond, MSGroup group1, MSGroup group2, ForceField forceField)	Create a joint between two chemical groups.
static PiOrbitalTorsion	PiOrbitalTorsion.piOrbitalTorsionFactory(Bond bond, ForceField forceField)	Attempt to create a new PiOrbitalTorsion based on the supplied bond and forceField.
void	Atom.setBond(Bond b)	Specify that this Atom is part of a Bond
void	BondedTerm.setBonds(Bond[] b)	Add constituent Bonds to the Term.
static TorsionTorsion	TorsionTorsion.torsionTorsionFactory(Bond firstBond, Angle angle, Bond lastBond, ForceField forceField)	torsionTorsionFactory.

Method parameters in ffx.potential.bonded with type arguments of type Bond

Modifier and Type	Method	Description
static void	AminoAcidUtils.assignAminoAcidAtomTypes(Residue residue, Residue previousResidue, Residue nextResidue, ForceField forceField, List<Bond> bondList)	assignAminoAcidAtomTypes.
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 void	PolymerUtils.buildDisulfideBonds(List<Bond> ssBondList, MolecularAssembly molecularAssembly, List<Bond> bondList)	Assign parameters to disulfide bonds.
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, 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.

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

Modifier	Constructor	Description
	Angle(Bond b1, Bond b2)	Angle constructor
	AngleTorsion(Bond b1, Bond b2, Bond b3)	Create a AngleTorsion from 3 connected bonds (no error checking)
	PiOrbitalTorsion(Bond middleBond)	Pi-Orbital Torsion constructor.
	Torsion(Bond b1, Bond b2, Bond b3)	Create a Torsion from 3 connected bonds (no error checking)
	TorsionTorsion(Bond firstBond, Angle angle, Bond lastBond, boolean reversed)	Torsion-Torsion constructor.

Uses of Bond in ffx.potential.constraint

Method parameters in ffx.potential.constraint with type arguments of type Bond

Modifier and Type	Method	Description
static CcmaConstraint	CcmaConstraint.ccmaFactory(List<Bond> constrainedBonds, List<Angle> constrainedAngles, Atom[] allAtoms, double[] masses, double nonzeroCutoff)	Constructs a set of bond length Constraints to be satisfied using the Constaint Constraint Matrix Approximation, a parallelizable stable numeric method.

Uses of Bond in ffx.potential.parsers

Fields in ffx.potential.parsers with type parameters of type Bond

Modifier and Type	Field	Description
protected List<Bond>	SystemFilter.bondList	The bondList may be filled by the filters that extend SystemFilter.

Uses of Bond in ffx.potential.terms

Methods in ffx.potential.terms that return Bond

Modifier and Type	Method	Description
Bond	BondPotentialEnergy.getBond(int index)	Get the Bond at a given index.
Bond[]	BondPotentialEnergy.getBondArray()	Get an array of Bonds in this term.

Methods in ffx.potential.terms that return types with arguments of type Bond

Modifier and Type	Method	Description
List<Bond>	BondPotentialEnergy.getBonds()	Get an unmodifiable view of the Bonds in this term.

Methods in ffx.potential.terms with parameters of type Bond

Modifier and Type	Method	Description
boolean	BondPotentialEnergy.addBond(Bond bond)	Add a Bond to this term.
boolean	BondPotentialEnergy.addBonds(Bond[] bonds)	Add an array of Bonds to this term.
boolean	BondPotentialEnergy.removeBond(Bond bond)	Remove a Bond from this term.

Method parameters in ffx.potential.terms with type arguments of type Bond

Modifier and Type	Method	Description
boolean	BondPotentialEnergy.addBonds(List<Bond> bonds)	Add a list of Bonds to this term.

Constructor parameters in ffx.potential.terms with type arguments of type Bond

Modifier	Constructor	Description
	BondPotentialEnergy(String name, int forceGroup, List<Bond> bonds)	Create a BondPotentialEnergy initialized with a list of bonds and force group.
	BondPotentialEnergy(String name, Collection<Bond> bonds)	Create a BondPotentialEnergy initialized with a collection of bonds.