Uses of Class
ffx.potential.bonded.Rotamer

Packages that use Rotamer

Package	Description
ffx.algorithms.optimize.manybody	The manybody package implements many-body rotamer optimization infrastructure, including distance matrices, an energy expansion (self, two-body, three-body, and four-body), Dead-end elimination criteria, Goldstein elimination criteria, and supporting data structures for efficient optimization.
ffx.potential.bonded	The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
ffx.potential.parameters	The Parameters package stores force field atom types, bond types, etc, and keywords that define the potential.

Uses of Rotamer in ffx.algorithms.optimize.manybody

Methods in ffx.algorithms.optimize.manybody with parameters of type Rotamer

Modifier and Type	Method	Description
double	EnergyExpansion.getSelf(int i, int ri, Rotamer rot, boolean excludeFMod)	Return a previously computed self-energy.

Uses of Rotamer in ffx.potential.bonded

Methods in ffx.potential.bonded that return Rotamer

Modifier and Type	Method	Description
static Rotamer[]	Rotamer.defaultRotamerFactory(Residue residue)	Factory method to construct an original-coordinates Rotamer from a residue.
static Rotamer[]	Rotamer.defaultRotamerFactory(Residue residue, TitrationUtils titrationUtils)	Factory method to construct an original-coordinates Rotamer from a residue.
Rotamer	Residue.getRotamer()	Get the current rotamer.
Rotamer	RotamerLibrary.RotamerGuess.getRotamer()
Rotamer[]	MultiResidue.getRotamers()	Return all currently set rotamers.
Rotamer[]	Residue.getRotamers()	Return all currently set rotamers.
Rotamer[]	RotamerLibrary.getRotamers(AminoAcidUtils.AminoAcid3 name)	Return an array of Rotamers for the given amino acid.
Rotamer[]	RotamerLibrary.getRotamers(AminoAcidUtils.AminoAcid3 name, TitrationUtils titrationUtils)	Return an array of Rotamers for the given amino acid.
Rotamer[]	RotamerLibrary.getRotamers(NucleicAcidUtils.NucleicAcid3 name)	Return an array of Rotamers for the given nucleic acid.
Rotamer[]	MultiResidue.setRotamers(RotamerLibrary library)	Resets the rotamers for this residue, potentially incorporating the original coordinates if RotamerLibrary's original coordinates rotamer flag has been set.
Rotamer[]	Residue.setRotamers()	Sets the original coordinate rotamers for titratable residues RotamerLibrary's original coordinates rotamer flag has been set.
Rotamer[]	Residue.setRotamers(RotamerLibrary library)	Resets the rotamers for this residue, potentially incorporating the original coordinates if RotamerLibrary's original coordinates rotamer flag has been set.

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

Modifier and Type	Method	Description
static void	RotamerLibrary.applyRotamer(Residue residue, Rotamer rotamer)	Applies a Rotamer to a Residue by calling applyAARotamer or applyNARotamer.
static void	RotamerLibrary.applyRotamer(Residue residue, Rotamer rotamer, boolean independent)	Version of applyRotamer which allows for chain context-independent drawing of nucleic acid Rotamers.
void	Residue.setRotamer(Rotamer rotamer)	Set the current rotamer.
String	Residue.toString(Rotamer rotamer)	A descriptive string based on a given rotamer.

Uses of Rotamer in ffx.potential.parameters

Methods in ffx.potential.parameters with parameters of type Rotamer

Modifier and Type	Method	Description
double	TitrationUtils.getTotalRotamerPhBias(Rotamer[] rotamers)
void	TitrationUtils.updateResidueParameters(Residue residue, Rotamer rotamer)	Update force field parameters for the side-chain atoms of the given residue based on the rotamer amino acid type.