Uses of Enum Class
ffx.potential.bonded.NucleicAcidUtils.NucleicAcid3

Packages that use NucleicAcidUtils.NucleicAcid3

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

Uses of NucleicAcidUtils.NucleicAcid3 in ffx.potential.bonded

Fields in ffx.potential.bonded declared as NucleicAcidUtils.NucleicAcid3

Modifier and Type	Field	Description
NucleicAcidUtils.NucleicAcid3	Rotamer.nucleicAcid3	The N.A. name of this residue (or null for a A.A.).

Fields in ffx.potential.bonded with type parameters of type NucleicAcidUtils.NucleicAcid3

Modifier and Type	Field	Description
static final HashMap<NucleicAcidUtils.NucleicAcid1,NucleicAcidUtils.NucleicAcid3>	NucleicAcidUtils.NA1toNA3	Constant NA1toNA3
static final List<NucleicAcidUtils.NucleicAcid3>	NucleicAcidUtils.nucleicAcidList	Constant nucleicAcidList

Methods in ffx.potential.bonded that return NucleicAcidUtils.NucleicAcid3

Modifier and Type	Method	Description
NucleicAcidUtils.NucleicAcid3	Residue.getNucleicAcid3()	getNucleicAcid3.
NucleicAcidUtils.NucleicAcid3	Residue.getNucleicAcid3(boolean matchShortName)	Returns the NucleicAcid3 corresponding to this Residue, with additional robust checking for 1- or 2-letter names.
static NucleicAcidUtils.NucleicAcid3	NucleicAcidUtils.NucleicAcid3.parse(String name)	Best-guess parse of a String to an NA3.
static NucleicAcidUtils.NucleicAcid3	NucleicAcidUtils.NucleicAcid3.valueOf(String name)	Returns the enum constant of this class with the specified name.
static NucleicAcidUtils.NucleicAcid3[]	NucleicAcidUtils.NucleicAcid3.values()	Returns an array containing the constants of this enum class, in the order they are declared.

Methods in ffx.potential.bonded with parameters of type NucleicAcidUtils.NucleicAcid3

Modifier and Type	Method	Description
Rotamer[]	RotamerLibrary.getRotamers(NucleicAcidUtils.NucleicAcid3 name)	Return an array of Rotamers for the given nucleic acid.
static void	NamingUtils.renameCommonNucleicAcid(Residue residue, NucleicAcidUtils.NucleicAcid3 na3)	Renames atoms in common nucleic acids to PDB standard.
static void	NamingUtils.renameCommonNucleobase(Atom N19, Atom C1s, NucleicAcidUtils.NucleicAcid3 na3)	Renames the atoms of the common nucleobases (A, C, G, T, U, and deoxy variants).

Constructors in ffx.potential.bonded with parameters of type NucleicAcidUtils.NucleicAcid3

Modifier	Constructor	Description
	Rotamer(NucleicAcidUtils.NucleicAcid3 nucleicAcid3, double... values)	Constructor for Rotamer.
	Rotamer(NucleicAcidUtils.NucleicAcid3 nucleicAcid3, ResidueState residueState, double... values)	Constructor for Rotamer.
	Rotamer(NucleicAcidUtils.NucleicAcid3 nucleicAcid3, ResidueState residueState, TitrationUtils titrationUtils, double... values)	Constructor for Rotamer.