Uses of Enum Class
ffx.potential.bonded.AminoAcidUtils.AminoAcid3

Packages that use AminoAcidUtils.AminoAcid3

Package	Description
ffx.algorithms.misc	The Misc package contains a few miscellaneous algorithms.
ffx.potential.bonded	The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions, etc.
ffx.potential.extended	The Extended package is progress toward support for constant pH molecular dynamics using extended system variables (i.e. lambda dynamics on protonation).
ffx.potential.parameters	The Parameters package stores force field atom types, bond types, etc, and keywords that define the potential.

Uses of AminoAcidUtils.AminoAcid3 in ffx.algorithms.misc

Methods in ffx.algorithms.misc with parameters of type AminoAcidUtils.AminoAcid3

Modifier and Type	Method	Description
void	GenerateRotamers.setBaselineAARes(AminoAcidUtils.AminoAcid3 aa3)	Sets a standard amino acid to be the baseline for rotamer generation.

Uses of AminoAcidUtils.AminoAcid3 in ffx.potential.bonded

Fields in ffx.potential.bonded declared as AminoAcidUtils.AminoAcid3

Modifier and Type	Field	Description
AminoAcidUtils.AminoAcid3	Rotamer.aminoAcid3	The A.A. name of this residue (or null for a N.A.).

Fields in ffx.potential.bonded with type parameters of type AminoAcidUtils.AminoAcid3

Modifier and Type	Field	Description
static final HashMap<AminoAcidUtils.AminoAcid1,AminoAcidUtils.AminoAcid3>	AminoAcidUtils.AA1toAA3	Constant AA1toAA3
static final List<AminoAcidUtils.AminoAcid3>	AminoAcidUtils.aminoAcidList	Constant aminoAcidList

Methods in ffx.potential.bonded that return AminoAcidUtils.AminoAcid3

Modifier and Type	Method	Description
static AminoAcidUtils.AminoAcid3	AminoAcidUtils.getAminoAcid(String residueName)	getAminoAcid.
AminoAcidUtils.AminoAcid3	MultiResidue.getAminoAcid3()	getAminoAcid3.
AminoAcidUtils.AminoAcid3	Residue.getAminoAcid3()	getAminoAcid3.
static AminoAcidUtils.AminoAcid3	AminoAcidUtils.getAminoAcid3From1(String residueName)	This method takes a one letter amino acid code and converts it to a three letter amino acid code.
static AminoAcidUtils.AminoAcid3	AminoAcidUtils.AminoAcid3.valueOf(String name)	Returns the enum constant of this class with the specified name.
static AminoAcidUtils.AminoAcid3[]	AminoAcidUtils.AminoAcid3.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 AminoAcidUtils.AminoAcid3

Modifier and Type	Method	Description
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.
static void	AminoAcidUtils.removeH1_H2_H3(AminoAcidUtils.AminoAcid3 aminoAcid, Residue residue)	Only the first nitrogen should have H1, H2 and H3 atoms, unless it's an NME cap.
static void	NamingUtils.renameCommonAminoAcids(Residue residue, AminoAcidUtils.AminoAcid3 aa3, Atom CA, Atom CB)	Renames atoms in common amino acids to PDB standard.
boolean	MultiResidue.setActiveResidue(AminoAcidUtils.AminoAcid3 aa)	Method may be redundant with requestSetActiveResidue.

Constructors in ffx.potential.bonded with parameters of type AminoAcidUtils.AminoAcid3

Modifier	Constructor	Description
	Rotamer(AminoAcidUtils.AminoAcid3 aminoAcid3, double... values)	Constructor for Rotamer.
	Rotamer(AminoAcidUtils.AminoAcid3 aminoAcid3, ResidueState residueState, double... values)	Constructor for Rotamer.
	Rotamer(AminoAcidUtils.AminoAcid3 aminoAcid3, ResidueState residueState, TitrationUtils titrationUtils, double... values)	Constructor for Rotamer.
	Rotamer(AminoAcidUtils.AminoAcid3 aminoAcid3, TitrationUtils titrationUtils, double... values)	Constructor for Rotamer.

Uses of AminoAcidUtils.AminoAcid3 in ffx.potential.extended

Fields in ffx.potential.extended declared as AminoAcidUtils.AminoAcid3

Modifier and Type	Field	Description
final AminoAcidUtils.AminoAcid3[]	ExtendedSystem.residueNames	Array of AminoAcid3 initialized to match the number of atoms in the system.

Uses of AminoAcidUtils.AminoAcid3 in ffx.potential.parameters

Fields in ffx.potential.parameters declared as AminoAcidUtils.AminoAcid3

Modifier and Type	Field	Description
final AminoAcidUtils.AminoAcid3	TitrationUtils.Titration.deprotForm
final AminoAcidUtils.AminoAcid3	TitrationUtils.Titration.protForm

Methods in ffx.potential.parameters with parameters of type AminoAcidUtils.AminoAcid3

Modifier and Type	Method	Description
double	TitrationUtils.getRotamerPhBias(AminoAcidUtils.AminoAcid3 AA3)
static int	TitrationUtils.getTitratingHydrogenDirection(AminoAcidUtils.AminoAcid3 aminoAcid3, Atom atom)
static boolean	TitrationUtils.isTitratingHeavy(AminoAcidUtils.AminoAcid3 aminoAcid3, Atom atom)	Used to keep track of heavy atoms with changing polarizability.
static boolean	TitrationUtils.isTitratingHydrogen(AminoAcidUtils.AminoAcid3 aminoAcid3, Atom atom)