Uses of Enum Class
ffx.potential.bonded.AminoAcidUtils.AminoAcid3
Package
Description
The Misc package contains a few miscellaneous algorithms.
The Bonded package implements bonded molecular mechanics terms such as bonds, angles, torsions,
etc.
The Extended package is progress toward support for constant pH molecular dynamics using extended
system variables (i.e. lambda dynamics on protonation).
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
Modifier and TypeMethodDescriptionvoid
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
Modifier and TypeFieldDescriptionRotamer.aminoAcid3
The A.A. name of this residue (or null for a N.A.).Modifier and TypeFieldDescriptionstatic final HashMap
<AminoAcidUtils.AminoAcid1, AminoAcidUtils.AminoAcid3> AminoAcidUtils.AA1toAA3
ConstantAA1toAA3
static final List
<AminoAcidUtils.AminoAcid3> AminoAcidUtils.aminoAcidList
ConstantaminoAcidList
Modifier and TypeMethodDescriptionstatic AminoAcidUtils.AminoAcid3
AminoAcidUtils.getAminoAcid
(String residueName) getAminoAcid.MultiResidue.getAminoAcid3()
getAminoAcid3.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
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.Modifier and TypeMethodDescriptionRotamer[]
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.ModifierConstructorDescriptionRotamer
(AminoAcidUtils.AminoAcid3 aminoAcid3, double... values) Constructor for Rotamer.Rotamer
(AminoAcidUtils.AminoAcid3 aminoAcid3, int rotIndex, 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.Rotamer
(AminoAcidUtils.AminoAcid3 aminoAcid3, TitrationUtils titrationUtils, int rotIndex, double... values) -
Uses of AminoAcidUtils.AminoAcid3 in ffx.potential.extended
Modifier and TypeFieldDescriptionfinal 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
Modifier and TypeFieldDescriptionTitrationUtils.Titration.deprotForm
TitrationUtils.Titration.protForm
Modifier and TypeMethodDescriptiondouble
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)