Uses of Interface
org.biojava.nbio.structure.AminoAcid

Packages that use AminoAcid

Package	Description
org.biojava.nbio.structure	Interfaces and classes for protein structure (PDB).

Uses of AminoAcid in org.biojava.nbio.structure

Classes in org.biojava.nbio.structure that implement AminoAcid

Modifier and Type	Class and Description
class	AminoAcidImpl AminoAcid inherits most from Hetatom.

Methods in org.biojava.nbio.structure that return AminoAcid

Modifier and Type	Method and Description
static AminoAcid	StandardAminoAcid.getAminoAcid(String name) get a standard amino acid.
AminoAcid	Mutator.mutateResidue(AminoAcid oldAmino, String newType) create a new residue which is of the new type.

Methods in org.biojava.nbio.structure with parameters of type AminoAcid

Modifier and Type	Method and Description
static Atom	Calc.createVirtualCBAtom(AminoAcid amino) creates a virtual C-beta atom. this might be needed when working with GLY thanks to Peter Lackner for a python template of this method.
static double	Calc.getPhi(AminoAcid a, AminoAcid b) Calculate the phi angle.
static double	Calc.getPsi(AminoAcid a, AminoAcid b) Calculate the psi angle.
static boolean	Calc.isConnected(AminoAcid a, AminoAcid b) Test if two amino acids are connected, i.e. if the distance from C to N < 2.5 Angstrom.
AminoAcid	Mutator.mutateResidue(AminoAcid oldAmino, String newType) create a new residue which is of the new type.