Uses of Class
ProGAL.proteins.structure.Atom

Packages that use Atom

ProGAL.proteins.beltaStructure.loop
ProGAL.proteins.structure
ProGAL.proteins.structure.generators

Uses of Atom in ProGAL.proteins.beltaStructure.loop

Fields in ProGAL.proteins.beltaStructure.loop declared as Atom

Atom[]

LoopStructure.targetAtoms

Constructors in ProGAL.proteins.beltaStructure.loop with parameters of type Atom

LoopStructure(SecondaryStructure ss, int seg1, int seg2, Atom[] targetAtoms)

Uses of Atom in ProGAL.proteins.structure

Fields in ProGAL.proteins.structure declared as Atom

Atom	CBond.a1
Atom	CBond.a2

Methods in ProGAL.proteins.structure that return Atom

Atom	AminoAcid.atom(int atomNumber)
Atom	AminoAcidChain.atom(int res, int atomNumber)
Atom	AminoAcidChain.atom(int res, java.lang.String name)
Atom	AminoAcid.atom(java.lang.String name)
Atom[]	AminoAcidChain.atoms()
Atom[]	AminoAcid.atoms()
Atom	Atom.clone()

Constructors in ProGAL.proteins.structure with parameters of type Atom

AminoAcid(char type, Atom[] atoms)

CBond(Atom a1, Atom a2)

Uses of Atom in ProGAL.proteins.structure.generators

Methods in ProGAL.proteins.structure.generators that return Atom

Atom[]	HeavyAtomAminoAcidGenerator.generateAtoms(char type)
Atom[]	CABAminoAcidGenerator.generateAtoms(char type)
Atom[]	AtomGenerator.generateAtoms(char type)
Atom[]	AllAtomAminoAcidGenerator.generateAtoms(char type)