Uses of Class
jgromacs.data.Atom

Packages that use Atom

jgromacs.analysis	jgromacs.analysis is a collection of classes providing static methods for various analysis tasks
jgromacs.data	jgromacs.data is a collection of classes representing multiple levels of structural data

Uses of Atom in jgromacs.analysis

Methods in jgromacs.analysis that return Atom

static Atom

Distances.findClosestAtom(Structure s, IndexSet atomset, IndexSet referenceset) Returns the atom from a given atom set that is closest to a reference set of atoms

Methods in jgromacs.analysis with parameters of type Atom

static IndexSet

Distances.getAtomIndicesInRadius(Structure s, Atom atom, double radius) Returns the index set of atoms in a structure that are closer to a reference atom than a given radius

Uses of Atom in jgromacs.data

Methods in jgromacs.data that return Atom

Atom	Residue.getAlphaCarbon() Returns the alpha carbon atom if any (otherwise returns null)
Atom	Structure.getAtom(int i) Returns atom #i of the structure
Atom	Residue.getAtom(int i) Returns atom #i of the residue
Atom	Structure.getAtomByIndex(int index) Returns the atom of given index
Atom	Residue.getAtomByIndex(int index) Returns the atom of given index
Atom	Residue.getAtomByName(java.lang.String name) Returns the atom of name
Atom	Structure.getAtomInResidueOfIndex(int residueindex, int i) Returns atom #i of the residue of given index
Atom	Structure.getAtomInResidueOfIndex(int residueindex, java.lang.String chainID, int i) Returns atom #i of the residue of given index and chain ID
Atom	Residue.getBetaCarbon() Returns the beta carbon atom if any (otherwise returns null)
Atom	Residue.getCarbonylOxygen() Returns the carbonyl oxygen atom of amino acid
Atom	Residue.getCTerminalCarbon() Returns the C-terminal carbon atom of amino acid
Atom	Residue.getDeltaCarbon() Returns the delta carbon atom if any (otherwise returns null)
Atom	Residue.getEpsilonCarbon() Returns the epsilon carbon atom if any (otherwise returns null)
Atom	Residue.getGammaCarbon() Returns the gamma carbon atom if any (otherwise returns null)
Atom	Residue.getNTerminalNitrogen() Returns the N-terminal nitrogen atom of amino acid
Atom	Residue.getZetaCarbon() Returns the zeta carbon atom if any (otherwise returns null)

Methods in jgromacs.data that return types with arguments of type Atom

java.util.ArrayList<Atom>

Residue.getAtomsAsArrayList() Returns the list of atoms as an ArrayList object

Methods in jgromacs.data with parameters of type Atom

void	Residue.addAtom(Atom atom) Adds a new atom to the residue
void	Structure.addAtomToResidue(int i, Atom atom) Adds the given atom to residue #i
void	Structure.addAtomToResidueOfIndex(int index, Atom atom) Adds the given atom to the residue of given index
double	Atom.distance(Atom other) Returns the Euclidean distance between this atom and another atom
boolean	Residue.isAtomIn(Atom atom) Returns true if the given atom is in the residue
void	Structure.removeAtom(Atom atom) Removes the given atom from the structure
void	Residue.removeAtom(Atom atom) Removes the given atom from the residue
void	Residue.setAtom(int i, Atom atom) Replaces atom #i of the residue with the given atom
void	Structure.setAtomInResidue(int i, int j, Atom atom) Replaces atom #j of residue #i with a new atom
void	Structure.setAtomInResidueOfIndex(int index, int i, Atom atom) Replaces atom #i of the residue of given index with a new atom