Uses of Class
starfish.chemistry.Atom

Packages that use Atom

starfish.chemistry

Uses of Atom in starfish.chemistry

Fields in starfish.chemistry declared as Atom

Atom	SpatialSet.atom
Atom[]	DistanceConstraint.atom1
Atom[]	DistanceConstraint.atom2
Atom[]	MoleculePrimitives.atoms
Atom	Bond.begin
Atom	Bond.end
Atom	Entity.firstAtom
Atom	Entity.lastAtom
Atom	DistanceConstraint.next
Atom	Atom.next
Atom	Atom.parent
Atom	DistanceConstraint.previous
Atom	Atom.previous
Atom	Atom.rotGroup
Atom	Atom.rotUnit

Methods in starfish.chemistry that return Atom

Atom	SpatialSetGroup.getAnAtom()
static Atom	Molecule.getAtom(tcl.lang.Interp interp, MolFilter molFilter)
Atom	Residue.getAtom(java.lang.String name)
Atom	Compound.getAtom(java.lang.String name)
static Atom	Molecule.getAtomByName(tcl.lang.Interp interp, java.lang.String name)
static Atom[][]	NoeCmd.getAtoms(tcl.lang.Interp interp, starfish.datasets.peaks.Peak peak)
Atom	Entity.getFirstAtom()
Atom	Atom.getParent()
Atom[]	Atom.getPartners(int targetANum, int shells)
Atom[]	Residue.getPseudo(java.lang.String pseudoName)
static Atom	Molecule.getStartAtom(Molecule molecule)

Methods in starfish.chemistry that return types with arguments of type Atom

java.util.ArrayList<Atom>	Compound.getAtoms(java.lang.String match)
java.util.ArrayList<Atom>	Molecule.getAttachedHydrogens(Atom atom)

Methods in starfish.chemistry with parameters of type Atom

void	Residue.addAtom(Atom atom)
void	Compound.addAtom(Atom atom)
static int	Atom.addBond(Atom atom1, Atom atom2, int order)
static int	Atom.addBond(Atom atom1, Atom atom2, int order, int stereo)
static int	Molecule.buildTree(tcl.lang.Interp interp, Molecule molecule, Atom startAtom, java.util.Vector atomList, MTree mTree)
static int	Atom.calcBond(Atom atom1, Atom atom2, int order)
static int	Atom.calcBond(Atom atom1, Atom atom2, int order, int stereo)
static int	AtomUtil.checkPattern(tcl.lang.Interp interp, Atom[] atoms, java.lang.String[] pattern, java.lang.String[] relation)
int	Molecule.getAtoms(int iStructure, Atom[] atoms)
java.util.ArrayList<Atom>	Molecule.getAttachedHydrogens(Atom atom)
void	Atom.removeBondTo(Atom atom)
void	PPMv.setValid(boolean valid, Atom atom)

Constructors in starfish.chemistry with parameters of type Atom

Bond(Atom begin, Atom end)

DistanceConstraint(starfish.datasets.peaks.Peak p, Atom a1, Atom a2, double newScale)

SpatialSet(java.lang.String name, Atom atom)

SpatialSetGroup(Atom[] atoms)