Uses of Interface
org.simtk.molecularstructure.atom.Atom

Packages that use Atom

org.simtk.molecularstructure
org.simtk.molecularstructure.atom

Uses of Atom in org.simtk.molecularstructure

Methods in org.simtk.molecularstructure that return Atom

Atom	ResidueClass.getAtom(java.lang.String atomName) Get the atom with the given name.
Atom	Residue.getAtom(java.lang.String atomName)

Methods in org.simtk.molecularstructure that return types with arguments of type Atom

java.util.Set<Atom>	ResidueClass.atoms() Override atoms() method to use a class that can index by atom name
java.util.Set<Atom>	MolecularClass.atoms()
java.util.Set<Atom>	Molecular.atoms()
java.util.Set<Atom>	ResidueClass.getHydrogenBondAcceptors()
java.util.Set<Atom>	Residue.getHydrogenBondAcceptors()
java.util.Set<Atom>	ResidueClass.getHydrogenBondDonors()
java.util.Set<Atom>	Residue.getHydrogenBondDonors()

Methods in org.simtk.molecularstructure with parameters of type Atom

void	ResidueClass.updateAtomPosition(Atom atom)
void	Residue.updateAtomPosition(Atom atom)

Uses of Atom in org.simtk.molecularstructure.atom

Classes in org.simtk.molecularstructure.atom that implement Atom

class

AtomClass

Methods in org.simtk.molecularstructure.atom that return types with arguments of type Atom

java.util.Set<Atom>	AtomClass.bonds()
java.util.Collection<Atom>	Atom.bonds()

Methods in org.simtk.molecularstructure.atom with parameters of type Atom

double	AtomClass.distance(Atom atom2)
double	Atom.distance(Atom atom2)