Uses of Class
org.episteme.natural.chemistry.Atom

Packages that use Atom

Package	Description
org.episteme.natural.biology
org.episteme.natural.chemistry
org.episteme.natural.chemistry.computational.quantum
org.episteme.natural.chemistry.loaders.cml	Provides the org.episteme.natural.chemistry.loaders.cml module.
org.episteme.natural.ui.viewers.chemistry
org.episteme.natural.ui.viewers.chemistry.backends

Uses of Atom in org.episteme.natural.biology

Methods in org.episteme.natural.biology that return types with arguments of type Atom

Modifier and Type	Method	Description
List<Atom>	Protein.Residue.getAtoms()

Methods in org.episteme.natural.biology with parameters of type Atom

Modifier and Type	Method	Description
void	Protein.Residue.addAtom(Atom atom)

Uses of Atom in org.episteme.natural.chemistry

Classes in org.episteme.natural.chemistry that implement interfaces with type arguments of type Atom

Modifier and Type	Class	Description
class	MolecularGraph	Represents a molecule as a graph of atoms and bonds.

Fields in org.episteme.natural.chemistry declared as Atom

Modifier and Type	Field	Description
final Atom	MolecularGraph.Bond.source
final Atom	MolecularGraph.Bond.target

Methods in org.episteme.natural.chemistry that return Atom

Modifier and Type	Method	Description
Atom	Bond.getAtom1()
Atom	Bond.getAtom2()
Atom	Bond.getOtherAtom(Atom atom)	Returns the other atom in the bond.
Atom	Radical.getRadicalAtom()	Returns the atom representing the radical center.

Methods in org.episteme.natural.chemistry that return types with arguments of type Atom

Modifier and Type	Method	Description
Set<Graph.Edge<Atom>>	MolecularGraph.edges()
List<Atom>	MolecularGraph.getAtoms()
List<Atom>	Molecule.getAtoms()
Map<Atom, List<MolecularGraph.Bond>>	MolecularGraph.getConnections()	connection table: Mapinvalid input: '<'Atom, List>
List<Atom>	Molecule.getNeighbors(Atom atom)	Gets all neighbors of an atom.
Set<Atom>	Radical.getUnboundedAtoms()	Returns the set of atoms that are not fully bonded (potential bonding sites).
Set<Atom>	MolecularGraph.neighbors(Atom vertex)
Set<Atom>	MolecularGraph.vertices()

Methods in org.episteme.natural.chemistry with parameters of type Atom

Modifier and Type	Method	Description
void	MolecularGraph.addAtom(Atom atom)
void	Molecule.addAtom(Atom atom)
void	MolecularGraph.addBond(Atom a, Atom b, MolecularGraph.BondType type)
boolean	MolecularGraph.addEdge(Atom source, Atom target)
boolean	MolecularGraph.addVertex(Atom vertex)
boolean	Bond.contains(Atom atom)	Is this atom part of the bond?
int	MolecularGraph.degree(Atom vertex)
Quantity<Length>	Atom.distanceTo(Atom other)	Distance to another atom.
List<Bond>	Molecule.getBondsFor(Atom atom)	Gets all bonds connected to an atom.
List<Atom>	Molecule.getNeighbors(Atom atom)	Gets all neighbors of an atom.
Atom	Bond.getOtherAtom(Atom atom)	Returns the other atom in the bond.
Set<Atom>	MolecularGraph.neighbors(Atom vertex)

Constructors in org.episteme.natural.chemistry with parameters of type Atom

Modifier	Constructor	Description
	Bond(Atom atom1, Atom atom2)
	Bond(Atom atom1, Atom atom2, BondType type)
	Bond(Atom source, Atom target, MolecularGraph.BondType type)

Uses of Atom in org.episteme.natural.chemistry.computational.quantum

Methods in org.episteme.natural.chemistry.computational.quantum with parameters of type Atom

Modifier and Type	Method	Description
static double	AnalyticIntegrals.nuclearAttraction(BasisFunction a, BasisFunction b, Atom atom)

Uses of Atom in org.episteme.natural.chemistry.loaders.cml

Methods in org.episteme.natural.chemistry.loaders.cml that return Atom

Modifier and Type	Method	Description
Atom	CMLBridge.convertAtom(CMLAtom cmlAtom)	Converts a CML atom to a Episteme Atom.

Method parameters in org.episteme.natural.chemistry.loaders.cml with type arguments of type Atom

Modifier and Type	Method	Description
Bond	CMLBridge.convertBond(CMLBond cmlBond, Map<String,Atom> atomMap)	Converts a CML bond to a Episteme Bond.

Uses of Atom in org.episteme.natural.ui.viewers.chemistry

Methods in org.episteme.natural.ui.viewers.chemistry with parameters of type Atom

Modifier and Type	Method	Description
void	MolecularRenderer.drawAtom(Atom atom)	Draw a single atom.

Uses of Atom in org.episteme.natural.ui.viewers.chemistry.backends

Methods in org.episteme.natural.ui.viewers.chemistry.backends with parameters of type Atom

Modifier and Type	Method	Description
void	JavaFXMolecularRenderer.drawAtom(Atom atom)
void	JmolMolecularRenderer.drawAtom(Atom atom)
void	PyMOLMolecularRenderer.drawAtom(Atom atom)
void	VMDMolecularRenderer.drawAtom(Atom atom)