Uses of Interface
org.simtk.molecularstructure.Molecule

Packages that use Molecule

org.simtk.moleculargraphics
org.simtk.moleculargraphics.cartoon
org.simtk.molecularstructure
org.simtk.molecularstructure.nucleicacid
org.simtk.molecularstructure.protein

Uses of Molecule in org.simtk.moleculargraphics

Methods in org.simtk.moleculargraphics with parameters of type Molecule

void	ActiveMoleculeBroadcaster.fireSetActiveMolecle(Molecule m)
void	SequencePane.setActiveMolecule(Molecule molecule)
void	SequenceCartoonCanvas.setActiveMolecule(Molecule molecule)
void	ActiveMoleculeListener.setActiveMolecule(Molecule m)

Uses of Molecule in org.simtk.moleculargraphics.cartoon

Methods in org.simtk.moleculargraphics.cartoon with parameters of type Molecule

void	WireFrameActor.addMolecule(Molecule molecule)
void	WireFrame.addMolecule(Molecule m)
void	TubeAndStickTrace.addMolecule(Molecule m)
void	RopeAndCylinder.addMolecule(Molecule m)
void	RichardsonProteinRibbon.addMolecule(Molecule molecule)
void	ResidueSpheres.addMolecule(Molecule m)
void	ResidueSphereActor.addMolecule(Molecule molecule)
void	ProteinRibbon.addMolecule(Molecule m)
void	NucleotideStickCartoon.addMolecule(Molecule molecule)
void	MoleculeTensorCartoon.addMolecule(Molecule molecule)
void	MoleculeCartoon.addMolecule(Molecule molecule)
void	MoleculeBlobs.addMolecule(Molecule m)
protected void	MoleculeBlobActor.addMolecule(Molecule molecule)
abstract void	GlyphCartoon.addMolecule(Molecule molecule)
void	FineRibbonCartoon.addMolecule(Molecule m)
void	DuplexResidueWedge.addMolecule(Molecule molecule)
void	DuplexCylinderCartoon.addMolecule(Molecule molecule)
void	CappedBondActor.addMolecule(Molecule molecule)
void	BondStickCartoon.addMolecule(Molecule molecule)
void	BasePairRod.addMolecule(Molecule molecule)
void	BasePairRibbon.addMolecule(Molecule m)
void	BasePairOval.addMolecule(Molecule molecule)
void	BasePairConnectorStick.addMolecule(Molecule molecule)
void	BaseConnectorTube.addMolecule(Molecule molecule)
void	BallAndStickCartoon.addMolecule(Molecule m)
void	BackboneTubeCartoon.addMolecule(Molecule molecule)
void	BackboneStick.addMolecule(Molecule molecule)
void	BackboneCurve.addMolecule(Molecule molecule)
void	AtomSpheres.addMolecule(Molecule m)
void	AtomSphereActor.addMolecule(Molecule molecule)
void	ProteinRibbon.hide(Molecule m)
void	ProteinRibbon.show(Molecule m)

Constructors in org.simtk.moleculargraphics.cartoon with parameters of type Molecule

MoleculeBlobActor(Molecule molecule, double resolution)

MoleculeTensorActor(Molecule molecule)

NewBackboneCurveActor(double width, double thickness, Molecule molecule)

Uses of Molecule in org.simtk.molecularstructure

Subinterfaces of Molecule in org.simtk.molecularstructure

interface

Biopolymer

Classes in org.simtk.molecularstructure that implement Molecule

class	BiopolymerClass
class	MoleculeClass

Methods in org.simtk.molecularstructure that return Molecule

static Molecule	MoleculeClass.createFactoryPDBMolecule(java.io.LineNumberReader reader) Read one molecule from a PDB format stream.
static Molecule	MoleculeClass.createFactoryPDBMolecule(java.lang.String fileName)
static Molecule	MoleculeClass.createFactoryPDBMolecule(java.net.URL url)
Molecule	MoleculeCollection.getMolecule(int i)

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

java.util.Collection<Molecule>

MoleculeCollection.molecules()

Uses of Molecule in org.simtk.molecularstructure.nucleicacid

Classes in org.simtk.molecularstructure.nucleicacid that implement Molecule

class	DNA
class	NucleicAcid
class	RNA

Uses of Molecule in org.simtk.molecularstructure.protein

Subinterfaces of Molecule in org.simtk.molecularstructure.protein

interface	LocatedProtein
interface	Protein

Classes in org.simtk.molecularstructure.protein that implement Molecule

class

PDBProteinClass