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Adenylate Alanine AminoAcid Angle Angle.Range Angle.Units Arginine Asparagine Aspartate Atom AtomClass AtomPosition AtomSet BasePair BasePair.BondOrientation BasePair.EdgeType BaseStack BaseTriple BetaStrand Biopolymer BiopolymerClass Chemical ChemicalElement ChemicalElementClass ColorName CommandLineInterface Cylinder Cysteine Cytidylate DNA DoubleRing Duplex FileNameFilter FunctionalGroup Glutamate Glutamine Glycine Guanylate Hairpin Hash3D Helix Histidine HomogeneousTransform HomogeneousTransformClass Inositate InsufficientAtomsException InsufficientPointsException Isoleucine JamaMatrix JLinkLabel Leucine Line3D LineCommand LoadPdbUrlProcess LocatedProtein Location Lysine MassBody MassBodyClass MathMatrix MathMatrixClass MathVector MathVectorClass Matrix3D Matrix3DClass MatrixSizeMismatchException Methionine Molecular MolecularClass Molecule MoleculeAcquisitionMethodDialog MoleculeClass MoleculeCollection MoleculeMVCModel MonitoredProcess MutableHomogeneousTransform MutableMathMatrix MutableMathVector MutableMatrix3D MutableVector2D MutableVector3D MVCModel MVCView MyJFileFilter NucleicAcid Nucleotide ObservableInterface ParameterSetModel PDBProteinClass Phenylalanine Plane3D ProgrammerLogicProblem ProgressDialog ProgressDialogClass ProgressManager ProgressPanel Proline Protein Pseudoknot Purine Pyrimidine Residue ResidueBackbone ResidueClass ResidueType ResidueTypeClass RNA RnamlDocument RnamlExportDocument SecondaryStructure SecondaryStructureClass SecondaryStructureClass.SourceType Selectable SelectionBroadcaster SelectionListener SemiCylinder SequenceAlignment Serine SimpleObservable Stopwatch Superposition TestSuperposition Threonine Throbber Thymidylate Tryptophan Tyrosine UncompressInputStream UndoableDialog UndoRedoMechanism UnknownAminoAcid Uridylate Valine Vector2D Vector2DClass Vector3D Vector3DClass Vector3DFloatArrayWrapper VectorSizeException WebPDB