A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

S

SADDLE_BROWN - Static variable in class org.simtk.util.ColorName

SALMON - Static variable in class org.simtk.util.ColorName

SALMON1 - Static variable in class org.simtk.util.ColorName

SALMON2 - Static variable in class org.simtk.util.ColorName

SALMON3 - Static variable in class org.simtk.util.ColorName

SALMON4 - Static variable in class org.simtk.util.ColorName

SANDY_BROWN - Static variable in class org.simtk.util.ColorName

scalarsName - Variable in class org.simtk.moleculargraphics.cartoon.vtkSetScalarsFilter

ScaleBar - Class in org.simtk.moleculargraphics

ScaleBar(StructureCanvas) - Constructor for class org.simtk.moleculargraphics.ScaleBar

scaleBar - Variable in class org.simtk.moleculargraphics.StructureCanvas

scaleByAtom - Variable in class org.simtk.moleculargraphics.cartoon.AtomSphereActor

scaleByBoundingBox() - Method in class org.simtk.moleculargraphics.StructureCanvas

scaleByNormal() - Method in class org.simtk.moleculargraphics.cartoon.GlyphCartoon

scaleByNormal() - Method in class org.simtk.moleculargraphics.cartoon.TensorGlyphCartoon

scaleNone() - Method in class org.simtk.moleculargraphics.cartoon.GlyphCartoon

scaleNone() - Method in class org.simtk.moleculargraphics.cartoon.TensorGlyphCartoon

SEA_GREEN - Static variable in class org.simtk.util.ColorName

SEA_GREEN1 - Static variable in class org.simtk.util.ColorName

SEA_GREEN2 - Static variable in class org.simtk.util.ColorName

SEA_GREEN3 - Static variable in class org.simtk.util.ColorName

SEA_GREEN4 - Static variable in class org.simtk.util.ColorName

SEASHELL - Static variable in class org.simtk.util.ColorName

SEASHELL1 - Static variable in class org.simtk.util.ColorName

SEASHELL2 - Static variable in class org.simtk.util.ColorName

SEASHELL3 - Static variable in class org.simtk.util.ColorName

SEASHELL4 - Static variable in class org.simtk.util.ColorName

SecondaryStructure - Interface in org.simtk.molecularstructure

Base class for alpha helices, beta strands, beta sheets, and RNA duplexes

SecondaryStructureCanvas - Class in org.simtk.toon.secstruct

SecondaryStructureCanvas(ResidueHighlightBroadcaster) - Constructor for class org.simtk.toon.secstruct.SecondaryStructureCanvas

SecondaryStructureClass - Class in org.simtk.molecularstructure

SecondaryStructureClass() - Constructor for class org.simtk.molecularstructure.SecondaryStructureClass

SecondaryStructureClass(int) - Constructor for class org.simtk.molecularstructure.SecondaryStructureClass

SecondaryStructureClass(Collection<Residue>) - Constructor for class org.simtk.molecularstructure.SecondaryStructureClass

SecondaryStructureClass(Collection<Residue>, int) - Constructor for class org.simtk.molecularstructure.SecondaryStructureClass

SecondaryStructureClass(Collection<Residue>, int, String) - Constructor for class org.simtk.molecularstructure.SecondaryStructureClass

SecondaryStructureClass.SourceType - Enum in org.simtk.molecularstructure

SecondaryStructureDiagram - Interface in org.simtk.toon.secstruct

SecondaryStructureDiagramClass - Class in org.simtk.toon.secstruct

SecondaryStructureDiagramClass() - Constructor for class org.simtk.toon.secstruct.SecondaryStructureDiagramClass

secondaryStructures() - Method in interface org.simtk.molecularstructure.Biopolymer

secondaryStructures() - Method in class org.simtk.molecularstructure.BiopolymerClass

secondaryStructures() - Method in interface org.simtk.molecularstructure.Residue

secondaryStructures() - Method in class org.simtk.molecularstructure.ResidueClass

select(Selectable) - Method in interface org.simtk.util.SelectionListener

Selectable - Interface in org.simtk.util

selectedObjects - Variable in class org.simtk.util.SelectionBroadcaster

selectedSourceTypes - Variable in class org.simtk.moleculargraphics.Tornado

SelectionBroadcaster - Class in org.simtk.util

SelectionBroadcaster() - Constructor for class org.simtk.util.SelectionBroadcaster

SelectionListener - Interface in org.simtk.util

SELENIUM - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass

selfUnit() - Method in class org.simtk.geometry3d.MathVectorClass

selfUnit() - Method in interface org.simtk.geometry3d.MutableMathVector

SemiCylinder - Class in org.simtk.geometry3d

SemiCylinder(Vector3D, Vector3D, double, Vector3DClass) - Constructor for class org.simtk.geometry3d.SemiCylinder

SequenceAlignment - Class in org.simtk.molecularstructure

SequenceAlignment(Biopolymer, Biopolymer) - Constructor for class org.simtk.molecularstructure.SequenceAlignment

SequenceCanvas - Class in org.simtk.moleculargraphics

SequenceCanvas() - Constructor for class org.simtk.moleculargraphics.SequenceCanvas

SequenceCartoonCanvas - Class in org.simtk.moleculargraphics

SequenceCartoonCanvas(ResidueHighlightBroadcaster, TornadoSequenceCanvas) - Constructor for class org.simtk.moleculargraphics.SequenceCartoonCanvas

SequencePane - Class in org.simtk.moleculargraphics

SEQUENCING_NUCLEOTIDE_COLOR_SCHEME - Static variable in class org.simtk.moleculargraphics.cartoon.SequencingNucleotideColorScheme

SequencingNucleotideColorScheme - Class in org.simtk.moleculargraphics.cartoon

SequencingNucleotideColorScheme() - Constructor for class org.simtk.moleculargraphics.cartoon.SequencingNucleotideColorScheme

serialVersionUID - Static variable in class org.simtk.moleculargraphics.BufferedCanvas

serialVersionUID - Static variable in class org.simtk.moleculargraphics.CylinderPanel

serialVersionUID - Static variable in class org.simtk.moleculargraphics.SequenceCartoonCanvas

serialVersionUID - Static variable in class org.simtk.moleculargraphics.SequencePane

serialVersionUID - Static variable in class org.simtk.moleculargraphics.Tornado3DCanvas

serialVersionUID - Static variable in exception org.simtk.util.ProgrammerLogicProblem

Serine - Class in org.simtk.molecularstructure.protein

Serine() - Constructor for class org.simtk.molecularstructure.protein.Serine

set(int, int, double) - Method in class Jama.Matrix

Set a single element.

set(int, int, double) - Method in class org.simtk.geometry3d.JamaMatrix

set(int, int, double) - Method in class org.simtk.geometry3d.MathMatrixClass

set(int, double) - Method in class org.simtk.geometry3d.MathVectorClass

set(int, int, double) - Method in interface org.simtk.geometry3d.MutableMathMatrix

set(int, double) - Method in interface org.simtk.geometry3d.MutableMathVector

set(int, double) - Method in class org.simtk.geometry3d.Vector3DFloatArrayWrapper

setActiveMolecule(Molecule) - Method in interface org.simtk.moleculargraphics.ActiveMoleculeListener

setActiveMolecule(Molecule) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

setActiveMolecule(Molecule) - Method in class org.simtk.moleculargraphics.SequencePane

setAtomName(String) - Method in interface org.simtk.molecularstructure.atom.Atom

setAtomName(String) - Method in class org.simtk.molecularstructure.atom.AtomClass

setBackgroundColor(Color) - Method in class org.simtk.moleculargraphics.MolApp

setBackgroundColor(Color) - Method in class org.simtk.moleculargraphics.ScaleBar

setBackgroundColor(Color) - Method in class org.simtk.moleculargraphics.StructureCanvas

setBackgroundColor(Color) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

setBond_orient(BasePair.BondOrientation) - Method in class org.simtk.molecularstructure.nucleicacid.BasePair

setBond_orient(String) - Method in class org.simtk.molecularstructure.nucleicacid.BasePair

setCancelled(boolean) - Method in interface org.simtk.gui.ProgressDialog

setCancelled(boolean) - Method in class org.simtk.gui.ProgressDialogClass

setCancelled(boolean) - Method in class org.simtk.gui.ProgressPanel

setChanged() - Method in class org.simtk.mvc.SimpleObservable

setColor(Object, Color) - Method in class org.simtk.moleculargraphics.cartoon.AtomColorScheme

setColumn(int, MathVector) - Method in class org.simtk.geometry3d.MathMatrixClass

setColumn(int, MathVector) - Method in interface org.simtk.geometry3d.MutableMathMatrix

setCoordinates(Vector3D) - Method in interface org.simtk.molecularstructure.atom.Atom

setCoordinates(Vector3D) - Method in class org.simtk.molecularstructure.atom.AtomClass

setCoordinates(Vector3D) - Method in class org.simtk.molecularstructure.atom.AtomPosition

setCovalentRadius(double) - Method in class org.simtk.molecularstructure.atom.ChemicalElementClass

setCpkColors() - Method in class org.simtk.moleculargraphics.cartoon.AtomColorScheme

setCurrentPath(String) - Method in class org.simtk.moleculargraphics.Tornado

setCurrentPath(String) - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog

setDefaultColor(Color) - Method in class org.simtk.moleculargraphics.cartoon.ToonColors

setDefaultPdbId(String) - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog

setDescription(String) - Method in class org.simtk.util.MyJFileFilter

setDiagram(SecondaryStructureDiagram) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

setDisplaySourceTypes(Collection<SecondaryStructureClass.SourceType>) - Method in interface org.simtk.molecularstructure.Molecule

setDisplaySourceTypes(Collection<SecondaryStructureClass.SourceType>) - Method in class org.simtk.molecularstructure.MoleculeClass

SetDistance(double) - Method in class org.simtk.moleculargraphics.cartoon.vtkGrowPointsFilter

setEdge(Residue, BasePair.EdgeType) - Method in class org.simtk.molecularstructure.nucleicacid.BasePair

setEdge(Residue, String) - Method in class org.simtk.molecularstructure.nucleicacid.BasePair

setElement(ChemicalElement) - Method in class org.simtk.molecularstructure.atom.AtomClass

setElementName(String) - Method in class org.simtk.molecularstructure.atom.ChemicalElementClass

setElementSymbol(String) - Method in class org.simtk.molecularstructure.atom.ChemicalElementClass

setGlycosyl(String) - Method in class org.simtk.molecularstructure.ResidueClass

setGlyphSource(vtkPolyData) - Method in class org.simtk.moleculargraphics.cartoon.GlyphCartoon

setGlyphSource(vtkPolyData) - Method in class org.simtk.moleculargraphics.cartoon.TensorGlyphCartoon

setHelixType(HelixType) - Method in class org.simtk.molecularstructure.protein.Helix

setHighlightColor(Color) - Method in class org.simtk.moleculargraphics.ResidueHighlightBroadcaster

setInputStructureFileName(String) - Method in class org.simtk.molecularstructure.MoleculeCollection

setLeftEdgePixel(int) - Method in class org.simtk.moleculargraphics.SequenceCanvas

setMass(double) - Method in class org.simtk.molecularstructure.atom.ChemicalElementClass

setMatrix(int, int, int, int, Matrix) - Method in class Jama.Matrix

Set a submatrix.

setMatrix(int[], int[], Matrix) - Method in class Jama.Matrix

Set a submatrix.

setMatrix(int[], int, int, Matrix) - Method in class Jama.Matrix

Set a submatrix.

setMatrix(int, int, int[], Matrix) - Method in class Jama.Matrix

Set a submatrix.

setMaximumSize(Dimension) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

setMaximumSize(Dimension) - Method in class org.simtk.moleculargraphics.SequencePane

setMaximumSize(Dimension) - Method in class org.simtk.moleculargraphics.StructureCanvas

setMaximumSize(Dimension) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

setMessage(String) - Method in class org.simtk.moleculargraphics.Tornado

setMinimumSize(Dimension) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

setMinimumSize(Dimension) - Method in class org.simtk.moleculargraphics.SequencePane

setMinimumSize(Dimension) - Method in class org.simtk.moleculargraphics.StructureCanvas

setMinimumSize(Dimension) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

setMolecule(Biopolymer) - Method in class org.simtk.moleculargraphics.SequenceCanvas

setMolecule(Biopolymer) - Method in interface org.simtk.molecularstructure.SecondaryStructure

setMolecule(Biopolymer) - Method in class org.simtk.molecularstructure.SecondaryStructureClass

setNewParameters(Object) - Method in class org.simtk.gui.UndoableDialog

setNextResidue(Residue) - Method in interface org.simtk.molecularstructure.Residue

setNextResidue(Residue) - Method in class org.simtk.molecularstructure.ResidueClass

setParameters(Object) - Method in class org.simtk.gui.ParameterSetModel

setParentContainer(JComponent) - Method in class org.simtk.moleculargraphics.SequenceCanvas

setPdbChainId(String) - Method in class org.simtk.molecularstructure.MoleculeClass

setPdbId(String) - Method in class org.simtk.molecularstructure.MoleculeCollection

setPdbId(String) - Method in class org.simtk.pdb.LoadPdbUrlProcess

setPdbId(String) - Method in class org.simtk.pdb.MoleculeAcquisitionMethodDialog

setPdbInsertionCode(char) - Method in class org.simtk.molecularstructure.ResidueClass

setPreferredSize(Dimension) - Method in class org.simtk.moleculargraphics.SequenceCartoonCanvas

setPreferredSize(Dimension) - Method in class org.simtk.moleculargraphics.StructureCanvas

setPreferredSize(Dimension) - Method in class org.simtk.toon.secstruct.SecondaryStructureCanvas

setPreviousResidue(Residue) - Method in interface org.simtk.molecularstructure.Residue

setPreviousResidue(Residue) - Method in class org.simtk.molecularstructure.ResidueClass

setPucker(String) - Method in class org.simtk.molecularstructure.ResidueClass

setRange(Angle.Range) - Method in class org.simtk.geometry3d.Angle

setResidue(Residue) - Method in class org.simtk.molecularstructure.atom.AtomClass

setResidueCenterBroadcaster(ResidueCenterBroadcaster) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

setResidueHighlightBroadcaster(ResidueHighlightBroadcaster) - Method in class org.simtk.moleculargraphics.Tornado3DCanvas

setResidueNumber(int) - Method in interface org.simtk.molecularstructure.Residue

setResidueNumber(int) - Method in class org.simtk.molecularstructure.ResidueClass

setRotation(Matrix3D) - Method in class org.simtk.geometry3d.HomogeneousTransformClass

setRotation(Matrix3D) - Method in interface org.simtk.geometry3d.MutableHomogeneousTransform

setRow(int, MathVector) - Method in class org.simtk.geometry3d.MathMatrixClass

setRow(int, MathVector) - Method in interface org.simtk.geometry3d.MutableMathMatrix

SetScalars(String) - Method in class org.simtk.moleculargraphics.cartoon.vtkSetScalarsFilter

setScale(double) - Method in class org.simtk.moleculargraphics.cartoon.AtomSphereActor

setSequenceColor(Color) - Method in class org.simtk.moleculargraphics.SequenceCanvas

setSize(int, int) - Method in class org.simtk.moleculargraphics.vtkSwingPanel

setSource(String) - Method in interface org.simtk.molecularstructure.SecondaryStructure

setSource(String) - Method in class org.simtk.molecularstructure.SecondaryStructureClass

setStartTime(Date) - Method in interface org.simtk.gui.ProgressDialog

setStartTime(Date) - Method in class org.simtk.gui.ProgressDialogClass

setStartTime(Date) - Method in class org.simtk.gui.ProgressPanel

setStereoCrossEye() - Method in class org.simtk.moleculargraphics.StructureCanvas

setStereoInterlaced() - Method in class org.simtk.moleculargraphics.StructureCanvas

setStereoLeftEye() - Method in class org.simtk.moleculargraphics.StructureCanvas

setStereoOff() - Method in class org.simtk.moleculargraphics.StructureCanvas

setStereoRedBlue() - Method in class org.simtk.moleculargraphics.StructureCanvas

setStereoRightEye() - Method in class org.simtk.moleculargraphics.StructureCanvas

setStrand_orient(String) - Method in class org.simtk.molecularstructure.nucleicacid.BasePair

SetThickness(double) - Method in class org.simtk.moleculargraphics.cartoon.vtkArrowWidthFilter

SetThickness(double) - Method in class org.simtk.moleculargraphics.cartoon.vtkPreExtrusionCenteringFilter

SetThickness(double) - Method in class org.simtk.moleculargraphics.cartoon.vtkTaperedWidthFilter

setTitle(String) - Method in class org.simtk.molecularstructure.MoleculeCollection

setTorsionAngle(double) - Method in class org.simtk.moleculargraphics.EthaneDemo

setTranslation(Vector3D) - Method in class org.simtk.geometry3d.HomogeneousTransformClass

setTranslation(Vector3D) - Method in interface org.simtk.geometry3d.MutableHomogeneousTransform

setUnits(Angle.Units) - Method in class org.simtk.geometry3d.Angle

setUpLights() - Method in class org.simtk.moleculargraphics.StructureCanvas

setUpMenuBar() - Method in class org.simtk.moleculargraphics.EthaneDemo

setValue(double, Angle.Units) - Method in class org.simtk.geometry3d.Angle

setValue(double) - Method in class org.simtk.geometry3d.Angle

setVanDerWaalsRadius(double) - Method in class org.simtk.molecularstructure.atom.ChemicalElementClass

setWait(String) - Method in class org.simtk.moleculargraphics.Tornado

SetWidth(double) - Method in class org.simtk.moleculargraphics.cartoon.vtkArrowWidthFilter

SetWidth(double) - Method in class org.simtk.moleculargraphics.cartoon.vtkTaperedWidthFilter

setX(double) - Method in interface org.simtk.geometry3d.MutableVector2D

setX(double) - Method in interface org.simtk.geometry3d.MutableVector3D

setX(double) - Method in class org.simtk.geometry3d.Vector2DClass

setX(double) - Method in class org.simtk.geometry3d.Vector3DClass

setY(double) - Method in interface org.simtk.geometry3d.MutableVector2D

setY(double) - Method in interface org.simtk.geometry3d.MutableVector3D

setY(double) - Method in class org.simtk.geometry3d.Vector2DClass

setY(double) - Method in class org.simtk.geometry3d.Vector3DClass

setZ(double) - Method in interface org.simtk.geometry3d.MutableVector3D

setZ(double) - Method in class org.simtk.geometry3d.Vector3DClass

shortValue() - Method in class org.simtk.geometry3d.Angle

show() - Method in interface org.simtk.moleculargraphics.cartoon.Hidable

show() - Method in class org.simtk.moleculargraphics.cartoon.HidableActorClass

show() - Method in class org.simtk.moleculargraphics.cartoon.ProteinRibbon

show(Molecule) - Method in class org.simtk.moleculargraphics.cartoon.ProteinRibbon

sideChainGroup - Static variable in class org.simtk.molecularstructure.protein.AminoAcid

SIENNA - Static variable in class org.simtk.util.ColorName

SIENNA1 - Static variable in class org.simtk.util.ColorName

SIENNA2 - Static variable in class org.simtk.util.ColorName

SIENNA3 - Static variable in class org.simtk.util.ColorName

SIENNA4 - Static variable in class org.simtk.util.ColorName

SIGNED - Static variable in class org.simtk.geometry3d.Angle.Range

SILVER - Static variable in class org.simtk.util.ColorName

SimpleObservable - Class in org.simtk.mvc

Observable with public setChanged() method

SimpleObservable() - Constructor for class org.simtk.mvc.SimpleObservable

sin() - Method in class org.simtk.geometry3d.Angle

SingularValueDecomposition - Class in Jama

Singular Value Decomposition.

SingularValueDecomposition(Matrix) - Constructor for class Jama.SingularValueDecomposition

Construct the singular value decomposition

skip(long) - Method in class org.simtk.util.UncompressInputStream

SKY_BLUE - Static variable in class org.simtk.util.ColorName

SKY_BLUE1 - Static variable in class org.simtk.util.ColorName

SKY_BLUE2 - Static variable in class org.simtk.util.ColorName

SKY_BLUE3 - Static variable in class org.simtk.util.ColorName

SKY_BLUE4 - Static variable in class org.simtk.util.ColorName

SLATE_BLUE - Static variable in class org.simtk.util.ColorName

SLATE_BLUE1 - Static variable in class org.simtk.util.ColorName

SLATE_BLUE2 - Static variable in class org.simtk.util.ColorName

SLATE_BLUE3 - Static variable in class org.simtk.util.ColorName

SLATE_BLUE4 - Static variable in class org.simtk.util.ColorName

SLATE_GRAY - Static variable in class org.simtk.util.ColorName

SLATE_GRAY1 - Static variable in class org.simtk.util.ColorName

SLATE_GRAY2 - Static variable in class org.simtk.util.ColorName

SLATE_GRAY3 - Static variable in class org.simtk.util.ColorName

SLATE_GRAY4 - Static variable in class org.simtk.util.ColorName

SLATE_GREY - Static variable in class org.simtk.util.ColorName

SNOW - Static variable in class org.simtk.util.ColorName

SNOW1 - Static variable in class org.simtk.util.ColorName

SNOW2 - Static variable in class org.simtk.util.ColorName

SNOW3 - Static variable in class org.simtk.util.ColorName

SNOW4 - Static variable in class org.simtk.util.ColorName

SODIUM - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass

solve(Matrix) - Method in class Jama.CholeskyDecomposition

Solve A*X = B

solve(Matrix) - Method in class Jama.LUDecomposition

Solve A*X = B

solve(Matrix) - Method in class Jama.Matrix

Solve A*X = B

solve(Matrix) - Method in class Jama.QRDecomposition

Least squares solution of A*X = B

solveTranspose(Matrix) - Method in class Jama.Matrix

Solve X*A = B, which is also A'*X' = B'

sourceType - Variable in class org.simtk.molecularstructure.SecondaryStructureClass

splash(URL) - Static method in class org.simtk.splashscreen.SplashWindow

splash(Image) - Static method in class org.simtk.splashscreen.SplashWindow

SplashWindow - Class in org.simtk.splashscreen

Spline3D - Class in org.simtk.moleculargraphics

Spline3D() - Constructor for class org.simtk.moleculargraphics.Spline3D

splineX - Variable in class org.simtk.moleculargraphics.Spline3D

splineY - Variable in class org.simtk.moleculargraphics.Spline3D

splineZ - Variable in class org.simtk.moleculargraphics.Spline3D

SPRING_GREEN - Static variable in class org.simtk.util.ColorName

SPRING_GREEN1 - Static variable in class org.simtk.util.ColorName

SPRING_GREEN2 - Static variable in class org.simtk.util.ColorName

SPRING_GREEN3 - Static variable in class org.simtk.util.ColorName

SPRING_GREEN4 - Static variable in class org.simtk.util.ColorName

stateChanged(ChangeEvent) - Method in class org.simtk.moleculargraphics.EthaneDemo

STEEL_BLUE - Static variable in class org.simtk.util.ColorName

STEEL_BLUE1 - Static variable in class org.simtk.util.ColorName

STEEL_BLUE2 - Static variable in class org.simtk.util.ColorName

STEEL_BLUE3 - Static variable in class org.simtk.util.ColorName

STEEL_BLUE4 - Static variable in class org.simtk.util.ColorName

stepNutation(double) - Method in class org.simtk.moleculargraphics.StructureCanvas

Stopwatch - Class in org.simtk.util

Stopwatch() - Constructor for class org.simtk.util.Stopwatch

straightLine - Variable in class org.simtk.toon.secstruct.BasePairPosition

strand_orient - Variable in class org.simtk.molecularstructure.nucleicacid.BasePair

strandWidth - Variable in class org.simtk.moleculargraphics.cartoon.RichardsonProteinRibbon

StructureCanvas - Class in org.simtk.moleculargraphics

StructureCanvas() - Constructor for class org.simtk.moleculargraphics.StructureCanvas

subToons - Variable in class org.simtk.moleculargraphics.cartoon.MoleculeCartoonClass

sugarGroup - Static variable in class org.simtk.molecularstructure.nucleicacid.Nucleotide

SULFUR - Static variable in class org.simtk.molecularstructure.atom.ChemicalElementClass

Superposition - Class in org.simtk.geometry3d

Superposition() - Constructor for class org.simtk.geometry3d.Superposition

svd() - Method in class Jama.Matrix

Singular Value Decomposition