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G

Ga - Static variable in class edu.sdsc.mbt.util.Element
GeneralFragmentPanel - class edu.sdsc.sirius.builder.GeneralFragmentPanel.
GeneralFragmentPanel() - Constructor for class edu.sdsc.sirius.builder.GeneralFragmentPanel
Geometry - class edu.sdsc.mbt.viewers.GLViewerImpl.Geometry.: This class provides the base functionality for geometry factory objects.
Geometry() - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.Geometry
GeometryEntity - class edu.sdsc.mbt.viewers.GLViewerImpl.GeometryEntity.: Geometry is the base class for the geometry description of all structure objects in a scene.
GeometryEntity() - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.GeometryEntity: Empty constructor for a GeometryEntity object.
GeometryEvent - class edu.sdsc.sirius.dialogs.GeometryEvent.
GeometryEvent(DisplayDialog) - Constructor for class edu.sdsc.sirius.dialogs.GeometryEvent
GlAxesRenderable - class edu.sdsc.mbt.viewers.GLViewerImpl.GlAxesRenderable.: Draw X-Y-Z axes at the world origin (0.0, 0.0, 0.0).
GlAxesRenderable() - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.GlAxesRenderable: Construct a X-Y-Z axes renderable.
GlExtrusion - class edu.sdsc.mbt.viewers.GLViewerImpl.GlExtrusion.: Creates a geometry factory that uses JOGL/OpenGL to draw a generalized extrusion.
GlExtrusion(float[][], float[][], float[][], float[][], float[][], boolean, boolean, boolean, float) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.GlExtrusion: Primary Constructor.
GlExtrusion(float[][], float[][], float[][], float[][], float[][]) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.GlExtrusion: Secondary Constructor.
GlExtrusion(float[][], float[][], float[][], float[][]) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.GlExtrusion: Secondary Constructor.
GlExtrusion(float[][], float[][], float[][]) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.GlExtrusion: Secondary Constructor.
GlExtrusion(float[][], float[][]) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.GlExtrusion: Secondary Constructor.
GlGeometryViewer - class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer.: Define the GlGeometryViewer class.
GlGeometryViewer() - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer: Construct an instance of the class.
GlRenderable - interface edu.sdsc.mbt.viewers.GLViewerImpl.GlRenderable.: Provides an interface with which the GlGeometryViewer class can render a visible representation of some data.
GvPickEvent - class edu.sdsc.mbt.viewers.GLViewerImpl.GvPickEvent.: GvPickEvent.java
Please complete these missing tags
GvPickEvent() - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.GvPickEvent
GvPickEventListener - interface edu.sdsc.mbt.viewers.GLViewerImpl.GvPickEventListener.: GvPickEventListener.java
Please complete these missing tags
gapdist - Static variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.AlignmentSettings
gapext - Static variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.AlignmentSettings
gapopen - Static variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.AlignmentSettings
generateBonds() - Method in class edu.sdsc.mbt.StructureMap: Generate a complete set of Bond objects from the Atom records.
generateBonds(Structure) - Static method in class edu.sdsc.mbt.util.BondFactory: Return a vector of Bond objects extracted from a Structure using 1.8 as the bondLimit distance.
generateBonds(Structure, double) - Static method in class edu.sdsc.mbt.util.BondFactory: Return a vector of Bond objects extracted from a Structure using the specified bondLimit distance.
generateCovalentBonds(Vector, double, boolean) - Static method in class edu.sdsc.mbt.util.BondFactory: Given a vector of Atom objects, return a Vector of Bond objects.
generateCovalentBonds(Vector) - Static method in class edu.sdsc.mbt.util.BondFactory: Given a vector of Atom objects, return a Vector of Bond objects.
generateFragments() - Method in class edu.sdsc.mbt.Chain: Regenerate the vector of Fragment objects from the fragments RangeMap.
generateFragments() - Method in class edu.sdsc.mbt.StructureMap: Generate secondary structure fragments for the Structure.
generateNormals(IntrinsicCrossSection, FrenetTrihedron) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.AffineCrossSection
generateNormals(FrenetTrihedron) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection
generatePoints(IntrinsicCrossSection, FrenetTrihedron) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.AffineCrossSection
generatePoints(FrenetTrihedron) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection
get(String) - Static method in class edu.sdsc.mbt.viewables.AtomColorRegistry: Get an AtomColor implementation by name.
get(String) - Static method in class edu.sdsc.mbt.viewables.AtomLabelRegistry: Get an AtomLabel implementation by name.
get(String) - Static method in class edu.sdsc.mbt.viewables.AtomRadiusRegistry: Get an AtomRadius implementation by name.
get(String) - Static method in class edu.sdsc.mbt.viewables.BondColorRegistry: Get an BondColor implementation by name.
get(String) - Static method in class edu.sdsc.mbt.viewables.BondFormRegistry: Get an BondForm implementation by name.
get(String) - Static method in class edu.sdsc.mbt.viewables.BondLabelRegistry: Get an BondLabel implementation by name.
get(String) - Static method in class edu.sdsc.mbt.viewables.BondRadiusRegistry: Get an BondRadius implementation by name.
get(String) - Static method in class edu.sdsc.mbt.viewables.ChainColorRegistry: Get an ChainColor implementation by name.
get(String) - Static method in class edu.sdsc.mbt.viewables.FragmentColorRegistry: Get an FragmentColor implementation by name.
get(String) - Static method in class edu.sdsc.mbt.viewables.FragmentFormRegistry: Get an FragmentForm implementation by name.
get(String) - Static method in class edu.sdsc.mbt.viewables.ResidueColorRegistry: Get an ResidueColor implementation by name.
get(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Path: Gets the component of this Path at the given level.
getAcc() - Method in class edu.sdsc.sirius.dialogs.TableImpl.InterProDataBlock
getAccession() - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock
getActiveComponent() - Method in class edu.sdsc.sirius.viewers.TreeViewer.InfoViewer
getAlgorithm() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Interpolator: Get the interpolation algorithm.
getAlignedResidues(Entry) - Method in class edu.sdsc.sirius.viewers.SequenceViewer: This method returns a Vector of Residues that correspond to sequence of the given Entry If no residue is present at the given position, null is used
getAllAttachmentPoints(String) - Static method in class edu.sdsc.sirius.builder.FragmentRegistry
getAllData() - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataSet: Returns a hash containing mappings of entry ids to the corresponding DataBlocks.
getAlphaAtom() - Method in class edu.sdsc.mbt.Residue: Get the alpha (backbone) Atom (eg: "CA" or "P") for this amino acid or nucleic acid residue (or -1 for ligands).
getAlphaAtomIndex() - Method in class edu.sdsc.mbt.Residue: Get the alpha (backbone) Atom (eg: "CA" or "P") index for this amino acid or nucleic acid residue (or -1 for ligands).
getAltLoc() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Return the value of the "alternate location indicator".
getAminoAcidLetter(String) - Static method in class edu.sdsc.mbt.util.CodonInfo: Returns the amino acid letter code for the given 3-letter codon tuple.
getAminoAcidLetter(String, String, String) - Static method in class edu.sdsc.mbt.util.CodonInfo: Returns the amino acid letter code for the given 3-letter codon tuple.
getAminoacids() - Static method in class edu.sdsc.sirius.util.ProteinProperties
getAngle(Vec3d, Vec3d, Vec3d) - Static method in class edu.sdsc.mbt.util.Algebra: Calculates the angle formed by the three points.
getAngleBetweenVectors(double[], double[]) - Static method in class edu.sdsc.mbt.util.Algebra
getAngleConnections() - Method in class edu.sdsc.mbt.StructureMap: Get all combination of three atoms connected through the central atom and forming an angle Each item is an array of three Atoms
getAnnotationComponent() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.MonitorRenderable
getApplication() - Method in class edu.sdsc.sirius.dialogs.TableImpl.InterProDataBlock
getApplicationFrame() - Method in class Viewer
getApplicationFrame() - Method in interface edu.sdsc.sirius.util.Manager: Returns a reference to the frame of the main application.
getAsString() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Path: Returns this Path as a plain String.
getAsStrings() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Path: Returns this Path as array containing the elements of the Path.
getAspectRatio() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
getAtom(int) - Method in class edu.sdsc.mbt.Bond: Get the specified Atom record that forms this Bond.
getAtom(int) - Method in class edu.sdsc.mbt.Residue: Return the specified Atom record contained in this Residue.
getAtom(int) - Method in class edu.sdsc.mbt.StructureMap: Get the Atom at the specified index.
getAtom() - Method in class edu.sdsc.mbt.util.OctreeAtomItem: Return the Atom associated with this data item.
getAtom(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue: Return the nth Atom in this residue.
getAtomColor(Atom, float[]) - Method in interface edu.sdsc.mbt.viewables.AtomColor
getAtomColor(Atom, float[]) - Method in class edu.sdsc.mbt.viewables.AtomColorByCharge: Produce a color based upon the residue element type.
getAtomColor(Atom, float[]) - Method in class edu.sdsc.mbt.viewables.AtomColorByElement: Produce a color based upon the atom element type.
getAtomColor(Color) - Static method in class edu.sdsc.mbt.viewables.AtomColorFactory
getAtomColor(Atom, float[]) - Method in class edu.sdsc.mbt.viewables.AtomColorUniform: Produce a color based upon the residue element type.
getAtomColor(StructureComponent) - Method in class edu.sdsc.mbt.viewables.StructureStyles
getAtomColorStyleReference() - Method in class edu.sdsc.mbt.viewables.StructureStyles
getAtomColorStyles() - Method in class edu.sdsc.mbt.viewables.StructureStyles
getAtomColors() - Method in class edu.sdsc.sirius.export.StyleMap
getAtomCoordinateAverage() - Method in class edu.sdsc.mbt.StructureMap: Return the coordinate average for a Structure's atom coordinates.
getAtomCoordinateAverage(Structure) - Static method in class edu.sdsc.mbt.util.AtomStats: Return the coordinate average for a Structure's atom coordinates.
getAtomCoordinateBounds() - Method in class edu.sdsc.mbt.StructureMap: Return the coordinate bounds for a Structure's atom coordinates.
getAtomCoordinateBounds(Structure) - Static method in class edu.sdsc.mbt.util.AtomStats: Return the coordinate bounds for given a Structure.
getAtomCoordinates(Atom) - Static method in class edu.sdsc.mbt.util.Algebra: Returns coordinates of the given Atom in 3d space.
getAtomCount() - Method in class edu.sdsc.mbt.Chain: Get the number of Atoms contained in the Residues of this Chain.
getAtomCount() - Method in class edu.sdsc.mbt.Residue: Return the number of Atom records contained in this Residue.
getAtomCount() - Method in class edu.sdsc.mbt.StructureMap: Return the total Atom count extracted from the Structure.
getAtomCount() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue: Return the number of atoms in this residue.
getAtomIndex(Atom) - Method in class edu.sdsc.mbt.Residue
getAtomIndex(Atom) - Method in class edu.sdsc.mbt.StructureMap: Get the index of the specified Atom.
getAtomLabel(Atom) - Method in interface edu.sdsc.mbt.viewables.AtomLabel
getAtomLabel(Atom) - Method in class edu.sdsc.mbt.viewables.AtomLabelByAtomCompound: Produce a label based upon the atom name.
getAtomLabel(Atom) - Method in class edu.sdsc.mbt.viewables.AtomLabelByAtomElement: Produce a label based upon the atom element.
getAtomLabel(Atom) - Method in class edu.sdsc.mbt.viewables.AtomLabelByAtomName: Produce a label based upon the atom name.
getAtomLabel(Atom) - Method in class edu.sdsc.mbt.viewables.AtomLabelByChainId: Produce a label based upon the atom chain_id.
getAtomLabel(Atom) - Method in class edu.sdsc.mbt.viewables.AtomLabelNone: Produce a null label.
getAtomPaths() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper: Returns an array containing all of the edu.sdsc.sirius.viewers.StructureViewerImpl.pdb.Atom-level Paths in this PdbWrapper.
getAtomPaths(Path[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper
getAtomPaths() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getAtomPaths(Path[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getAtomPaths() - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getAtomPaths(Path[]) - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getAtomRadius(int) - Static method in class edu.sdsc.mbt.util.ElementProperties: Get the radius of the given element number.
getAtomRadius(String) - Static method in class edu.sdsc.mbt.util.ElementProperties: Get the radius of the given element name.
getAtomRadius(short) - Static method in class edu.sdsc.mbt.util.ElementProperties
getAtomRadius(Atom) - Method in interface edu.sdsc.mbt.viewables.AtomRadius
getAtomRadius(Atom) - Method in class edu.sdsc.mbt.viewables.AtomRadiusByConstant: Produce a radius based upon the atom element type.
getAtomRadius(Atom) - Method in class edu.sdsc.mbt.viewables.AtomRadiusByCpk: Produce a radius based upon the atom element type.
getAtomRadius(Atom) - Method in class edu.sdsc.mbt.viewables.AtomRadiusByScaledCpk: Produce a radius based upon the atom element type.
getAtomRadius(StructureComponent) - Method in class edu.sdsc.mbt.viewables.StructureStyles: Set the style for the given structure component and then fire an event to all listeners.
getAtomRadiusStyleReference() - Method in class edu.sdsc.mbt.viewables.StructureStyles
getAtomRadiusStyles() - Method in class edu.sdsc.mbt.viewables.StructureStyles
getAtomRenderingQuality() - Method in class edu.sdsc.sirius.export.StyleMap
getAtomRenderingStyle() - Method in class edu.sdsc.sirius.export.StyleMap
getAtomSelection() - Method in class edu.sdsc.sirius.export.StyleMap
getAtomSetAssignment() - Method in class edu.sdsc.sirius.export.StyleMap
getAtomSetNames() - Method in class edu.sdsc.sirius.export.StateObject
getAtomSetNames() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getAtomSets() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getAtomToAtoms() - Method in class edu.sdsc.mbt.StructureMap
getAtomToBonds() - Method in class edu.sdsc.mbt.StructureMap
getAtomToLabels() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getAtomToResidueLabels() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getAtomVisibility() - Method in class edu.sdsc.sirius.export.StyleMap
getAtoms() - Method in class edu.sdsc.mbt.Residue: Return Vector of Atoms that are contained in this Residue.
getAtoms(Atom) - Method in class edu.sdsc.mbt.StructureMap
getAtoms() - Method in class edu.sdsc.mbt.StructureMap
getAtoms() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue: Return an array containing all atoms in the residue.
getAtoms() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper: Returns an array of all Atoms in this PdbWrapper.
getAtoms(Path[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper: Returns an array of Atoms corresponding to the Atom-level Paths that were supplied.
getAtoms() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getAtoms(Path[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getAtoms() - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getAtoms(Path[]) - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getAttachmentPoint(String) - Static method in class edu.sdsc.sirius.builder.FragmentRegistry
getAttachments() - Method in class edu.sdsc.sirius.builder.FragmentRecord
getAuthor() - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock
getAuthors() - Method in class edu.sdsc.mbt.StructureInfo: Get the authors of this entry.
getBFactor() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Return the temperature factor of the atom.
getBackgroundColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByCharge
getBackgroundColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByHydrophobicity
getBackgroundColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByType
getBackgroundColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorDefault
getBackgroundColor(Color) - Static method in class edu.sdsc.mbt.viewables.ResidueColorFactory: Returns a ResidueColorUniform object in response to the requested Color for residue cell background
getBackgroundColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorScaled
getBackgroundColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorUniform
getBackgroundColor() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
getBackupSequences() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getBaseCount() - Static method in class edu.sdsc.mbt.util.NucleicAcidInfo: Returns the number of nucleic acid base name tuples in the database.
getBiOrthogonalVector(double[], double[]) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometryUtils: returns a vector that is orthogonal to both input vectors
getBinormal() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron
getBinormal() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Trihedron: Get the binormal vector.
getBond(int) - Method in class edu.sdsc.mbt.StructureMap: Get the Bond at the specified index.
getBondColor(Bond, float[]) - Method in interface edu.sdsc.mbt.viewables.BondColor: Provides the primary color for a bond.
getBondColor(Bond, float[]) - Method in class edu.sdsc.mbt.viewables.BondColorByAtomColor
getBondColor(Bond, float[]) - Method in class edu.sdsc.mbt.viewables.BondColorByElement
getBondColor(StructureComponent) - Method in class edu.sdsc.mbt.viewables.StructureStyles
getBondColorStyleReference() - Method in class edu.sdsc.mbt.viewables.StructureStyles
getBondColorStyles() - Method in class edu.sdsc.mbt.viewables.StructureStyles
getBondCount() - Method in class edu.sdsc.mbt.StructureMap: Get a count of bonds contained in this StructureMap.
getBondForm(Bond) - Method in interface edu.sdsc.mbt.viewables.BondForm
getBondForm(Bond) - Method in class edu.sdsc.mbt.viewables.BondFormOrder
getBondForm(Bond) - Method in class edu.sdsc.mbt.viewables.BondFormSimple
getBondForm(Bond) - Method in class edu.sdsc.mbt.viewables.BondFormSplit
getBondGeometry(Atom) - Static method in class edu.sdsc.mbt.util.ElementProperties
getBondIndex(Bond) - Method in class edu.sdsc.mbt.StructureMap: Get the index of the specified Bond.
getBondLabel(Bond) - Method in interface edu.sdsc.mbt.viewables.BondLabel
getBondLabel(Bond) - Method in class edu.sdsc.mbt.viewables.BondLabelByDistance: Produce a label based upon the bond atom distance.
getBondLabel(Bond) - Method in class edu.sdsc.mbt.viewables.BondLabelNone: Produce a null label.
getBondLength(int, int) - Static method in class edu.sdsc.mbt.util.ElementProperties
getBondLength(short, short) - Static method in class edu.sdsc.mbt.util.ElementProperties
getBondLocation(Bond) - Static method in class edu.sdsc.sirius.util.StructureMath: Returns a location of the bond, with the lookAt vector pointed along the bond and the up vector being orthogonal to the plane of the bond and one of the atoms the third vector is computed automatically The position is at the heavy atom
getBondMap() - Static method in class edu.sdsc.sirius.util.DNAProperties
getBondMap() - Static method in class edu.sdsc.sirius.util.ProteinProperties
getBondMapping(String) - Static method in class edu.sdsc.sirius.util.DNAProperties
getBondMapping(String) - Static method in class edu.sdsc.sirius.util.ProteinProperties
getBondRadius(Bond) - Method in interface edu.sdsc.mbt.viewables.BondRadius: Provides the primary radius for a bond.
getBondRadius(Bond) - Method in class edu.sdsc.mbt.viewables.BondRadiusAsStick: Produce the primary radius (in pixel units) as a constant value.
getBondRadius(Bond) - Method in class edu.sdsc.mbt.viewables.BondRadiusAsWire: Produce the primary radius (in pixel units) as a constant value.
getBondRadius(Bond) - Method in class edu.sdsc.mbt.viewables.BondRadiusByAtomRadius: Produce the primary radius based upon the first atom radius.
getBondRadius(Bond) - Method in class edu.sdsc.mbt.viewables.BondRadiusByScaledAtomRadius: Produce the primary radius based upon the first atom radius.
getBondRadius(StructureComponent) - Method in class edu.sdsc.mbt.viewables.StructureStyles
getBondRadiusStyleReference() - Method in class edu.sdsc.mbt.viewables.StructureStyles
getBondRadiusStyles() - Method in class edu.sdsc.mbt.viewables.StructureStyles
getBondToBonds() - Method in class edu.sdsc.mbt.StructureMap
getBondUniqueness() - Method in class edu.sdsc.mbt.StructureMap
getBonds(Atom) - Method in class edu.sdsc.mbt.StructureMap: Return a Vector of all Bond objects connected to the given Atom object.
getBonds(Bond) - Method in class edu.sdsc.mbt.StructureMap: Return a Vector of bonds that are neighbors of the argument
getBonds(Vector) - Method in class edu.sdsc.mbt.StructureMap: Return a Vector of all Bond objects connected to the given Atom objects.
getBonds() - Method in class edu.sdsc.mbt.StructureMap
getBonds(double) - Method in class edu.sdsc.mbt.util.Octree: ???
getBondsVector(double) - Method in class edu.sdsc.mbt.util.Octree: Return the vector of all potential covalent bonds.
getBufferedImage() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
getBumps() - Method in class edu.sdsc.sirius.export.StateObject
getBumps() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getCellBackgroundDefault() - Static method in class edu.sdsc.mbt.viewables.ResidueColorRegistry
getCellColor(Cell) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles
getCellColors() - Method in class edu.sdsc.sirius.export.StateObject
getCellResidueMapping() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getCells() - Method in class edu.sdsc.mbt.Sequence
getCenter() - Method in class edu.sdsc.mbt.StructureMap
getCenter() - Method in class edu.sdsc.sirius.io.FragmentEntry
getChain() - Method in class edu.sdsc.mbt.Fragment: Get the chain to which this Fragment belongs.
getChain(Atom) - Method in class edu.sdsc.mbt.StructureMap: Get the Chain object to which this Atom belongs.
getChain(String) - Method in class edu.sdsc.mbt.StructureMap: Get the Chain object given its ID.
getChain(int) - Method in class edu.sdsc.mbt.StructureMap: Return the Chain at the given chain index.
getChain(int[]) - Method in class edu.sdsc.mbt.util.DerivedInformation
getChain(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Model: Get the nth Chain from this Model.
getChainById() - Method in class edu.sdsc.mbt.StructureMap
getChainColor(Chain, float[]) - Method in interface edu.sdsc.mbt.viewables.ChainColor
getChainColor(Chain, float[]) - Method in class edu.sdsc.mbt.viewables.ChainColorById: Produce a color based upon the chain id.
getChainCount() - Method in class edu.sdsc.mbt.StructureMap: Return the chain count extracted from the Structure.
getChainCount() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Model: Get the number of Chains in this Model.
getChainId() - Method in class edu.sdsc.mbt.Chain: Return the chain ID by asking the first Atom of the first Residue.
getChainId() - Method in class edu.sdsc.mbt.Residue: Get the chain id (as it is assigned in the first Atom record).
getChainId() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Return the name of the chain to which this atom belongs.
getChainId() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Chain: Return the chain identifier.
getChainId() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue: Return the chain identifier for this residue.
getChainIndex(Chain) - Method in class edu.sdsc.mbt.StructureMap: Get the index of the specified Chain.
getChainPaths() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper: Returns an array containing all of the edu.sdsc.sirius.viewers.StructureViewerImpl.pdb.Chain-level Paths in this PdbWrapper.
getChainPaths() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getChainPaths() - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getChains() - Method in class edu.sdsc.mbt.StructureMap: Return the chains from the Structure.
getChains() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Model: Get an array of all the Chains in this Model.
getChains() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper: Returns an array of all Chains in this PdbWrapper.
getChains(Path[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper: Returns an array of Chains corresponding to the Chain-level Paths that were supplied.
getChains() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getChains(Path[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getChains() - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getChains(Path[]) - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getCharge() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Return the electrical charge on this atom.
getChild(int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.TransformGroupRenderable
getChildCount() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.TransformGroupRenderable
getChildren(Object) - Method in class edu.sdsc.mbt.StructureMap: Return the Structure or StructureComponent children objects.
getCircle(int[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.VirtualSphere2: Get the parameters for the screen-space constraining 2D circle as {x,y,r}.
getClassName() - Static method in class edu.sdsc.mbt.Atom
getClassName() - Static method in class edu.sdsc.mbt.Bond: This method returns the fully qualified name of this class.
getClassName() - Static method in class edu.sdsc.mbt.Chain: This method returns the fully qualified name of this class.
getClassName() - Static method in class edu.sdsc.mbt.Coil
getClassName() - Static method in class edu.sdsc.mbt.Conformation
getClassName() - Static method in class edu.sdsc.mbt.Fragment: This method returns the fully qualified name of this class.
getClassName() - Static method in class edu.sdsc.mbt.Helix
getClassName() - Static method in class edu.sdsc.mbt.Residue: This method returns the fully qualified name of this class.
getClassName() - Static method in class edu.sdsc.mbt.Strand
getClassName() - Static method in class edu.sdsc.mbt.StructureComponent: This method returns the fully qualified name of this class.
getClassName() - Static method in class edu.sdsc.mbt.StructureInfo
getClassName() - Static method in class edu.sdsc.mbt.Symmetry
getClassName() - Static method in class edu.sdsc.mbt.Turn
getClassification() - Method in class edu.sdsc.mbt.Chain: Return the chain classification by asking the first residue.
getClassification() - Method in class edu.sdsc.mbt.Residue: Return the compound classification for this residue.
getClosedFlag() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle: Get the closed/open Polygon flag
getClosestResidueIndex(float[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Returns the index of the closest residue to the given point, with the given color.
getCodeFromLetter(String) - Static method in class edu.sdsc.mbt.util.AminoAcidInfo: Returns the 3-letter code equivalent for the given letter.
getCodeFromLetter(byte) - Static method in class edu.sdsc.mbt.util.AminoAcidInfo: Returns the 3-letter code equivalent for the given letter.
getCodeFromLetter(byte) - Static method in class edu.sdsc.mbt.util.NucleicAcidInfo
getCodeFromLetter(String) - Static method in class edu.sdsc.sirius.util.DeletionInfo: Returns the 3-letter code equivalent for the given letter.
getCodeFromLetter(byte) - Static method in class edu.sdsc.sirius.util.DeletionInfo: Returns the 3-letter code equivalent for the given letter.
getCodonCount() - Static method in class edu.sdsc.mbt.util.CodonInfo: Returns the number of codon/amino-acid tuples in the database.
getCollapseOn() - Method in class edu.sdsc.mbt.util.RangeMap: Get flag to enable/disable collapse feature.
getColor() - Method in class edu.sdsc.mbt.AnnotationComponent
getColor() - Method in class edu.sdsc.mbt.ArrowComponent
getColor() - Method in class edu.sdsc.mbt.HydrogenBondComponent
getColor() - Method in class edu.sdsc.mbt.LabelComponent
getColor() - Method in class edu.sdsc.mbt.MonitorComponent
getColor() - Method in class edu.sdsc.mbt.ResidueLabelComponent
getColor() - Method in class edu.sdsc.mbt.StericBumpComponent
getColor(int[]) - Method in class edu.sdsc.mbt.util.DerivedInformation
getColor(float, float[]) - Method in interface edu.sdsc.mbt.viewables.ColorMap: Given a normalized float (0.0-1.0) value, the getColor method should return an interpolated RGB color value.
getColor(float, float[]) - Method in class edu.sdsc.mbt.viewables.ConservationColorMap: Given a normalized float (0.0-1.0) value, the getColor method returns an interpolated RGB color value based upon the user-defined color knots.
getColor(float, float[]) - Method in class edu.sdsc.mbt.viewables.InterpolatedColorMap: Given a normalized float (0.0-1.0) value, the getColor method returns an interpolated RGB color value based upon the user-defined color knots.
getColor() - Method in class edu.sdsc.mbt.viewables.ResidueAnnotation
getColor(String) - Method in class edu.sdsc.sirius.rasmol.AminoColorScheme
getColor(String, String) - Static method in class edu.sdsc.sirius.rasmol.ColorManager
getColor(String) - Method in interface edu.sdsc.sirius.rasmol.ColorScheme
getColor(String) - Method in class edu.sdsc.sirius.rasmol.CpkColorScheme
getColor(String) - Method in class edu.sdsc.sirius.rasmol.StructureColorScheme
getColor(Color) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.StyleManager: This method takes a color required by the application, e.g.
getColor(float[]) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.StyleManager
getColorMap() - Method in class edu.sdsc.mbt.viewables.AtomColorByCharge: Get the ColorMap used to color by hydrophobicity.
getColorMap() - Method in class edu.sdsc.mbt.viewables.ChainColorById: Get the ColorMap used to color by Id.
getColorMap() - Method in class edu.sdsc.mbt.viewables.ResidueColorByCharge: Get the ColorMap used to color by hydrophobicity.
getColorMap() - Method in class edu.sdsc.mbt.viewables.ResidueColorByHydrophobicity: Get the ColorMap used to color by hydrophobicity.
getColorMap() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Returns the color map from a given set of float arrays.
getColorScheme(String) - Static method in class edu.sdsc.sirius.rasmol.ColorManager
getColors() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.AffineCrossSection
getColors() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Extrusion
getColors() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection
getColumnCount() - Method in class edu.sdsc.sirius.dialogs.TableImpl.BlastResultPanel
getColumnCount() - Method in class edu.sdsc.sirius.dialogs.TableImpl.PubmedResultPanel
getColumnCount() - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel
getColumnCount() - Method in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel
getCompoundCode() - Method in class edu.sdsc.mbt.Residue: Get the 3-letter compound code for this residue.
getCompoundName() - Method in class edu.sdsc.mbt.StructureInfo: Get the name of this macromolecular structure.
getConformationType() - Method in class edu.sdsc.mbt.Fragment: Get the Conformation type for this Fragment.
getConformationType() - Method in class edu.sdsc.mbt.Residue: Get the secondary structure conformation type that is assigned to this residue.
getConservation() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getConservationColor(double) - Static method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.StyleManager
getContainerBounds() - Method in class Viewer
getContainerBounds() - Method in interface edu.sdsc.sirius.util.Manager: Returns bounds of the application frame as a Rectangle object
getContent() - Method in class com.jgoodies.uif_lite.panel.SimpleInternalFrame: Returns the content - null, if none has been set.
getContiguousValue(int, int) - Method in class edu.sdsc.mbt.util.RangeMap: Get the value object asocciated with the given start and end indexes.
getCoordinate() - Method in class edu.sdsc.mbt.util.OctreeAtomItem: Return the coordinate of the Atom.
getCoordinate() - Method in interface edu.sdsc.mbt.util.OctreeDataItem: Return the coordinate for this data item.
getCoordinate() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Return the coordinate of this atom as a Vec3f.
getCoordinates() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Hermite
getCurrentAttachmentAtom() - Method in class edu.sdsc.sirius.builder.FragmentRecord
getCurrentConfiguration() - Method in class edu.sdsc.mbt.viewables.ElementPreferences: Read currently set element color preferences from ElementStyles
getCustomFragmentRecords() - Static method in class edu.sdsc.sirius.builder.FragmentRegistry
getData(int) - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataSet: Returns a DataBlock stored at the specified index.
getDataBlock(int) - Method in class edu.sdsc.sirius.dialogs.TableImpl.BlastResultPanel
getDataBlock(int) - Method in class edu.sdsc.sirius.dialogs.TableImpl.PubmedResultPanel
getDataListerDialog() - Method in class Viewer
getDataListerDialog() - Method in interface edu.sdsc.sirius.util.Manager
getDataType() - Method in class edu.sdsc.sirius.io.AlnEntryLoader
getDataType() - Method in interface edu.sdsc.sirius.io.EntryLoader
getDataType() - Method in class edu.sdsc.sirius.io.FastaEntryLoader
getDataType() - Method in class edu.sdsc.sirius.io.Mol2EntryLoader
getDataType() - Method in class edu.sdsc.sirius.io.MsfEntryLoader
getDataType() - Method in class edu.sdsc.sirius.io.PdbEntryLoader
getDataType() - Method in class edu.sdsc.sirius.io.SDFEntryLoader
getDatabaseID() - Method in class edu.sdsc.sirius.io.Entry
getDatabaseSource() - Method in class edu.sdsc.sirius.io.Entry
getDefault() - Static method in class edu.sdsc.mbt.viewables.AtomColorRegistry: Get the default AtomColor implementation.
getDefault() - Static method in class edu.sdsc.mbt.viewables.AtomLabelRegistry: Get the default AtomLabel implementation.
getDefault() - Static method in class edu.sdsc.mbt.viewables.AtomRadiusRegistry: Get the default AtomRadius implementation.
getDefault() - Static method in class edu.sdsc.mbt.viewables.BondColorRegistry: Get the default BondColor implementation.
getDefault() - Static method in class edu.sdsc.mbt.viewables.BondFormRegistry: Get the default BondForm implementation.
getDefault() - Static method in class edu.sdsc.mbt.viewables.BondLabelRegistry: Get the default BondLabel implementation.
getDefault() - Static method in class edu.sdsc.mbt.viewables.BondRadiusRegistry: Get the default BondRadius implementation.
getDefault() - Static method in class edu.sdsc.mbt.viewables.ChainColorRegistry: Get the default ChainColor implementation.
getDefault() - Static method in class edu.sdsc.mbt.viewables.FragmentColorRegistry: Get the default FragmentColor implementation.
getDefault() - Static method in class edu.sdsc.mbt.viewables.FragmentFormRegistry: Get the default FragmentForm implementation.
getDefault() - Static method in class edu.sdsc.mbt.viewables.ResidueColorRegistry: Get the default ResidueColor implementation.
getDefaultColor() - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.StyleManager
getDefaultName() - Static method in class edu.sdsc.mbt.viewables.AtomColorRegistry: Return the name of the default AtomColor impelementation.
getDefaultName() - Static method in class edu.sdsc.mbt.viewables.AtomLabelRegistry: Return the name of the default AtomLabel impelementation.
getDefaultName() - Static method in class edu.sdsc.mbt.viewables.AtomRadiusRegistry: Return the name of the default AtomRadius impelementation.
getDefaultName() - Static method in class edu.sdsc.mbt.viewables.BondColorRegistry: Return the name of the default BondColor impelementation.
getDefaultName() - Static method in class edu.sdsc.mbt.viewables.BondFormRegistry: Return the name of the default BondForm impelementation.
getDefaultName() - Static method in class edu.sdsc.mbt.viewables.BondLabelRegistry: Return the name of the default BondLabel impelementation.
getDefaultName() - Static method in class edu.sdsc.mbt.viewables.BondRadiusRegistry: Return the name of the default BondRadius impelementation.
getDefaultName() - Static method in class edu.sdsc.mbt.viewables.ChainColorRegistry: Return the name of the default ChainColor impelementation.
getDefaultName() - Static method in class edu.sdsc.mbt.viewables.FragmentColorRegistry: Return the name of the default FragmentColor impelementation.
getDefaultName() - Static method in class edu.sdsc.mbt.viewables.FragmentFormRegistry: Return the name of the default FragmentForm impelementation.
getDefaultName() - Static method in class edu.sdsc.mbt.viewables.ResidueColorRegistry: Return the name of the default ResidueColor impelementation.
getDefaultTab() - Method in class edu.sdsc.sirius.util.TabListCellRenderer
getDelimiter() - Static method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Path: Gets the delimiter character used to separate path elements when the Path is converted to a String.
getDescription() - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Filter
getDescription() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtom
getDescription() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomAll
getDescription() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByChain
getDescription() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByName
getDescription() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterAtomByType
getDescription() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNum
getDescription() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterCaByResNumAndCh
getDescription() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterResidue
getDescription() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.FilterResidueByName
getDescription() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.LogicalGroup
getDescription() - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock: Returns entry description.
getDescription() - Method in class edu.sdsc.sirius.io.Entry
getDescription() - Method in class edu.sdsc.sirius.util.FileNameFilter
getDeterminationMethod() - Method in class edu.sdsc.mbt.StructureInfo: Get the exerimental method used to determine this compound.
getDiameters() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle: Get the number of vertices
getDihedralAngle(Vec3d, Vec3d, Vec3d, Vec3d) - Static method in class edu.sdsc.mbt.util.Algebra: Calculates the dihedral angle defined by four points
getDimension() - Method in class edu.sdsc.mbt.util.Octree: ???
getDisjointFragments(Vector, Vector) - Method in class edu.sdsc.mbt.util.DerivedInformation
getDisplacementVector(Bond, double[], double) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometryUtils
getDisplayDialog() - Method in class Viewer
getDisplayDialog() - Method in interface edu.sdsc.sirius.util.Manager: Returns a reference to the currently displayed DisplayDialog.
getDisplayDialogStatus() - Method in class Viewer
getDisplayDialogStatus() - Method in interface edu.sdsc.sirius.util.Manager: Indicates whether any dialogs are currently open.
getDisplayList(GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Renderable: If the renderable is dirty, regenerate the display list and set the dirty state to false, then return the display list.
getDisplayParameters() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getDistance() - Method in class edu.sdsc.mbt.Bond: Get the distance for the bond.
getDistance(Atom, Atom) - Static method in class edu.sdsc.mbt.Bond
getDistance() - Method in class edu.sdsc.mbt.StericBumpComponent
getDistance(double[], double[]) - Method in class edu.sdsc.mbt.util.Octree: Methods to operate with vectors.
getDistanceMonitors() - Method in class edu.sdsc.sirius.export.StateObject
getDivider() - Method in class edu.sdsc.sirius.util.DialogLayout
getDnaPairing(String) - Static method in class edu.sdsc.mbt.util.NucleicAcidInfo: Returns the base pair pairing for DNA.
getDrawable() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
getDummyAtoms() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getEditMode() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getElement() - Method in class edu.sdsc.mbt.Atom
getElement(int) - Static method in class edu.sdsc.mbt.util.PeriodicTable: Get an Element by its atomic number.
getElement(String) - Static method in class edu.sdsc.mbt.util.PeriodicTable: Get an Element by its symbol.
getElement(short) - Static method in class edu.sdsc.mbt.util.PeriodicTable
getElement() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Return the chemical element of this atom.
getElementByWeight(double) - Static method in class edu.sdsc.mbt.util.PeriodicTable
getElementColor(int) - Static method in class edu.sdsc.mbt.util.ElementProperties: Get the RGB color of the given element number.
getElementColor(String) - Static method in class edu.sdsc.mbt.util.ElementProperties: Get the RGB color of the given element name.
getElementCount() - Static method in class edu.sdsc.mbt.util.ElementProperties: Get the number of elements for which style information is represented by this class.
getElementCount() - Static method in class edu.sdsc.mbt.util.PeriodicTable: Return the number of Elements stored in this table.
getElementName(int) - Static method in class edu.sdsc.mbt.util.PeriodicTable: Get an Element name by its atomic number.
getElementName(String) - Static method in class edu.sdsc.mbt.util.PeriodicTable: Get an Element name by its symbol.
getElementNumber(String) - Static method in class edu.sdsc.mbt.util.PeriodicTable: Get an Element atomic number by its symbol.
getElementSymbol(int) - Static method in class edu.sdsc.mbt.util.PeriodicTable
getElementSymbol(short) - Static method in class edu.sdsc.mbt.util.PeriodicTable
getElementValency(int) - Static method in class edu.sdsc.mbt.util.ElementProperties
getElementValency(String) - Static method in class edu.sdsc.mbt.util.ElementProperties
getElementValency(short) - Static method in class edu.sdsc.mbt.util.ElementProperties
getElementWeight(int) - Static method in class edu.sdsc.mbt.util.PeriodicTable: Get an Element atomic weight by its atomic number.
getElementWeight(String) - Static method in class edu.sdsc.mbt.util.PeriodicTable: Get an Element atomic weight by its symbol.
getElementWeight(short) - Static method in class edu.sdsc.mbt.util.PeriodicTable
getEnd() - Method in class edu.sdsc.mbt.util.DoubleRange: Returns the end value.
getEnd() - Method in class edu.sdsc.mbt.util.IntRange: Returns the end value.
getEnd() - Method in class edu.sdsc.sirius.dialogs.TableImpl.InterProDataBlock
getEndResidueIndex() - Method in class edu.sdsc.mbt.Fragment: Get the end Reisude index for this Fragment.
getEndResidues() - Method in class edu.sdsc.mbt.StructureMap
getEntries() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getEntriesByType(int) - Method in class edu.sdsc.mbt.viewables.StructureDocument
getEntry(int) - Method in class edu.sdsc.mbt.viewables.StructureDocument: Returns one of the loaded Entries by index
getEntry() - Method in class edu.sdsc.sirius.util.FileCloseListener
getEntry(Sequence) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getEntry(Structure) - Method in class edu.sdsc.sirius.viewers.StructureViewer
getEntryById(String) - Method in class edu.sdsc.mbt.viewables.StructureDocument: Returns a reference to an Entry by its id.
getEntryByName(String) - Method in class edu.sdsc.mbt.viewables.StructureDocument: Returns a reference to an Entry by its name.
getEntryCount() - Method in class edu.sdsc.mbt.viewables.StructureDocument: Returns count of Entries currently in the application
getEntryId() - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock: Returns database id as a String.
getEntryName(String) - Method in class edu.sdsc.sirius.io.AlnEntryLoader: Returns the name of the Entry in the event of its loading.
getEntryName(String) - Method in class edu.sdsc.sirius.io.FastaEntryLoader: Returns the name of the Entry in the event of its loading.
getEntryName(String) - Method in class edu.sdsc.sirius.io.MsfEntryLoader: Returns the name of the Entry in the event of its loading.
getEntryNames() - Method in class edu.sdsc.mbt.viewables.StructureDocument: This method returns a list of currently loaded entry names and is used by the entry loading mechanism to check ahead of time whether a particular entry has been loaded.
getEv() - Method in class edu.sdsc.sirius.dialogs.TableImpl.InterProDataBlock
getEvalue() - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock
getEyePosition() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
getFarDistance() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
getFileEntryLoader(String) - Static method in class edu.sdsc.sirius.io.EntryFactory: Return a reference to a named FileEntryLoader object.
getFileEntryLoaderNames() - Static method in class edu.sdsc.sirius.io.EntryFactory: Return a list of currently registered FileEntryLoader names.
getFillDisorderedGaps() - Method in class edu.sdsc.mbt.StructureMap: Should we "fill in" the disordered residue gaps with random coil when we load fragments?
getFilter() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Selection
getFogFar() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
getFogNear() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
getFolder() - Method in class edu.sdsc.sirius.workbench.WBEntry: Returns label of the folder where this WBEntry is located in the Workbench database
getFolderCount() - Method in class edu.sdsc.sirius.workbench.WBManager: Returns the number of folders in the user's workbench account.
getFolderLabel(Entry) - Method in class edu.sdsc.sirius.workbench.WBManager: Returns name of the folder that the specified Entry came from.
getFolderLabels() - Method in class edu.sdsc.sirius.workbench.WBManager: Returns labels of all folders in the user's workbench account as a Vector
getFont() - Method in class edu.sdsc.mbt.LabelComponent
getFont() - Method in class edu.sdsc.mbt.ResidueLabelComponent
getFontSize() - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceScalePanel: Returns the current font size in points.
getFontSizeHints() - Method in class com.jgoodies.looks.demo.Settings
getForm() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Geometry: Please complete the missing tags for main
getFormat() - Method in class edu.sdsc.sirius.workbench.WBEntry: Returns a String representation of data format used to store this data item in the Workbench database
getFormattedNumber(double, int) - Static method in class edu.sdsc.sirius.util.StringUtils: digits specifies how many digits after the decimal point should be left
getFragment(int) - Method in class edu.sdsc.mbt.Chain: Get the specified Fragment object.
getFragment() - Method in class edu.sdsc.mbt.Residue: Get the parent fragment (if any) for this residue.
getFragment(int) - Method in class edu.sdsc.mbt.StructureMap: Get the Fragment at the specified index.
getFragmentColor(Fragment, float[]) - Method in interface edu.sdsc.mbt.viewables.FragmentColor
getFragmentColor(Fragment, float[]) - Method in class edu.sdsc.mbt.viewables.FragmentColorByType: Produce a color based upon the conformation type.
getFragmentCount() - Method in class edu.sdsc.mbt.Chain: Get the number of fragments (residue ranges) currently assigned to this chain.
getFragmentCount() - Method in class edu.sdsc.mbt.StructureMap: Return the total Fragment count extracted from the Structure.
getFragmentEndResidue(int) - Method in class edu.sdsc.mbt.Chain: Get the end residue index for the given fragment.
getFragmentForm(Fragment) - Method in interface edu.sdsc.mbt.viewables.FragmentForm
getFragmentForm(Fragment) - Method in class edu.sdsc.mbt.viewables.FragmentFormCartoon: Produce a fragment style for a cartoon representation.
getFragmentForm(Fragment) - Method in class edu.sdsc.mbt.viewables.FragmentFormCylinder: Produce a fragment style for a cylinder representation.
getFragmentForm(Fragment) - Method in class edu.sdsc.mbt.viewables.FragmentFormLadder: Produce a fragment style for a ladder representation.
getFragmentForm(Fragment) - Method in class edu.sdsc.mbt.viewables.FragmentFormRibbon: Produce a fragment style for a ribbon representation.
getFragmentForm(Fragment) - Method in class edu.sdsc.mbt.viewables.FragmentFormTube: Produce a fragment style for a tube representation.
getFragmentForm(Fragment) - Method in class edu.sdsc.mbt.viewables.FragmentFormWireframe: Produce a fragment style for a wireframe representation.
getFragmentGroupName() - Method in class edu.sdsc.sirius.builder.CustomFragmentPanel
getFragmentGroupName() - Method in interface edu.sdsc.sirius.builder.FragmentGroupPanel
getFragmentGroupName() - Method in class edu.sdsc.sirius.builder.GeneralFragmentPanel
getFragmentGroupName() - Method in class edu.sdsc.sirius.builder.ProteinFragmentPanel
getFragmentGroupPanel(String) - Method in class edu.sdsc.sirius.builder.BuilderPanel
getFragmentId() - Method in class edu.sdsc.sirius.io.FragmentEntry
getFragmentIndex(Fragment) - Method in class edu.sdsc.mbt.StructureMap: Get the index of the specified Fragment.
getFragmentPanels() - Static method in class edu.sdsc.sirius.builder.FragmentRegistry
getFragmentRecord(int) - Static method in class edu.sdsc.sirius.builder.FragmentRegistry
getFragmentRecords() - Static method in class edu.sdsc.sirius.builder.FragmentRegistry
getFragmentStartResidue(int) - Method in class edu.sdsc.mbt.Chain: Get the start residue index for the given fragment.
getFragmentType(int) - Method in class edu.sdsc.mbt.Chain: Get the conformation type currently assigned to the given fragment.
getFragments() - Method in class edu.sdsc.mbt.Chain: Get the fragments for this chain.
getFragments() - Method in class edu.sdsc.mbt.StructureMap
getFragments(Vector, Vector) - Method in class edu.sdsc.mbt.util.DerivedInformation
getFrameIcon() - Method in class com.jgoodies.uif_lite.panel.SimpleInternalFrame: Returns the frame's icon.
getFrenetTrihedron() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.AffineCrossSection
getFromOriginMatrix(Atom) - Static method in class edu.sdsc.sirius.util.StructureMath
getFromOriginMatrix(double[]) - Static method in class edu.sdsc.sirius.util.StructureMath
getFullAminoAcidName(String) - Static method in class edu.sdsc.sirius.util.ProteinProperties
getGeometry() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.MbtRenderable
getGeometryViewer() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getHBondInfoVector(double) - Method in class edu.sdsc.mbt.util.Octree
getHBonds(double) - Method in class edu.sdsc.mbt.util.Octree: ???
getHBonds() - Method in class edu.sdsc.sirius.export.StateObject
getHBonds() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getHBondsVector(double) - Method in class edu.sdsc.mbt.util.Octree: ???
getHGap() - Method in class edu.sdsc.sirius.util.DialogLayout
getHGap() - Method in class edu.sdsc.sirius.util.ExtensionLayout
getHNaming(String) - Static method in class edu.sdsc.sirius.util.ProteinProperties
getHeaderTitle() - Method in class edu.sdsc.sirius.dialogs.TableImpl.ColumnData
getHiddenSequences() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getHighlightState() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry
getHydrophobicity() - Method in class edu.sdsc.mbt.Residue: Return the Hydrophobicity of the amino acid residue as a normalized value from 0.0 to 1.0 inclusive.
getHydrophobicityColor(String) - Static method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.StyleManager
getHydrophobicityFromCode(String) - Static method in class edu.sdsc.mbt.util.AminoAcidInfo: Returns hydrophobicity given the 3-letter code.
getId() - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock
getId() - Method in class edu.sdsc.sirius.io.Entry
getId() - Method in class edu.sdsc.sirius.workbench.WBEntry: Returns Workbench database identificator assigned to this item
getIdCode() - Method in class edu.sdsc.mbt.StructureInfo: Get the PDB-ID code by which this entry is registered.
getIdCode() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper: Returns the ID code for this PDB entry.
getImage() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
getImagePreviewPanel() - Method in class Viewer
getImagePreviewPanel() - Method in interface edu.sdsc.sirius.util.Manager
getIndependentAtoms() - Method in class edu.sdsc.sirius.export.StateObject
getIndependentComponents() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getIndependentResidues() - Method in class edu.sdsc.sirius.export.StateObject
getIndependentStructure() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getIndependentStructureIndex() - Method in class edu.sdsc.sirius.export.StateObject
getIndex() - Method in class edu.sdsc.mbt.util.OctreeAtomItem: Return the index associated with this data item.
getIndex() - Method in interface edu.sdsc.mbt.util.OctreeDataItem: Return the data index associated with this data item.
getIndexColorModel() - Static method in class edu.sdsc.mbt.image.ImageHandler
getIndexOf(Sequence) - Method in class edu.sdsc.sirius.io.SequenceEntry
getInitialCoordinates(Structure) - Method in class edu.sdsc.sirius.viewers.StructureViewer
getInsCode() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Return the insertion code for this atom.
getIntrinsicCrossSection(CrossSectionStyle, Vector3f) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionBuilder: Return a IntrinsicCrossSection polygon
getInverseMatrix(double[][]) - Static method in class edu.sdsc.mbt.util.Algebra
getIonRadius(int) - Static method in class edu.sdsc.mbt.util.ElementProperties
getItem() - Method in class edu.sdsc.sirius.util.FileCloseListener
getJournal() - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock
getKnotColor(int, float[]) - Method in class edu.sdsc.mbt.viewables.InterpolatedColorMap: Get the color at the specified knot index.
getKnotCount() - Method in class edu.sdsc.mbt.viewables.InterpolatedColorMap: Returns the number of knots in the color map.
getKnotLocation(int) - Method in class edu.sdsc.mbt.viewables.InterpolatedColorMap: Get the location value of the specified knot.
getKnotWeight() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Hermite
getKnots(float[][]) - Method in class edu.sdsc.mbt.viewables.InterpolatedColorMap: Get the knots used by the color map.
getLabelColor() - Method in class edu.sdsc.sirius.export.StyleMap
getLabelForId(String) - Method in class edu.sdsc.sirius.workbench.WBManager: Method returns user-supplied label of a workbench data item when given its id
getLabelSelection() - Method in class edu.sdsc.sirius.export.StyleMap
getLabelSize() - Method in class edu.sdsc.sirius.export.StyleMap
getLabelText() - Method in class edu.sdsc.sirius.export.StyleMap
getLabelType() - Method in class edu.sdsc.mbt.LabelComponent
getLabelType() - Method in class edu.sdsc.mbt.ResidueLabelComponent
getLabeledResidueIndices() - Method in class edu.sdsc.sirius.export.StyleMap
getLabels() - Method in class edu.sdsc.sirius.export.StyleMap
getLabels() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getLastUsedDirectory() - Method in class Viewer
getLastUsedDirectory() - Method in interface edu.sdsc.sirius.util.Manager
getLetterFromCode(String) - Static method in class edu.sdsc.mbt.util.AminoAcidInfo: Returns the character code equivalent for the given 3-letter code.
getLetterFromCode(String) - Static method in class edu.sdsc.sirius.util.DeletionInfo: Returns the character code equivalent for the given 3-letter code.
getLetterFromName(String) - Static method in class edu.sdsc.mbt.util.NucleicAcidInfo: Returns the full name equivalent for the given character code.
getLevelCount() - Static method in class edu.sdsc.mbt.util.Status: Get the number of supported level values.
getLevelName(int) - Static method in class edu.sdsc.mbt.util.Status: Get the human-reable name corresponding to the given level number.
getLigandCount() - Method in class edu.sdsc.mbt.StructureMap: Return the ligand (het group) count.
getLigandResidue(int) - Method in class edu.sdsc.mbt.StructureMap: Return the Residue for a given ligand index.
getLigands() - Method in class edu.sdsc.mbt.StructureMap
getLinearRotationMatrix(double, double[]) - Static method in class edu.sdsc.sirius.util.StructureMath
getLinearTranslationMatrix(double[]) - Static method in class edu.sdsc.sirius.util.StructureMath
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class edu.sdsc.sirius.util.TabListCellRenderer
getLoadedStructures() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getLoaderName() - Method in class edu.sdsc.sirius.io.AlnEntryLoader
getLoaderName() - Method in interface edu.sdsc.sirius.io.EntryLoader: Returns the common name for the loader implementation.
getLoaderName() - Method in class edu.sdsc.sirius.io.FastaEntryLoader: Returns the common name for the loader implementation.
getLoaderName() - Method in class edu.sdsc.sirius.io.Mol2EntryLoader: Returns name of the loader.
getLoaderName() - Method in class edu.sdsc.sirius.io.MsfEntryLoader
getLoaderName() - Method in class edu.sdsc.sirius.io.PdbEntryLoader: Returns name of the loader.
getLoaderName() - Method in class edu.sdsc.sirius.io.SDFEntryLoader
getLookAt() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
getLookAt() - Method in class edu.sdsc.sirius.io.FragmentEntry
getMatchedSequences() - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel
getMax() - Method in class edu.sdsc.mbt.util.RangeMap: Get the maximum range index.
getMaxCoordinate() - Method in class edu.sdsc.mbt.StructureMap
getMaxNumberOfChildren() - Method in class edu.sdsc.mbt.util.Octree: ???
getMenuBar3DHint() - Method in class com.jgoodies.looks.demo.Settings
getMenuBarHeaderStyle() - Method in class com.jgoodies.looks.demo.Settings
getMenuBarPlasticBorderStyle() - Method in class com.jgoodies.looks.demo.Settings
getMenuBarWindowsBorderStyle() - Method in class com.jgoodies.looks.demo.Settings
getMetadata() - Method in class edu.sdsc.sirius.io.Entry
getMin() - Method in class edu.sdsc.mbt.util.RangeMap: Get the minimum range index.
getMinCoordinate() - Method in class edu.sdsc.mbt.StructureMap
getMinimumSize() - Method in class edu.sdsc.sirius.dialogs.JFontPreviewPanel
getMinimumSize() - Method in class edu.sdsc.sirius.viewers.StatusPanel
getMinimumSize() - Method in class edu.sdsc.sirius.viewers.StructureViewer: Make sure that at least a minimal sized widget is maintained.
getModel(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Pdb: Get the nth Model from this Pdb.
getModelCount() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Pdb: Get the number of Models in this Pdb.
getModelNum() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Return the number of the model to which this atom belongs.
getModelNum() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Chain: Return the model number for this chain.
getModelNum() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Model: Get the model number.
getModelNum() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue: Returns the model number for this residue.
getModelPaths() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper: Returns an array containing all of the edu.sdsc.sirius.viewers.StructureViewerImpl.pdb.Model-level Paths in this PdbWrapper.
getModelPaths() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getModelPaths() - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getModels() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Pdb: Get the list of Models in this Pdb object.
getModels() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper: Returns an array of all Models in this PdbWrapper.
getModels(Path[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper: Returns an array of Models corresponding to the Model-level Paths that were supplied.
getModels() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getModels(Path[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getModels() - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getModels(Path[]) - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getMonitorDialog() - Method in class Viewer
getMonitorDialog() - Method in interface edu.sdsc.sirius.util.Manager: Returns a reference to the currently open dialog that manages current display markers (distances, hydrogen bonds, labels, etc)
getMonitors() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getName() - Method in class edu.sdsc.mbt.Sequence
getName() - Method in class edu.sdsc.mbt.StructureComponentRelation: Returns the name of this StructureComponentRelation object.
getName() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Return the name of this atom.
getName() - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock: Returns entry name.
getName() - Method in class edu.sdsc.sirius.dialogs.TableImpl.InterProDataBlock
getName() - Method in class edu.sdsc.sirius.io.Entry
getName() - Method in class edu.sdsc.sirius.rasmol.AminoColorScheme
getName() - Method in interface edu.sdsc.sirius.rasmol.ColorScheme
getName() - Method in class edu.sdsc.sirius.rasmol.CpkColorScheme
getName() - Method in class edu.sdsc.sirius.rasmol.StructureColorScheme
getName() - Method in class edu.sdsc.sirius.util.FileCloseListener
getName() - Method in class edu.sdsc.sirius.workbench.WBEntry: Returns user assigned label of the data item corresponding to this WBEntry
getNameCount() - Static method in class edu.sdsc.mbt.util.AminoAcidInfo: Returns the number of amino acid name tuples in the database.
getNameCount() - Static method in class edu.sdsc.sirius.util.DeletionInfo: Returns the number of amino acid name tuples in the database.
getNameFromCode(String) - Static method in class edu.sdsc.mbt.util.AminoAcidInfo: Returns the full name equivalent for the given 3-letter code.
getNameFromCode(String) - Static method in class edu.sdsc.sirius.util.DeletionInfo: Returns the full name equivalent for the given 3-letter code.
getNameFromLetter(byte) - Static method in class edu.sdsc.mbt.util.AminoAcidInfo: Returns the full name equivalent for the given letter.
getNameFromLetter(String) - Static method in class edu.sdsc.mbt.util.AminoAcidInfo: Returns the full name equivalent for the given character code.
getNameFromLetter(String) - Static method in class edu.sdsc.mbt.util.NucleicAcidInfo: Returns the nucleic acid base name equivalent for the given letter.
getNameFromLetter(byte) - Static method in class edu.sdsc.sirius.util.DeletionInfo: Returns the full name equivalent for the given letter.
getNameFromLetter(String) - Static method in class edu.sdsc.sirius.util.DeletionInfo: Returns the full name equivalent for the given character code.
getNearDistance() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
getNextSs() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Returns the next Secondary Structure geometry (in a chain for instance)
getNextToFirstCa() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: First CA coord (after smoothing) may be needed outside for imposing continuity Deprecated
getNextToFirstCaCoord() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: First CA coord (after smoothing) may be needed outside for imposing continuity
getNonBondedConnections() - Method in class edu.sdsc.mbt.StructureMap: Returns a Vector of arrays with pairs of atoms that don't form bonds
getNormal() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron
getNormal(float) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Hermite
getNormal() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Trihedron: Get the normal vector.
getNormalVector(double[], double[], double[]) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometryUtils: Get a Vector of normal to the plane defined by the three given points
getNormalizedVector(double[]) - Static method in class edu.sdsc.mbt.util.Algebra
getNormalizedVector(double[], double[]) - Static method in class edu.sdsc.mbt.util.Algebra
getNormals() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.AffineCrossSection
getNormals() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection
getNumber() - Method in class edu.sdsc.mbt.Residue
getNumberOfChains() - Method in class edu.sdsc.mbt.util.DerivedInformation
getNumberOfChildren() - Method in class edu.sdsc.mbt.util.Octree: ???
getObjectHash() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getObjectType() - Method in class edu.sdsc.mbt.StructureComponentRelation: Returns the object type of this StructureComponentRelation object.
getOcc() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Return the occupancy of this atom.
getOrganism() - Method in class edu.sdsc.sirius.io.Entry
getOrigin() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron
getOrigin() - Method in class edu.sdsc.sirius.util.VectorSet
getOutputLevel() - Static method in class edu.sdsc.mbt.util.Status: Get the output level for subsequent calls to the output method.
getPKATable() - Static method in class edu.sdsc.sirius.util.DNAProperties
getPKATable() - Static method in class edu.sdsc.sirius.util.ProteinProperties
getPOVContent(Manager, int, int, double, PrintWriter) - Static method in class edu.sdsc.sirius.ray.RayTraceUtil
getParam(int) - Method in class edu.sdsc.mbt.image.TileRenderer: Gets the parameters of this TileRender object
getParentApplication() - Method in class edu.sdsc.sirius.builder.CustomFragmentPanel
getParentApplication() - Method in interface edu.sdsc.sirius.builder.FragmentGroupPanel
getParentApplication() - Method in class edu.sdsc.sirius.builder.GeneralFragmentPanel
getParentApplication() - Method in class edu.sdsc.sirius.builder.ProteinFragmentPanel
getParents(Object) - Method in class edu.sdsc.mbt.StructureMap: Return the StructureComponent parent objects.
getPdb() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper: Returns the Path that points to the top-level PDB in this Wrapper.
getPdb(Path) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper
getPdb() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getPdb(Path) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getPdb() - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getPdb(Path) - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getPdbPath() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper: Returns the Path that points to the top-level PDB in this Wrapper.
getPdbPath() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getPdbPath() - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getPhiMap() - Method in class edu.sdsc.mbt.StructureMap
getPickLevel() - Static method in class edu.sdsc.mbt.util.PickUtils: Get the structure component pick level.
getPixel(int[], int, int, int) - Static method in class edu.sdsc.mbt.image.ImageUtils: Return one pixel (as 4-byte, 24-bit, 8-bit-per-component, ARGB int) given the raw pixel array returned by the getPixels method.
getPixels(Image) - Static method in class edu.sdsc.mbt.image.ImageUtils: Return the pixels (as 4-byte, 24-bit, 8-bit-per-component, ARGB ints).
getPlasticTabStyle() - Method in class com.jgoodies.looks.demo.Settings
getPointOnVector(double[], double[], double) - Static method in class edu.sdsc.sirius.util.StructureMath: Get coordinates of a point on a vector that originates from a given point
getPointVertices() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.AffineCrossSection
getPolymerHeadAtom() - Method in class edu.sdsc.mbt.Residue: Get the polymer "head" atom for this amino acid or nucleic acid residue (or null for ligands).
getPolymerTailAtom() - Method in class edu.sdsc.mbt.Residue: Get the polymer "tail" atom for this amino acid or nucleic acid residue (or null for ligands).
getPosition() - Method in class edu.sdsc.mbt.Residue
getPreferences() - Method in class Viewer
getPreferences() - Method in interface edu.sdsc.sirius.util.Manager: Returns current StylesPreferences.
getPreferredSize() - Method in class edu.sdsc.sirius.dialogs.JFontPreviewPanel
getPreviousNormal() - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron
getPreviousSs() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Returns the previous Secondary Structure geometry (in a chain for instance)
getPreviousToLastCa() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Get Previous to last CA coord (after smoothing) may be needed outside for imposing continuity Deprecated
getPreviousToLastCaCoord() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Previous to last CA coord (after smoothing) may be needed outside for imposing continuity
getPriestleSteps() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry
getPrimaryReference() - Method in class edu.sdsc.mbt.StructureInfo: Get the primary citation reference for this entry.
getPsiMap() - Method in class edu.sdsc.mbt.StructureMap
getPsiPhi(Residue) - Method in class edu.sdsc.mbt.StructureMap
getQuality() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Geometry: Gets the rendering quality level (0.0 meaning lowest quality but faster rendering, and 1.0 meaning highest quality but slower rendering).
getQuality() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GeometryEntity: Get the quality parameter.
getRMSD(Structure, Structure) - Static method in class edu.sdsc.sirius.util.StructureMath
getRadius() - Method in class edu.sdsc.mbt.viewables.AtomRadiusByConstant: Get the constant radius.
getRadius() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.VirtualSphere2
getRamaViewers() - Method in class edu.sdsc.sirius.export.StateObject
getRamachandranViewer(Structure) - Method in class Viewer
getRamachandranViewer(Structure) - Method in interface edu.sdsc.sirius.util.Manager
getRange(int) - Method in class edu.sdsc.mbt.util.RangeMap: Get the range currently associated with the given rangeIndex.
getRangeCount() - Method in class edu.sdsc.mbt.util.RangeMap: Get the number of ranges currently assigned to this map.
getRangeEnd(int) - Method in class edu.sdsc.mbt.util.RangeMap: Get the endIndex for the given rangeIndex.
getRangeStart(int) - Method in class edu.sdsc.mbt.util.RangeMap: Get the startIndex for the given rangeIndex.
getRangeValue(int) - Method in class edu.sdsc.mbt.util.RangeMap: Get the value currently associated with the given rangeIndex.
getRasmolReader() - Method in class Viewer
getRasmolReader() - Method in interface edu.sdsc.sirius.util.Manager
getReferenceAtom() - Method in class edu.sdsc.mbt.Bond
getRelation(String) - Static method in class edu.sdsc.mbt.StructureComponentRegistry: Get an existing StructureComponent relation.
getRelationCount() - Static method in class edu.sdsc.mbt.StructureComponentRegistry: Return the number of registered StructureComponent relations.
getRelationNames() - Static method in class edu.sdsc.mbt.StructureComponentRegistry: Return an Enumeration of String values for all registered StructureComponent relations.
getReleaseDate(int[]) - Method in class edu.sdsc.mbt.StructureInfo: Get the date on which this entry was released.
getRenderables() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getResName() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Return the name of the residue to which this atom belongs
getResName() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue: Return the name of this residue.
getResNickName() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue: Return the nickname (abbreviated name) of this residue
getResNum() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Return the number of the residue to which this atom belong.
getResNum() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue: Return the number of this residue.
getResidue(int) - Method in class edu.sdsc.mbt.Chain: Return the specified Residue record contained in this Chain.
getResidue(int) - Method in class edu.sdsc.mbt.Fragment
getResidue(Atom) - Method in class edu.sdsc.mbt.StructureMap: Get the Residue object to which this Atom belongs.
getResidue(int) - Method in class edu.sdsc.mbt.StructureMap: Return the start Atom index for a given residue index.
getResidue(String) - Method in class edu.sdsc.mbt.StructureMap: Get the Residue object by its chain and residue id.
getResidue(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Chain: Get the nth Residue from this Chain.
getResidueByChainAndResidueId() - Method in class edu.sdsc.mbt.StructureMap
getResidueCellMapping() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getResidueColor(Residue, float[]) - Method in interface edu.sdsc.mbt.viewables.ResidueColor: Assign appropriate color to the specified Residue
getResidueColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByCharge: Produce a color based upon the residue element type.
getResidueColor(double, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByCharge
getResidueColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByElement: Produce a color based upon the residue element type.
getResidueColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByHydrophobicity: Produce a color based upon the residue element type.
getResidueColor(double, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByHydrophobicity
getResidueColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByType: Produce a color based upon the residue.
getResidueColor(double, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorByType
getResidueColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorDefault: Produce a color based upon the residue element type.
getResidueColor(Color) - Static method in class edu.sdsc.mbt.viewables.ResidueColorFactory: Returns a ResidueColorUniform object in response to the requested Color for a Residue
getResidueColor(float[]) - Static method in class edu.sdsc.mbt.viewables.ResidueColorFactory
getResidueColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorScaled: Produce a color based upon the color map values.
getResidueColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.ResidueColorUniform: Produce a color based upon the residue element type.
getResidueColor(StructureComponent) - Method in class edu.sdsc.mbt.viewables.StructureStyles
getResidueColorScaled(HashMap) - Static method in class edu.sdsc.mbt.viewables.ResidueColorFactory: Returns a ResidueColorScaled object for the given map.
getResidueColorScaled() - Static method in class edu.sdsc.mbt.viewables.ResidueColorFactory: Returns blank ResidueColorScaled object.
getResidueColorStyleReference() - Method in class edu.sdsc.mbt.viewables.StructureStyles
getResidueColorStyles() - Method in class edu.sdsc.mbt.viewables.StructureStyles
getResidueColors() - Method in class edu.sdsc.sirius.export.StyleMap
getResidueCount() - Method in class edu.sdsc.mbt.Chain: Return the number of Residue records contained in this Chain.
getResidueCount() - Method in class edu.sdsc.mbt.Fragment
getResidueCount() - Method in class edu.sdsc.mbt.StructureMap: Return the residue count extracted from the Structure.
getResidueCount() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Chain: Return the number of Residues in this Chain.
getResidueId() - Method in class edu.sdsc.mbt.Residue: Get the residue id (as it is assigned in the first Atom record).
getResidueIndex(Residue) - Method in class edu.sdsc.mbt.Chain: Return the specified Residue index in this Chain.
getResidueIndex(Residue) - Method in class edu.sdsc.mbt.Fragment
getResidueIndex(Residue) - Method in class edu.sdsc.mbt.StructureMap: Get the index of the specified Residue.
getResidueIndexInChain(Residue) - Method in class edu.sdsc.mbt.Fragment
getResidueLabelColor() - Method in class edu.sdsc.sirius.export.StyleMap
getResidueLabelSelection() - Method in class edu.sdsc.sirius.export.StyleMap
getResidueLabelSize() - Method in class edu.sdsc.sirius.export.StyleMap
getResidueLabelText() - Method in class edu.sdsc.sirius.export.StyleMap
getResidueLabels() - Method in class edu.sdsc.sirius.export.StyleMap
getResidueMax() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getResiduePaths() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper: Returns an array containing all of the edu.sdsc.sirius.viewers.StructureViewerImpl.pdb.Residue-level Paths in this PdbWrapper.
getResiduePaths() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getResiduePaths() - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getResidueSetAssignment() - Method in class edu.sdsc.sirius.export.StyleMap
getResidueToFragment() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getResidues() - Method in class edu.sdsc.mbt.Fragment
getResidues() - Method in class edu.sdsc.mbt.StructureMap
getResidues() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Chain: Get the Residues in this Chain.
getResidues() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper: Returns an array of all Residues in this PdbWrapper.
getResidues(Path[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper: Returns an array of Residues corresponding to the Residue-level Paths that were supplied.
getResidues() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getResidues(Path[]) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getResidues() - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getResidues(Path[]) - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getReverseVector(double[]) - Static method in class edu.sdsc.mbt.util.Algebra
getRibbonColor(Residue, float[]) - Method in interface edu.sdsc.mbt.viewables.RibbonColor: Assign appropriate color to the specified Residue
getRibbonColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.RibbonColorDefault: Produce a color based upon the residue element type.
getRibbonColor(Color) - Static method in class edu.sdsc.mbt.viewables.RibbonColorFactory: Returns a ResidueColorUniform object in response to the requested Color for a Residue
getRibbonColor(StructureComponent, ResidueColor) - Static method in class edu.sdsc.mbt.viewables.RibbonColorFactory
getRibbonColor(float[]) - Static method in class edu.sdsc.mbt.viewables.RibbonColorFactory
getRibbonColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.RibbonColorUniform: Produce a color based upon the residue element type.
getRibbonColor(StructureComponent) - Method in class edu.sdsc.mbt.viewables.StructureStyles
getRibbonColor(Residue, float[]) - Method in class edu.sdsc.mbt.viewables.StructureStyles
getRibbonColorStyleReference() - Method in class edu.sdsc.mbt.viewables.StructureStyles
getRibbonColorStyles() - Method in class edu.sdsc.mbt.viewables.StructureStyles
getRibbonColors() - Method in class edu.sdsc.sirius.export.StyleMap
getRibbonDiameter(Chain) - Method in class edu.sdsc.mbt.viewables.StructureStyles
getRibbonForm() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.ChainGeometry
getRibbonQuality(Chain) - Method in class edu.sdsc.mbt.viewables.StructureStyles
getRibbonQuality() - Method in class edu.sdsc.sirius.export.StyleMap
getRibbonType(Chain) - Method in class edu.sdsc.mbt.viewables.StructureStyles
getRibbonVis() - Method in class edu.sdsc.sirius.export.StyleMap
getRibbons() - Method in class edu.sdsc.sirius.export.StyleMap
getRnaDnaPairing(String) - Static method in class edu.sdsc.mbt.util.NucleicAcidInfo: Returns the base pair pairing for RNA-DNA interaction.
getRnaRnaPairing(String) - Static method in class edu.sdsc.mbt.util.NucleicAcidInfo: Returns the base pair pairing for RNA-RNA interaction.
getRotatedAtoms(StructureMap, Bond, Atom) - Static method in class edu.sdsc.sirius.util.StructureMath
getRotationCenter() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
getRotationMatrix(double[], double[]) - Static method in class edu.sdsc.sirius.util.StructureMath
getRotationMatrix(double, double[]) - Static method in class edu.sdsc.sirius.util.StructureMath
getScale() - Method in class edu.sdsc.mbt.viewables.AtomRadiusByScaledCpk: Get the CPK radius scale factor.
getScalePanel() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getScrollableTracksViewportWidth() - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultTable
getSecondaryStructures() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.FilePdbWrapper
getSecondaryStructures() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io.UrlPdbWrapper
getSecondaryStructures() - Method in interface edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.PdbWrapper
getSegId() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Returns the segment identifier for this atom.
getSelected() - Method in class edu.sdsc.mbt.AnnotationComponent
getSelected() - Method in class edu.sdsc.mbt.ArrowComponent
getSelected() - Method in class edu.sdsc.mbt.HydrogenBondComponent
getSelected() - Method in class edu.sdsc.mbt.LabelComponent
getSelected() - Method in class edu.sdsc.mbt.MonitorComponent
getSelected() - Method in class edu.sdsc.mbt.ResidueLabelComponent
getSelected() - Method in class edu.sdsc.mbt.StericBumpComponent
getSelected() - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock
getSelectedCells() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getSelectedChains() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getSelectedColumns() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getSelectedColumns() - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceScalePanel: Returns a list of the columns that are currently selected.
getSelectedFont() - Method in class edu.sdsc.sirius.dialogs.JFontChooser: Returns the currently selected font.
getSelectedLookAndFeel() - Method in class com.jgoodies.looks.demo.Settings
getSelectedPaths() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Selection
getSelectedPaths() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.SelectionOfAtoms
getSelectedPaths() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.SelectionOfResidues
getSelectedRowCount() - Method in class edu.sdsc.sirius.dialogs.TableImpl.BlastResultPanel
getSelectedRowCount() - Method in class edu.sdsc.sirius.dialogs.TableImpl.PubmedResultPanel
getSelectedRowCount() - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel
getSelectedRowCount() - Method in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel
getSelectedRows() - Method in class edu.sdsc.sirius.dialogs.TableImpl.BlastResultPanel
getSelectedRows() - Method in class edu.sdsc.sirius.dialogs.TableImpl.PubmedResultPanel
getSelectedRows() - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel
getSelectedRows() - Method in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel
getSelectedSequences() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getSelectedSequences() - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel
getSelectedTheme() - Method in class com.jgoodies.looks.demo.Settings
getSelection() - Method in class edu.sdsc.mbt.viewables.StructureStyles
getSelectionColor(float[]) - Static method in class edu.sdsc.mbt.viewables.StylesPreferences
getSelectionFlag() - Method in class edu.sdsc.mbt.viewables.StructureStyles
getSequence() - Method in class edu.sdsc.mbt.Sequence
getSequence() - Method in class edu.sdsc.sirius.io.SequenceEntry: Returns the Structure object holding the 3D information.
getSequence(int) - Method in class edu.sdsc.sirius.io.SequenceEntry
getSequence() - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles: Return a reference to our Sequence object.
getSequenceCount() - Method in class edu.sdsc.sirius.io.SequenceEntry
getSequenceDefault() - Static method in class edu.sdsc.mbt.viewables.ResidueColorRegistry
getSequenceIndex() - Method in class edu.sdsc.sirius.export.StyleMap
getSequenceName() - Method in class edu.sdsc.sirius.io.SequenceEntry
getSequenceName(int) - Method in class edu.sdsc.sirius.io.SequenceEntry
getSequenceObjects() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getSequenceSelected() - Method in class edu.sdsc.sirius.export.StyleMap
getSequenceStyles() - Method in class edu.sdsc.mbt.Sequence
getSequenceViewer() - Method in class Viewer
getSequenceViewer() - Method in interface edu.sdsc.sirius.util.Manager: Returns a reference to SequenceViewer
getSequences() - Method in class edu.sdsc.sirius.export.StateObject
getSequences() - Method in class edu.sdsc.sirius.io.SequenceEntry
getSequences() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getSerialNumber() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Return the atom serial number.
getSetColor() - Method in class edu.sdsc.mbt.LabelComponent
getSetColor() - Method in class edu.sdsc.mbt.ResidueLabelComponent
getSetFlag() - Method in class edu.sdsc.sirius.dialogs.ColorEvent
getSetFlag() - Method in interface edu.sdsc.sirius.dialogs.DisplayDialogEvent
getSetFlag() - Method in class edu.sdsc.sirius.dialogs.GeometryEvent
getSetFlag() - Method in class edu.sdsc.sirius.dialogs.HydrogenEvent
getSetFlag() - Method in class edu.sdsc.sirius.dialogs.LabelEvent
getSetFlag() - Method in class edu.sdsc.sirius.dialogs.RenderingEvent
getSetFlag() - Method in class edu.sdsc.sirius.dialogs.RibbonColorEvent
getSetFlag() - Method in class edu.sdsc.sirius.dialogs.RibbonEvent
getSetFlag() - Method in class edu.sdsc.sirius.dialogs.StericEvent
getSetFlag() - Method in class edu.sdsc.sirius.dialogs.StructureEvent
getSetFlag() - Method in class edu.sdsc.sirius.dialogs.ViewEvent
getSetFlag() - Method in class edu.sdsc.sirius.dialogs.VisibilityEvent
getSetFlag() - Method in class edu.sdsc.sirius.dialogs.WeightEvent
getSharpVector(double[], double[], double[]) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometryUtils
getShowOrder() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometry: Get the state of showing/hiding a representation of bond order.
getSideChain(String) - Static method in class edu.sdsc.sirius.util.DataService
getSideColor() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.AffineCrossSection
getSideColor() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection
getSingleLetterAminoAcidName(String) - Static method in class edu.sdsc.sirius.util.ProteinProperties
getSource() - Method in class edu.sdsc.sirius.dialogs.ColorEvent: Returns the source of the event.
getSource() - Method in interface edu.sdsc.sirius.dialogs.DisplayDialogEvent
getSource() - Method in class edu.sdsc.sirius.dialogs.GeometryEvent
getSource() - Method in class edu.sdsc.sirius.dialogs.HydrogenEvent
getSource() - Method in class edu.sdsc.sirius.dialogs.LabelEvent
getSource() - Method in class edu.sdsc.sirius.dialogs.RenderingEvent
getSource() - Method in class edu.sdsc.sirius.dialogs.RibbonColorEvent: Returns the source of the event.
getSource() - Method in class edu.sdsc.sirius.dialogs.RibbonEvent
getSource() - Method in class edu.sdsc.sirius.dialogs.StericEvent
getSource() - Method in class edu.sdsc.sirius.dialogs.StructureEvent
getSource() - Method in class edu.sdsc.sirius.dialogs.ViewEvent
getSource() - Method in class edu.sdsc.sirius.dialogs.VisibilityEvent
getSource() - Method in class edu.sdsc.sirius.dialogs.WeightEvent
getSourceSpecies() - Method in class edu.sdsc.mbt.StructureInfo: Get the source species of this compound.
getSourceUrl() - Method in class edu.sdsc.sirius.io.Entry
getSplitBondColor(Bond, float[]) - Method in interface edu.sdsc.mbt.viewables.BondColor: Provides the secondary color for a SPLIT bond (@see BondForm).
getSplitBondColor(Bond, float[]) - Method in class edu.sdsc.mbt.viewables.BondColorByAtomColor
getSplitBondColor(Bond, float[]) - Method in class edu.sdsc.mbt.viewables.BondColorByElement
getSplitBondRadius(Bond) - Method in interface edu.sdsc.mbt.viewables.BondRadius: Provides the secondary radius for a SPLIT bond (@see BondForm).
getSplitBondRadius(Bond) - Method in class edu.sdsc.mbt.viewables.BondRadiusAsStick: Produce the secondary radius (in pixel units) as a constant value.
getSplitBondRadius(Bond) - Method in class edu.sdsc.mbt.viewables.BondRadiusAsWire: Produce the secondary radius (in pixel units) as a constant value.
getSplitBondRadius(Bond) - Method in class edu.sdsc.mbt.viewables.BondRadiusByAtomRadius: Produce the secondary radius based upon the second atom radius.
getSplitBondRadius(Bond) - Method in class edu.sdsc.mbt.viewables.BondRadiusByScaledAtomRadius: Produce the secondary radius based upon the second atom radius.
getSsFlags() - Method in class edu.sdsc.mbt.util.DerivedInformation
getSsShape(int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.HelixGeometry: Returns the general appearance of the helix shape, i.e.
getStart() - Method in class edu.sdsc.mbt.util.DoubleRange: Returns the start value.
getStart() - Method in class edu.sdsc.mbt.util.IntRange: Returns the start value.
getStart() - Method in class edu.sdsc.sirius.dialogs.TableImpl.InterProDataBlock
getStartResidue() - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel
getStartResidueIndex() - Method in class edu.sdsc.mbt.Fragment: Get the start Reisude index for this Fragment.
getStartSequence() - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel
getStatus() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.ChainGeometry
getStatus() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Geometry
getStructure() - Method in class edu.sdsc.mbt.StructureComponent: Get the Structure to which a StructureComponent instance belongs.
getStructure() - Method in class edu.sdsc.mbt.StructureMap: Returns the Structure object used to construct this StructureMap.
getStructure() - Method in class edu.sdsc.sirius.io.StructureEntry: Returns the Structure object holding the 3D information.
getStructure(Hashtable, String) - Static method in class edu.sdsc.sirius.util.IOHandler
getStructure() - Method in class edu.sdsc.sirius.viewers.RamachandranViewer
getStructure(Entry) - Method in class edu.sdsc.sirius.viewers.StructureViewer
getStructureBrowser() - Method in class Viewer
getStructureBrowser() - Method in interface edu.sdsc.sirius.util.Manager
getStructureComponent() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.MbtRenderable: Return the StructureComponent for this MbtRenderable.
getStructureComponentByIndex(String, int) - Method in class edu.sdsc.mbt.Structure: Get the values for any StructureSomponent subclass by its type-specific index.
getStructureComponentCount(String) - Method in class edu.sdsc.mbt.Structure: Counts components of the specified type that exist in the structure.
getStructureComponentRelations(String, StructureComponent) - Method in class edu.sdsc.mbt.Structure: Given a StructureComponentRelation name and a StructureComponent, create and return a StructureComponentIterator which will selectively return the related subset of StructureComponent objects.
getStructureComponentType() - Method in class edu.sdsc.mbt.Atom: This method returns the fully qualified name of this class.
getStructureComponentType() - Method in class edu.sdsc.mbt.Bond: This method returns the fully qualified name of this class.
getStructureComponentType() - Method in class edu.sdsc.mbt.Chain: This method returns the fully qualified name of this class.
getStructureComponentType() - Method in class edu.sdsc.mbt.Coil: This method returns the fully qualified name of this class.
getStructureComponentType() - Method in class edu.sdsc.mbt.Fragment: This method returns the fully qualified name of this class.
getStructureComponentType() - Method in class edu.sdsc.mbt.Helix: This method returns the fully qualified name of this class.
getStructureComponentType() - Method in class edu.sdsc.mbt.Residue: This method returns the fully qualified name of this class.
getStructureComponentType() - Method in class edu.sdsc.mbt.Strand: This method returns the fully qualified name of this class.
getStructureComponentType() - Method in class edu.sdsc.mbt.StructureComponent: This method returns the fully qualified name of this class.
getStructureComponentType() - Method in class edu.sdsc.mbt.StructureInfo: This method returns the fully qualified name of this class.
getStructureComponentType() - Method in class edu.sdsc.mbt.Symmetry: This method returns the fully qualified name of this class.
getStructureComponentType() - Method in class edu.sdsc.mbt.Turn: This method returns the fully qualified name of this class.
getStructureDocument() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getStructureDocument() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getStructureId() - Method in class edu.sdsc.sirius.io.StructureEntry
getStructureMap() - Method in class edu.sdsc.mbt.Structure: Return the StructureMap object that describes the derived (implied) hierarchy of primary and secondary structure data for the Structure.
getStructureMap() - Method in class edu.sdsc.mbt.viewables.StructureStyles: Return a reference to our StructureMap object.
getStructureName(Structure) - Method in class edu.sdsc.sirius.viewers.StructureViewer
getStructureStyles() - Method in class edu.sdsc.mbt.StructureMap: Return the StructureStyles object that describes the style (authored) attributes needed to produce consistant views of StructureMap elements.
getStructureViewer() - Method in class Viewer
getStructureViewer() - Method in interface edu.sdsc.sirius.util.Manager: Returns a reference to the StructureViewer
getStructures() - Method in class edu.sdsc.sirius.export.StateObject
getStyle() - Method in class edu.sdsc.mbt.viewables.ResidueAnnotation
getStyleMap() - Method in class edu.sdsc.sirius.export.StateObject
getStyleMap() - Method in class edu.sdsc.sirius.viewers.SequenceViewer
getStyleName() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle: Get the Style Name
getStyleReference() - Method in class edu.sdsc.mbt.viewables.StructureStyles
getStyleType() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle: Get the Style Type
getSubApplet() - Method in class AppletLauncher3D: Helper method to make it easier to call methods on the sub-applet from JavaScript.
getSubApplet() - Method in class SiriusAppletLauncher: Helper method to make it easier to call methods on the sub-applet from JavaScript.
getSubjectType() - Method in class edu.sdsc.mbt.StructureComponentRelation: Returns the subject type of this StructureComponentRelation object.
getSuperimpose() - Method in class Viewer
getSuperimpose() - Method in interface edu.sdsc.sirius.util.Manager
getSymbolFromThreeLetters(String) - Static method in class edu.sdsc.sirius.util.DNAProperties
getTab(int) - Method in class edu.sdsc.sirius.util.TabListCellRenderer
getTabs() - Method in class edu.sdsc.sirius.util.TabListCellRenderer
getTangent() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron
getTangent(float) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Hermite
getTangent() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Trihedron: Get the tangent vector.
getText() - Method in class edu.sdsc.mbt.LabelComponent
getText() - Method in class edu.sdsc.mbt.ResidueLabelComponent
getTitle() - Method in class com.jgoodies.uif_lite.panel.SimpleInternalFrame: Returns the frame's title text.
getTitle() - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock
getToOriginMatrix(Atom) - Static method in class edu.sdsc.sirius.util.StructureMath
getToOriginMatrix(double[]) - Static method in class edu.sdsc.sirius.util.StructureMath
getToolBar() - Method in class com.jgoodies.uif_lite.panel.SimpleInternalFrame: Returns the current toolbar, null if none has been set before.
getToolBar3DHint() - Method in class com.jgoodies.looks.demo.Settings
getToolBarHeaderStyle() - Method in class com.jgoodies.looks.demo.Settings
getToolBarPlasticBorderStyle() - Method in class com.jgoodies.looks.demo.Settings
getToolBarWindowsBorderStyle() - Method in class com.jgoodies.looks.demo.Settings
getToolTipLocation(MouseEvent) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel: Return the tool-tip help location when the user moves the cursor over the residues.
getToolTipText(MouseEvent) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel: Return the tool-tip help text when the user moves the cursor over the residues.
getTorsionConnections() - Method in class edu.sdsc.mbt.StructureMap
getTransform(double[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.TransformGroupRenderable: xxx.
getTransformedCoordinates() - Method in class edu.sdsc.sirius.viewers.StructureViewer
getTranslationMap() - Static method in class edu.sdsc.sirius.util.DNAProperties
getType() - Method in class edu.sdsc.mbt.AnnotationComponent
getType() - Method in class edu.sdsc.mbt.ArrowComponent
getType() - Method in class edu.sdsc.mbt.HydrogenBondComponent
getType() - Method in class edu.sdsc.mbt.LabelComponent
getType() - Method in class edu.sdsc.mbt.MonitorComponent
getType() - Method in class edu.sdsc.mbt.ResidueLabelComponent
getType() - Method in class edu.sdsc.mbt.StericBumpComponent
getType() - Method in class edu.sdsc.sirius.workbench.WBEntry: Returns data type of the correspoding item in the Workbench database (structure, view, etc.)
getTypeColor(String) - Method in class edu.sdsc.mbt.viewables.FragmentColorByType: Get the color used for the given conformation type.
getTypeColor(String) - Static method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.StyleManager
getTypeCount() - Static method in class edu.sdsc.mbt.StructureComponentRegistry: Return the number of registered StructureComponent types.
getTypeForId(String) - Method in class edu.sdsc.sirius.workbench.WBManager: Method returns integer type of a data item when given its id
getTypeForId(String, boolean) - Method in class edu.sdsc.sirius.workbench.WBManager: This method looks up type of the item when given its id.
getTypeName(String) - Static method in class edu.sdsc.mbt.StructureComponentRegistry: Get an existing StructureComponent type name for the given String.
getTypeNames() - Static method in class edu.sdsc.mbt.StructureComponentRegistry: Return an Enumeration of String values for all registered StructureComponent types.
getUniqueId() - Static method in class edu.sdsc.sirius.util.DataService
getUnit() - Method in class edu.sdsc.mbt.util.DoubleRange: Returns a unit that indicates what type of range this is (a Double)
getUnit() - Method in class edu.sdsc.mbt.util.IntRange: Returns a unit that indicates what type of range this is (an Integer)
getUnit() - Method in interface edu.sdsc.mbt.util.Range: Method that returns an object of the type contained in the Range.
getUp() - Method in class edu.sdsc.sirius.io.FragmentEntry
getUpVector() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
getUrlString() - Method in class edu.sdsc.mbt.Structure: This method returns a string which represents the URL from which the structure instance was produced.
getUserData() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry: Returns information (annotation) provided by the user
getVGap() - Method in class edu.sdsc.sirius.util.DialogLayout
getVGap() - Method in class edu.sdsc.sirius.util.ExtensionLayout
getValue(int) - Method in class edu.sdsc.mbt.util.RangeMap: Get the value object asocciated with the given index.
getValueMap() - Method in class edu.sdsc.mbt.viewables.AtomColorByCharge
getValueMap() - Method in interface edu.sdsc.mbt.viewables.ResidueColor: Gets value map used to assign residue colors.
getValueMap() - Method in class edu.sdsc.mbt.viewables.ResidueColorByCharge
getValueMap() - Method in class edu.sdsc.mbt.viewables.ResidueColorByElement
getValueMap() - Method in class edu.sdsc.mbt.viewables.ResidueColorByHydrophobicity
getValueMap() - Method in class edu.sdsc.mbt.viewables.ResidueColorByType
getValueMap() - Method in class edu.sdsc.mbt.viewables.ResidueColorDefault
getValueMap() - Method in class edu.sdsc.mbt.viewables.ResidueColorScaled
getValueMap() - Method in class edu.sdsc.mbt.viewables.ResidueColorUniform
getValueMap() - Method in interface edu.sdsc.mbt.viewables.RibbonColor: Gets value map used to assign residue colors.
getValueMap() - Method in class edu.sdsc.mbt.viewables.RibbonColorDefault
getValueMap() - Method in class edu.sdsc.mbt.viewables.RibbonColorUniform
getVector(double[], double[]) - Static method in class edu.sdsc.mbt.util.Algebra
getVector(int) - Method in class edu.sdsc.sirius.util.VectorSet
getVectorAngle(double[], double[], double[]) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometryUtils
getVectorAngle(double[], double[]) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometryUtils
getVectorDifference(double[], double[]) - Static method in class edu.sdsc.mbt.util.Algebra: subtract function
getVectorNormals() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection
getVectorSum(double[], double[]) - Static method in class edu.sdsc.mbt.util.Algebra
getVectorVertices() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection
getVertexColors() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle: Set the vertex colors
getVertexCount() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.AffineCrossSection
getVertexCount() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle: Get the number of vertices
getVertexCount() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection
getVertices() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection
getView() - Method in class edu.sdsc.sirius.export.StateObject
getViewPoint(double[], double) - Static method in class edu.sdsc.mbt.util.Algebra: Calculate the position of the view point on Z axis, given the center of the viewed structure and the required distance
getViewer() - Method in class edu.sdsc.sirius.viewers.RamachandranViewerImpl.RamachandranViewerDialog
getViewerParameters() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer
getViewers() - Method in class edu.sdsc.mbt.viewables.StructureDocument
getVisibilityMap() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry
getVisible() - Method in class edu.sdsc.mbt.AnnotationComponent
getVisible() - Method in class edu.sdsc.mbt.ArrowComponent
getVisible() - Method in class edu.sdsc.mbt.HydrogenBondComponent
getVisible() - Method in class edu.sdsc.mbt.LabelComponent
getVisible() - Method in class edu.sdsc.mbt.MonitorComponent
getVisible() - Method in class edu.sdsc.mbt.ResidueLabelComponent
getVisible() - Method in class edu.sdsc.mbt.StericBumpComponent
getWBEntryCount() - Method in class edu.sdsc.sirius.workbench.WBManager: Returns the number of items in the user's Workbench account
getWBList() - Method in class edu.sdsc.sirius.workbench.WBManager: This method retrieves list of data items and registers them with the WBManager
getWBManager() - Method in class Viewer
getWBManager() - Method in interface edu.sdsc.sirius.util.Manager
getWeight() - Method in class edu.sdsc.mbt.util.Octree: ???
getWorkbenchId(Entry) - Method in class edu.sdsc.sirius.workbench.WBManager: If a loaded Entry actually came from Workbench, this method returns its workbench id.
getX() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Return the X-coordinate of this atom.
getY() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Return the Y-coordinate of this atom.
getYear() - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataBlock
getZ() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Atom: Return the Z-coordinate of this atom.
group_name - Variable in class edu.sdsc.mbt.util.Element
group_number - Variable in class edu.sdsc.mbt.util.Element

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