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

D

DATA_SEQUENCE - Static variable in class edu.sdsc.sirius.io.Entry

DATA_STRUCTURE - Static variable in class edu.sdsc.sirius.io.Entry

DELETE - Static variable in class edu.sdsc.sirius.dialogs.StructureEditDialog

DELETE_ATOM - Static variable in class edu.sdsc.sirius.dialogs.StructureEventRegistry

DNAProperties - class edu.sdsc.sirius.util.DNAProperties.

This class stores information about bonding in standard amino acids and is used by the pdb loader to create bonds

DNAProperties() - Constructor for class edu.sdsc.sirius.util.DNAProperties

DOUBLE_FACE - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle

Standard - Styles: Plane Single Face

DataBlock - class edu.sdsc.sirius.dialogs.TableImpl.DataBlock.

This class stores information about a database entry used to display it in search and loading dialogs.

DataBlock() - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.DataBlock

DataBlock(String) - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.DataBlock

DataListerDialog - class edu.sdsc.sirius.dialogs.DataListerDialog.

This class implements a dialog that displays the currently loaded entries.

DataListerDialog(JFrame, Manager, StructureDocument, FileEntryLoader, Vector, File) - Constructor for class edu.sdsc.sirius.dialogs.DataListerDialog

Constructor that creates the dialog.

DataListerDialog(JFrame, Manager, StructureDocument, FileEntryLoader, Vector, URL) - Constructor for class edu.sdsc.sirius.dialogs.DataListerDialog

DataService - class edu.sdsc.sirius.util.DataService.

DataService() - Constructor for class edu.sdsc.sirius.util.DataService

DataSet - class edu.sdsc.sirius.dialogs.TableImpl.DataSet.

This class is a container for DataBlocks and is used to ship information about multiple entries at once.

DataSet() - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.DataSet

Constructor that intializes storage hashes.

DataWBListerDialog - class edu.sdsc.sirius.dialogs.DataWBListerDialog.

This class implements a dialog that displays the currently loaded entries.

DataWBListerDialog(JFrame, Manager, StructureDocument, String, Vector, String) - Constructor for class edu.sdsc.sirius.dialogs.DataWBListerDialog

Constructor that creates the dialog.

Debug - class edu.sdsc.mbt.viewers.StructureViewerImpl.util.Debug.

Utility class to add debugging to an application.

Debug(String, int) - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.util.Debug

Initialize debugging.

DeletionInfo - class edu.sdsc.sirius.util.DeletionInfo.

Provides static information about Amino Acids such as character codes, 3-letter codes, and full names.

DeletionInfo() - Constructor for class edu.sdsc.sirius.util.DeletionInfo

DerivedInformation - class edu.sdsc.mbt.util.DerivedInformation.

DerivedInformation is a class that encapsulates methods that produce information derivable from data in the source file.

DerivedInformation(Structure) - Constructor for class edu.sdsc.mbt.util.DerivedInformation

DerivedInformation(Structure, StructureMap) - Constructor for class edu.sdsc.mbt.util.DerivedInformation

DialogConstants - class edu.sdsc.sirius.dialogs.DialogConstants.

This class contains constants used by the dialogs originating from the SequenceViewer.

DialogConstants() - Constructor for class edu.sdsc.sirius.dialogs.DialogConstants

DialogLayout - class edu.sdsc.sirius.util.DialogLayout.

DialogLayout() - Constructor for class edu.sdsc.sirius.util.DialogLayout

DialogLayout(int, int) - Constructor for class edu.sdsc.sirius.util.DialogLayout

DihedralDialog - class edu.sdsc.sirius.dialogs.DihedralDialog.

DihedralDialog(JFrame, Manager, StructureViewer) - Constructor for class edu.sdsc.sirius.dialogs.DihedralDialog

DisplayDialog - interface edu.sdsc.sirius.dialogs.DisplayDialog.

DisplayDialogEvent - interface edu.sdsc.sirius.dialogs.DisplayDialogEvent.

DisplayDialogListener - interface edu.sdsc.sirius.dialogs.DisplayDialogListener.

DisplayParameters - class edu.sdsc.sirius.viewers.SequenceViewerImpl.DisplayParameters.

DisplayParameters() - Constructor for class edu.sdsc.sirius.viewers.SequenceViewerImpl.DisplayParameters

DistanceDialog - class edu.sdsc.sirius.dialogs.DistanceDialog.

DistanceDialog(JFrame, Manager, StructureViewer) - Constructor for class edu.sdsc.sirius.dialogs.DistanceDialog

DistributionViewer - class edu.sdsc.sirius.dialogs.DistributionViewer.

DistributionViewer(JFrame, StructureDocument, HashMap) - Constructor for class edu.sdsc.sirius.dialogs.DistributionViewer

DoubleRange - class edu.sdsc.mbt.util.DoubleRange.

This class implements a container for a range of two double values.

DoubleRange(double, double) - Constructor for class edu.sdsc.mbt.util.DoubleRange

Constructor initialized with two values

data - Variable in class edu.sdsc.mbt.StructureComponentEvent

data - Variable in class edu.sdsc.mbt.viewers.GLViewerImpl.MoveEvent

dataType - Variable in class edu.sdsc.mbt.LabelComponent

dataType - Variable in class edu.sdsc.mbt.ResidueLabelComponent

defaultCellBackgroundColor - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

defaultColumns - Static variable in class edu.sdsc.sirius.dialogs.TableImpl.BlastResultPanel

defaultColumns - Static variable in class edu.sdsc.sirius.dialogs.TableImpl.PubmedResultPanel

defaultColumns - Static variable in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel

defaultColumns - Static variable in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel

defaultGeometry - Static variable in class edu.sdsc.sirius.viewers.StructureViewer

defaultLAF - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

deleteCustomFragment(String) - Static method in class edu.sdsc.sirius.builder.FragmentRegistry

deleteCustomFragment(String) - Static method in class edu.sdsc.sirius.builder.FragmentUtil

deleteGappedColumn(int) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel

deleteHydrogen(Atom, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

This method serves to delete hydrogens without creating any dummy atoms.

deleteLastUndoState() - Method in class edu.sdsc.sirius.viewers.StructureViewer

deleteResidue(Cell) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles

deleteSelected() - Method in class edu.sdsc.sirius.workbench.WBListPanel

Deletes selected item from the user's Workbench account

deleteSelectedAtoms() - Method in class edu.sdsc.sirius.viewers.StructureViewer

deleteStructureComponent(StructureComponent, boolean, boolean) - Method in class edu.sdsc.mbt.viewables.StructureStyles

TODO temporarily use StructureStyles as a handler of component events.

depth() - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Path

Returns the depth of this Path.

deriveBondOrder - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

deriveBondOrders() - Method in class edu.sdsc.mbt.StructureMap

This method walks over all bonds in the structure and calculates orders based on their geometry

description - Variable in class edu.sdsc.sirius.dialogs.TableImpl.BlastLineData

description - Variable in class edu.sdsc.sirius.dialogs.TableImpl.LineData

description - Variable in class edu.sdsc.sirius.util.StructureItem

deselectButtons(FragmentGroupPanel) - Method in class edu.sdsc.sirius.builder.BuilderPanel

Deselects fragment buttons on all panels except for the one requesting the action

deselectButtons() - Method in class edu.sdsc.sirius.builder.CustomFragmentPanel

deselectButtons() - Method in interface edu.sdsc.sirius.builder.FragmentGroupPanel

deselectButtons() - Method in class edu.sdsc.sirius.builder.GeneralFragmentPanel

deselectButtons() - Method in class edu.sdsc.sirius.builder.ProteinFragmentPanel

destroy() - Method in class AppletLauncher3D

destroy() - Method in class SiriusAppletLauncher

destructor() - Method in class Viewer

destructor() - Method in class edu.sdsc.sirius.viewers.RamachandranViewer

detectBonds() - Method in class edu.sdsc.mbt.StructureMap

This method detects missing bonds without removing any existing ones.

detectBumps(Vector, double, boolean, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

Boolean parameter determines whether to look for bumps between the members of the set and the rest of the display

detectBumps(Vector, Vector, double, boolean, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

detectHydrogenBonds(Vector, Vector, double, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

detectLigandBonds() - Method in class edu.sdsc.mbt.StructureMap

dictionaryPath - Static variable in class edu.sdsc.sirius.builder.FragmentRegistry

dihedralAngle(double[], double[], double[], double[]) - Static method in class edu.sdsc.mbt.util.Algebra

Calculate the dihedral angle defined by four virtex coordinates.

disableStatus() - Static method in class edu.sdsc.mbt.util.Status

disconnect(int) - Method in class edu.sdsc.sirius.viewers.RamachandranViewer

display(GLAutoDrawable) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

GLEventListener interface - display method:

displayAction() - Method in class Viewer

displayAction() - Method in interface edu.sdsc.sirius.util.Manager

displayChanged(GLAutoDrawable, boolean, boolean) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

GLEventListener interface - displayChanged method:

displayColumn(String, boolean) - Method in class edu.sdsc.sirius.dialogs.TableImpl.BlastResultPanel

displayColumn(String, boolean) - Method in class edu.sdsc.sirius.dialogs.TableImpl.PubmedResultPanel

displayColumn(String, boolean) - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel

displayComponentInfo(StructureComponent) - Method in class edu.sdsc.sirius.viewers.TreeViewer.InfoViewer

displayErrorMessage(String) - Method in class Viewer

displayErrorMessage(String) - Method in interface edu.sdsc.sirius.util.Manager

Displays an error message.

displayExceptionMessage(String, Exception) - Method in class Viewer

displayExceptionMessage(String, Exception) - Method in interface edu.sdsc.sirius.util.Manager

Displays an error message with an option to display details of the exception.

displayMessage(String) - Method in class Viewer

displayMessage(String) - Method in interface edu.sdsc.sirius.util.Manager

Displays a message in an information dialog.

displayMessage(String) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

displayRamachandranPlot(Structure) - Method in class Viewer

displayRamachandranPlot(Structure) - Method in interface edu.sdsc.sirius.util.Manager

displayTextMessage(String, String) - Method in class Viewer

displayTextMessage(String, String) - Method in interface edu.sdsc.sirius.util.Manager

displayToolbar - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

displayURL(String) - Static method in class edu.sdsc.sirius.util.BrowserControl

displayWaitScreen() - Method in class Viewer

displayWaitScreen() - Method in interface edu.sdsc.sirius.util.Manager

Displays a wait screen.

distance(double[], double[]) - Static method in class edu.sdsc.mbt.util.Algebra

Compute the distance between two virtex coordinates.

distance(Vec3d, Vec3d) - Static method in class edu.sdsc.mbt.util.Algebra

Compute the distance between coordinates using double values

distance(Vec3f, Vec3f) - Static method in class edu.sdsc.mbt.util.Algebra

Compute the distance between coordinates using float values

distance(Atom, Atom) - Static method in class edu.sdsc.mbt.util.BondFactory

Return the coordinate distance between two Atom objects.

distance(FrenetTrihedron) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.FrenetTrihedron

dna_bases - Static variable in class edu.sdsc.mbt.util.NucleicAcidInfo

Letter codes of the 4 nitrogenous bases for DNA.

doRcsbLoad(String) - Method in class Viewer

doRcsbLoad(String) - Method in interface edu.sdsc.sirius.util.Manager

Loads entries from the PDB ftp server.

dockRama - Static variable in class edu.sdsc.mbt.viewables.StylesPreferences

dot(Vector3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Vector3f

dotProduct(double[], double[]) - Static method in class edu.sdsc.mbt.util.Algebra

Return the vector dot product between v1 and v2.

dotProduct(float[], float[]) - Static method in class edu.sdsc.mbt.util.Algebra

download(URL, File) - Method in class edu.sdsc.sirius.io.FileTransfer

Copy a file from a remote URL to a local file on hard disk.

draw(AnnotationComponent, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.AnnotationGeometry

Please complete the missing tags for main

draw(StructureComponent, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.ArrowGeometry

draw(AnnotationComponent, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.ArrowGeometry

Please complete the missing tags for main

draw(StructureComponent, StructureStyles, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.AtomGeometry

Please complete the missing tags for main

draw(Atom, StructureStyles, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.AtomGeometry

draw(StructureComponent, StructureStyles, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.AtomLineGeometry

Please complete the missing tags for main

draw(Atom, StructureStyles, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.AtomLineGeometry

Please complete the missing tags for main

draw(GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.BackboneLine

draw(StructureComponent, StructureStyles, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometry

Please complete the missing tags for main

draw(Bond, StructureStyles, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometry

Please complete the missing tags for main

draw(StructureComponent, StructureStyles, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.ChainGeometry

Please complete the missing tags for main

draw(Chain, StructureStyles, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.ChainGeometry

Please complete the missing tags for main

draw(GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Extrusion

draw(StructureComponent, StructureStyles, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Geometry

Please complete the missing tags for main

draw(GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlAxesRenderable

Draw the X-Y-Z axes.

draw(GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlExtrusion

Draw the extrusion with the specified JOGL context using the current extrusion state.

draw(GL, GLU, GLUT) - Method in interface edu.sdsc.mbt.viewers.GLViewerImpl.GlRenderable

Draw the content.

draw(StructureComponent, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.LabelGeometry

draw(AnnotationComponent, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.LabelGeometry

Please complete the missing tags for main

draw(GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.MbtRenderable

Tell the geometry to redraw its representation for this renderable.

draw(StructureComponent, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.MonitorGeometry

draw(AnnotationComponent, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.MonitorGeometry

Please complete the missing tags for main

draw(GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.MonitorRenderable

Tell the geoemtry to redraw its representation for this renderable.

draw(StructureComponent, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.ResidueLabelGeometry

draw(AnnotationComponent, GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.ResidueLabelGeometry

Please complete the missing tags for main

draw(GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.TransformGroupRenderable

drawCone(GL, GLU, GLUT, double, boolean, double, int, int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.ArrowGeometry

drawCylinder(GL, GLU, GLUT, double, boolean, double, float, int, int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.ArrowGeometry

drawCylinder(GL, GLU, GLUT, double, boolean, double, boolean, float, int, int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.AtomLineGeometry

Please complete the missing tags for main

drawCylinder(GL, GLU, GLUT, double, boolean, double, boolean, float, int, int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.BondGeometry

Please complete the missing tags for main

drawFigure(GL, GLU, GLUT, CrossSectionStyle, Vector3f[], FrenetTrihedron[], Color[], boolean[], boolean[], int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.CoilGeometry

drawFigure(GL, GLU, GLUT, CrossSectionStyle, Vector3f[], Vector3f[], FrenetTrihedron[], Color[], boolean[], boolean[], int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.StrandGeometry

Returns the scene graph component associated with the Strand defined by the underlying data

drawJoglGeometry(GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.CoilGeometry

drawJoglGeometry(GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GeometryEntity

Return the BranchGroup object representing the geometrical shape contained by this GeometryEntity object.

drawJoglGeometry(GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.HelixGeometry

drawJoglGeometry(GL, GLU, GLUT) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.StrandGeometry

Returns a Java3D object representing a strand and eventually any other GeometryEntity that this object contains as a child.

drawSs(Chain, GL, GLU, GLUT, StructureMap, StructureStyles, boolean) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry

Builds a scene of the secondary structures, the list of SS being the one produced by the StructureMap argument based on what is explicitely available in the data source file or from the Kabsch-Sander algorithm.

drawSs(Chain, GL, GLU, GLUT, StructureMap, StructureStyles, boolean, int, int, int, int) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry

Builds a scene of the secondary structures, the list of SS being the one produced by the StructureMap argument based on what is explicitely available in the data source file or from the Kabsch-Sander algorithm.

drawSs(Chain, GL, GLU, GLUT, StructureMap, StructureStyles, boolean, int, int, int, int, int) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry

Builds a scene of the secondary structures, the list of SS being the one produced by the StructureMap argument based on what is explicitely available in the data source file or from the Kabsch-Sander algorithm.

drawSs(Chain, GL, GLU, GLUT, StructureMap, StructureStyles, boolean, float, float, float, float, int, int, int, int, int, int, int, int, int) - Static method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry

Builds a scene of the secondary structures, the list of SS being the one produced by the StructureMap argument based on what is explicitely available in the data source file or from the Kabsch-Sander algorithm.

dx - Variable in class edu.sdsc.mbt.viewers.GLViewerImpl.MoveEvent

dy - Variable in class edu.sdsc.mbt.viewers.GLViewerImpl.MoveEvent