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

R

RAINBOW - Static variable in class edu.sdsc.mbt.viewables.InterpolatedColorMap

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

Standard - Styles: Rectangular CrossSection

REFERENCE_COMMON - Static variable in class edu.sdsc.sirius.dialogs.DialogConstants

Use the common ruler to define the residue numbers.

REFERENCE_DEFINED - Static variable in class edu.sdsc.sirius.dialogs.DialogConstants

Reference sequence option: reference sequence is is typed in the dialog.

REFERENCE_SELECTED - Static variable in class edu.sdsc.sirius.dialogs.DialogConstants

Reference sequence option: use selected sequence as reference.

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

Standard - Styles: POLYGONAL CrossSection

RELATION_CONFORMATION_ATOMS - Static variable in class edu.sdsc.mbt.StructureComponentRegistry

This is a static convenience field provided so that user code does not have to create a local variable name to store a cached relation.

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

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

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

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

Constants that define rendering quality.

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

Constants that define structure rendering modes for each atom to allow different rendering of defined structure fragments.

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

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

RENDER_TIMEOUT - Static variable in class edu.sdsc.sirius.ray.RayTraceUtil

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

REPLACE_SELECTION - Static variable in class edu.sdsc.sirius.dialogs.DialogConstants

RIBBON - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.HelixGeometry

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

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

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

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

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

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

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

Standard - Styles: POLYGONAL ROUNDED CrossSection

RamachandranViewer - class edu.sdsc.sirius.viewers.RamachandranViewer.

RamachandranViewer(Structure) - Constructor for class edu.sdsc.sirius.viewers.RamachandranViewer

RamachandranViewerDialog - class edu.sdsc.sirius.viewers.RamachandranViewerImpl.RamachandranViewerDialog.

RamachandranViewerDialog(JFrame, RamachandranViewer) - Constructor for class edu.sdsc.sirius.viewers.RamachandranViewerImpl.RamachandranViewerDialog

Range - interface edu.sdsc.mbt.util.Range.

Interface that defines the range identification method.

RangeMap - class edu.sdsc.mbt.util.RangeMap.

The RangeMap class provides a means to map an integer value (such as an index) that falls in a fixed range (min and max) to application-supplied Objects.

RangeMap(int, int, Object) - Constructor for class edu.sdsc.mbt.util.RangeMap

Construct a RangeMap object with the specified min, max, and default value.

RasmolReader - class edu.sdsc.sirius.rasmol.RasmolReader.

This class provides a static method for reading rasmol input scripts with one line being input at a time.

RasmolReader(StructureViewer) - Constructor for class edu.sdsc.sirius.rasmol.RasmolReader

RayTraceUtil - class edu.sdsc.sirius.ray.RayTraceUtil.

This class provides methods to process the currently displayed scene and record a POV input file for ray tracing.

RayTraceUtil() - Constructor for class edu.sdsc.sirius.ray.RayTraceUtil

RayTracerDialog - class edu.sdsc.sirius.dialogs.RayTracerDialog.

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

RelationFilter - class edu.sdsc.mbt.filters.RelationFilter.

Defines a StructureComponentFilter sub-class which handles the filtering of StructureComponent objects that are related to the StructureComponent subject parameter.

RelationFilter(StructureComponentRelation, StructureComponent) - Constructor for class edu.sdsc.mbt.filters.RelationFilter

Constructs a RelationFilter for the given StructureComponentRelation instance and StructureComponent subject parameters.

Relation_Conformation_Atom - class edu.sdsc.mbt.Relation_Conformation_Atom.

This class represents a relationship between the Conformation and the Atom StructureComponent class.

Relation_Conformation_Atom() - Constructor for class edu.sdsc.mbt.Relation_Conformation_Atom

Constructs a relation between Conformation and Atom objects.

Renderable - class edu.sdsc.mbt.viewers.GLViewerImpl.Renderable.

Provides a renderable object which contains all properties needed to regenerate geometry for a visible representation of some data.

Renderable() - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.Renderable

Constructor with basic initialization (empty display list and dirty).

RenderingDialog - class edu.sdsc.sirius.dialogs.RenderingDialog.

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

RenderingEvent - class edu.sdsc.sirius.dialogs.RenderingEvent.

RenderingEvent(DisplayDialog) - Constructor for class edu.sdsc.sirius.dialogs.RenderingEvent

ReplaceAtomDialog - class edu.sdsc.sirius.dialogs.ReplaceAtomDialog.

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

ReplaceResidueDialog - class edu.sdsc.sirius.dialogs.ReplaceResidueDialog.

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

Residue - class edu.sdsc.mbt.Residue.

Implements a StructureComponent container for residue information.

Residue(String) - Constructor for class edu.sdsc.mbt.Residue

Constructor variant used when there will likely be no atom list (eg: when only sequence data is loaded).

Residue() - Constructor for class edu.sdsc.mbt.Residue

Constructor variant used when there will likely be an atom list.

Residue - class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue.

The Residue class stores a list of all Atoms which form a single residue.

Residue() - Constructor for class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue

ResidueAnnotation - class edu.sdsc.mbt.viewables.ResidueAnnotation.

ResidueAnnotation() - Constructor for class edu.sdsc.mbt.viewables.ResidueAnnotation

ResidueAnnotation(int, Color) - Constructor for class edu.sdsc.mbt.viewables.ResidueAnnotation

ResidueColor - interface edu.sdsc.mbt.viewables.ResidueColor.

This interface defines how all ResidueColor implementation classes should generate a color for a given Residue.

ResidueColorByCharge - class edu.sdsc.mbt.viewables.ResidueColorByCharge.

This class implements the ResidueColor interface by applying a color to the given Residue by using hydrophobicity.

ResidueColorByElement - class edu.sdsc.mbt.viewables.ResidueColorByElement.

This class implements the ResidueColor interface by applying a color to the given Residue by using hydrophobicity.

ResidueColorByHydrophobicity - class edu.sdsc.mbt.viewables.ResidueColorByHydrophobicity.

This class implements the ResidueColor interface by applying a color to the given Residue by using hydrophobicity.

ResidueColorByType - class edu.sdsc.mbt.viewables.ResidueColorByType.

This class implements the ResidueColor interface by applying a color to the given Residue by its nature (a color scheme similar to that used by BioEdit).

ResidueColorDefault - class edu.sdsc.mbt.viewables.ResidueColorDefault.

This class implements the ResidueColor interface by applying a color to the given Residue by using hydrophobicity.

ResidueColorFactory - class edu.sdsc.mbt.viewables.ResidueColorFactory.

This class implements a dispatcher keeping track of the currently available ResidueColors.

ResidueColorFactory() - Constructor for class edu.sdsc.mbt.viewables.ResidueColorFactory

ResidueColorRegistry - class edu.sdsc.mbt.viewables.ResidueColorRegistry.

A class used to register ResidueColor implementation objects.

ResidueColorRegistry() - Constructor for class edu.sdsc.mbt.viewables.ResidueColorRegistry

ResidueColorScaled - class edu.sdsc.mbt.viewables.ResidueColorScaled.

This class implements the ResidueColor interface by applying a color to the given Residue by using hydrophobicity.

ResidueColorUniform - class edu.sdsc.mbt.viewables.ResidueColorUniform.

This class implements the ResidueColor interface by applying a color to the given Residue by using hydrophobicity.

ResidueLabelComponent - class edu.sdsc.mbt.ResidueLabelComponent.

ResidueLabelComponent(Residue, int, int, String) - Constructor for class edu.sdsc.mbt.ResidueLabelComponent

ResidueLabelComponent(Residue, int, int, String, boolean, float[]) - Constructor for class edu.sdsc.mbt.ResidueLabelComponent

ResidueLabelDialog - class edu.sdsc.sirius.dialogs.ResidueLabelDialog.

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

ResidueLabelGeometry - class edu.sdsc.mbt.viewers.GLViewerImpl.ResidueLabelGeometry.

Construct a new object for generating bond geometry using default

ResidueLabelGeometry() - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.ResidueLabelGeometry

Construct a new MonitorGeometry object.

ResidueRenameDialog - class edu.sdsc.sirius.dialogs.ResidueRenameDialog.

ResidueRenameDialog(JFrame) - Constructor for class edu.sdsc.sirius.dialogs.ResidueRenameDialog

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

This class implements a panel used to display sequence data retrieved from a database.

ResultPanel(JFrame, DataSet, Manager, int) - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel

Constructs the ResultPanel when created as in a frame typically storing search results.

ResultPanel(JDialog, DataSet, Manager, int) - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel

Constructs the ResultPanel when created as in a dialog typically as a browsing and loading interface.

ResultPanel(JDialog, DataSet, Manager, int, Vector, HashMap) - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel

ResultPanelCallable - interface edu.sdsc.sirius.dialogs.TableImpl.ResultPanelCallable.

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

This class implements a frame holder for ResultPanel and is used to display search results.

ResultPanelFrame(Manager, int) - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.ResultPanelFrame

Constructor that instantiates the frame with the Manager object that will process entry loading.

ResultPanelFrame(DataSet, Manager, int) - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.ResultPanelFrame

Constructor that instantiates the frame with the Manager object that will process entry loading.

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

This class extends JTable and implements a custom table to display database contents or search results.

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

Constructs the table.

RibbonColor - interface edu.sdsc.mbt.viewables.RibbonColor.

This interface defines how all ResidueColor implementation classes should generate a color for a given Residue.

RibbonColorDefault - class edu.sdsc.mbt.viewables.RibbonColorDefault.

This class implements the ResidueColor interface by applying a color to the given Residue by using hydrophobicity.

RibbonColorDialog - class edu.sdsc.sirius.dialogs.RibbonColorDialog.

This class impements a dialog box used to color the currently displayed structures.

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

Constructor that builds the dialog.

RibbonColorEvent - class edu.sdsc.sirius.dialogs.RibbonColorEvent.

This class impements a color event object storing the user selections from the ColorDialog.

RibbonColorEvent(DisplayDialog) - Constructor for class edu.sdsc.sirius.dialogs.RibbonColorEvent

The constructor initialized with the parent dialog.

RibbonColorFactory - class edu.sdsc.mbt.viewables.RibbonColorFactory.

This class implements a dispatcher keeping track of the currently available ResidueColors.

RibbonColorFactory() - Constructor for class edu.sdsc.mbt.viewables.RibbonColorFactory

RibbonColorUniform - class edu.sdsc.mbt.viewables.RibbonColorUniform.

This class implements the ResidueColor interface by applying a color to the given Residue by using hydrophobicity.

RibbonDialog - class edu.sdsc.sirius.dialogs.RibbonDialog.

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

RibbonEvent - class edu.sdsc.sirius.dialogs.RibbonEvent.

RibbonEvent(DisplayDialog) - Constructor for class edu.sdsc.sirius.dialogs.RibbonEvent

RotateBondDialog - class edu.sdsc.sirius.dialogs.RotateBondDialog.

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

radius - Variable in class edu.sdsc.mbt.ArrowComponent

radius - Variable in class edu.sdsc.sirius.dialogs.GeometryEvent

radius - Variable in class edu.sdsc.sirius.dialogs.ViewEvent

readBlocking(InputStream, byte[], int, int) - Method in class edu.sdsc.sirius.io.FileTransfer

Reads exactly len bytes from the input stream into the byte array.

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

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

This method is used to read in fragments from the files in the location specified in FragmentRegistry class.

readHeaders(File) - Method in class edu.sdsc.sirius.io.PdbEntryLoader

readHeaders(URL) - Method in class edu.sdsc.sirius.io.PdbEntryLoader

readHeaders(String) - Method in class edu.sdsc.sirius.io.SDFEntryLoader

readHeaders(File) - Method in class edu.sdsc.sirius.io.SDFEntryLoader

readLine(Manager, String, String, boolean) - Method in class edu.sdsc.sirius.rasmol.RasmolReader

readPDB(File) - Static method in class edu.sdsc.sirius.util.IOHandler

readPDBHeaders(String) - Static method in class edu.sdsc.sirius.util.IOHandler

readPreferences() - Method in class edu.sdsc.mbt.viewables.ElementPreferences

Open current color settings from persistent storage.

readPreferences() - Method in class edu.sdsc.mbt.viewables.StylesPreferences

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

refreshList() - Method in class edu.sdsc.sirius.dialogs.EntryListerDialog

registerEntry(Entry) - Method in class edu.sdsc.sirius.workbench.WBManager

Associate a loaded entry with the Workbench item

registerResidueSelection(Entry, Residue, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

Blank method for compliance with the Viewer interface.

registerStructureComponentRemoval(StructureComponent) - Method in class edu.sdsc.mbt.viewables.StructureStyles

rejectedPaths - Static variable in class edu.sdsc.mbt.util.Octree

reloadContent() - Method in class edu.sdsc.mbt.viewables.StructureDocument

remove(int) - Method in class edu.sdsc.mbt.util.RangeMap

Remove an index (decreasing the range maximum by 1 and causing all subsequent index values to be decreased by 1).

remove(String) - Static method in class edu.sdsc.mbt.viewables.AtomColorRegistry

Remove an existing AtomColor implementation.

remove(String) - Static method in class edu.sdsc.mbt.viewables.AtomLabelRegistry

Remove an existing AtomLabel implementation.

remove(String) - Static method in class edu.sdsc.mbt.viewables.AtomRadiusRegistry

Remove an existing AtomRadius implementation.

remove(String) - Static method in class edu.sdsc.mbt.viewables.BondColorRegistry

Remove an existing BondColor implementation.

remove(String) - Static method in class edu.sdsc.mbt.viewables.BondFormRegistry

Remove an existing BondForm implementation.

remove(String) - Static method in class edu.sdsc.mbt.viewables.BondLabelRegistry

Remove an existing BondLabel implementation.

remove(String) - Static method in class edu.sdsc.mbt.viewables.BondRadiusRegistry

Remove an existing BondRadius implementation.

remove(String) - Static method in class edu.sdsc.mbt.viewables.ChainColorRegistry

Remove an existing ChainColor implementation.

remove(String) - Static method in class edu.sdsc.mbt.viewables.FragmentColorRegistry

Remove an existing FragmentColor implementation.

remove(String) - Static method in class edu.sdsc.mbt.viewables.FragmentFormRegistry

Remove an existing FragmentForm implementation.

remove(String) - Static method in class edu.sdsc.mbt.viewables.ResidueColorRegistry

Remove an existing ResidueColor implementation.

removeAllAtoms() - Method in class edu.sdsc.mbt.Residue

Remove all Atom records from this Residue.

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

Remove all Bond objects from the StructureMap.

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

removeAllResidues() - Method in class edu.sdsc.mbt.Chain

Remove all Residue records from this Chain.

removeAnnotationComponent(AnnotationComponent, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

removeAtom(Atom) - Method in class edu.sdsc.mbt.Residue

removeAtom(int) - Method in class edu.sdsc.mbt.Residue

Remove the specified Atom record from this Residue.

removeAtom(Atom) - Method in class edu.sdsc.mbt.StructureMap

This method removes an atom from the structure

removeAtom(Atom) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue

Remove the supplied Atom from the Residue.

removeAtom(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Residue

Remove the nth Atom from the Residue.

removeBond(Bond) - Method in class edu.sdsc.mbt.StructureMap

Remove a Bond from the StructureMap.

removeBond(int) - Method in class edu.sdsc.mbt.StructureMap

Remove a Bond from the StructureMap.

removeBump(StericBumpComponent, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

removeChain(Chain) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Model

Remove the given Chain from this Model.

removeChain(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Model

Remove the nth Chain from the Model.

removeChild(GlRenderable) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.TransformGroupRenderable

xxx.

removeChildren() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.TransformGroupRenderable

removeCloseListener(Entry) - Method in class Viewer

Called by the structure or sequence viewer when an entry is added or removed internally, without clicking the close menu items

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

Updates the close menu in response to programmatically closed or created entries

removeCloseMenuItem(FileCloseListener) - Method in class Viewer

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

removeData(String) - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataSet

Removes a DataBlock from this set based on the id of the entry it represents.

removeData(DataBlock) - Method in class edu.sdsc.sirius.dialogs.TableImpl.DataSet

Removes a DataBlock from this set

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

removeEntry(Entry) - Method in class edu.sdsc.mbt.viewables.StructureDocument

Remove an Entry from this StructureDocument.

removeEntry(String) - Method in class edu.sdsc.mbt.viewables.StructureDocument

Remove an Entry from this StructureDocument.

removeEntry(Entry) - Method in class edu.sdsc.sirius.dialogs.DataListerDialog

removeEntry(Entry) - Method in class edu.sdsc.sirius.dialogs.DataWBListerDialog

removeEntry(Entry) - Method in interface edu.sdsc.sirius.dialogs.ListerDialog

removeEntryByName(String) - Method in class edu.sdsc.mbt.viewables.StructureDocument

removeEntryLoader(String) - Static method in class edu.sdsc.sirius.io.EntryFactory

Remove (un-register) an EntryLoader object by its name thus preventing the EntryFactory class from loadng data with it.

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

removeHBond(HydrogenBondComponent, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

removeLabel(LabelComponent, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

removeLabel(ResidueLabelComponent, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

removeLayoutComponent(Component) - Method in class edu.sdsc.sirius.util.DialogLayout

removeLayoutComponent(Component) - Method in class edu.sdsc.sirius.util.ExtensionLayout

removeModel(Model) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Pdb

Remove the given Model from the Pdb.

removeModel(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Pdb

Remove the nth Model from the Pdb.

removeMonitor(MonitorComponent, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

removeMonitors(Structure, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

Remove all monitors for a specific structure.

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

removeMoveEventListener(MoveEventListener) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

Remove a pick event listener.

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

removePickEventListener(GvPickEventListener) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

Remove a pick event listener.

removeRamachandranDialog(Viewer) - Method in class Viewer

removeRamachandranDialog(Structure) - Method in class Viewer

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

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

removeRelation(String) - Static method in class edu.sdsc.mbt.StructureComponentRegistry

Un-register an existing StructureComponent relation.

removeRenderable(Renderable) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

Remove a renderable object from the scene.

removeResidue(int) - Method in class edu.sdsc.mbt.Chain

Remove the specified Residue record from this Chain.

removeResidue(Residue) - Method in class edu.sdsc.mbt.Chain

removeResidue(Residue) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Chain

Remove the given Residue from the Chain.

removeResidue(int) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.Chain

Remove the nth Residue Residue from the Chain.

removeRibbon(Chain, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

removeRibbonDiameter(Chain) - Method in class edu.sdsc.mbt.viewables.StructureStyles

removeRibbonQuality(Chain) - Method in class edu.sdsc.mbt.viewables.StructureStyles

removeRibbonType(Chain) - Method in class edu.sdsc.mbt.viewables.StructureStyles

removeSelection() - Method in class edu.sdsc.sirius.dialogs.DataListerDialog

removeSelection() - Method in class edu.sdsc.sirius.dialogs.DataWBListerDialog

removeSequence(Sequence) - Method in class edu.sdsc.sirius.io.SequenceEntry

removeSequence(Sequence) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

removeSequenceStylesEventListener(SequenceStylesEventListener) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles

removeServicePanel(FragmentGroupPanel) - Static method in class edu.sdsc.sirius.builder.FragmentRegistry

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

Remove a StatusListener object in order to stop recieving StatusEvent messages.

removeStructureComponentEventListener(StructureComponentEventListener) - Method in class edu.sdsc.mbt.viewables.StructureStyles

removeStructureComponentEventListener(StructureComponentEventListener) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles

removeStructureStylesEventListener(StructureStylesEventListener) - Method in class edu.sdsc.mbt.viewables.StructureStyles

Please complete the missing tags for main

removeType(String) - Static method in class edu.sdsc.mbt.StructureComponentRegistry

Un-register an existing StructureComponent type.

removeViewer(Viewer) - Method in class edu.sdsc.mbt.viewables.StructureDocument

Remove a Viewer from the list of viewers.

removeWaitScreen() - Method in class Viewer

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

Removes wait screen.

renameEntry(Entry, String) - Method in class Viewer

renameEntry(Entry, String) - Method in class edu.sdsc.mbt.viewables.StructureDocument

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

Triggers renaming of the specified Entry

renameSequence(Sequence, String) - Method in class edu.sdsc.mbt.viewables.StructureDocument

This method is called when individual sequences from composite entries are renamed in the sequence viewer

renameSequence(Sequence, String) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

This method rename the specified sequence with the provided name.

renameSequence(String) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles

renameStructure(Structure, String) - Method in class edu.sdsc.sirius.viewers.StructureViewer

render - Variable in class edu.sdsc.mbt.Atom

Inidcates whether this atom is ionized, hence which radius should be used for rendering

render - Variable in class edu.sdsc.mbt.Bond

render - Variable in class edu.sdsc.mbt.Chain

render - Variable in class edu.sdsc.mbt.Residue

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

renderBondOrder - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache

renderRequested - Static variable in class edu.sdsc.sirius.ray.RayTraceUtil

renderable - Variable in class edu.sdsc.mbt.viewers.GLViewerImpl.GvPickEvent

renderables - Variable in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

renderingAction() - Method in class Viewer

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

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

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

Numeric values that reflect quality of rendering.

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

repaintTree() - Method in class edu.sdsc.sirius.monitors.MonitorDialog

replaceResidue(Sequence, int, String) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

This method is called internally by SequencePanel.

replaceResidue(Sequence, Cell, String) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel

replaceResidue(Sequence, int, String) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel

replaceResidue(Cell, String) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStyles

replaceResidue(Residue, String) - Method in class edu.sdsc.sirius.viewers.StructureViewer

replaceStructureComponent(StructureComponent, String) - Method in class edu.sdsc.mbt.viewables.StructureStyles

requestImage(int, int, int, int, int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

reset(int, int, Object) - Method in class edu.sdsc.mbt.util.RangeMap

Reset the entire RangeMap by setting new max, min and default values, and by clearing all existing ranges.

resetColor() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry

Resets the whole fragment to the original color map.

resetCoordinates() - Method in class edu.sdsc.mbt.StericBumpComponent

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

resetFog(double[], double) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

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

Get the current stereo display state (ie: is it enabled or disabled?)

resetGeometryColor() - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry

Resets the vertex color in the geometry shape of this SsGeometry object.

resetPanel() - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceScalePanel

resetPopup() - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceScalePanel

Returns the panel popup menu to the defaults.

resetRibbonColor(int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry

Resets the color of the portion of SS sorounding residue at index.

resetStylesDefaults() - Static method in class edu.sdsc.mbt.viewables.StylesPreferences

This method uses hard-coded defaults to restore the configuration of the application.

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

Reset the camera view to point at the origin, with an eye position at Z = -1, with a Y-up orientation.

resetView(double[], double, boolean) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

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

Reset the viewpoint so that all geometry can be seen.

resetViewOnLoad - Static variable in class Viewer

reshape(GLAutoDrawable, int, int, int, int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

GLEventListener interface - reshape method:

residue - Variable in class edu.sdsc.mbt.Atom

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

residue - Variable in class edu.sdsc.sirius.io.SideChain

residue - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.Cell

residueCode - Variable in class edu.sdsc.sirius.io.SideChain

residueId - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.Cell

residue_id - Variable in class edu.sdsc.mbt.Atom

Residue/Sequence ID.

resizePanel(Dimension) - Method in class edu.sdsc.sirius.dialogs.TableImpl.BlastResultPanel

Handles repainting of the table panel in response to resizing of the container frame.

resizePanel(Dimension) - Method in class edu.sdsc.sirius.dialogs.TableImpl.PubmedResultPanel

Handles repainting of the table panel in response to resizing of the container frame.

resizePanel(Dimension) - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel

Handles repainting of the table panel in response to resizing of the container frame.

resizePanel(Dimension) - Method in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel

Handles repainting of the table panel in response to resizing of the container frame.

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

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

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

restoreState(StateObject, Manager, StructureViewer, SequenceViewer) - Static method in class edu.sdsc.sirius.export.StateHandler

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

ribbon - Variable in class edu.sdsc.mbt.Residue

ribbonColor - Variable in class edu.sdsc.sirius.dialogs.RibbonColorEvent

The actual value of the chosen color.

ribbonDiameter - Variable in class edu.sdsc.mbt.viewables.StructureStyles

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

ribbonDiameter - Variable in class edu.sdsc.sirius.dialogs.RibbonEvent

ribbonDisplay - Static variable in class edu.sdsc.sirius.dialogs.ComponentRibbonDialog

ribbonDisplay - Static variable in class edu.sdsc.sirius.dialogs.RayTracerDialog

ribbonDisplay - Static variable in class edu.sdsc.sirius.dialogs.RibbonDialog

ribbonDisplayAction() - Method in class Viewer

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

ribbonQuality - Variable in class edu.sdsc.sirius.dialogs.PreferencesCache

ribbonQuality - Variable in class edu.sdsc.sirius.dialogs.RibbonEvent

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

ribbonType - Variable in class edu.sdsc.sirius.dialogs.RibbonEvent

right - Variable in class edu.sdsc.sirius.util.Location

rightPadded(String, int, String) - Static method in class edu.sdsc.sirius.util.StringUtils

Pads a String on the right.

rightPadded(String, int, char) - Static method in class edu.sdsc.sirius.util.StringUtils

Pads a String on the right.

righthand - Variable in class edu.sdsc.mbt.Helix

TRUE=righthanded, FALSE=lefthanded

rmsd(Vector, Vector) - Static method in class edu.sdsc.sirius.util.StructureMath

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

Letter codes of the 4 nitrogenous bases for RNA.

rotate(double[], int, int) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.GlGeometryViewer

this method simulates rotation of the loaded structure(s) by transforming the camera position and direction positive values of rotation angle correspond to counterclockwise rotation when looking down the positive axis

rotate(float, Vec3f, Vec3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection

rotate(float, Vec3f) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.IntrinsicCrossSection

rotateCoordinates(double[], double[], double, Vector) - Static method in class edu.sdsc.sirius.util.StructureMath

rotateStructure(double[], Atom, double, Vector) - Static method in class edu.sdsc.sirius.util.StructureMath

Note that the argument is in degrees, and they get converted into radians

rotationCenter - Variable in class edu.sdsc.sirius.export.ViewerParameters

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

Convert the angle-axis {angle,x,y,z} rotation vector to a 16-element rotation matrix.