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

C

C - Static variable in class edu.sdsc.mbt.util.Element

CANCEL_OPTION - Static variable in class edu.sdsc.sirius.dialogs.JFontChooser

Value returned by showDialog upon a cancel.

CAlphaAtomFilter - class edu.sdsc.mbt.filters.CAlphaAtomFilter.

Defines an AtomFilter sub-class which accepts only C-Alpha Atom objects.

CAlphaAtomFilter() - Constructor for class edu.sdsc.mbt.filters.CAlphaAtomFilter

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

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

CHAIN_COLOR - Static variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.StyleManager

CHANGE_ADDED - Static variable in class edu.sdsc.mbt.viewables.StructureDocumentEvent

Objects were added.

CHANGE_RELOAD - Static variable in class edu.sdsc.mbt.viewables.StructureDocumentEvent

CHANGE_REMOVED - Static variable in class edu.sdsc.mbt.viewables.StructureDocumentEvent

Objects were removed.

CHANGE_RENAMED - Static variable in class edu.sdsc.mbt.viewables.StructureDocumentEvent

CLOSE_ENTRY - Static variable in class edu.sdsc.sirius.dialogs.EntryListerDialog

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

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

COLOR_BY_CHAIN - Static variable in class edu.sdsc.sirius.dialogs.ColorDialog

COLOR_BY_CHAIN - Static variable in class edu.sdsc.sirius.dialogs.ComponentColorDialog

COLOR_BY_CHAIN - Static variable in class edu.sdsc.sirius.dialogs.RibbonColorDialog

COLOR_BY_CHARGE - Static variable in class edu.sdsc.sirius.dialogs.ColorDialog

COLOR_BY_CHARGE - Static variable in class edu.sdsc.sirius.dialogs.ComponentColorDialog

COLOR_BY_ELEMENT - Static variable in class edu.sdsc.sirius.dialogs.ColorDialog

COLOR_BY_ELEMENT - Static variable in class edu.sdsc.sirius.dialogs.ComponentColorDialog

COLOR_BY_ELEMENT - Static variable in class edu.sdsc.sirius.dialogs.RibbonColorDialog

COLOR_CUSTOM - Static variable in class edu.sdsc.sirius.dialogs.ColorDialog

COLOR_CUSTOM - Static variable in class edu.sdsc.sirius.dialogs.ComponentColorDialog

COLOR_CUSTOM - Static variable in class edu.sdsc.sirius.dialogs.RibbonColorDialog

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

COMPOUND_AMINO_ACID - Static variable in class edu.sdsc.mbt.Residue

Residue compound classification is an amino acid.

COMPOUND_CLASSIFICATIONS - Static variable in class edu.sdsc.mbt.Residue

COMPOUND_DELETION - Static variable in class edu.sdsc.mbt.Residue

Residue compound classification as a deletion.

COMPOUND_LIGAND - Static variable in class edu.sdsc.mbt.Residue

Residue compound classification is a ligand.

COMPOUND_NUCLEIC_ACID - Static variable in class edu.sdsc.mbt.Residue

Residue compound is a nucleic acid.

CONSERVATION_COLOR - Static variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.StyleManager

COSINE - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.Interpolator

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

CUBIC - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.Interpolator

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

Ca - Static variable in class edu.sdsc.mbt.util.Element

Cd - Static variable in class edu.sdsc.mbt.util.Element

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

This class is intended to store information and coloring and selection state of a residue cell in the SequenceViewer.

Cell(Sequence, int, String, Residue, int) - Constructor for class edu.sdsc.sirius.viewers.SequenceViewerImpl.Cell

Cell(Sequence, int, String, Residue) - Constructor for class edu.sdsc.sirius.viewers.SequenceViewerImpl.Cell

Cell(int, String, Residue) - Constructor for class edu.sdsc.sirius.viewers.SequenceViewerImpl.Cell

Cell(Sequence, int, String) - Constructor for class edu.sdsc.sirius.viewers.SequenceViewerImpl.Cell

CenterDialog - class edu.sdsc.sirius.dialogs.CenterDialog.

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

Chain - class edu.sdsc.mbt.Chain.

Implements a StructureComponent container for chain information.

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

Construct a Chain.

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

Stores the Residues belonging to a particular polypeptide chain.

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

ChainColor - interface edu.sdsc.mbt.viewables.ChainColor.

This interface defines how all ChainColor implementation classes should generate a color for a given Chain.

ChainColorById - class edu.sdsc.mbt.viewables.ChainColorById.

This class implements the ChainColor interface by applying a color to the given Chain by using its chainId.

ChainColorRegistry - class edu.sdsc.mbt.viewables.ChainColorRegistry.

A class used to register ChainColor implementation objects.

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

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

ChainGeometry.java
Please complete these missing tags

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

Construct a new ChainGeometry object.

ChargeDialog - class edu.sdsc.sirius.dialogs.ChargeDialog.

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

Cl - Static variable in class edu.sdsc.mbt.util.Element

CodonInfo - class edu.sdsc.mbt.util.CodonInfo.

Provides static information about mRNA Codons such nucleic acid tuple / amino acid code mapping.

CodonInfo() - Constructor for class edu.sdsc.mbt.util.CodonInfo

Coil - class edu.sdsc.mbt.Coil.

Implements a StructureComponent container for Coil conformation (secondary structure) data.

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

Creates a new Coil object.

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

CoilGeometry is a SsGeometry container that, primarily, manages the geometry of a random coil.

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

Constructs a CoilGeometry objects with default values for the number of facets, segments, and cross section style.

Color3f - class edu.sdsc.mbt.viewers.GLViewerImpl.util.Color3f.

Color3f() - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.util.Color3f

Color3f(Color) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.util.Color3f

Color3f(Color3f) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.util.Color3f

Color3f(float, float, float) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.util.Color3f

ColorDialog - class edu.sdsc.sirius.dialogs.ColorDialog.

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

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

Constructor that builds the dialog.

ColorEvent - class edu.sdsc.sirius.dialogs.ColorEvent.

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

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

The constructor initialized with the parent dialog.

ColorManager - class edu.sdsc.sirius.rasmol.ColorManager.

ColorManager() - Constructor for class edu.sdsc.sirius.rasmol.ColorManager

ColorMap - interface edu.sdsc.mbt.viewables.ColorMap.

This interface defines how all ColorMap implementation classes should generate a color for a given normalized float (0.0-1.0).

ColorScheme - interface edu.sdsc.sirius.rasmol.ColorScheme.

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

This class extends JTable and enables custom cell coloring.

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

Constructor that initializes the table.

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

Container class storing column attributes.

ColumnData(String, String, int, int) - Constructor for class edu.sdsc.sirius.dialogs.TableImpl.ColumnData

Constructor.

CommandPanel - class edu.sdsc.sirius.rasmol.CommandPanel.

CommandPanel(JFrame, Manager) - Constructor for class edu.sdsc.sirius.rasmol.CommandPanel

This panel contains command-line and text panel for entering and running scripting commands that control appearance of the loaded structures

ComponentColorDialog - class edu.sdsc.sirius.dialogs.ComponentColorDialog.

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

ComponentColorDialog(JFrame, Manager, StructureViewer, String, StructureComponent, boolean) - Constructor for class edu.sdsc.sirius.dialogs.ComponentColorDialog

Constructor that builds the dialog.

ComponentRenderingDialog - class edu.sdsc.sirius.dialogs.ComponentRenderingDialog.

ComponentRenderingDialog(JFrame, Manager, StructureViewer, String, StructureComponent) - Constructor for class edu.sdsc.sirius.dialogs.ComponentRenderingDialog

ComponentRibbonDialog - class edu.sdsc.sirius.dialogs.ComponentRibbonDialog.

ComponentRibbonDialog(JFrame, Manager, StructureViewer, String, Chain, boolean) - Constructor for class edu.sdsc.sirius.dialogs.ComponentRibbonDialog

Conformation - class edu.sdsc.mbt.Conformation.

Implements a an abstract StructureComponent container for conformation (secondary structure) data.

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

ConservationColorMap - class edu.sdsc.mbt.viewables.ConservationColorMap.

This class implements the ColorMap interface by generating a linear interpolated color from a list of user-defined color knots.

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

Construct an empty InterpolatedColorMap.

Coordinate - class edu.sdsc.mbt.util.Coordinate.

Coordinate(float, float, float) - Constructor for class edu.sdsc.mbt.util.Coordinate

Coordinate(String, String, String) - Constructor for class edu.sdsc.mbt.util.Coordinate

CpkColorScheme - class edu.sdsc.sirius.rasmol.CpkColorScheme.

CpkColorScheme() - Constructor for class edu.sdsc.sirius.rasmol.CpkColorScheme

CreateBondDialog - class edu.sdsc.sirius.dialogs.CreateBondDialog.

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

CreateSequenceDialog - class edu.sdsc.sirius.dialogs.CreateSequenceDialog.

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

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

CrossSectionBuilder class: produces closed polygons based on the description in a given CrossSectionStyle.

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

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

CrossSectionStyle class encapsulates descriptors of the cross section of the ribon used for building SS.

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

Creates a CrossSectionStyle with nothing set initially

CrossSectionStyle(boolean, int, float[]) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle

Creates a minimal-defined CrossSectionStyle from given polygon type (closed of open), number of vertices and diameter

CrossSectionStyle(int, float[]) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.CrossSectionStyle

Creates a CrossSectionStyle from a predefined list and with a given diameter set.

Cu - Static variable in class edu.sdsc.mbt.util.Element

CustomFragmentPanel - class edu.sdsc.sirius.builder.CustomFragmentPanel.

CustomFragmentPanel() - Constructor for class edu.sdsc.sirius.builder.CustomFragmentPanel

cache - Static variable in class edu.sdsc.mbt.viewables.AtomColorFactory

cache - Static variable in class edu.sdsc.mbt.viewables.ResidueColorFactory

Hashes that keep track of produced objects and are cleared when the factory is reset

cache - Static variable in class edu.sdsc.mbt.viewables.RibbonColorFactory

Hashes that keep track of produced objects and are cleared when the factory is reset

cache2 - Static variable in class edu.sdsc.mbt.viewables.ResidueColorFactory

cache2 - Static variable in class edu.sdsc.mbt.viewables.RibbonColorFactory

cache3 - Static variable in class edu.sdsc.mbt.viewables.ResidueColorFactory

cache3 - Static variable in class edu.sdsc.mbt.viewables.RibbonColorFactory

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

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

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

canLoad(String) - Method in class edu.sdsc.sirius.io.AlnEntryLoader

Checks whether the file can be used to load entries.

canLoad(File) - Method in class edu.sdsc.sirius.io.AlnEntryLoader

Checks whether an EntrySet can be loaded from the given File.

canLoad(URL) - Method in class edu.sdsc.sirius.io.AlnEntryLoader

Checks whether an EntrySet can be loaded from the given URL.

canLoad(String) - Method in interface edu.sdsc.sirius.io.EntryLoader

Returns true if the loader is capable of loading the structure, or false otherwise.

canLoad(String) - Method in class edu.sdsc.sirius.io.FastaEntryLoader

Returns true if the loader is capable of loading the entry, or false otherwise.

canLoad(File) - Method in class edu.sdsc.sirius.io.FastaEntryLoader

Returns true if the Entry can be read from the given File object.

canLoad(URL) - Method in class edu.sdsc.sirius.io.FastaEntryLoader

Returns true if the Entry can be read from the given URL object.

canLoad(File) - Method in interface edu.sdsc.sirius.io.FileEntryLoader

Returns true if the loader is capable of loading the entry, or false otherwise.

canLoad(URL) - Method in interface edu.sdsc.sirius.io.FileEntryLoader

Returns true if the loader is capable of loading the entry, or false otherwise.

canLoad(String) - Method in class edu.sdsc.sirius.io.Mol2EntryLoader

Returns true if the loader is capable of loading the structure, or false otherwise.

canLoad(File) - Method in class edu.sdsc.sirius.io.Mol2EntryLoader

Returns true if the Entry can be read from the given File object.

canLoad(URL) - Method in class edu.sdsc.sirius.io.Mol2EntryLoader

Returns true if the Entry can be read from the given URL object.

canLoad(String) - Method in class edu.sdsc.sirius.io.MsfEntryLoader

Checks whether the file can be used to load entries.

canLoad(File) - Method in class edu.sdsc.sirius.io.MsfEntryLoader

Checks whether an EntrySet can be loaded from the given File.

canLoad(URL) - Method in class edu.sdsc.sirius.io.MsfEntryLoader

Checks whether an EntrySet can be loaded from the given URL.

canLoad(String) - Method in class edu.sdsc.sirius.io.PdbEntryLoader

Returns true if the loader is capable of loading the structure, or false otherwise.

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

Returns true if the Entry can be read from the given File object.

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

Returns true if the Entry can be read from the given URL object.

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

canLoad(URL) - Method in class edu.sdsc.sirius.io.SDFEntryLoader

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

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

cancelSelection() - Method in class edu.sdsc.sirius.dialogs.JFontChooser

This method is called when the user presses the cancel button.

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

cell - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceStylesEvent

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

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

cellHeight - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.DisplayParameters

cellMargin - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.DisplayParameters

cellWidth - Variable in class edu.sdsc.sirius.viewers.SequenceViewerImpl.DisplayParameters

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

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

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

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

Chain/Asymetric unit ID.

change - Variable in class edu.sdsc.mbt.viewables.StructureDocumentEvent

The kind of change that occured in the StructureDocument.

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

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

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

chargesUserAssigned - Variable in class edu.sdsc.mbt.StructureMap

check - Variable in class edu.sdsc.sirius.dialogs.StructureEvent

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

This method checks whether the atom should be represented as a dummy

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

This method is a Residue-level utility optimized to run a limited check within the residue affected by a visibility event

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

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

This method searches through selected atoms and determines whether any atom on the other end of any of the bonds is visible with invisible bonds or a dummy is no longer needed This way the search is only within the selected area, rather than the entire structure

checkHydrogens(Structure, StructureViewer, float) - Static method in class edu.sdsc.sirius.util.StructureMath

This method runs through the structure and adds hydrogens where necessary, based on tabulated element valencies.

checkHydrogens(Atom, StructureViewer, float, boolean) - Static method in class edu.sdsc.sirius.util.StructureMath

clear(Structure) - Method in class edu.sdsc.sirius.rasmol.RasmolReader

clear() - Method in class edu.sdsc.sirius.rasmol.RasmolReader

clear() - Method in class edu.sdsc.sirius.viewers.StatusPanel

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

Clear the entire RangeMap by setting everything to the default value.

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

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

clearCellSelection(boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

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

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

clearData() - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanelFrame

Clear data from the display.

clearDisplay(boolean) - Method in class edu.sdsc.sirius.viewers.TreeViewer.InfoViewer

clearEntries(boolean) - Method in class Viewer

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

Removes all entries from the application.

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

Clear the specified range by setting it to the default value.

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

Remove all renderable objects from the scene.

clearResidueColors() - Static method in class edu.sdsc.mbt.viewables.ResidueColorFactory

Clears all residue color hashes.

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

clearRibbonColors() - Static method in class edu.sdsc.mbt.viewables.RibbonColorFactory

Clears all residue color hashes.

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

Removes selection of the rows.

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

Removes selection of the rows.

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

Removes selection of the rows.

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

Removes selection of the rows.

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

clearSelection() - Method in class edu.sdsc.sirius.monitors.MonitorPanel

clearSelection() - Method in class edu.sdsc.sirius.rasmol.RasmolReader

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

Deselects the tree.

clearStructureEntries() - Method in class Viewer

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

Clear only the entries that have structure representation.

clone() - Method in class edu.sdsc.mbt.Atom

Clone this object.

clone() - Method in class edu.sdsc.mbt.Bond

Clone this object.

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

Clone this object.

clone() - Method in class edu.sdsc.mbt.Coil

Clone this object.

clone() - Method in class edu.sdsc.mbt.Conformation

Clone this object.

clone() - Method in class edu.sdsc.mbt.Fragment

Clone this object.

clone() - Method in class edu.sdsc.mbt.Helix

Clone this object.

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

Clone this object.

clone() - Method in class edu.sdsc.mbt.Strand

Clone this object.

clone() - Method in class edu.sdsc.mbt.StructureComponent

Clone this object.

clone() - Method in class edu.sdsc.mbt.StructureInfo

Clone this object.

clone() - Method in class edu.sdsc.mbt.Symmetry

Clone this object.

clone() - Method in class edu.sdsc.mbt.Turn

Clone this object.

closeBuilderDialog() - Method in class Viewer

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

Closes the builder dialog

closeCommandPanel() - Method in class Viewer

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

closeImagePreviewPanel() - Method in class Viewer

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

closeMonitorDialog() - Method in class Viewer

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

Closes the dialog that manages display markers

closeSequencePanel() - Method in class Viewer

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

Closes the panel that displays sequence data

closeStructureBrowserPanel() - Method in class Viewer

closestAtom(StructureComponent, double[]) - Static method in class edu.sdsc.mbt.util.PickUtils

Find the atom object within the specified structure component which is closest to the given coordinate.

code - Variable in class edu.sdsc.sirius.builder.FragmentRecord

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

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

color - Variable in class edu.sdsc.mbt.HydrogenBondComponent

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

color - Variable in class edu.sdsc.mbt.MonitorComponent

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

color - Variable in class edu.sdsc.mbt.StericBumpComponent

color - Variable in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Color3f

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

colorAction() - Method in class Viewer

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

colorCache - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry

colorHidden - Variable in class edu.sdsc.sirius.viewers.StructureViewer

Flag that indicates whether hidden structure components should be included in coloring

colorMap - Static variable in class edu.sdsc.sirius.rasmol.RasmolReader

colorReference - Static variable in class edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry

This hash is used to look up float[] values by a reference to a Color object

colorRibbon(Chain, int, Color) - Method in class edu.sdsc.sirius.viewers.StructureViewer

colorType - Static variable in class edu.sdsc.sirius.dialogs.ColorDialog

Static variable that determines which type of coloring coloring is used.

colorType - Variable in class edu.sdsc.sirius.dialogs.ColorEvent

Variable that denotes the type of coloring: by element, by specified color, etc.

colorType - Static variable in class edu.sdsc.sirius.dialogs.ComponentColorDialog

Static variable that determines which type of coloring coloring is used.

colorType - Static variable in class edu.sdsc.sirius.dialogs.RibbonColorDialog

Static variable that determines which type of coloring coloring is used.

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

Variable that denotes the type of coloring: by cartoon setting, by specified color, etc.

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

columnAlign - Variable in class edu.sdsc.sirius.dialogs.TableImpl.BlastResultPanel

columnAlign - Variable in class edu.sdsc.sirius.dialogs.TableImpl.PubmedResultPanel

columnAlign - Variable in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel

columnAlign - Variable in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel

columnWidths - Variable in class edu.sdsc.sirius.dialogs.TableImpl.BlastResultPanel

columnWidths - Variable in class edu.sdsc.sirius.dialogs.TableImpl.PubmedResultPanel

columnWidths - Variable in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel

columnWidths - Variable in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel

com.jgoodies.looks.demo - package com.jgoodies.looks.demo

com.jgoodies.uif_lite.component - package com.jgoodies.uif_lite.component

com.jgoodies.uif_lite.panel - package com.jgoodies.uif_lite.panel

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

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

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

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

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

Variable that denotes whether the ribbon is colored with the structure

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

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

compare(Object, Object) - Method in class edu.sdsc.sirius.viewers.SequenceComparator

compareTo(Object) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.Cell

componentId - Variable in class edu.sdsc.sirius.dialogs.ColorEvent

String representation of the component picked in the StructureViewer.

componentId - Variable in class edu.sdsc.sirius.dialogs.HydrogenEvent

componentId - Variable in class edu.sdsc.sirius.dialogs.LabelEvent

componentId - Variable in class edu.sdsc.sirius.dialogs.RenderingEvent

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

String representation of the component picked in the StructureViewer.

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

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

componentId - Variable in class edu.sdsc.sirius.dialogs.VisibilityEvent

componentId - Variable in class edu.sdsc.sirius.dialogs.WeightEvent

componentToLabel(StructureComponent) - Static method in class edu.sdsc.sirius.util.DataService

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

Compound 3-letter code.

compute(int, int, int, int, double[]) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.VirtualSphere2

Determine the axis and angle (in radians) of rotation from two screen coordinates and relative to the virtual sphere cue circle.

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

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

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

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

This method calculates phi-psi angles for the protein structure and saves the values in the hashmaps If the structure contains no amino acids, false is returned.

computePhiPsi(Residue, HashMap) - Method in class edu.sdsc.mbt.StructureMap

computeResidueMax(boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewer

connect(Structure, int) - Method in class edu.sdsc.sirius.viewers.RamachandranViewer

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

Tests for containment.

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

Tests whether the Residue contains a particular Atom.

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

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

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

convertMol2ToString(Structure, boolean, StructureViewer, HashMap) - Static method in class edu.sdsc.sirius.util.IOHandler

Flag fragment denotes whether this string will be used to write out a custom fragment.

convertStructureToPdb(Structure, Manager) - Static method in class edu.sdsc.sirius.util.IOHandler

convertStructureToSDF(Structure, String, HashMap) - Static method in class edu.sdsc.sirius.util.IOHandler

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

The x,y,z coordinate in angstroms.

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

coordinates - Variable in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Quat4f

coordinates - Variable in class edu.sdsc.mbt.viewers.GLViewerImpl.util.Vector3f

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

copy(StructureComponent) - Method in class edu.sdsc.mbt.Atom

Copy all of the field values from the parameter object into "this".

copy(StructureComponent) - Method in class edu.sdsc.mbt.Bond

Copy all of the field values from the parameter object into "this".

copy(StructureComponent) - Method in class edu.sdsc.mbt.Chain

Copy all of the field values from the parameter object into "this".

copy(StructureComponent) - Method in class edu.sdsc.mbt.Coil

Copy all of the field values from the parameter object into "this".

copy(StructureComponent) - Method in class edu.sdsc.mbt.Conformation

Copy all of the field values from the parameter object into "this".

copy(StructureComponent) - Method in class edu.sdsc.mbt.Fragment

Copy all of the field values from the parameter object into "this".

copy(StructureComponent) - Method in class edu.sdsc.mbt.Helix

Copy all of the field values from the parameter object into "this".

copy(StructureComponent) - Method in class edu.sdsc.mbt.Residue

Copy all of the field values from the parameter object into "this".

copy(StructureComponent) - Method in class edu.sdsc.mbt.Strand

Copy all of the field values from the parameter object into "this".

copy(StructureComponent) - Method in class edu.sdsc.mbt.StructureComponent

Copy all of the field values from the parameter object into "this".

copy(StructureComponent) - Method in class edu.sdsc.mbt.StructureInfo

Copy all of the field values from the parameter object into "this".

copy(StructureComponent) - Method in class edu.sdsc.mbt.Symmetry

Copy all of the field values from the parameter object into "this".

copy(StructureComponent) - Method in class edu.sdsc.mbt.Turn

Copy all of the field values from the parameter object into "this".

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

Copy a file.

copy(InputStream, OutputStream, long) - Method in class edu.sdsc.sirius.io.FileTransfer

Copy an InputStream to an OutputStream.

copy(InputStream, OutputStream) - Method in class edu.sdsc.sirius.io.FileTransfer

Copy an InputStream to an OutputStream, until EOF.

copy() - Method in class edu.sdsc.sirius.util.VectorSet

count - Variable in class edu.sdsc.mbt.Symmetry

The count of the number of symmetry copies.

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

Return the number of registered AtomColor impelementations.

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

Return the number of registered AtomLabel impelementations.

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

Return the number of registered AtomRadius impelementations.

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

Return the number of registered BondColor impelementations.

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

Return the number of registered BondForm impelementations.

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

Return the number of registered BondLabel impelementations.

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

Return the number of registered BondRadius impelementations.

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

Return the number of registered ChainColor impelementations.

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

Return the number of registered FragmentColor impelementations.

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

Return the number of registered FragmentForm impelementations.

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

Return the number of registered ResidueColor impelementations.

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

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

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

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

create() - Static method in class edu.sdsc.mbt.viewables.AtomColorByCharge

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.AtomColorByElement

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.AtomColorUniform

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.AtomLabelByAtomCompound

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.AtomLabelByAtomElement

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.AtomLabelByAtomName

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.AtomLabelByChainId

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.AtomLabelNone

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.AtomRadiusByConstant

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.AtomRadiusByCpk

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.AtomRadiusByScaledCpk

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.BondColorByAtomColor

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.BondColorByElement

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.BondFormOrder

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.BondFormSimple

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.BondFormSplit

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.BondLabelByDistance

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.BondLabelNone

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.BondRadiusAsStick

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.BondRadiusAsWire

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.BondRadiusByAtomRadius

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.BondRadiusByScaledAtomRadius

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.ChainColorById

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.FragmentColorByType

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.FragmentFormCartoon

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.FragmentFormCylinder

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.FragmentFormLadder

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.FragmentFormRibbon

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.FragmentFormTube

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.FragmentFormWireframe

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.ResidueColorByCharge

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.ResidueColorByElement

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.ResidueColorByHydrophobicity

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.ResidueColorByType

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.ResidueColorDefault

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.ResidueColorScaled

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.ResidueColorUniform

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.RibbonColorDefault

Return the singleton instance of this class.

create() - Static method in class edu.sdsc.mbt.viewables.RibbonColorUniform

Return the singleton instance of this class.

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

createDefault() - Static method in class com.jgoodies.looks.demo.Settings

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

createImagePopup() - Method in class edu.sdsc.sirius.dialogs.DistributionViewer

createLabel(Atom, int, int, String, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

createLabel(Atom, int, int, String, boolean, float[], boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

createLabel(Residue, int, int, String, boolean, float[], boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

createMonitor(Atom, Atom, String, float[], boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

Creates a distance monitor

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

createPrintableImage(int, int, int, int) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceScalePanel

This method creates a BufferedImage of the requested part of the scale that is used for printing.

createRibbon(Chain, int, float, float, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

createRibbonInSelection(int, float, float, boolean) - Method in class edu.sdsc.sirius.viewers.StructureViewer

createSet(String, Vector) - Method in class edu.sdsc.sirius.viewers.StructureViewer

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

createStrippedScrollPane(Component) - Static method in class com.jgoodies.uif_lite.component.Factory

Creates and answers a JScrollPane that has an empty border.

createStrippedSplitPane(int, Component, Component, double) - Static method in class com.jgoodies.uif_lite.component.Factory

Creates and returns a JSplitPane that has empty borders.

createStrippedSplitPane(int, Component, Component) - Static method in class com.jgoodies.uif_lite.component.UIFSplitPane

Constructs a UIFSplitPane, i.e.

createStructureComponentIterator(StructureComponentFilter) - Method in class edu.sdsc.mbt.Structure

Given a StructureComponentFilter, create and return an iterator which will selectively return a subset of structure components.

createTablePopup() - Method in class edu.sdsc.sirius.dialogs.DistributionViewer

createTextSample(Font) - Method in class edu.sdsc.sirius.dialogs.PreferencesDialog

createToolBarButton(Action) - Static method in class com.jgoodies.uif_lite.component.Factory

Creates and answers an AbstractButton configured for use in a JToolBar.

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

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

Compute the vector cross product between v1 and v2 storing the output in result.

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

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

currentIndices - Variable in class edu.sdsc.sirius.dialogs.TableImpl.BlastResultPanel

currentIndices - Variable in class edu.sdsc.sirius.dialogs.TableImpl.PubmedResultPanel

currentIndices - Variable in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel

currentIndices - Variable in class edu.sdsc.sirius.dialogs.TableImpl.TableViewPanel

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

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