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

E

ERROR_OPTION - Static variable in class edu.sdsc.sirius.dialogs.JFontChooser
Value returned by showDialog upon an error.
EXTENT_GLOBAL - Static variable in class edu.sdsc.mbt.StructureComponentEvent
 
EXTENT_LOCAL - Static variable in class edu.sdsc.mbt.StructureComponentEvent
 
EXTENT_RECURSIVE - Static variable in class edu.sdsc.mbt.StructureComponentEvent
 
EXTRACT - Static variable in class edu.sdsc.sirius.dialogs.StructureEditDialog
 
Element - class edu.sdsc.mbt.util.Element.
A container object to hold information about an element from the periodic table.
Element(String, String, int, double, int, String, int, String) - Constructor for class edu.sdsc.mbt.util.Element
Construct an Element object from the given attribute values.
ElementPreferences - class edu.sdsc.mbt.viewables.ElementPreferences.
This class encapsulates element color settings and is used to provide persistence to user settings by saving current colors to filesystem storage and reading them when loading the application and opening the element editing dialog.
ElementPreferences() - Constructor for class edu.sdsc.mbt.viewables.ElementPreferences
 
ElementProperties - class edu.sdsc.mbt.util.ElementProperties.
 
ElementProperties() - Constructor for class edu.sdsc.mbt.util.ElementProperties
 
ElementSelectionDialog - class edu.sdsc.sirius.dialogs.ElementSelectionDialog.
Used in atom replacement dialog to pick the new element
ElementSelectionDialog(JFrame, String, ElementSettable) - Constructor for class edu.sdsc.sirius.dialogs.ElementSelectionDialog
 
ElementSelectionPanel - class edu.sdsc.sirius.dialogs.ElementSelectionPanel.
An example program which exersises the PeriodicTable class.
ElementSelectionPanel(ElementSelectionDialog) - Constructor for class edu.sdsc.sirius.dialogs.ElementSelectionPanel
Construct an instance of this class using the content described by the PeriodicTable and ElementStyles classes.
ElementSelectionPanel.PtButton - class edu.sdsc.sirius.dialogs.ElementSelectionPanel.PtButton.
An inner class which knows how to draw an element tile.
ElementSelectionPanel.PtButton(Element) - Constructor for class edu.sdsc.sirius.dialogs.ElementSelectionPanel.PtButton
 
ElementSelectionPanel.PtListener - class edu.sdsc.sirius.dialogs.ElementSelectionPanel.PtListener.
An inner class which knows how to respond to a click on an element tile.
ElementSelectionPanel.PtListener(Element, ElementSelectionPanel, JButton) - Constructor for class edu.sdsc.sirius.dialogs.ElementSelectionPanel.PtListener
 
ElementSettable - interface edu.sdsc.mbt.util.ElementSettable.
 
ElementStylesDialog - class edu.sdsc.sirius.dialogs.ElementStylesDialog.
 
ElementStylesDialog(JFrame, Manager) - Constructor for class edu.sdsc.sirius.dialogs.ElementStylesDialog
 
ElementStylesEditor - class edu.sdsc.sirius.dialogs.ElementStylesEditor.
An example program which exersises the PeriodicTable class.
ElementStylesEditor() - Constructor for class edu.sdsc.sirius.dialogs.ElementStylesEditor
Construct an instance of this class using the content described by the PeriodicTable and ElementStyles classes.
ElementStylesEditor.PtButton - class edu.sdsc.sirius.dialogs.ElementStylesEditor.PtButton.
An inner class which knows how to draw an element tile.
ElementStylesEditor.PtButton(Element) - Constructor for class edu.sdsc.sirius.dialogs.ElementStylesEditor.PtButton
 
ElementStylesEditor.PtListener - class edu.sdsc.sirius.dialogs.ElementStylesEditor.PtListener.
An inner class which knows how to respond to a click on an element tile.
ElementStylesEditor.PtListener(Element, ElementStylesEditor, JButton) - Constructor for class edu.sdsc.sirius.dialogs.ElementStylesEditor.PtListener
 
Entry - class edu.sdsc.sirius.io.Entry.
 
Entry() - Constructor for class edu.sdsc.sirius.io.Entry
 
EntryFactory - class edu.sdsc.sirius.io.EntryFactory.
Provides a master instantiation factory for Structure objects.
EntryFactory() - Constructor for class edu.sdsc.sirius.io.EntryFactory
 
EntryListerDialog - class edu.sdsc.sirius.dialogs.EntryListerDialog.
This class implements a dialog that displays the currently loaded entries.
EntryListerDialog(JFrame, Manager, boolean, StructureDocument, int) - Constructor for class edu.sdsc.sirius.dialogs.EntryListerDialog
Constructor that creates the dialog.
EntryLoader - interface edu.sdsc.sirius.io.EntryLoader.
Defines the standard interface for classes which know how to load Entry objects.
ExtensionLayout - class edu.sdsc.sirius.util.ExtensionLayout.
 
ExtensionLayout() - Constructor for class edu.sdsc.sirius.util.ExtensionLayout
 
ExtensionLayout(int, int) - Constructor for class edu.sdsc.sirius.util.ExtensionLayout
 
Extrusion - class edu.sdsc.mbt.viewers.GLViewerImpl.Extrusion.
Extrusion is the main building block for ribbon-like secondary structure representations
Extrusion(int, int, int[], AffineCrossSection[], Color[], boolean[], boolean[], int, boolean, boolean) - Constructor for class edu.sdsc.mbt.viewers.GLViewerImpl.Extrusion
 
echofilter - Static variable in class edu.sdsc.sirius.util.BlastSettings
 
editCopy(Sequence, int) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel
 
editCut(Sequence, int) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel
 
editPaste(Sequence, int) - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequencePanel
 
edu.sdsc.mbt - package edu.sdsc.mbt
 
edu.sdsc.mbt.filters - package edu.sdsc.mbt.filters
This package provides classes which enable filtering or subsetting of a structure's constituent components.
edu.sdsc.mbt.image - package edu.sdsc.mbt.image
 
edu.sdsc.mbt.util - package edu.sdsc.mbt.util
This package provides classes which implement extra functionality on top of the core MBT classes (that is, capabilities that are not absolutely required by, or would otherwise overcomplicate, the core classes).
edu.sdsc.mbt.viewables - package edu.sdsc.mbt.viewables
This package provides classes which enable molecular biology data to be represented as visible/renderable viewable objects, plus, this package defines a top-level StructureDocument object to encapsulate the complete state of these objects and properties.
edu.sdsc.mbt.viewers.GLViewerImpl - package edu.sdsc.mbt.viewers.GLViewerImpl
 
edu.sdsc.mbt.viewers.GLViewerImpl.util - package edu.sdsc.mbt.viewers.GLViewerImpl.util
 
edu.sdsc.mbt.viewers.StructureViewerImpl.pdb - package edu.sdsc.mbt.viewers.StructureViewerImpl.pdb
 
edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io - package edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.io
 
edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util - package edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util
 
edu.sdsc.mbt.viewers.StructureViewerImpl.util - package edu.sdsc.mbt.viewers.StructureViewerImpl.util
 
edu.sdsc.mbt.viewers.StructureViewerImpl.vec - package edu.sdsc.mbt.viewers.StructureViewerImpl.vec
 
edu.sdsc.sirius.builder - package edu.sdsc.sirius.builder
 
edu.sdsc.sirius.dialogs - package edu.sdsc.sirius.dialogs
 
edu.sdsc.sirius.dialogs.TableImpl - package edu.sdsc.sirius.dialogs.TableImpl
 
edu.sdsc.sirius.export - package edu.sdsc.sirius.export
 
edu.sdsc.sirius.io - package edu.sdsc.sirius.io
This package provides classes which enable molecular biology data sets (such as protein structures, sequence data, etc) to be loaded into an MBT application as a Structure object.
edu.sdsc.sirius.monitors - package edu.sdsc.sirius.monitors
 
edu.sdsc.sirius.rasmol - package edu.sdsc.sirius.rasmol
 
edu.sdsc.sirius.ray - package edu.sdsc.sirius.ray
 
edu.sdsc.sirius.util - package edu.sdsc.sirius.util
 
edu.sdsc.sirius.viewers - package edu.sdsc.sirius.viewers
 
edu.sdsc.sirius.viewers.RamachandranViewerImpl - package edu.sdsc.sirius.viewers.RamachandranViewerImpl
 
edu.sdsc.sirius.viewers.SequenceViewerImpl - package edu.sdsc.sirius.viewers.SequenceViewerImpl
 
edu.sdsc.sirius.viewers.TreeViewer - package edu.sdsc.sirius.viewers.TreeViewer
 
edu.sdsc.sirius.workbench - package edu.sdsc.sirius.workbench
 
element - Variable in class edu.sdsc.mbt.Atom
The element symbol.
element - Variable in class edu.sdsc.sirius.dialogs.StructureEvent
 
enableCommonSelection(boolean) - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel
 
enablePopup() - Method in class edu.sdsc.sirius.viewers.SequenceViewerImpl.SequenceScalePanel
Enables display of sequence names by turning on the corresponding popup menu item.
enableStatus() - Static method in class edu.sdsc.mbt.util.Status
 
enableTooltips(boolean) - Method in class edu.sdsc.sirius.dialogs.TableImpl.BlastResultPanel
 
enableTooltips(boolean) - Method in class edu.sdsc.sirius.dialogs.TableImpl.PubmedResultPanel
 
enableTooltips(boolean) - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanel
 
enableTooltips(boolean) - Method in class edu.sdsc.sirius.dialogs.TableImpl.ResultPanelFrame
 
end - Variable in class edu.sdsc.mbt.ArrowComponent
 
end - Variable in class edu.sdsc.mbt.MonitorComponent
 
end - Variable in class edu.sdsc.mbt.StericBumpComponent
 
endTile(GL) - Method in class edu.sdsc.mbt.image.TileRenderer
Must be called after rendering the scene
end_chain - Variable in class edu.sdsc.mbt.Conformation
This value corresponds to the end Atom.chain_id value.
end_compound - Variable in class edu.sdsc.mbt.Conformation
For example, "ALA", "GLU", "LYS", etc.
end_residue - Variable in class edu.sdsc.mbt.Conformation
This value corresponds to the end Atom.residue_id value.
entry - Variable in class edu.sdsc.mbt.viewables.StructureDocumentEvent
The Structure object that was effected in the StructureDocument.
entryAdded(Entry, boolean) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
 
entryRemoved(Entry) - Method in class edu.sdsc.sirius.viewers.SequenceViewer
 
equalLookAtVectors(Location) - Method in class edu.sdsc.sirius.util.Location
 
equalPositions(Location) - Method in class edu.sdsc.sirius.util.Location
 
equalUpVectors(Location) - Method in class edu.sdsc.sirius.util.Location
 
equalVectors(Location) - Method in class edu.sdsc.sirius.util.Location
 
equals(Object) - Method in class edu.sdsc.mbt.Bond
One Bond is equal to another Bond if they hashCode values are equal.
equals(Object) - Method in class edu.sdsc.mbt.Fragment
One Fragment is equal to another Fragment if the indexes are equal.
equals(Geometry) - Method in class edu.sdsc.mbt.viewers.GLViewerImpl.Geometry
Please complete the missing tags for main
equals(Object) - Method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Path
Compares the specified object with this Path to determine equality.
equals(Location) - Method in class edu.sdsc.sirius.util.Location
 
equals(Object) - Method in class edu.sdsc.sirius.viewers.SequenceComparator
 
eraseTooltip() - Method in class edu.sdsc.sirius.dialogs.DistributionViewer
 
evalue - Variable in class edu.sdsc.sirius.dialogs.TableImpl.BlastLineData
 
eventType - Variable in class edu.sdsc.sirius.dialogs.StructureEvent
 
exp - Static variable in class edu.sdsc.sirius.util.BlastSettings
 
expandSelection - Static variable in class edu.sdsc.sirius.viewers.TreeViewer.StructureBrowser
 
expandToNode(StructureComponent) - Method in class edu.sdsc.sirius.viewers.TreeViewer.StructureBrowser
 
expandToNode(Cell) - Method in class edu.sdsc.sirius.viewers.TreeViewer.StructureBrowser
 
expandToNodes(Vector) - Method in class edu.sdsc.sirius.viewers.TreeViewer.StructureBrowser
 
exportPreferences(OutputStream) - Method in class edu.sdsc.mbt.viewables.StylesPreferences
 
exportState(StructureViewer, SequenceViewer, String) - Static method in class edu.sdsc.sirius.export.StateHandler
 
extract(Path[], boolean[], boolean) - Static method in class edu.sdsc.mbt.viewers.StructureViewerImpl.pdb.util.Strain
 

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