- UAMU_FILE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
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- undoConformation(boolean) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
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- uniformBackground - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
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- uniqueRandom - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.AlgorithmSettings
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- UniqueRandom - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
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Random Class generates new Unique Random numbers.
- UniqueRandom(long) - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.UniqueRandom
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Creates a new Unique Random number by using the seed.
- uniqueRandomSeed - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.AlgorithmSettings
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- update() - Method in class org.cellmicrocosmos.cm2.dataobjects.Constraint_3D
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- update() - Method in class org.cellmicrocosmos.cm2.gui.CompatibilityPanel
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- UPDATE_FILENAME - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.IO
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- updateAfterLayerChange() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
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- upDateAll() - Method in class org.cellmicrocosmos.cm2.gui.elements.ComponentView
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updates all tables
- updateAllBonds() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
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- updateAllFileAttributes() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
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- updateAtomColors() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
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- updateCanvas() - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.Display
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- updateColors() - Method in class org.cellmicrocosmos.cm2.gui.elements.ComponentView
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- updateColors() - Method in class org.cellmicrocosmos.cm2.gui.elements.StatisticsView
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- updateCurrentView() - Method in class org.cellmicrocosmos.cm2.gui.elements.PropertiesView
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- updateDisplayOfMicroDomains() - Method in class org.cellmicrocosmos.cm2.functionality3d.MicroDomainManager
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- updateDistanceScale(double) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
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Update the distance for the stereoscopic effect.
- updateDistanceScale(double) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
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- updateGeometry(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
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Updates the Geometry (needs to be called after one or more
applyAtomPosition() calls)
- updateGeometry() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
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Updates the Geometry (needs to be called after one or more
applyAtomPosition() calls)
- updateGeometry() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
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Updates the geometry of this Molecule.
- updateIntersectionDisplay() - Method in class org.cellmicrocosmos.cm2.functionality3d.IntersectionsDisplayer
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- updateIntersectionDisplay(StatusDialog) - Method in class org.cellmicrocosmos.cm2.functionality3d.IntersectionsDisplayer
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- updateLayers() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
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- updateLights() - Method in class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
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Recalculates the pointlight positions regarding to the current camera
position
- updateMembraneInfo(boolean) - Method in class org.cellmicrocosmos.cm2.pluginmanager.CalculationManager
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- updateMembraneStatistics(MembraneModel, int) - Method in class org.cellmicrocosmos.cm2.gui.elements.StatisticsView
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- updateMicroDomainsIn3D() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
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- updateMicroDomainsIn3D() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
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- updatePanels() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
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Updates the information shown in the toolbars
- updateProperties() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
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- updateProperties() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
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- updateSelection() - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
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- updateShape3D() - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
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- updateSpinner() - Method in class org.cellmicrocosmos.cm2.gui.elements.ComponentView
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- updateTextArea() - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.ControlPanel
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- updateVisualAtomPositionsOnly() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
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- upper - Variable in class org.cellmicrocosmos.cm2.dataobjects.MyBounds
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- upper - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.AutoBox
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- userAddsLipid(String, String, int, int, int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
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- userAddsLipid(String, String, int, int, int) - Method in interface org.cellmicrocosmos.cm2.interfaces.DatabaseViewListener
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- userAddsProtein(String, String, int, int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
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- userAddsProtein(String, String, int, int) - Method in interface org.cellmicrocosmos.cm2.interfaces.DatabaseViewListener
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- userChangedModelForFile(File, int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
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- userChangedModelForFile(File, int) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
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- userChangedStereoEnable(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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- userChangedStereoEnable(boolean) - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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- userChangedStereoSlider() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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- userChangedStereoSlider() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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- userChoseAnalyzeMembrane() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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- userChoseAnalyzeMembrane() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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- userChoseGeneratePDBFile(File) - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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Called when User chooses to generate a PDB file
(Uses the current membrane if the last opened file was a restored PDB file
called when user chooses to generate the Membrane
- userChoseGeneratePDBFile(File) - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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Called when User chooses to generate a PDB file
(Uses the current membrane if the last opened file was a restored PDB file
- userChoseGromacsCall() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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Called when user chose generate a PDB-File using Gromacs
- userchoseLoadDB() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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called when user chooses to load a DB
- userchoseLoadDB() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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Called when User chooses to load a DB
- userChoseLoadMembrane() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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Called when user chose to load a Membrane
- userChoseLoadMembrane() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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Called when User chooses to load a membrane
- userChoseNewDB() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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Called when user chooses to create a new DataBase
- userChoseNewDB() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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Called when User chooses to create a new DB
- userChoseNewMembrane() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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Called when user chose to create a new Membrane
- userChoseNewMembrane() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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Called when User chooses to create a new Membrane
- userChosePreviewMembrane(int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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- userChosePreviewMembrane(int) - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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- userChoseQuickLoadMembrane(File) - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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Called when user clicked on one of the quickloaditems
- userChoseQuickLoadMembrane(File) - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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- userChoseQuickSaveMembrane() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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Called when user chose to quicksave current Membrane
- userChoseQuickSaveMembrane() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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Called when User chooses to quicksave the current Membrane
- userChoseSaveImage() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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Called when user chose to save current Screenshot.
- userChoseSaveImage() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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Called when User chooses to save a Screenshot
- userChoseSaveMembrane() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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Called when user chose to save a Membrane
- userChoseSaveMembrane() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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Called when User chooses to save a membrane
- userChoseSaveTimeProtocol(Vector<String>) - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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Called when user chose to save a Time Protocol
- userChoseSaveTimeProtocol(Vector<String>) - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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Called when User chooses to save the algorithm time protocol
- userChoseShowTimeProtocol() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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Called when user chose to show the current Algorithm Time Protocol
- userChoseShowTimeProtocol() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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Called when User chooses to show the algorithm time protocol
- userClicked3DSettings(Point) - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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- userClicked3DSettings(Point) - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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- userClickedEditorMode(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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- userClickedEditorMode(boolean) - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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- userClickedOpenExternal() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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- userClickedOpenExternal() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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- userClickedOpenRCSB() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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Invoked when user wants to open the SearchView
- userClickedOpenRCSB() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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- userClickedOpenRestrictionDialog() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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- userClickedOpenRestrictionDialog() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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- userClickedUniformBackground() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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- userClosesGlobalDBView() - Method in class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
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- userClosesGlobalDBView() - Method in interface org.cellmicrocosmos.cm2.interfaces.DatabaseViewListener
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- userOpensGlobalDBView() - Method in class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
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- userOpensGlobalDBView(String, String) - Method in class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
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- userOpensGlobalDBView() - Method in interface org.cellmicrocosmos.cm2.interfaces.DatabaseViewListener
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- userOpensGlobalDBView(String, String) - Method in interface org.cellmicrocosmos.cm2.interfaces.DatabaseViewListener
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- userWantToChangeModel(File, int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
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- userWantToChangeModel(File, int) - Method in interface org.cellmicrocosmos.cm2.interfaces.DatabaseViewListener
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- userWantToPreviewMolecule(File, int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
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- userWantToPreviewMolecule(File, int) - Method in interface org.cellmicrocosmos.cm2.interfaces.DatabaseViewListener
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- userWantToSeeProperties(File, int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
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- userWantToSeeProperties(File, int) - Method in interface org.cellmicrocosmos.cm2.interfaces.DatabaseViewListener
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- useSystemLookandFeel - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool
-