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