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D

DatabaseIO - Class in org.cellmicrocosmos.cm2.io
The class that read and writes the Database contents
DatabaseIO() - Constructor for class org.cellmicrocosmos.cm2.io.DatabaseIO
 
DatabaseOperations() - Constructor for class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
 
databaseOperations - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
 
DatabaseView - Class in org.cellmicrocosmos.cm2.gui.elements
The local database view.
DatabaseView() - Constructor for class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
The constructor builds up the database Gui without setting any contents yet
DatabaseViewListener - Interface in org.cellmicrocosmos.cm2.interfaces
Listener that is used for the DatabaseView
DataPool - Class in org.cellmicrocosmos.cm2.engine
This class serves as a singleton and will store all shared data.
DataPool() - Constructor for class org.cellmicrocosmos.cm2.engine.DataPool
 
DataPool.AlgorithmSettings - Class in org.cellmicrocosmos.cm2.engine
A subclass that stores the current Algorithm settings.
DataPool.APLVoroSettings - Class in org.cellmicrocosmos.cm2.engine
This class is needed to setup the direct path to APL@Voro
DataPool.AtomValues - Class in org.cellmicrocosmos.cm2.engine
 
DataPool.CoordinateTransformationSettings - Class in org.cellmicrocosmos.cm2.engine
A subclass that stores the current Coordinate Transformation settings.
DataPool.DNDBridge - Class in org.cellmicrocosmos.cm2.engine
Used for Drag and Drop.
DataPool.InternetSettings - Class in org.cellmicrocosmos.cm2.engine
 
DataPool.IO - Class in org.cellmicrocosmos.cm2.engine
 
DataPool.J3DSettings - Class in org.cellmicrocosmos.cm2.engine
A subclass that stores our J3d settings.
DataPool.JmolSettings - Class in org.cellmicrocosmos.cm2.engine
This class is needed to setup the direct path to Jmol, including the java -jar execution string.
DataPool.LimitationSettings - Class in org.cellmicrocosmos.cm2.engine
A subclass that stores the current limitation settings.
DataPool.PPESettings - Class in org.cellmicrocosmos.cm2.engine
A subclass that stores the current Protein Placement Expansion settings.
dataset - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.GraphPanel
 
date - Variable in class org.cellmicrocosmos.cm2.io.MembraneMetaInfo
 
DB() - Constructor for class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.DB
 
dbContainsCode(Object) - Method in class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
 
dbContainsCode(String) - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
 
dbContainsCode(Object) - Method in interface org.cellmicrocosmos.cm2.interfaces.DatabaseViewListener
 
dbContainsPdbFile(File) - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Tests if an Entry with the passed File already exists in both tables
dbContainsPdbFile(File) - Method in interface org.cellmicrocosmos.cm2.interfaces.EditDBEntryDialogListener
 
deactivate() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.DNDBridge
Discards the current Protein
DEBUG() - Constructor for class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.DEBUG
 
DEFAULT_ALGORITHM_DIRECTORY - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
DEFAULT_APLVORO_EXECUTION_LINK - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
DEFAULT_COVALENT_RADIUS - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.ATOMVALUES
 
DEFAULT_DATABASE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
DEFAULT_DB_DIRECTORY - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
Default_DB_File - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.IO
 
DEFAULT_DOWNLOAD_LINK - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
DEFAULT_INCOMING_DIRECTORY - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
DEFAULT_JMOL_EXECUTION_LINK - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
DEFAULT_LIPID_COLOR - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.MOLECULE_DEFAULTS
Default Color for Lipids (used if no other can be found) Also used for table grids
DEFAULT_MEMBRANE_DIRECTORY - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
DEFAULT_OPM_DOWNLOAD_LINK - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
DEFAULT_PDB_DIRECTORY - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
DEFAULT_PREVIEW_IMAGE_LINK - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
DEFAULT_PROTEIN_COLOR - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.MOLECULE_DEFAULTS
Default Color for Proteins (used if no other can be found) Also used for table grids
DEFAULT_RCSB_SITE_LINK - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
DEFAULT_SEARCH_ENTRIES_LINK - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
DEFAULT_SHOW_PROTOCOL - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.ALGORITHMS
 
DEFAULT_SIZE_OF_MEMBRANE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.MEMBRANE_SIZES
 
DEFAULT_START_IN_BACKGROUND - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.ALGORITHMS
 
DEFAULT_UNIQUE_RANDOM - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.ALGORITHMS
 
DEFAULT_UNIQUE_RANDOM_SEED - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.ALGORITHMS
 
DEFAULT_VANDERWAALS_RADIUS - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.ATOMVALUES
 
defaultArea - Variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
DEFAULTDBDIRECTORY - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.IO
 
DEFAULTINCOMINGDIRECTORY - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.IO
 
DEFAULTMEMBRANEDIRECTORY - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.IO
 
DEFAULTMICRODOMAINCOLOR - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
DEFAULTPDBDIRECTORY - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.IO
 
deleteAllAt(String) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.ConfigIO
deletes the Value(s) stored by the given key so that new ones can be added without keeping the old ones
deleteAllAt(String) - Static method in class org.cellmicrocosmos.cm2.misc.ConfigParser
deletes the Value(s) stored by the given key so that new ones can be added without keeping the old ones
deleteDir(File, boolean) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
 
deleteExampleLipidAtExtra(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Removes the example lipid at specified index
deleteExampleLipidAtIntra(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Removes the example lipid at specified index
deleteExampleLipidExtra(Lipid_3D) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
deleteExampleLipidIntra(Lipid_3D) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
deleteLipidAtExtra(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
deletes the Lipid that has the given index
deleteLipidAtIntra(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
deletes the Lipid that has the given index
deleteLipidExtra(Lipid_3D) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
deletes the specified lipid
deleteLipidIntra(Lipid_3D) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
deletes the specified lipid
deleteMolecule(Molecule_3D) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
deletes the passed Molecule of any kind
deleteProtein(Protein_3D) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
deletes the passed Protein
deleteProteinAt(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
deletes the Protein at specified index
DETAIL_AMBIENT_LIGHT - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
DETAIL_DEFAULTVERTICES - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
DETAIL_MIN_PRECISION - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
DETAIL_POLYGON_MODE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
DETAIL_PRECISION_MODIFIER - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
DETAIL_SHININESS_LIPIDS - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
DETAIL_SHININESS_PROTEINS - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
DEVELOPER_EDITION - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GUI_SETTINGS_AND_CONTROLS
The Developer Edition comes with the PlugIn-Manager, which allows to work with user generated algorithms.
DEVELOPER_EDITION_NAME - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GENERAL
 
dia - Variable in class org.cellmicrocosmos.cm2.io.ReversePDBParser
 
DISABLE_ROTATE - Static variable in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Constructor flag to disable rotate
DISABLE_TRANSLATE - Static variable in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Constructor flag to disable translate
DISABLE_ZOOM - Static variable in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Constructor flag to disable zoom
discardChanges() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.ChangeSizeDialog
 
Display - Class in org.cellmicrocosmos.cm2.coarsegrainsupport
Describes the display of the MoleculeEditor
Display(MoleculeEditor) - Constructor for class org.cellmicrocosmos.cm2.coarsegrainsupport.Display
 
displayAdditionalInformation(Atom_3D, float) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
displayAlgorithmInfo(String) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
displayAlgorithmProgress(int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
displayAlgorithmProgress(int) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
displayAlgoritmInfo(String) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
displayAlgoritmInfo(String) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
displayedLayerChanged(int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
displayedLayerChanged(int) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
displayInformation(String) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Displays the passed information in string representation beneath the MembraneView during Algorithm Performance.
displayOPMAtoms(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
dispose() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.J3DSettingsDialog
 
dispose() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.PdbSettingsWindow
 
dispose() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.ProtocolDialog
 
dispose() - Method in class org.cellmicrocosmos.cm2.gui.PDBFileBrowser
 
disposeLater() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.StatusDialog
Use method to make a secure disposal of the StatusDialog.
distance(Molecule, Molecule, boolean) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the distance between mol1 and mol2.
distance(Point3f, Point3f, boolean) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the distance between tow positions.
Distributor - Class in org.cellmicrocosmos.cm2.membranepackingalgorithms
Distributes lipids onto a membrane trying to reach the pre-defined absolute lipid numbers.
Distributor() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
 
DND_TIMER_COUNTDOWN - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GUI_SETTINGS_AND_CONTROLS
The Time the user has to hold down the mouse button to start DragNDrop
DNDBridge() - Constructor for class org.cellmicrocosmos.cm2.engine.DataPool.DNDBridge
 
DNDCursor - Static variable in class org.cellmicrocosmos.cm2.misc.Cm2_IconDepot
 
DnDEventOccured(Point) - Method in class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
 
DnDEventOccured(Point) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
DnDEventOccured(Point) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Called, when a drag event is recognized in the database table.
DnDEventOccured(Point) - Method in interface org.cellmicrocosmos.cm2.interfaces.DatabaseViewListener
 
DnDEventOccured(Point) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
DNDFinished(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
 
DNDFinished(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
DnDFinished(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Finishes the DND.
DNDFinished(boolean) - Method in interface org.cellmicrocosmos.cm2.interfaces.DatabaseViewListener
 
DNDFinished(boolean) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
DO_BORDER_CHECK_WHEN_LOADING - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
doBorderCutoff(Atom[]) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
 
dock() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
NOT MEANT TO BE USED BY PLUGIN DEVELOPERS!
dockScreen(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
dockScreen(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
dockScreen(boolean) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
doLayout() - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.ControlPanel
 
doLayout() - Method in class org.cellmicrocosmos.cm2.gui.elements.ComponentView
 
doLayout() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Overrides doLayout
doLayout() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
sets the prefferedSize of the DrawableComponent ScrollPane
doLayout() - Method in class org.cellmicrocosmos.cm2.gui.elements.PropertiesView
 
domainID2ResNameAtPosition - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.LimitationSettings
 
doProxySettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
 
doProxySettings() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
 
doProxySettings() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
 
DOUBLE - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyNumberTextField
 
drawHud(Graphics2D) - Method in class org.cellmicrocosmos.cm2.functionality3d.Hud
 
drawingDomain - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool
 
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