- 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
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- 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
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- 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
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- 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
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- DETAIL_POLYGON_MODE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
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- DETAIL_PRECISION_MODIFIER - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
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- DETAIL_SHININESS_LIPIDS - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
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- 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
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- 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
-