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EditDBEntryDialog - Class in org.cellmicrocosmos.cm2.gui.dialogs
A Dialog that lets the user Edit an Entry in the DB.
EditDBEntryDialog(EditDBEntryDialogListener) - Constructor for class org.cellmicrocosmos.cm2.gui.dialogs.EditDBEntryDialog
 
EditDBEntryDialogListener - Interface in org.cellmicrocosmos.cm2.interfaces
Listener used by the Dialog where the DB Entries are edited
editEntry() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Opens a Dialog where the currently highlighted Entry can be edited
editMembers() - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
editMembrane(String) - Method in class org.cellmicrocosmos.cmX.mrna.MRNA
 
editor - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.ControlPanel
 
element - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
 
ELLIPSE - Static variable in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
enableAtomPerformanceMode - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
enableFastTransitions - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
enableGenerateButton(boolean) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
En or disables the generate options
enableMembraneButtons(boolean) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
en- or disable some mebrane options.
enablePPEAutomatic - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
enableSaveButtons(boolean) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
en- or disable the option to save the membrane
END_TOKEN - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONF_PARSER
 
endDocument() - Method in class org.cellmicrocosmos.cm2.io.ppe.transform.xml.SAXCustomizer
 
endElement(String, String, String) - Method in class org.cellmicrocosmos.cm2.io.ppe.toolbox.MIFHandler
 
endElement(String, String, String) - Method in class org.cellmicrocosmos.cm2.io.ppe.transform.xml.SAXCustomizer
 
Energies - Class in org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer
This class stores and handles values regarding the force field.
Energies(Atom_Level_Minimizer) - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Energies
 
EnergyFunction - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
This class must be overwritten in oder to create an own Enegry Functin for the Atom_level_minimizing Algorithm.
EnergyFunction() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.EnergyFunction
 
energyFunction(Molecule, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
The energy function returns a value which specifies the average distance to the neighbor molecules in the cutoff radius.
energyFunctions - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
 
engine - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
Engine - Class in org.cellmicrocosmos.cm2.engine
This class is the basement of the whole application; the basic usecases will be handled by this class.
Engine(StatusDialog, File, String) - Constructor for class org.cellmicrocosmos.cm2.engine.Engine
 
engine - Static variable in class org.cellmicrocosmos.cm2.engine.TestArea
 
Engine.BasicOperations - Class in org.cellmicrocosmos.cm2.engine
provides the basic file Operations for the application.
Engine.DatabaseOperations - Class in org.cellmicrocosmos.cm2.engine
Provides all Operations that may be started from the databaseview
Engine.J3DOperations - Class in org.cellmicrocosmos.cm2.engine
Operations concerning Detail Settings in the 3D scene.
Engine.MembraneOperations - Class in org.cellmicrocosmos.cm2.engine
Operations regarding the current Membrane
EnterMatrixDialog - Class in org.cellmicrocosmos.cm2.gui.dialogs
A Frame that lets the User type in the Values of the matrix and the y tanslation manually.
EnterMatrixDialog(Molecule_3D, Point) - Constructor for class org.cellmicrocosmos.cm2.gui.dialogs.EnterMatrixDialog
Constucts a Frame and shows the passed inital Data in its textfields
ENTRIES_FILE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
equalsType(Molecule_3D) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
execute() - Static method in class org.cellmicrocosmos.cm2.engine.TestArea
This method gets called when the test button got pressed
existsProfile(Molecule_3D, String, String) - Static method in class org.cellmicrocosmos.cm2.coarsegrainsupport.Molecule_Profile_IO
 
exitApplication() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
exits the Application, and causes the current settings to be saved
exitApplication() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
Called when User chooses to quit the application
exportAPLVoro - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.LimitationSettings
 
exportAPLVoro(Vector<String[]>, boolean) - Method in class org.cellmicrocosmos.cm2.io.PDBWriter
 
exportAPLVoroFile - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
 
exportTopology - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.LimitationSettings
 
exportTopology(Vector<String[]>) - Method in class org.cellmicrocosmos.cm2.io.PDBWriter
 
exportTopology - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
 
extendLeft(String, int) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
 
extendRight(String, int) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
 
EXTRA - Static variable in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
 
EXTRA - Static variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
EXTRA - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Used to specify the extracellular membrane side
extractFromJar(String, String) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
 
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