- EditDBEntryDialog - Class in org.cellmicrocosmos.cm2.gui.dialogs
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A Dialog that lets the user Edit an Entry in the DB.
- EditDBEntryDialog(EditDBEntryDialogListener) - Constructor for class org.cellmicrocosmos.cm2.gui.dialogs.EditDBEntryDialog
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- EditDBEntryDialogListener - Interface in org.cellmicrocosmos.cm2.interfaces
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Listener used by the Dialog where the DB Entries are edited
- editEntry() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
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Opens a Dialog where the currently highlighted Entry can be edited
- editMembers() - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
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- editMembrane(String) - Method in class org.cellmicrocosmos.cmX.mrna.MRNA
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- editor - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.ControlPanel
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- element - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
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- ELLIPSE - Static variable in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
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- enableAtomPerformanceMode - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
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- enableFastTransitions - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
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- enableGenerateButton(boolean) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
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En or disables the generate options
- enableMembraneButtons(boolean) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
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en- or disable some mebrane options.
- enablePPEAutomatic - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
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- enableSaveButtons(boolean) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
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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
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- endDocument() - Method in class org.cellmicrocosmos.cm2.io.ppe.transform.xml.SAXCustomizer
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- endElement(String, String, String) - Method in class org.cellmicrocosmos.cm2.io.ppe.toolbox.MIFHandler
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- endElement(String, String, String) - Method in class org.cellmicrocosmos.cm2.io.ppe.transform.xml.SAXCustomizer
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- Energies - Class in org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer
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This class stores and handles values regarding the force field.
- Energies(Atom_Level_Minimizer) - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Energies
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- EnergyFunction - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
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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
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- energyFunction(Molecule, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
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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
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- engine - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
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- Engine - Class in org.cellmicrocosmos.cm2.engine
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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
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- engine - Static variable in class org.cellmicrocosmos.cm2.engine.TestArea
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- Engine.BasicOperations - Class in org.cellmicrocosmos.cm2.engine
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provides the basic file Operations for the application.
- Engine.DatabaseOperations - Class in org.cellmicrocosmos.cm2.engine
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Provides all Operations that may be started from the databaseview
- Engine.J3DOperations - Class in org.cellmicrocosmos.cm2.engine
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Operations concerning Detail Settings in the 3D scene.
- Engine.MembraneOperations - Class in org.cellmicrocosmos.cm2.engine
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Operations regarding the current Membrane
- EnterMatrixDialog - Class in org.cellmicrocosmos.cm2.gui.dialogs
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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
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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
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- equalsType(Molecule_3D) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
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- execute() - Static method in class org.cellmicrocosmos.cm2.engine.TestArea
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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
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- exitApplication() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
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exits the Application, and causes the current settings to be saved
- exitApplication() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
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Called when User chooses to quit the application
- exportAPLVoro - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.LimitationSettings
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- exportAPLVoro(Vector<String[]>, boolean) - Method in class org.cellmicrocosmos.cm2.io.PDBWriter
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- exportAPLVoroFile - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
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- exportTopology - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.LimitationSettings
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- exportTopology(Vector<String[]>) - Method in class org.cellmicrocosmos.cm2.io.PDBWriter
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- exportTopology - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
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- extendLeft(String, int) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
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- extendRight(String, int) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
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- EXTRA - Static variable in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
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- EXTRA - Static variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
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- EXTRA - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
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Used to specify the extracellular membrane side
- extractFromJar(String, String) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
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