- pack() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.EditDBEntryDialog
-
Extends the dialogs pack method by setting the witdh regarding to the
space needed for the complete Filepath
- PAINT1Cursor - Static variable in class org.cellmicrocosmos.cm2.misc.Cm2_IconDepot
-
- PAINT2Cursor - Static variable in class org.cellmicrocosmos.cm2.misc.Cm2_IconDepot
-
- PAINT3Cursor - Static variable in class org.cellmicrocosmos.cm2.misc.Cm2_IconDepot
-
- paintBorder(Component, Graphics, int, int, int, int) - Method in class org.cellmicrocosmos.cm2.gui.MainGui.TabComponentNoBorder
-
- paintComponent(Graphics) - Method in class org.cellmicrocosmos.cm2.gui.MyFCAccessory
-
- paintComponent(Graphics) - Method in class org.cellmicrocosmos.cm2.gui.MyJRadioButton
-
- parallelProjection - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
-
- ParameterMatrixPanel - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
-
This panel will display a JTable that also has a scrollable row header.
- ParameterMatrixPanel(String[], TableCellRenderer, TableCellEditor) - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.ParameterMatrixPanel
-
Constructs a new ParamterMatrixPanel
- parseForElements(String) - Method in class org.cellmicrocosmos.cm2.io.ppe.toolbox.ConfParser
-
Generates an ArrayList with parsing-elements.
- parseForPortConfig(String) - Method in class org.cellmicrocosmos.cm2.io.ppe.toolbox.ConfParser
-
Generates an ArrayList with connection data.
- Particle - Class in org.cellmicrocosmos.cm2.dataobjects
-
The particles are extended atom models needed to represent
coarse grains.
- Particle(Atom_3D[]) - Constructor for class org.cellmicrocosmos.cm2.dataobjects.Particle
-
- particleAtomNames - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeProfile
-
- particleElementNames - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeProfile
-
- particleExtending - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
-
- particleIdentifier - Variable in class org.cellmicrocosmos.cm2.dataobjects.Particle
-
- particleIDs - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeProfile
-
- particleMemberIndices - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeProfile
-
- ParticlePropertiesPanel - Class in org.cellmicrocosmos.cm2.coarsegrainsupport
-
This class describes the panel to display or modify the textual properties of the selected particle(s)
- ParticlePropertiesPanel(MoleculeEditor, boolean, String, String, String, Color) - Constructor for class org.cellmicrocosmos.cm2.coarsegrainsupport.ParticlePropertiesPanel
-
- pauseAlgorithm - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
-
- PdbAttributes() - Constructor for class org.cellmicrocosmos.cm2.io.PdbReader_3D.PdbAttributes
-
- pdbbrowser - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool
-
- pdbCode - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeProfile
-
- PDBFileBrowser - Class in org.cellmicrocosmos.cm2.gui
-
The Frame that displays textual contents of a pdb file.
- PDBFileBrowser(File) - Constructor for class org.cellmicrocosmos.cm2.gui.PDBFileBrowser
-
- PDBFileBrowser(String[], String) - Constructor for class org.cellmicrocosmos.cm2.gui.PDBFileBrowser
-
Constructs a new Frame.
- PdbReader_3D - Class in org.cellmicrocosmos.cm2.io
-
The new pdb reader.
- PdbReader_3D() - Constructor for class org.cellmicrocosmos.cm2.io.PdbReader_3D
-
- PdbReader_3D.PdbAttributes - Class in org.cellmicrocosmos.cm2.io
-
A kind of sheet that stores some strings.
- PDBSEARCH_FRAME_SCALE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GUI_SETTINGS_AND_CONTROLS
-
- pdbsettings - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool
-
- PdbSettingsWindow - Class in org.cellmicrocosmos.cm2.gui.dialogs
-
This dialog is used to change the PDB restriction settings.
- PdbSettingsWindow(Engine.MembraneOperations) - Constructor for class org.cellmicrocosmos.cm2.gui.dialogs.PdbSettingsWindow
-
Builds up the frame
- PDBTM - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.DB
-
- PDBTM - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.PPE_UPDATER
-
- PDBTM_ENTRY - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.MIFILE
-
- PDBTM_KEY - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONF_PARSER
-
- PdbTMConnection - Class in org.cellmicrocosmos.cm2.io.ppe.network.http
-
The PdbTMConnection establishes a connection to the
Protein Data Bank of Transmembrane Proteins.
- PdbTMConnection() - Constructor for class org.cellmicrocosmos.cm2.io.ppe.network.http.PdbTMConnection
-
Constructs a new PdbTMConnection.
- PDBWriter - Class in org.cellmicrocosmos.cm2.io
-
This class sets up all relevant data from the membrane model, computing it
into a proper pdb syntax and writing it into a file.
- PDBWriter(File, StatusDialog) - Constructor for class org.cellmicrocosmos.cm2.io.PDBWriter
-
Constructor of the class PDBWriter.
- performLipidCheck() - Method in class org.cellmicrocosmos.cm2.pluginmanager.CalculationManager
-
- performSearchInDownloadAPDB(String, String) - Method in class org.cellmicrocosmos.cm2.engine.Engine
-
- performSearchInDownloadAPDB(String, String) - Method in class org.cellmicrocosmos.cmX.mrna.MRNA
-
- performUpdate() - Method in class org.cellmicrocosmos.cm2.pluginmanager.PluginManager
-
- PICKED - Static variable in class org.cellmicrocosmos.cm2.functionality3d.SelectionBox
-
- pickMolecules(Molecule_3D[]) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
-
- pickMolecules(Molecule_3D[]) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
-
- PickNDragManager - Class in org.cellmicrocosmos.cm2.functionality3d
-
Manages all picking and movement operations in the 3d view
- PickNDragManager(Canvas3D, IntersectManager, CameraMode, PickCanvas, PointLight, PointLight, PointLight, Hud) - Constructor for class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
-
Constructs the PND manager and registers all required references
- placeNewLipidDuringSimulationBorder(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
-
Try to add new molecules on the north, east, south or west border.
- placeNewLipidDuringSimulationRandom(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
-
Try to add new molecules somewhere inside the membrane.
- plot - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.GraphPanel
-
- Plugin - Class in org.cellmicrocosmos.cm2.pluginmanager
-
This class contains the MembranePackingAlgorithm compiled
from a .jar or .java file.
- Plugin() - Constructor for class org.cellmicrocosmos.cm2.pluginmanager.Plugin
-
- PLUGIN_FILE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
-
- PluginIO - Class in org.cellmicrocosmos.cm2.pluginmanager
-
This class parses the different information located in a
MembranePackingAlgorithm.
- PluginIO() - Constructor for class org.cellmicrocosmos.cm2.pluginmanager.PluginIO
-
- PluginManager - Class in org.cellmicrocosmos.cm2.pluginmanager
-
This class manages the different MembranePackingAlgorithms.
- PluginManager() - Constructor for class org.cellmicrocosmos.cm2.pluginmanager.PluginManager
-
- plugins - Variable in class org.cellmicrocosmos.cm2.pluginmanager.PluginManager
-
- POLYGON - Static variable in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
-
- polygon_mode - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
-
- popUp() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.ChangeSizeDialog
-
Constructs the Gui referring to the mode and the model and shows the
Dialog.
- popUp() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.ManageTitleSectionDialog
-
Constructs the Gui and shows the Dialog.
- popUp() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.NewMembraneDialog
-
Constructs the Gui
- popup3DSettingsDialog(Point) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
-
- popup3DSettingsDialog(Point) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
-
- popUpAttrsDialog() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
-
- popUpAttrsDialog() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
-
- popUpChangeSize(Point) - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
-
- popUpChangeSize(Point) - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
-
- popUpGUI(Component, String, String) - Static method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmGUI
-
opens a JDialog in which the JComponent that u have designed will be
displayed.
- popupHelp() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.HelpDialog
-
Builds up the frame, initializes the tree and makes them appear on
screen.
- popupHelp(int) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.HelpDialog
-
Builds up the frame, initializes the tree and makes them appear on
screen.
- popupHelp(Object) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.HelpDialog
-
- popUpHelpIfItsApplicationsFirstRun() - Static method in class org.cellmicrocosmos.cm2.gui.dialogs.HelpDialog
-
Called at startup Opens the Help if the programm is started for the first
time
- popUpLayoutDescription(RootWindow) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
-
This is for development purposes only.
- PORT_SUBKEY - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONF_PARSER
-
- position - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
-
- position - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
-
- positionAfterReading - Variable in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
-
- positions - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeProfile
-
- possibleDirections - Static variable in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
-
- PPE_AUTOMATIC - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
-
- PPE_CONSTANTS - Class in org.cellmicrocosmos.cm2.io.ppe.toolbox
-
PPE_CONSTANTS contains some subclasses with defined constants.
- PPE_CONSTANTS() - Constructor for class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS
-
- PPE_CONSTANTS.CONF_PARSER - Class in org.cellmicrocosmos.cm2.io.ppe.toolbox
-
CONF_PARSER contains constants belonging to the ppe.conf.
- PPE_CONSTANTS.CONNECTION - Class in org.cellmicrocosmos.cm2.io.ppe.toolbox
-
CONNECTION contains constants which are necessary for the connections.
- PPE_CONSTANTS.DB - Class in org.cellmicrocosmos.cm2.io.ppe.toolbox
-
IO contains constants for the input and output of the
Protein Placement Expansion.
- PPE_CONSTANTS.IO - Class in org.cellmicrocosmos.cm2.io.ppe.toolbox
-
IO contains constants for the input and output of the
Protein Placement Expansion.
- PPE_CONSTANTS.MIFILE - Class in org.cellmicrocosmos.cm2.io.ppe.toolbox
-
MIFILE contains constants which are necessary for the
generation of a MIFile by the MIFHandler.
- PPE_CONSTANTS.PPE_UPDATER - Class in org.cellmicrocosmos.cm2.io.ppe.toolbox
-
PPE_UPDATER contains constants which are necessary for
generating an update.txt.
- PPE_UPDATER() - Constructor for class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.PPE_UPDATER
-
- PPESettings() - Constructor for class org.cellmicrocosmos.cm2.engine.DataPool.PPESettings
-
- PPEUpdater - Class in org.cellmicrocosmos.cm2.io.ppe.toolbox
-
The class PPEUpdater updates the pdbtm.mif and looks for
new data bank updates of the different protein data banks.
- PPEUpdater() - Constructor for class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPEUpdater
-
- precision_modifier - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
-
- prepare(MembranePackingAlgorithm) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
- prepare() - Method in class org.cellmicrocosmos.cm2.pluginmanager.CalculationManager
-
- prepareLength() - Method in class org.cellmicrocosmos.cm2.gui.Searcher
-
Determines the length of the file in rows for the length field Also
determines the number of rows that count as 1 percent of all rows
- PRINTOUT_JMOL_LOGS - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.DEBUG
-
if true, lets JMol printout Logs
- PRIORITY_GENERATE_MEMBRANE_THREAD - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.THREADS
-
- PRIORITY_LIPID_FILLING_ALGORITHMS - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.THREADS
-
- PRIORITY_LOAD_MEMBRANE_THREAD - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.THREADS
-
- PRIORITY_SEARCH_THREAD - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.THREADS
-
- projectFolder - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
-
- PropertiesView - Class in org.cellmicrocosmos.cm2.gui.elements
-
- PropertiesView() - Constructor for class org.cellmicrocosmos.cm2.gui.elements.PropertiesView
-
- propertyChange(PropertyChangeEvent) - Method in class org.cellmicrocosmos.cm2.gui.MyFCAccessory
-
- PROPORTIONAL_ZOOM - Static variable in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
-
Constructor flag to use proportional zoom, which determines
how much you zoom based on view's distance from the center of
rotation.
- ProportionalZoom(Object[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
-
Property which sets proportional zoom behavior.
- ProtCount - Variable in class org.cellmicrocosmos.cm2.io.MembraneMetaInfo
-
- Protein - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
-
This is an extension of the molecule class and is representing a protein
- Protein(Protein_3D, MembranePackingAlgorithm) - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.Protein
-
- Protein_3D - Class in org.cellmicrocosmos.cm2.dataobjects
-
An extended version of a molecule.
- Protein_3D() - Constructor for class org.cellmicrocosmos.cm2.dataobjects.Protein_3D
-
- PROTEINTYPE - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
-
Used to specify the PDB type for the database.
- ProtocolDialog - Class in org.cellmicrocosmos.cm2.gui.dialogs
-
This class is used to show the actual protocols generated by the
Membrane Packing Algorithms.
- ProtocolDialog() - Constructor for class org.cellmicrocosmos.cm2.gui.dialogs.ProtocolDialog
-
- proxyFTP - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
-
- proxyFTPport - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
-
- proxyHTTP - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
-
- proxyHTTPport - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
-
- proxyLogin - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
-
- proxyPassword - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
-
- proxyuse - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
-
- publicBranchGroup - Variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
-