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P

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
 
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