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object_3D - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
 
occupancy - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
 
openAPLVoroWithFile(File, File) - Static method in class org.cellmicrocosmos.cm2.engine.Engine
This opens the specified file in Jmol.
openJ3DSettingsWindow(Engine.J3DOperations, Point) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
Opens the j3d settings window.
openJmol() - Static method in class org.cellmicrocosmos.cm2.engine.Engine
This opens Jmol.
openJmolWithFile(File) - Static method in class org.cellmicrocosmos.cm2.engine.Engine
This opens the specified file in Jmol.
openMembraneInJmol(String) - Method in class org.cellmicrocosmos.cmX.mrna.MRNA
 
openMoleculeEditorFromCV(Molecule_3D) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
openMoleculeEditorFromCV(Molecule_3D) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
openMoleculeEditorFromDB(File, int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
 
openMoleculeEditorFromDB(File, int) - Method in interface org.cellmicrocosmos.cm2.interfaces.DatabaseViewListener
 
openPdbFileBrowser(File) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
Opens the pdbfile text browser for the specified file.
openPdbSettingsWindow(Engine.MembraneOperations) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
Opens the pdb settings window.
openWebPageOnSystemBrowser(String) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
Tries to display the passed url in the Default OS Webbrowser
OPM - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.DB
 
OPM - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.PPE_UPDATER
 
OPM_DUMMY_LAYERS_IN_PDBEXPORT - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
OPM_ENTRY - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.MIFILE
 
OPM_FILENAME_ADDON - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
OPM_KEY - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONF_PARSER
 
opmAtoms - Variable in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
OPMConnection - Class in org.cellmicrocosmos.cm2.io.ppe.network.http
Initializes the OPM Connection.
OPMConnection() - Constructor for class org.cellmicrocosmos.cm2.io.ppe.network.http.OPMConnection
 
opmdownloadLink - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
 
OrbitBehaviorAdvanced - Class in org.cellmicrocosmos.cm2.functionality3d
This class is based on the original behavior from Sun: com.sun.j3d.utils.behaviors.vp.OrbitBehavior MODIFICATIONS: - Zoom-Support for PARALLEL_PROJECTION changes by Bjoern Sommer bjoern@CELLmicrocosmos.org Moves the View around a point of interest when the mouse is dragged with a mouse button pressed.
OrbitBehaviorAdvanced() - Constructor for class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Parameterless constructor for this behavior.
OrbitBehaviorAdvanced(Canvas3D) - Constructor for class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Creates a new OrbitBehavior
OrbitBehaviorAdvanced(Canvas3D, int, MembraneViewListener) - Constructor for class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Creates a new OrbitBehavior
org.cellmicrocosmos.cm2 - package org.cellmicrocosmos.cm2
 
org.cellmicrocosmos.cm2.coarsegrainsupport - package org.cellmicrocosmos.cm2.coarsegrainsupport
 
org.cellmicrocosmos.cm2.constants - package org.cellmicrocosmos.cm2.constants
 
org.cellmicrocosmos.cm2.dataobjects - package org.cellmicrocosmos.cm2.dataobjects
 
org.cellmicrocosmos.cm2.engine - package org.cellmicrocosmos.cm2.engine
 
org.cellmicrocosmos.cm2.functionality3d - package org.cellmicrocosmos.cm2.functionality3d
 
org.cellmicrocosmos.cm2.gui - package org.cellmicrocosmos.cm2.gui
 
org.cellmicrocosmos.cm2.gui.dialogs - package org.cellmicrocosmos.cm2.gui.dialogs
 
org.cellmicrocosmos.cm2.gui.elements - package org.cellmicrocosmos.cm2.gui.elements
 
org.cellmicrocosmos.cm2.interfaces - package org.cellmicrocosmos.cm2.interfaces
 
org.cellmicrocosmos.cm2.io - package org.cellmicrocosmos.cm2.io
 
org.cellmicrocosmos.cm2.io.ppe.network.http - package org.cellmicrocosmos.cm2.io.ppe.network.http
 
org.cellmicrocosmos.cm2.io.ppe.toolbox - package org.cellmicrocosmos.cm2.io.ppe.toolbox
 
org.cellmicrocosmos.cm2.io.ppe.transform.xml - package org.cellmicrocosmos.cm2.io.ppe.transform.xml
 
org.cellmicrocosmos.cm2.membranepackingalgorithm - package org.cellmicrocosmos.cm2.membranepackingalgorithm
 
org.cellmicrocosmos.cm2.membranepackingalgorithms - package org.cellmicrocosmos.cm2.membranepackingalgorithms
 
org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer - package org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer
 
org.cellmicrocosmos.cm2.misc - package org.cellmicrocosmos.cm2.misc
 
org.cellmicrocosmos.cm2.pluginmanager - package org.cellmicrocosmos.cm2.pluginmanager
 
org.cellmicrocosmos.cmX.mrna - package org.cellmicrocosmos.cmX.mrna
 
org.cellmicrocosmos.j3d.jogl - package org.cellmicrocosmos.j3d.jogl
 
org.cellmicrocosmos.j3d.jogl.lib - package org.cellmicrocosmos.j3d.jogl.lib
 
organizeDomains() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
originalConstraints - Variable in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
originalLength - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Bond
 
OTHERNOTES - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GENERAL
 
overallRenderMode - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
overrideExistingLipids() - Method in interface org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmInterface
 
overrideExistingLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.AdvancedRandomPlacing
 
overrideExistingLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
 
overrideExistingLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
 
overrideExistingLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.IntersectionDeleter
 
overrideExistingLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.LinearPlacing
 
overrideExistingLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.MembraneShifter
 
overrideExistingLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
 
overrideExistingLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
 
overrideExistingLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
 
overrideExistingLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
 
overrideExistingLipids() - Method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.ToolkitMembranePackingAlgorithm
 
overridesLipids() - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
overwriteCurrentMolecule(Molecule_3D) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.DNDBridge
Overwrites the current Protein
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