- object_3D - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
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- occupancy - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
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- openAPLVoroWithFile(File, File) - Static method in class org.cellmicrocosmos.cm2.engine.Engine
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This opens the specified file in Jmol.
- openJ3DSettingsWindow(Engine.J3DOperations, Point) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
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Opens the j3d settings window.
- openJmol() - Static method in class org.cellmicrocosmos.cm2.engine.Engine
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This opens Jmol.
- openJmolWithFile(File) - Static method in class org.cellmicrocosmos.cm2.engine.Engine
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This opens the specified file in Jmol.
- openMembraneInJmol(String) - Method in class org.cellmicrocosmos.cmX.mrna.MRNA
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- openMoleculeEditorFromCV(Molecule_3D) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
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- openMoleculeEditorFromCV(Molecule_3D) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
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- openMoleculeEditorFromDB(File, int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
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- openMoleculeEditorFromDB(File, int) - Method in interface org.cellmicrocosmos.cm2.interfaces.DatabaseViewListener
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- openPdbFileBrowser(File) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
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Opens the pdbfile text browser for the specified file.
- openPdbSettingsWindow(Engine.MembraneOperations) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
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Opens the pdb settings window.
- openWebPageOnSystemBrowser(String) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
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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
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- OPM - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.PPE_UPDATER
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- OPM_DUMMY_LAYERS_IN_PDBEXPORT - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
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- OPM_ENTRY - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.MIFILE
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- OPM_FILENAME_ADDON - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
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- OPM_KEY - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONF_PARSER
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- opmAtoms - Variable in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
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- OPMConnection - Class in org.cellmicrocosmos.cm2.io.ppe.network.http
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Initializes the OPM Connection.
- OPMConnection() - Constructor for class org.cellmicrocosmos.cm2.io.ppe.network.http.OPMConnection
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- opmdownloadLink - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
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- OrbitBehaviorAdvanced - Class in org.cellmicrocosmos.cm2.functionality3d
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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
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Parameterless constructor for this behavior.
- OrbitBehaviorAdvanced(Canvas3D) - Constructor for class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
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Creates a new OrbitBehavior
- OrbitBehaviorAdvanced(Canvas3D, int, MembraneViewListener) - Constructor for class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
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Creates a new OrbitBehavior
- org.cellmicrocosmos.cm2 - package org.cellmicrocosmos.cm2
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- org.cellmicrocosmos.cm2.coarsegrainsupport - package org.cellmicrocosmos.cm2.coarsegrainsupport
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- org.cellmicrocosmos.cm2.constants - package org.cellmicrocosmos.cm2.constants
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- org.cellmicrocosmos.cm2.dataobjects - package org.cellmicrocosmos.cm2.dataobjects
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- org.cellmicrocosmos.cm2.engine - package org.cellmicrocosmos.cm2.engine
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- org.cellmicrocosmos.cm2.functionality3d - package org.cellmicrocosmos.cm2.functionality3d
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- org.cellmicrocosmos.cm2.gui - package org.cellmicrocosmos.cm2.gui
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- org.cellmicrocosmos.cm2.gui.dialogs - package org.cellmicrocosmos.cm2.gui.dialogs
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- org.cellmicrocosmos.cm2.gui.elements - package org.cellmicrocosmos.cm2.gui.elements
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- org.cellmicrocosmos.cm2.interfaces - package org.cellmicrocosmos.cm2.interfaces
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- org.cellmicrocosmos.cm2.io - package org.cellmicrocosmos.cm2.io
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- org.cellmicrocosmos.cm2.io.ppe.network.http - package org.cellmicrocosmos.cm2.io.ppe.network.http
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- 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
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- org.cellmicrocosmos.cm2.membranepackingalgorithm - package org.cellmicrocosmos.cm2.membranepackingalgorithm
-
- org.cellmicrocosmos.cm2.membranepackingalgorithms - package org.cellmicrocosmos.cm2.membranepackingalgorithms
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- 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
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- 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
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- 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
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- overridesLipids() - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
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- overwriteCurrentMolecule(Molecule_3D) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.DNDBridge
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Overwrites the current Protein