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SAVEIMAGE - Variable in class org.cellmicrocosmos.cm2.io.FileIOHandler
 
SAVEMEMBRANE - Variable in class org.cellmicrocosmos.cm2.io.FileIOHandler
 
saveOPMDummyLayersInPDB - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.PPESettings
 
saveProfile(Molecule_3D, String) - Static method in class org.cellmicrocosmos.cm2.coarsegrainsupport.Molecule_Profile_IO
 
SAVEPROTOCOL - Variable in class org.cellmicrocosmos.cm2.io.FileIOHandler
 
SAXCustomizer - Class in org.cellmicrocosmos.cm2.io.ppe.transform.xml
The SAXCustomizer reduces the pdbtmall.xml in a program-internal file format.
SAXCustomizer(int, Connection) - Constructor for class org.cellmicrocosmos.cm2.io.ppe.transform.xml.SAXCustomizer
Constructs a new SAXCustomizer.
scale(float) - Method in class org.cellmicrocosmos.cm2.dataobjects.MyBounds
 
scale(float) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.AutoBox
Scales all values with a specified factor
scr2 - Variable in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
 
Searcher - Class in org.cellmicrocosmos.cm2.gui
This class can search the entries.idx of the RCSB-Database for strings.
Searcher() - Constructor for class org.cellmicrocosmos.cm2.gui.Searcher
 
SearchListener - Interface in org.cellmicrocosmos.cm2.interfaces
An interface used for delivering matches
select(Molecule_3D, int) - Method in class org.cellmicrocosmos.cm2.gui.elements.ComponentView
 
selectByCode(String, int) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Selects all protein instances that have the passed pdb code
selectByCode(String, int) - Method in class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
Selects all proteins instances that have the passed code
selectFromCV(Molecule_3D, int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
selectFromCV(Molecule_3D, int) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
SelectionBox - Class in org.cellmicrocosmos.cm2.functionality3d
The selection box which is drawn around a selected molecule is handled here.
SelectionBox(Molecule_3D, int) - Constructor for class org.cellmicrocosmos.cm2.functionality3d.SelectionBox
 
selectProteinsByCode(String, int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
selectProteinsByCode(String, int) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
sendToSystemTray() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
This method hides a CmME instance in the SystemTray.
sendToSystemTray() - Method in class org.cellmicrocosmos.cm2.pluginmanager.CalculationManager
 
set(Atom_3D[]) - Method in class org.cellmicrocosmos.cm2.dataobjects.Particle
 
setAcceptButton(JButton) - Method in class org.cellmicrocosmos.cm2.functionality3d.MicroDomainManager
 
setActive(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine
 
setActive(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
En-or disables the picking
setAlgorithmdescription(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
setAlgorithmname(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
setAlgorithmStringRepresentation(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
setAlgoritmProgress(int) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
setAllCapabilitysForBranchGroup(BranchGroup) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
sets up capabilitys for BranchGroup
setAllCapabilitysForShape3D(Shape3D) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
Sets up the required capabilities for a molecule
setAllCapabilitysForTransformGroup(TransformGroup) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
sets up capabilitys for TransformGroup
setAllEnabled(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
 
setAllEnabled(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
setAllEnabled(boolean) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
setAmbientBrightness(float) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Sets the ambient colors brightness
setAntialiasingEnabled(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.J3DOperations
 
setAtomicMass(float) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
setAuthor(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Sets the author string
setAuthor(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets the author of the Ppdb file.
setBarsVisible(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.CoordinateBar
 
setBrightEditorAppearance(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Sets the appearance of the editor.
setBrightLookAndFeel() - Static method in class org.cellmicrocosmos.cm2.gui.MainGui
 
setBrightnessForAmbientLight(float) - Method in class org.cellmicrocosmos.cm2.engine.Engine.J3DOperations
 
setCalculationEnabled() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
setCalculationEnabled(boolean) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
sets calculation button enabled if ExampleLipids are added to the membranemodel
setCalculationEnabled() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
setCameraModeWhileAligning(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.Hud
 
setChainIDs(Set<String>) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets the characters of the chain ids used in the underlying pdb file.
setChanged(boolean) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
setCode(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Sets the code string
setColor(Color) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets the color for this object.
setColor(Color3f) - Method in class org.cellmicrocosmos.cm2.functionality3d.CoordinateBar
 
setColor(Color3f) - Method in class org.cellmicrocosmos.cm2.functionality3d.Raster
 
setComboBoxData(String[], String) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditorToolbar
 
setComputeAbsoluteValues(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Set if absolute values are used during the computation process instead of percental values.
setComputeAbsoluteValues(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
The ComponentView uses absolute values instead of percental values to compute the lipid distribution.
setComputeAbsoluteValues(boolean) - Method in class org.cellmicrocosmos.cm2.gui.elements.ComponentView
The ComponentView uses absolute values instead of percental values to compute the lipid distribution.
setComputeAbsoluteValues(boolean) - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
 
setComputeAbsoluteValues(boolean) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Use this method to change the Membrane Editor distribution mode to - support absolute values if true - support percental values if false
setConfigFile(File) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.ConfigIO
Sets the path of the Config File;
setConfigFile(File) - Static method in class org.cellmicrocosmos.cm2.misc.ConfigParser
Sets the path of the Config File;
setContents(Document) - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Set up the tables values according to a DOM-Tree in an Document that was produced in the Parser.
setContentsFile(File) - Method in class org.cellmicrocosmos.cm2.gui.GlobalDatabaseBrowser
Sets the file for the Entries
setContentsFile(int, JLabel) - Static method in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPEUpdater
Set the ContenFile information of the file defined by the database.
setCountOfOPM(String) - Method in class org.cellmicrocosmos.cm2.io.ppe.network.http.OPMConnection
 
setCurrentFile(File) - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Sets the current File.
setCurrentlyColliding(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.Hud
 
setCurrentMembraneFile(File) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
sets the currently opened Membranefile
setCurrentProfileName(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
setDarkLookAndFeel() - Static method in class org.cellmicrocosmos.cm2.gui.MainGui
 
setData(Point2d[][]) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.GraphPanel
Sets the coordinates of the graphs.
setDatabaseViewListener(DatabaseViewListener) - Method in class org.cellmicrocosmos.cm2.gui.GlobalDatabaseBrowser
Adds a DatabaseListener to this Instance
setDate(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
sets the date string
setDate(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets the date
setDecimalPlaces(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
setDefaultConformation() - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
setDefaultTitle(String) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
sets the default Title for the MainFrame
setDisplayedProgress(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Displays the given progress beneath the MembraneView during Algorithm performance.
setDomainID(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
setDomainPaintMode(int) - Method in class org.cellmicrocosmos.cm2.functionality3d.MicroDomainManager
 
setEnabled(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
setEnabled(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
en- or disables the movable camera.
setEnabled(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
En- or disables the 3d display
setEnabled(boolean) - Method in class org.cellmicrocosmos.cm2.gui.elements.ComponentView
 
setEnabled(boolean) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
enables buttons in the toolbar if a membrane model exists
setEnabled(boolean) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
En-or disables all toolbar and menubar buttons
setEnableLight1(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
En-or disables light1
setEnableLight2(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
En-or disables light2 (containing of 2 light sources that can only be activated together)
setEnergy(double) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Can be used to store an energy value for this atom
setExpdta(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
setExtendedPlugin(boolean) - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
setEyeDistance(double) - Method in class org.cellmicrocosmos.cm2.engine.Engine.J3DOperations
 
setEyePosition(Point3d, Point3d) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.Display
Sets the eyeposition given per parameter.
setFile(File) - Method in class org.cellmicrocosmos.cm2.gui.Searcher
Sets the searcher to the entries file
setFirstRow(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
 
setFixedSize(int, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyNumberTextField
 
setForbidDraggingInFreeLookMode(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.J3DOperations
 
setGeometryType(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
setHeader(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Sets the header string
setHeader(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets the description of the Protein.
setHighlighted(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
setID(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.Protein_3D
Sets the ID of the protein
setInAlgorithmMode(JButton, JCheckBox, JCheckBox, JButton, Component) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
setInformation(String) - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
setInitialState() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
Sets up the initial state.
setJavapath(String) - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
setJrnl(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
setKeywds(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
setLastGeneratedMembraneFile(File) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
setLastModified(long) - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
setLayerId(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.Layer
 
setLayerID(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
setLayoutFile(File) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
set the location of the layout file.
setLight1Enabled(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.J3DOperations
 
setLight2Enabled(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.J3DOperations
 
setList(ArrayList<String>) - Method in class org.cellmicrocosmos.cm2.io.ppe.network.http.Connection
 
setListenerAndPrepare(MembraneViewListener, GuiListener, CalculationManager) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Deprecated.
setListenerAndPrepare(MembraneViewListener, GuiListener, DatabaseViewListener, CalculationManager) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
NOT MEANT TO BE USED BY PLUGIN DEVELOPERS!
setListenerAndPrepare(MembranePackingAlgorithm) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Use this method to inherit listeners from one algorithm to the next one.
setMainFrameTitle(String) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
sets the specified String as the Mainframe's Title.
setMembraneHasBeenEditedAgain(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
sets the state of membraneHasBeenEditedAgain
setMembraneHasBeenEditedAgain(boolean) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
sets the state of membraneHasBeenEditedAgain
setMembraneImage(Image) - Method in class org.cellmicrocosmos.cm2.functionality3d.Hud
 
setMembranePackingAlgorithm(MembranePackingAlgorithm) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.EnergyFunction
Gets called at startup and passes a reference to the underLying MembraneAlgortihm
setMembraneSide(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.Lipid_3D
 
setMembraneViewListener(MembraneViewListener) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
 
setMinRadius(double) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Sets the minimum radius for the OrbitBehavior.
setModelcount(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
setModelSet(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets the model index this molecule was constructed from
setMouseBehavior(MouseRotate) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
setMouseSensitivity(double) - Method in class org.cellmicrocosmos.cm2.engine.Engine.J3DOperations
 
setMouseSensitivity(double) - Method in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
Sets the mousesensitivity synchroniously for rotation, zoom and translation
setMRNA(MRNA) - Static method in class org.cellmicrocosmos.cm2.engine.Engine
 
setName(String) - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
setNormalMode() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
setOriginalFile(File) - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
setOriginalHeight(float) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
setOverridesLipids(Boolean) - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
setOwnThread(Thread) - Static method in class org.cellmicrocosmos.cm2.engine.Engine
 
setParallelProjection(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.J3DOperations
 
setPDBcode(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets the PDBcode
setPDBFile(File) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets this molecule's pdb file
setPDBTMRotation(Matrix3f) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets the PDBTM rotation matrix extracted from a PDBTM XML file.
Parameter rotation has to be not null.
setPDBTMTranslation(float) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets the y-coordinate of the molecules bounding center after transforming by the PPE.
Parameter center has to be a number.
setPercent(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.Lipid_3D
Sets the percentage of this lipid
setPercentages(int, int, String, int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
Set percentages of the ComponentView.
setPercentages(int, int, String, int) - Method in class org.cellmicrocosmos.cm2.gui.elements.ComponentView
AutoSets other percentages for all lipis on one membrane side
setPercentages(int, int, String, int) - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
 
setPercentages(int, int, String, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Set the percentages of the ComponentView.
setPickable(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets the shape to pickable.
setPicked(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets this protein picked or unpicked.
setPickedMolecules(Molecule_3D[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
 
setPickNDragManager(PickNDragManager) - Method in class org.cellmicrocosmos.cm2.functionality3d.Hud
 
setPolygonMode(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Changes the PolygonMode for all Molecules during 3d runtime
setPosition(Point3f) - Method in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
Sets the position.
setPosition(float, float) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets the Position of the instance of the Protein in the membrane
setPosition(Point3f) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
setPosition(Point3f) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Sets and applies a new position to this atom.
setPosition(Point3f) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
sets the position of the molecule.
setPositionIsInAValidSpace(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets, wether this protein is in a valid space (that means not colliding with anything) or not.
setPreferredSize(Dimension) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Sets the preferred size for the 3d display
setPreferredSize(Dimension) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.GraphPanel
 
setProfile(String) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
setProgress(String, int, boolean) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.StatusDialog
Update the current Progress that should be shown
setProportionalZoom(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Set proportional zoom behavior.
setRasterVisible(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.Raster
Creates a raster.
setRemark(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
sets the comment string
setRenderingAttributes(Appearance) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
The given Appearance is assigned to the RenderingAttributes.
setRenderMode(Integer) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets and applies the specified render mode (see contants fields) if the objects are currently live, else it does nothing.
setReverseRotate(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Set reverse rotate behavior.
setReverseTranslate(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Set reverse translate behavior.
setReverseZoom(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Set reverse zoom behavior.
setRotateEnable(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
 
setRotateEnable(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Enables or disables rotation.
setRotationCenter(Point3d) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Sets the center around which the View rotates.
setRotationMatrix(Matrix3f) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets the rotaion matrix for this object
setRotationMatrix(Matrix3f) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
sets the rotation matrix.
setRotFactors(double, double) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Sets the rotation x and y factors.
setRotXFactor(double) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Sets the rotation x factor.
setRotYFactor(double) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Sets the rotation y factor.
setRubberband(Rectangle) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.Display
 
setSeed(long) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.UniqueRandom
Set the actual used seed.
setSelectedLayer(int) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
 
setShininess(int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Changes the shininess for all Molecules during 3d runtime
setShowAxis(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
setShowAxis(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
En-or disables the axis bars in the view.
setShowAxis(boolean) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
setShowRaster(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
En-or disables the Raster painted on the Plane in the view.
setSimpleRandom() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Set the Random Number Generator to SimpleRandom.
setSize(Dimension) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Sets the size of the membrane
setSortByType(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Set if the lipids in the membrane PDB file are sorted by type during export.
setSOURCE(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
sets a list of species
setSOURCE(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
setStartInBackgroundAllowed(boolean) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
This should be true [Default] for every algorithm which does not use the method getRuntimeControlPanel().
setStartInBackgroundSelected(boolean) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
NOT MEANT TO BE USED BY PLUGIN DEVELOPERS!
setStartingTime(long) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Get the optionally defined starting time.
setState(String) - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
setStereoAvailable(boolean) - Static method in class org.cellmicrocosmos.cm2.engine.Engine
 
setStereoEnable(JCheckBox) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
 
setStereoSliderPosition(JLabel) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
 
setStereoView(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
setStereoViewAutoFocusMode(int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
setStereoViewAutoFocusMode(int) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Set the actual Stereo View Auto Focus Mode.
setStereoViewAutoFocusMode(int) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
setStereoViewMode(int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
setStereoViewMode(int) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Set the actual Stereo View Mode.
setStereoViewMode(int) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
setStereoViewScalingMode(int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
setStereoViewScalingMode(int) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Set the actual Stereo View Scaling Mode.
setStereoViewScalingMode(int) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
setSupportsAbsoluteValues(Boolean) - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
setSupportsMDs(Boolean) - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
setTerminationTime(long) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Get the optionally defined termination time.
settings - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyData
 
SETTINGS_DIR - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.IO
 
setTitle(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Sets the title String
setTitle(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets the description of the Protein.
setToolbarsEnabled(boolean) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
setTransFactors(double, double) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Sets the translation x and y factors.
setTransform(Transform3D) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
setTranslateEnable(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Enables or disables translate.
setTransparent(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
This method sets the molecule into transparent mode.
setTransparent(boolean, boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets the transparency and the picking value of the molecule.
setTransXFactor(double) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Sets the translation x factor.
setTransYFactor(double) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Sets the translation y factor.
setTrianglePoints(Point3f[]) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets the triangle points for this object.
setType(String) - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
setUniformBackground(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.J3DOperations
 
setUniformBackground(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
setUniqueRandom(long) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Set the Random Number Generator to UniqueRandom based on the defined seed.
setUnrotatedBounds(Box) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
setupAnalyzeMembraneButton() - Static method in class org.cellmicrocosmos.cm2.gui.MainGui
 
setUpButtons() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.PdbSettingsWindow
 
SetUpConnectionsDialog - Class in org.cellmicrocosmos.cm2.gui.dialogs
A Dialog that lets the User set up connections preferences
SetUpConnectionsDialog(GuiListener) - Constructor for class org.cellmicrocosmos.cm2.gui.dialogs.SetUpConnectionsDialog
Assembles the Gui
setUpMolecule(Molecule_3D, int) - Static method in class org.cellmicrocosmos.cm2.functionality3d.Atom_Creator_3D
 
setUrl(URL) - Method in class org.cellmicrocosmos.cm2.io.ppe.network.http.Connection
 
setUseAtomColors(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets if the Molecule should be displayed using atom colors in Covalent or Van Der Waals Mode.
setUserData(Object) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Can be used to store any Object to associate it with this atom
setValid(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
setViewByMode(int, Point3f) - Method in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
sets the view by the mode.
setViewByMode(int, Point3f) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Switches the camera to the requested view.
setViewingPlatform(ViewingPlatform) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Sets the ViewingPlatform for this behavior.
setViewToMode(int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.J3DOperations
 
setYHeight(float) - Method in class org.cellmicrocosmos.cm2.dataobjects.Layer
 
setYTranslation(float) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Sets the current Y-translation in angstrom for this object.
setYTranslation(float) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
sets the y translation NOTE: If this molecule is already added to the membrane model this will immediately move the molecule.
setZoomEnable(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
 
setZoomEnable(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Enables or disables zoom.
setZoomFactor(double) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Sets the zoom factor.
shakeMolecule(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
Simple method to change position and rotation of a molecule at random.
shape - Variable in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
shapeCollisionCheck - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
shapeIt(Molecule_3D) - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D
 
sharedGroupsOfMolecules - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool
 
sharedGroupsRenderModeOfMolecules - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool
 
sharedOPMGroupsOfMolecules - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool
 
shiftXZ - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.CoordinateTransformationSettings
 
shiftXZ() - Method in class org.cellmicrocosmos.cm2.io.Compatibility
 
shiftXZ - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
 
SHIFTXZ_BOUNDS_CENTER - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
 
SHIFTXZ_NONE - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
 
SHIFTXZ_PHYSICAL_CENTER - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
 
shiftY - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.CoordinateTransformationSettings
 
shiftY() - Method in class org.cellmicrocosmos.cm2.io.Compatibility
 
shiftY - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
 
SHIFTY_AUTO_MEDIAN - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
 
SHIFTY_BOTTOM - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
 
SHIFTY_NONE - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
 
SHIFTY_PHYSICAL_CENTER - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
 
shininess_lipids - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
shininess_proteins - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
SHORT_NAME_OF_THIS_PROGRAM - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GENERAL
 
SHOW_UI_BACKGROUND - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GUI_SETTINGS_AND_CONTROLS
Decides if the background color of the UI is also used for the 3D universe
showAllMultilayers(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
showAllMultiLayers - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
showAllMultilayers(boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.J3DOperations
 
showBordersAndTitles(boolean) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
Switches visibility of borders and titles on or off
showBtn - Variable in class org.cellmicrocosmos.cm2.gui.elements.MembraneView.IntersectionPanel
 
showInputDialog(Component, String, String, String[], String[], String) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
 
showLipid(Lipid_3D) - Method in class org.cellmicrocosmos.cm2.gui.elements.PropertiesView
 
showMembraneInfo() - Method in class org.cellmicrocosmos.cm2.gui.elements.PropertiesView
 
showProperties(File, int) - Method in class org.cellmicrocosmos.cm2.gui.elements.PropertiesView
Displays the specified properties
showProperties(Molecule_3D[]) - Method in class org.cellmicrocosmos.cm2.gui.elements.PropertiesView
displays properties of the passed molecules
showProtocol - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.AlgorithmSettings
 
showRuntimeControls() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
showStereoView() - Method in class org.cellmicrocosmos.cm2.engine.Engine.J3DOperations
 
showStereoView() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
showStereoView() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
showToolbar(boolean) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
Switches visibility of the toolbar on or off
simpleMode() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
Creates rows of lipids.
SimpleRandom - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
Random Class generates simple random numbers.
SimpleRandom() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.SimpleRandom
Creates a new Unique Random number by using the seed.
simulateAnnealing() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
Fulfills the simulated annealing method.
simulateAnnealingStep(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
Tries to find a better place for randomly chosen lipids.
SimulatedAnnealing - Class in org.cellmicrocosmos.cm2.membranepackingalgorithms
This algorithm represents the power of geometrical based membrane simulations.
SimulatedAnnealing() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
generates a new SimulatedAnneling
size_x - Variable in class org.cellmicrocosmos.cm2.io.MembraneMetaInfo
 
size_y - Variable in class org.cellmicrocosmos.cm2.io.MembraneMetaInfo
 
sortAtoms() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
sortByType() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Check if the lipids in the membrane PDB file is sorted by type during export.
sortByType - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.CoordinateTransformationSettings
 
sortByType() - Method in class org.cellmicrocosmos.cm2.io.Compatibility
 
sortByType - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
 
sortMolecules() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
STANDALONE_NAME - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GENERAL
 
STANDARD_EDITION_NAME - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GENERAL
 
STANDARD_MULTILAYER_Y_TRANSLATION - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GUI_SETTINGS_AND_CONTROLS
the standard height for multilayers for the Add Multilayer dialog
STANDARD_MULTILAYERY_MOLECULE_HEIGHT - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GUI_SETTINGS_AND_CONTROLS
the standard height for multilayers for the Add Multilayer dialog
start() - Method in class org.cellmicrocosmos.cm2.pluginmanager.CalculationManager
 
Start - Class in org.cellmicrocosmos.cm2
The Entry Class of the Application.
Start() - Constructor for class org.cellmicrocosmos.cm2.Start
 
START_ELEMENT - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.MIFILE
 
START_TOKEN - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONF_PARSER
 
startDocument() - Method in class org.cellmicrocosmos.cm2.io.ppe.transform.xml.SAXCustomizer
 
startDomainChange(MicroDomain_3D) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
startDomainChange(MicroDomain_3D) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
startDomainMode(MicroDomain_3D) - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
 
startDomainMode(MicroDomain_3D) - Method in class org.cellmicrocosmos.cm2.functionality3d.MicroDomainManager
 
startDomainMode(MicroDomain_3D) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
startDomainMode(MicroDomain_3D) - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
 
startElement(String, String, String, Attributes) - Method in class org.cellmicrocosmos.cm2.io.ppe.toolbox.MIFHandler
 
startElement(String, String, String, Attributes) - Method in class org.cellmicrocosmos.cm2.io.ppe.transform.xml.SAXCustomizer
 
startInBackground - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.AlgorithmSettings
 
StartMain - Class in org.cellmicrocosmos.cm2.engine
The Entry Class of the Application.
StartMain() - Constructor for class org.cellmicrocosmos.cm2.engine.StartMain
 
startMain(String[]) - Static method in class org.cellmicrocosmos.cm2.engine.StartMain
Entry Point.
startMain() - Static method in class org.cellmicrocosmos.cm2.engine.StartMain
Start the program without any arguments directly.
startModelChange(Molecule_3D) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
startModelChange(Molecule_3D) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
startPainting(Point) - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
startSearching(String, boolean) - Method in class org.cellmicrocosmos.cm2.gui.Searcher
Starts to search for the passed string(s)
startSpecialMode(Molecule_3D, int) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
STARTUP_DIALOG_TEXT_FOREGROUND - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IMAGES_AND_ICONS
The text foreground colors for the startup dialog.
STARTUP_IMAGES - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IMAGES_AND_ICONS
images that are show at startup randomly (different Sizes allowed)
state - Variable in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
STATE_COMPILE_ERROR - Static variable in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
STATE_FILE_NOT_FOUND - Static variable in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
STATE_FILE_NOT_READABLE - Static variable in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
STATE_NO_ALGORITHMS - Static variable in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
STATE_READY - Static variable in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
stateChanged(ChangeEvent) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.ChangeSizeDialog
 
stateChanged(ChangeEvent) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.J3DSettingsDialog
 
stateChanged(ChangeEvent) - Method in class org.cellmicrocosmos.cm2.gui.elements.ComponentView
 
stateChanged(ChangeEvent) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
 
stateChanged(ChangeEvent) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
state changed method.
stateChanged(ChangeEvent) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
Handles User's GUI settings
StatisticsView - Class in org.cellmicrocosmos.cm2.gui.elements
The statistics displayed in the gui.
StatisticsView() - Constructor for class org.cellmicrocosmos.cm2.gui.elements.StatisticsView
The initialising constructor for this class with some test data and a previous TabbedPane constructed
StatusDialog - Class in org.cellmicrocosmos.cm2.gui.dialogs
A simple Dialog designed to show a Progress to the User.
StatusDialog(boolean) - Constructor for class org.cellmicrocosmos.cm2.gui.dialogs.StatusDialog
show only the label and the progressbar
StatusDialog(JButton, boolean) - Constructor for class org.cellmicrocosmos.cm2.gui.dialogs.StatusDialog
show the dialog also with the passed button inside
StatusDialog(String, boolean, Color) - Constructor for class org.cellmicrocosmos.cm2.gui.dialogs.StatusDialog
Show the dialog with an image and a small statusbar at the bottom
step - Variable in class org.cellmicrocosmos.cm2.gui.Searcher
 
STEREO_VIEW_DISTANCE_SCALE_MAX - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREO_VIEW_DISTANCE_SCALE_MIN - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREO_VIEW_DISTANCE_SCALE_STANDARD - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREO_VIEW_DISTANCE_SCALING - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREO_VIEW_MODE__OVER_UNDER__TOP_LEFT - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREO_VIEW_MODE__OVER_UNDER__TOP_RIGHT - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREO_VIEW_MODE__SIDE_BY_SIDE__LEFT_LEFT - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREO_VIEW_MODE__SIDE_BY_SIDE__LEFT_RIGHT - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREO_VIEW_MODE__STANDARD - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREO_VIEW_MODE_AUTOFOCUS__AUTO - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREO_VIEW_MODE_AUTOFOCUS__FIX - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREO_VIEW_MODE_AUTOFOCUS__STANDARD - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREO_VIEW_MODE_SCALING__DOUBLE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREO_VIEW_MODE_SCALING__NORMAL - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREO_VIEW_MODE_SCALING__STANDARD - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
stereoAvailable - Static variable in class org.cellmicrocosmos.cm2.engine.Engine
 
STEREOSCOPIC_3D_PERFORMANCE_MODE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREOSCOPIC_3D_QUAD_MODE_PREFERRED - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREOSCOPIC_3D_UPDATE_FOCUS - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREOVIEW_DEFAULT - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREOVIEW_MAX - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREOVIEW_MIN - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
STEREOVIEW_SCALE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
stereoViewAutoFocusMode - Variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
stereoViewMode - Variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
stereoViewScalingMode - Variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
STOP_ZOOM - Static variable in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Constructor flag that indicates zoom should stop when it reaches the minimum orbit radius set by setMinRadius().
stopAlgorithm() - Method in interface org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmInterface
 
stopAlgorithm() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.AdvancedRandomPlacing
 
stopAlgorithm() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
 
stopAlgorithm() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
 
stopAlgorithm() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.IntersectionDeleter
 
stopAlgorithm() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.LinearPlacing
 
stopAlgorithm() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.MembraneShifter
 
stopAlgorithm() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
 
stopAlgorithm() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
sets the breake flag.
stopAlgorithm() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
 
stopAlgorithm() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
 
stopAlgorithm() - Method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.ToolkitMembranePackingAlgorithm
 
storeCheckBoxValues() - Method in class org.cellmicrocosmos.cm2.gui.elements.ComponentView
 
storeRawPdbData(String, String[]) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
 
storeSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.AlgorithmSettings
Stores the settings into the config
storeSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.APLVoroSettings
 
storeSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.CoordinateTransformationSettings
Stores the settings into the config
storeSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
 
storeSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
Stores the settings into configParser
storeSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.JmolSettings
 
storeSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.LimitationSettings
Stores the settings into the config
storeSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.PPESettings
Stores the settings into the config
storeSettings() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
storeSizes() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Stores the sizes of the columns in the Config
storeXMLOfPdbTM() - Method in class org.cellmicrocosmos.cm2.io.ppe.network.http.PdbTMConnection
Generates a local copy to the pdbtmall.xml and fixes the PDBTM XML file which contains multiple tags.
SUB_TOKEN - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONF_PARSER
 
SUBDIR_PDB_ALL - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONNECTION
 
SUBDIR_PDBTM_ALL - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONNECTION
 
SUBDIR_PDBTM_ALPHA - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONNECTION
 
SUBDIR_PDBTM_BETA - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONNECTION
 
SUBDIR_PDBTM_XMLFILE - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONNECTION
 
supportsAbsoluteValues() - Method in interface org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmInterface
 
supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.AdvancedRandomPlacing
 
supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
 
supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
 
supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.IntersectionDeleter
 
supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.LinearPlacing
 
supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.MembraneShifter
 
supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
 
supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
 
supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
 
supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
 
supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.ToolkitMembranePackingAlgorithm
 
supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
supportsMDs() - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
supportsMicrodomains() - Method in interface org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmInterface
 
supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.AdvancedRandomPlacing
 
supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
 
supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
 
supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.IntersectionDeleter
 
supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.LinearPlacing
 
supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.MembraneShifter
 
supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
 
supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
 
supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
 
supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
 
supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.ToolkitMembranePackingAlgorithm
 
swapYZ - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.CoordinateTransformationSettings
 
swapYZ() - Method in class org.cellmicrocosmos.cm2.io.Compatibility
 
swapYZ - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
 
switchCursor(int) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.Display
 
switchRenderMode_While_Algorithm_Runs() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
switchToLayer(int) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
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