- 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
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- storeSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.CoordinateTransformationSettings
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Stores the settings into the config
- storeSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
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- storeSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
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Stores the settings into configParser
- storeSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.JmolSettings
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- storeSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.LimitationSettings
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Stores the settings into the config
- storeSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.PPESettings
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Stores the settings into the config
- storeSettings() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
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- storeSizes() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
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Stores the sizes of the columns in the Config
- storeXMLOfPdbTM() - Method in class org.cellmicrocosmos.cm2.io.ppe.network.http.PdbTMConnection
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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
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- SUBDIR_PDB_ALL - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONNECTION
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- SUBDIR_PDBTM_ALL - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONNECTION
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- SUBDIR_PDBTM_ALPHA - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONNECTION
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- SUBDIR_PDBTM_BETA - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONNECTION
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- SUBDIR_PDBTM_XMLFILE - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONNECTION
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- supportsAbsoluteValues() - Method in interface org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmInterface
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- supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.AdvancedRandomPlacing
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- supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
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- supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
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- supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.IntersectionDeleter
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- supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.LinearPlacing
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- supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.MembraneShifter
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- supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
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- supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
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- supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
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- supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
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- supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.ToolkitMembranePackingAlgorithm
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- supportsAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
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- supportsMDs() - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
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- supportsMicrodomains() - Method in interface org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmInterface
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- supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.AdvancedRandomPlacing
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- supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
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- supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
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- supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.IntersectionDeleter
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- supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.LinearPlacing
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- supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.MembraneShifter
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- supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
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- supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
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- supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
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- supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
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- supportsMicrodomains() - Method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.ToolkitMembranePackingAlgorithm
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- 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
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- switchCursor(int) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.Display
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- switchRenderMode_While_Algorithm_Runs() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
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- switchToLayer(int) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
-