- calcPercentages(int, int[]) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
-
Calculates the passed array of numbers
- calculate(MembranePackingAlgorithm) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
-
- calculate(MembranePackingAlgorithm) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
-
- calculateAtomicMass(Molecule_3D) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.AtomValues
-
- calculateEnergy(Atom, Atom, double, float, float) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.EnergyFunction
-
Return the Energy between the pair of passed Atoms.
- calculateLengthBetween(Point3f, Point3f) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
-
- calculateLevelExtremes(Point3f[]) - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D
-
Calculates all extremepoints in XZ directions from the passed list of
points.
- calculateLJPotential(Point3f, Point3f, Float, float, float) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Energies
-
- calculateLocation(int, int, float) - Method in class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
-
Converts the mouselocation on canvas to a location in the universe.
- calculateRadius() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
-
- calculateRadius() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
-
returns the radius the Molecule on the x/z plane.
- calculateTotalFileSize(int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
Returns the maximal FileSize of the current Membrane
- calculationManager - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
-
- CalculationManager - Class in org.cellmicrocosmos.cm2.pluginmanager
-
The CalculationManager performs the computation of the different algorithms.
- CalculationManager(Engine.MembraneOperations, MembranePackingAlgorithm, MembraneView, Engine.BasicOperations, Engine.DatabaseOperations, StatisticsView, PropertiesView) - Constructor for class org.cellmicrocosmos.cm2.pluginmanager.CalculationManager
-
- CalculationManager.CalculationThread - Class in org.cellmicrocosmos.cm2.pluginmanager
-
- CalculationThread() - Constructor for class org.cellmicrocosmos.cm2.pluginmanager.CalculationManager.CalculationThread
-
- CameraMode - Class in org.cellmicrocosmos.cm2.functionality3d
-
Handles the camera in the 3d view.
- CameraMode(Canvas3D, SimpleUniverse) - Constructor for class org.cellmicrocosmos.cm2.functionality3d.CameraMode
-
Equips the canvas with a camera mode
- canAddMoreExampleLipidsExtra(int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
- canAddMoreExampleLipidsIntra(int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
- CANCEL - Variable in class org.cellmicrocosmos.cm2.gui.dialogs.ChangeSizeDialog
-
- CANCEL - Variable in class org.cellmicrocosmos.cm2.gui.dialogs.EditDBEntryDialog
-
- CANCEL - Static variable in class org.cellmicrocosmos.cm2.gui.dialogs.NewMembraneDialog
-
- cancelCurrent() - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
-
- caretUpdate(CaretEvent) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.EnterMatrixDialog
-
Each time a change was made, values are checked for validity
- caretUpdate(CaretEvent) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyNumberTextField
-
- caseSensitiveChainIds - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.LimitationSettings
-
- caseSensitiveChainIds() - Method in class org.cellmicrocosmos.cm2.io.Compatibility
-
- cbAddLipids - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
-
- cbAlgoAddLipids - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
-
- cbAlgoAddLipids - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
-
- cbAlgoApproach - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
-
- cbAlgoApproach - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
-
- cbAlgoShake - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
-
- cbAlgoShake - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
-
- cbAlgoTwist - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
-
- cbAlgoTwist - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
-
- cbApproach - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
-
- cbShake - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
-
- cBtn - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.ParticlePropertiesPanel
-
- cbTwist - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
-
- center - Variable in class org.cellmicrocosmos.cm2.dataobjects.MyBounds
-
- center - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.AutoBox
-
- centerPoint - Variable in class org.cellmicrocosmos.cm2.dataobjects.Constraint_3D
-
- chainID - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
-
- chains - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.LimitationSettings
-
- changeAndApplyModel(int, boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
-
- changeAndApplyModel(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
-
- changeLayer(int) - Method in class org.cellmicrocosmos.cm2.gui.elements.StatisticsView
-
Switches the tabs when the displayed membrane side changes
- changeModelForFile(File, int) - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
-
- changeRenderModeFromAlgorithm() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
-
- changeRenderModeFromAlgorithm() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
-
- ChangeSizeDialog - Class in org.cellmicrocosmos.cm2.gui.dialogs
-
The dialog that allows the user to change the size of the membrane
- ChangeSizeDialog(Point, Engine, Point3f[], Shape[], Dimension) - Constructor for class org.cellmicrocosmos.cm2.gui.dialogs.ChangeSizeDialog
-
- characters(char[], int, int) - Method in class org.cellmicrocosmos.cm2.io.ppe.transform.xml.SAXCustomizer
-
Note: Character maybe run different times for one document pass!
- charge - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
-
- CHARS - Static variable in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
-
Creates a copy of the passed matrix.
- chart - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.GraphPanel
-
- chartPanel - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.GraphPanel
-
- checkAfterwards() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.ChangeSizeDialog
-
- checkCompatibility(String) - Method in class org.cellmicrocosmos.cm2.gui.CompatibilityPanel
-
- checkForModels(File) - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D
-
Tests (and only tests!) if the passed file contains multiple models
- checkJava3DVersion() - Method in class org.cellmicrocosmos.cm2.engine.Engine
-
Check if the correct Java3D Version is installed.
- cleanUpRawData() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
-
- clearAll(boolean, boolean, boolean, int) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
-
clears all Vectors.
- clearAllLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
-
Removes all added lipids from the membrane at once
- clearAllLipidsFrom3DandModel(int, int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
-
- clearAllLipidsFrom3DandModel(int, int) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
-
- clearExampleLipids() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
Removes all sample lipids from the model
- clearHashtable() - Static method in class org.cellmicrocosmos.cm2.functionality3d.IntersectionsDisplayer
-
- clearLipids() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
Removes all lipids from the membrane model (not the sample lipids) Also
clears the info about the last algorithm used
- clearLipids(int, int) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
-
clears the lipid Vector.
- clearLogs() - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.ControlPanel
-
- clearProteins() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
Removes all Proteins from the model
- clearSampleLipids() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
- clearSelection() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
-
clears the selection.
- clearView(boolean) - Method in class org.cellmicrocosmos.cm2.gui.elements.PropertiesView
-
- close() - Method in class org.cellmicrocosmos.cm2.gui.Searcher
-
- closeStreams() - Method in class org.cellmicrocosmos.cm2.io.ppe.transform.xml.SAXCustomizer
-
Tries to close all streams connected with the opened files.
- CM2_CONSTANTS - Class in org.cellmicrocosmos.cm2.constants
-
A number of major hardcoded variables are summarized here.
- CM2_CONSTANTS() - Constructor for class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS
-
- CM2_CONSTANTS.ALGORITHMS - Class in org.cellmicrocosmos.cm2.constants
-
- CM2_CONSTANTS.ATOMVALUES - Class in org.cellmicrocosmos.cm2.constants
-
- CM2_CONSTANTS.DEBUG - Class in org.cellmicrocosmos.cm2.constants
-
- CM2_CONSTANTS.GENERAL - Class in org.cellmicrocosmos.cm2.constants
-
- CM2_CONSTANTS.GUI_SETTINGS_AND_CONTROLS - Class in org.cellmicrocosmos.cm2.constants
-
- CM2_CONSTANTS.IMAGES_AND_ICONS - Class in org.cellmicrocosmos.cm2.constants
-
- CM2_CONSTANTS.IO - Class in org.cellmicrocosmos.cm2.constants
-
- CM2_CONSTANTS.J3D - Class in org.cellmicrocosmos.cm2.constants
-
J3D values
- CM2_CONSTANTS.MEMBRANE_SIZES - Class in org.cellmicrocosmos.cm2.constants
-
- CM2_CONSTANTS.MISC - Class in org.cellmicrocosmos.cm2.constants
-
- CM2_CONSTANTS.MOLECULE_DEFAULTS - Class in org.cellmicrocosmos.cm2.constants
-
- CM2_CONSTANTS.RENDERMODE - Class in org.cellmicrocosmos.cm2.constants
-
- CM2_CONSTANTS.THREADS - Class in org.cellmicrocosmos.cm2.constants
-
Priorities for some Threads.
- CM2_HOMEPAGE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GENERAL
-
- Cm2_IconDepot - Class in org.cellmicrocosmos.cm2.misc
-
Stores all icons for the application.
- Cm2_IconDepot() - Constructor for class org.cellmicrocosmos.cm2.misc.Cm2_IconDepot
-
- Cm2_Toolkit - Class in org.cellmicrocosmos.cm2.misc
-
A Toolkit that offers various useful Methods
- Cm2_Toolkit() - Constructor for class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
-
- Cm2_Toolkit.Membrane_Image2D_Generator - Class in org.cellmicrocosmos.cm2.misc
-
- Cm2_Toolkit.ToolkitMembranePackingAlgorithm - Class in org.cellmicrocosmos.cm2.misc
-
This class is only used for direct access to the different methods
of the MembranePackingAlgorithm interface.
- CM2AdditionalListener - Interface in org.cellmicrocosmos.cm2.interfaces
-
Listener that is used in the jmol Integration
- coarseGrain(Particle) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
-
- code - Variable in class org.cellmicrocosmos.cm2.io.MembraneMetaInfo
-
- color - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
-
- COLOR_COORDINATEBARS_BRIGHT - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
-
- COLOR_COORDINATEBARS_BRIGHT_WET - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
-
- COLOR_COORDINATEBARS_DARK - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
-
- COLOR_COORDINATEBARS_DARK_WET - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
-
- colors - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeProfile
-
- columnModel - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.ParameterMatrixPanel
-
- ColumnSorter - Class in org.cellmicrocosmos.cm2.gui
-
This comparator is used by the sortAllRows Method.
- ColumnSorter(int, boolean) - Constructor for class org.cellmicrocosmos.cm2.gui.ColumnSorter
-
- combineCurrentSelection() - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
-
- combineVectors(Vector<Object>, Vector<Object>) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
-
Puts the contents of first v1 and then v2 into a new Vector.
- comparator - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
-
- compare(Object, Object) - Method in class org.cellmicrocosmos.cm2.gui.ColumnSorter
-
compares two passed objects and returns an int value that tells in what
order these objects should be
- comparePDBTMtoOPM() - Method in class org.cellmicrocosmos.cm2.io.ppe.toolbox.MIFHandler
-
Use this method to compare both database entries to each other.
- compareTo(Object) - Method in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
-
- Compatibility - Class in org.cellmicrocosmos.cm2.io
-
The different compatibility settings for external PDB Viewers
shown in the PDB Property window.
- Compatibility() - Constructor for class org.cellmicrocosmos.cm2.io.Compatibility
-
- CompatibilityPanel - Class in org.cellmicrocosmos.cm2.gui
-
The compatibility panel is used to show the compatibility
of the actual PDB settings to external PDB viewers.
- CompatibilityPanel() - Constructor for class org.cellmicrocosmos.cm2.gui.CompatibilityPanel
-
- complain(String, String) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
-
- complainInternet() - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
-
- complainXML(String) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
-
- ComponentView - Class in org.cellmicrocosmos.cm2.gui.elements
-
- ComponentView() - Constructor for class org.cellmicrocosmos.cm2.gui.elements.ComponentView
-
- compressToJar(File, File) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
-
- COMPUTE_ABSOLUTE_VALUES - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.MISC
-
- computeAbsoluteValues - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
-
- CONF_FILENAME - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.IO
-
- CONF_PARSER() - Constructor for class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONF_PARSER
-
- CONFIG_FILE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
-
- ConfigIO - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
-
This class is for keeping various parameters as strings.
- ConfigIO() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.ConfigIO
-
- ConfigParser - Class in org.cellmicrocosmos.cm2.misc
-
This class is for keeping various parameters as strings.
- ConfigParser() - Constructor for class org.cellmicrocosmos.cm2.misc.ConfigParser
-
- configureTables() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
-
Configurates the Tables
- ConformationPanel - Class in org.cellmicrocosmos.cm2.coarsegrainsupport
-
This is the controlpanel used in the Conformation-Change-mode of the Molecule Editor
- ConformationPanel(MoleculeEditor) - Constructor for class org.cellmicrocosmos.cm2.coarsegrainsupport.ConformationPanel
-
- ConfParser - Class in org.cellmicrocosmos.cm2.io.ppe.toolbox
-
The ConfParser reads in the ppe.conf and generates different ArrayLists.
- ConfParser() - Constructor for class org.cellmicrocosmos.cm2.io.ppe.toolbox.ConfParser
-
Constructs a new ConfParser.
- Connection - Class in org.cellmicrocosmos.cm2.io.ppe.network.http
-
This is the abstract class for the connection to ftp/http files.
- Connection() - Constructor for class org.cellmicrocosmos.cm2.io.ppe.network.http.Connection
-
- CONNECTION() - Constructor for class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONNECTION
-
- Constraint_3D - Class in org.cellmicrocosmos.cm2.dataobjects
-
This class represents the constrains needed for the molecules.
- Constraint_3D(Atom_3D, Atom_3D) - Constructor for class org.cellmicrocosmos.cm2.dataobjects.Constraint_3D
-
- containsExampleLipidExtra(String, int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
- containsExampleLipidIntra(String, int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
- containsMolecules() - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
-
- containsMoleculeWithAbsoluteFilepath(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
- contents - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyData
-
- continuePainting(Point) - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
-
- ControlPanel - Class in org.cellmicrocosmos.cm2.coarsegrainsupport
-
This superclass describes a control panel that is displayed in the right half of the molecule editor
- ControlPanel(MoleculeEditor) - Constructor for class org.cellmicrocosmos.cm2.coarsegrainsupport.ControlPanel
-
- ControlPanel.TitledPanel - Class in org.cellmicrocosmos.cm2.coarsegrainsupport
-
- convertAtomNameToElementName(String) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
-
- convertFileSizeToString(long) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
-
Makes the passed Filesize to a string
- CoordinateBar - Class in org.cellmicrocosmos.cm2.functionality3d
-
The Coordinate System.
- CoordinateBar() - Constructor for class org.cellmicrocosmos.cm2.functionality3d.CoordinateBar
-
- coordinatesWouldExceedValidNumberRangeCurrently(MembraneModel) - Method in class org.cellmicrocosmos.cm2.io.PDBWriter
-
- CoordinateTransformationHints - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
-
A sheet with coordinate Transformation settings used by the reverse PDBParser
- CoordinateTransformationHints() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.CoordinateTransformationHints
-
- CoordinateTransformationSettings() - Constructor for class org.cellmicrocosmos.cm2.engine.DataPool.CoordinateTransformationSettings
-
- copy() - Method in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
-
Returns an exact clone of this instance
- copy(boolean, boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
-
Creates a new Protein / Lipid and copies all of its data.
- copy() - Method in class org.cellmicrocosmos.cm2.dataobjects.MyBounds
-
- copy() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.AutoBox
-
Copies this instance of the box
- copyFile(File, File) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
-
This method makes a copy of the given sourceFile to the defined destinationFile.
- copyMatrix(Matrix3f) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
-
Simply clones a matrix.
- copyMatrix(Matrix3f) - Static method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.RotationToolkit
-
Simply clones a matrix.
- copyMatrix(Matrix3f) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
-
- COPYRIGHT - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GENERAL
-
- countAtoms(int, int, int, boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
Counts the atoms for the specified group of molecules.
- countChains(int, int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
Counts the chains for the specified group of molecules.
- countMicroDomains() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
- countSampleLipids_Extracellular(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
-
Returns the number of lipid templates on the extracellular side of the
default area
- countSampleLipids_ExtraCellular() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MicroDomain
-
Returns the number of lipid templates on the extracellular side of this
microdomain
- countSampleLipids_Intracellular(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
-
Returns the number of lipid templates on the intracellular side of the
default area
- countSampleLipids_IntraCellular() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MicroDomain
-
Returns the number of lipid templates on the intracellular side of this
microdomain
- countTERs(int, int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
- countTotalLipidsThatAreAdded() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
-
Returns the number of all placed lipids in the membrane
- create2DImageOfCurrentMembrane(MembraneModel, int, boolean, boolean, boolean, int) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.Membrane_Image2D_Generator
-
- createAndAddANewExampleLipid(String, String, int, int, int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
Creates and adds a new sample Lipid with the passed parameters
- createAUnitMatrix() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
-
Creates a new unit matrix
- createAUnitMatrix() - Static method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.RotationToolkit
-
Creates a new unit matrix
- createAUnitMatrix() - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
-
- createCanvasPopUpMenu() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
-
- createCanvasPopUpMenu() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
-
- createCanvasPopUpMenu() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
-
- createCurrentDate() - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
-
- createDefaultEpsilons() - Static method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyDefaults
-
- createDefaultSigmas(Atom_Level_Minimizer) - Static method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyDefaults
-
- createImage(Molecule_3D, int, int) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.Membrane_Image2D_Generator
-
- createMembranePackingAlgorithm(Plugin, File) - Method in class org.cellmicrocosmos.cm2.pluginmanager.PluginManager
-
- createNewLipid(Lipid, int, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
-
Create a new lipid.
- createNextExtracellularLipid() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
-
Creates a new Lipid that can be placed in the membrane.
- createNextExtracellularLipid(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
-
Creates a new Lipid that can be placed in the membrane.
- createNextExtracellularLipid() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MicroDomain
-
Creates a new Lipid that can be placed in the membrane.
- createNextIntracellularLipid() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
-
Creates a new Lipid that can be placed in the membrane.
- createNextIntracellularLipid(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
-
Creates a new Lipid that can be placed in the membrane.
- createNextIntracellularLipid() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MicroDomain
-
Creates a new Lipid that can be placed in the membrane.
- createNextLipid(int, Lipid_3D[], int, int, MembranePackingAlgorithm) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
-
- createRandomCholesterolColor() - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
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- createRandomLayerID() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
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Chooses a random layerID of any layer that is in the model
- createRandomXZPosition(Rectangle) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
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Randomly creates a Point that has random x/z coordinates, including
decimal values
- createRow(int, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
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- createScaleFor2DImage() - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.Membrane_Image2D_Generator
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- CRITICAL_ATOM_COUNT - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
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- currentCGParticles - Variable in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
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- currentFunction - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Energies
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- currentLength - Variable in class org.cellmicrocosmos.cm2.dataobjects.Constraint_3D
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- CurrentMicroDomain - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
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- currentMoleculeAligning - Variable in class org.cellmicrocosmos.cm2.functionality3d.Hud
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- currentNeighbors - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
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- customizeThisFile(File, String) - Method in class org.cellmicrocosmos.cm2.io.ppe.transform.xml.SAXCustomizer
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Transforms the pdbtmall.xml from the given file into the pdbtm.mif.
- customizeThisFile(InputStream, String) - Method in class org.cellmicrocosmos.cm2.io.ppe.transform.xml.SAXCustomizer
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Transforms the pdbtmall.xml from the given InputStream into the pdbtm.mif.
- customizeThisFile(File, String) - Method in interface org.cellmicrocosmos.cm2.io.ppe.transform.xml.XMLCustomizer
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Transforms a given xml file in a program-internal file format.
- customizeThisFile(InputStream, String) - Method in interface org.cellmicrocosmos.cm2.io.ppe.transform.xml.XMLCustomizer
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Transforms a given xml file in a program-internal file format by using
an InputStream.