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C

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
 
createRandomLayerID() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Chooses a random layerID of any layer that is in the model
createRandomXZPosition(Rectangle) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Randomly creates a Point that has random x/z coordinates, including decimal values
createRow(int, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
 
createScaleFor2DImage() - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.Membrane_Image2D_Generator
 
CRITICAL_ATOM_COUNT - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
currentCGParticles - Variable in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
currentFunction - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Energies
 
currentLength - Variable in class org.cellmicrocosmos.cm2.dataobjects.Constraint_3D
 
CurrentMicroDomain - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
 
currentMoleculeAligning - Variable in class org.cellmicrocosmos.cm2.functionality3d.Hud
 
currentNeighbors - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
 
customizeThisFile(File, String) - Method in class org.cellmicrocosmos.cm2.io.ppe.transform.xml.SAXCustomizer
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
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
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
Transforms a given xml file in a program-internal file format by using an InputStream.
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