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G

GENERAL() - Constructor for class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GENERAL
 
generateGui() - Method in class org.cellmicrocosmos.cm2.gui.MainGui
builds up the gui with all added views
geo - Variable in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
geometry - Variable in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
geoObject - Variable in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
getActiveConstraints() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getAlgo() - Static method in class org.cellmicrocosmos.cm2.pluginmanager.CalculationManager
 
getAlgorithm_Directory_In_Workspace() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the Directory inside the Workspace Location for this Algorithm.
getAlgorithmDescription() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAlgorithmName() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAlgorithmStringRepresentation() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAlignedAtomCopies() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
returns a copy of all atoms of the molecule.
getAlignedAtoms() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getAlignedGeometricBounds() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns the current bounding box of this molecule.
getAlignedOPMAtoms() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getAlignedTrianglePoints() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns the copy of the original trianglepoints of this object computed to the correct alignment regarding to the translation and rotation of this molecule.
getAllAtomTypesOfMembraneModelSorted() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.AtomValues
 
getAllElementsOfMembraneModelSorted() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.AtomValues
 
getAllExampleLipidsExtra() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllExampleLipidsExtraInDomain(int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllExampleLipidsIntra() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllExampleLipidsIntraInDomain(int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllExampleLipidsOfTypeExtra(String, int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllExampleLipidsOfTypeExtra(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
getAllExampleLipidsOfTypeIntra(String, int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllExampleLipidsOfTypeIntra(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
getAllExampleLipidTypesExtra() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns a list of all types of sample lipids that occur in the membrane at least once
getAllExampleLipidTypesExtra() - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
getAllExampleLipidTypesExtraInDomain(int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllExampleLipidTypesIntra() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns a list of all types of sample lipids that occur in the membrane at least once
getAllExampleLipidTypesIntra() - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
getAllExampleLipidTypesIntraInDomain(int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllInternalBonds() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns a list of all bond objects associated with this atom.
getAllLipids() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Returns all rowdatas for Lipids
getAllLipids(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns a Vector with all lipids in the membrane of one side.
getAllLipidsExtra() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllLipidsExtraInDomain(int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllLipidsInDomain(int, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns a Vector with all lipids in the membrane of one domain and one side.
getAllLipidsIntra() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllLipidsIntraInDomain(int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllLipidsOfTypeExtra(String, int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllLipidsOfTypeIntra(String, int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllLipidTypes() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns a list of all types of lipids that occur in the membrane at least once
getAllLipidTypesExtraInDomain(int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllLipidTypesInMembraneExtra() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns a list of all types of proteins that occur in the extracellular membrane at least once
getAllLipidTypesInMembraneIntra() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns a list of all types of lipids that occur in the intracellular membrane at least once
getAllLipidTypesIntraInDomain(int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllMicroDomains(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllMoleculesInCurrentModel() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns all Molecule Instances that are currently in the Membrane Model, including all Layers and Microdomains.
getAllMoleculesInMembrane(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllMoleculesInMembrane() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllMoleculesInMembrane(int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllMoleculesInMembraneSortedBySide() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllMoleculesInMembraneSortedByType() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllParticleIDsOfMembraneModelSorted() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.AtomValues
 
getAllProfileNames(Molecule_3D, String) - Static method in class org.cellmicrocosmos.cm2.coarsegrainsupport.Molecule_Profile_IO
 
getAllProfiles(Molecule_3D, String) - Static method in class org.cellmicrocosmos.cm2.coarsegrainsupport.Molecule_Profile_IO
 
getAllProteins() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllProteins() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Returns all rowdatas for Proteins
getAllProteins() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns a Vector with all proteins in the membrane Will return all proteins that belong to the currently selected bilayer
getAllProteinsInDomain(int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllProteinsInDomain(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns a Vector with all proteins in the given domain Will return all proteins that belong to the currently selected bilayer domain.
getAllProteinsOfType(String, int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllProteinsOfType(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
getAllProteinTypes() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns a list of all types of proteins that occur in the membrane at least once
getAllProteinTypes() - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
getAllProteinTypesInDomain(int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getAllSampleLipids_ExtraCellular(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns all lipid templates of the extracellular side of this microdomain
getAllSampleLipids_ExtraCellular(int, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns all lipid templates of the extracellular side of this microdomain
getAllSampleLipids_ExtraCellular() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MicroDomain
Returns a copy of all lipid templates of the extracellular side of this microdomain
getAllSampleLipids_IntraCellular(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns all lipid templates of the intracellular side of this microdomain
getAllSampleLipids_IntraCellular(int, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns all lipid templates of the intracellular side of this microdomain
getAllSampleLipids_IntraCellular() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MicroDomain
Returns a copy of all lipid templates of the intracellular side of this microdomain
getAllSampleLipidsInModel() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns a list of all (!) lipid templates in the model
getAnEmptyDocument() - Static method in class org.cellmicrocosmos.cm2.io.DatabaseIO
Creates an Empty Document, used when a new Database is created from the Engine
getAppearance() - Method in class org.cellmicrocosmos.cm2.functionality3d.CoordinateBar
 
getApplicationName() - Method in class org.cellmicrocosmos.cm2.io.Compatibility
 
getArea() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Returns the area of the MembraneModel.
getArea() - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
Returns the area of the actual geometry shape.
getArea() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MicroDomain
Returns the area of the domain geometry.
getAtomCount() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns the atomcount of this molecule
getAtomicMass() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getAtomicMass() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns the atomic mass of this atom.
getAtomName() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns the name of this atom in its pdb-file entry
getAtoms(boolean, boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns a copy of all atoms for this instance in the right alignment.
getAuthor() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Returns the author string
getAuthor() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns the author of this pdb file
getAuthor() - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D.PdbAttributes
returns the AUTHOR
getBasementBranchGroup() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
getBondedNeighbor() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Bond
Returns the instance of the bonded neighbor of the atom that contains this bond
getBorderInsets(Component) - Method in class org.cellmicrocosmos.cm2.gui.MainGui.TabComponentNoBorder
 
getBoundingBox() - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
getBounds() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MicroDomain
Returns the bounding rectangle of the microdomain's defined area on the x/z plane
getBounds() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
returns the BoundingBox of the molecule.
getBranchGroup() - Method in class org.cellmicrocosmos.cm2.dataobjects.Constraint_3D
 
getBranchGroup() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getBranchGroup() - Method in class org.cellmicrocosmos.cm2.functionality3d.CoordinateBar
 
getBranchGroup() - Method in class org.cellmicrocosmos.cm2.functionality3d.Raster
 
getBranchGroup() - Method in class org.cellmicrocosmos.cm2.functionality3d.SelectionBox
 
getButton(Point) - Method in class org.cellmicrocosmos.cm2.functionality3d.Hud
 
getButtonName() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.EnergyFunction
Return the name for the RadioButton of this Algortihm here
getCamera() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Returns the camera
getCanvas() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Returns the canvas
getCenterPoint() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
Deprecated.
the equivalent method getPosition() should be used instead
getChainCount() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns the count of chains in the underlying pdb file
getChainID() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns the id of the atom's peptide chain as specifed in its pdb-file entry
getChainIDs() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns all chain ids used in the pdb file
getCharacterPosOf(char) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
 
getCharge() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns the fieldcharge as specifed in the pdb-file entry
getCode() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Returns the code string
getCode() - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D.PdbAttributes
Returns the Code that was found or null
getCollisionObjects() - Method in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
Returns the list of Objects, that have collided during the last run of a test.
getColor() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns the currently used color for this object
getColor(String) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.AtomValues
 
getComputeAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Check if absolute values are used during the computation process instead of percental values.
getComputeAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
Check if the ComponentView uses absolute values instead of percental values to compute the lipid distribution.
getComputeAbsoluteValues() - Method in class org.cellmicrocosmos.cm2.gui.elements.ComponentView
Check if the ComponentView uses absolute values instead of percental values to compute the lipid distribution.
getConfigFile() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.ConfigIO
Returns the config file
getConfigFile() - Static method in class org.cellmicrocosmos.cm2.misc.ConfigParser
Returns the config file
getContents() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Prepares a Document for the Dom Parser to save and return it
getCountOfOPM() - Method in class org.cellmicrocosmos.cm2.io.ppe.network.http.OPMConnection
 
getCountOfPdbAll() - Method in class org.cellmicrocosmos.cm2.io.ppe.network.http.PdbTMConnection
Obtains the number of all entries in the Protein Data Bank.
getCountOfPdbTM() - Method in class org.cellmicrocosmos.cm2.io.ppe.network.http.PdbTMConnection
Obtains the number of all entries in the Protein Data Bank of Transmembrane Proteins.
getCountOfPdbTMalpha() - Method in class org.cellmicrocosmos.cm2.io.ppe.network.http.PdbTMConnection
Obtains the number of all entries with alpha helices in the Protein Data Bank of Transmembrane Proteins.
getCountOfPdbTMbeta() - Method in class org.cellmicrocosmos.cm2.io.ppe.network.http.PdbTMConnection
Obtains the number of all entries with beta barrel in the Protein Data Bank of Transmembrane Proteins.
getCovalentRadius(String) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.AtomValues
 
getCovalentRadiusInAngstrom() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns the determined covalent radius of this atom
getCurrentEyePosition() - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.Display
 
getCurrentEyePosition() - Static method in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
 
getCurrentFile() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Returns the current File the DB is set to
getCurrentGuiMode() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
getCurrentIntersections(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getCurrentLayer() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
 
getCurrentLayerHeight() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
 
getCurrentLayerID() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
 
getCurrentLayerID() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the ID of the currently active layer
getCurrentLenght() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Bond
Deprecated.
getCurrentLength() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Bond
Returns the current length of this bond
getCurrentMembraneFile() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
Returns the currently opened Membranefile
getCurrentMolecule() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.DNDBridge
Returns the current Protein
getCurrentMolecules() - Method in class org.cellmicrocosmos.cm2.gui.elements.PropertiesView
 
getCurrentProfileName() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getCurrentRenderMode() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the current mode of rendering
getCurrentSelection() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
getCurrentSelection() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
getCutoff(Atom, Atom, float) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.EnergyFunction
Used to get the cutoff between this pair of atoms if "Autocutoff" is activated.
getDate() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns the date String
getDate() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getDate() - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D.PdbAttributes
Return the date that was found or null
getDecimalPlaces() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getDecimalPlaces() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Use this method to get the precision of the computation of the percentages (if isAbsoluteValuesSelected() is false, default mode of the MembraneEditor).
getDesiredAtomDistance() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the desired distance between atoms that the user can define.
getDialogFrame() - Static method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmGUI
Returns the JDialog, if it is required somehow
getDirection() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Bond
Returns the direction of the neighbor in respect to the atom this bond is associated with.
getDisplay() - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
Returns the Display of this MoleculeEditor.
getDomainID() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getDomainID() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MicroDomain
Returns the Domain_ID for this microdomain
getDomainIdentifier() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
Returns the ID-number of the microdomain that this molecule is assigned to
getElement() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns the field element as specifed in the pdb-file entry
getEmptyRowData(File) - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Creates and returns a new rowdata that is empty except for the path of the passed file
getEnergy() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns the stored energy value
getEntryAt(int) - Method in exception org.cellmicrocosmos.cm2.io.InvalidEntriesException
returns error at specified index
getEntryCount() - Method in exception org.cellmicrocosmos.cm2.io.InvalidEntriesException
returns the number of entries made
getExampleLipidAtExtra(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Returns the sample lipid at the specified index
getExampleLipidAtIntra(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Returns the sample lipid at the specified index
getExampleLipidsByPDBCodeExtra(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns all Sample Lipid individues which are of the specified type.
getExampleLipidsByPDBCodeIntra(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns all Sample Lipid individues which are of the specified type.
getExampleLipidsCountExtra() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Returns the count of example lipids
getExampleLipidsCountIntra() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Returns the count of example lipids
getExampleLipidsExtra() - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
getExampleLipidsIntra() - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
getExampleLipidTypeAlreadyInside(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Tests if a ExampleLipid with the passed PdbCode is already added
getEXPDTA() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getExtracellularLipidByPDBCode(String) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns a new extracellular lipid by given PDB-Code.
getFirstMoleculeThatHasFile(File, int, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Returns the first Molecule found that has the passed file in the specified group of molecules
getFrame() - Method in class org.cellmicrocosmos.cm2.gui.MainGui
Returns the Frame
getFullInformation() - Method in interface org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmInterface
 
getFullInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.AdvancedRandomPlacing
 
getFullInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
 
getFullInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
 
getFullInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.IntersectionDeleter
 
getFullInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.LinearPlacing
 
getFullInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.MembraneShifter
 
getFullInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
 
getFullInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
returns the full information about this algorithm
getFullInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
 
getFullInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
returns full information about this algorithm
getFullInformation() - Method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.ToolkitMembranePackingAlgorithm
 
getGeometryType() - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
Return the type of the Microdomain.
getGui() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.EnergyFunction
Here you may return the gui for this.
getHeader() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Returns the header string
getHeader() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getHeader() - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D.PdbAttributes
Returns the Header that was found or null
getHighestExampleLipid(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Returns the lipid with the higest percentage in the specified group
getHighlightedDomainID() - Method in class org.cellmicrocosmos.cm2.gui.elements.ComponentView
 
getHighlightedID() - Method in class org.cellmicrocosmos.cm2.functionality3d.MicroDomainManager
 
getHighlightedMicroDomain() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
getHighlightedMicroDomain() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
getHints(File) - Method in class org.cellmicrocosmos.cm2.io.ReversePDBParser
 
getHostParticle(Atom_3D) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getHud() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
getID() - Method in class org.cellmicrocosmos.cm2.dataobjects.Protein_3D
Returns the ID of the protein
getImageLarge() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getImageSmall() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getInformation() - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
getInputStreamFromXML() - Method in class org.cellmicrocosmos.cm2.io.ppe.network.http.OPMConnection
 
getInputStreamFromXML() - Method in class org.cellmicrocosmos.cm2.io.ppe.network.http.PdbTMConnection
Generates an InputStream to the pdbtmall.xml.
getIntersectedBorders(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns all borders the molecule intersects with.
getIntersectedMolecules(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the molecules the passed lipid intersects with.
getIntersectionsDisplayer() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
getIntersectManager() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
getIntracellularLipidByPDBCode(String) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns a newintracellular lipid by given PDB-Code.
getJ3DBranchGroup() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
getJ3DBranchGroup() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
getJ3DBranchGroup() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
For Java 3D experts only! Here it is possible to add custom Java3D-based objects.
getJavapath() - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
getJRNL() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getKEYWDS() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getLastGeneratedMembraneFile() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getLastLaunchedEngine() - Static method in class org.cellmicrocosmos.cm2.engine.StartMain
Retrieves the engine of the program.
getLastModified() - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
getLayer(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getLayerAtIndex(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the Layer Object at the specified index
getLayerByID(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getLayerByLayerID(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the Layer that has the specified Layer ID or null if the Layer doesn't exist
getLayerCount() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getLayerCount() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the number of Layers in the model
getLayerId() - Method in class org.cellmicrocosmos.cm2.dataobjects.Layer
 
getLayerID() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getLayerID() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MicroDomain
Returns the Layer_ID for this microdomain
getLayerID() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
Returns the ID-number of the Layer that this molecule is assigned to
getLipidAtExtra(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns the lipid at the specified index
getLipidAtIntra(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns the lipid at the specified index
getLipidCountExtra() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns the current number of lipids in the model
getLipidCountIntra() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns the current number of lipids in the model
getLipidInMembraneHeight(Lipid) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the scaled height in the membrane of the given lipid.
getLipidsByPDBCodeExtra(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns all Lipid individues which are of the specified type.
getLipidsByPDBCodeIntra(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns all Lipid individues which are of the specified type.
getLipidsInRadiusExcept(Molecule, int, Vector<Molecule>) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns all lipids within the given radius of the molecule mol.
getLipidTypeAlreadyInside(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Tests if a Lipid with the passed PdbCode is already inside the Membrane
getList() - Method in class org.cellmicrocosmos.cm2.io.ppe.network.http.Connection
 
getLower(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns the lower corner of the current boundingbox.
getLowestPossibleReturnValue() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.EnergyFunction
Should return the lowest value possible that could be a result of the calculateEnergy method.
getLowestValuePossibleMultiplied() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Energies
 
getMainBranchGroup() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
getMainFrame() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
getMainFrame() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
getMassValue() - Method in class org.cellmicrocosmos.cm2.dataobjects.Particle
 
getMassValue(String) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.AtomValues
 
getMaxRadius_XZ() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
Compares the widht (x) and the height (z) of the molecule's current boundingbox and returns the largest of these two values
getMembrane3D() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
returns the MembraneDisplay instance
getMembraneArea() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the Area of the whole Membrane in A².
getMembraneBounds2D() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Similar to getMembraneSize(), but this returns the bounds as a rectangle object
getMembraneHasBeenEditedAgain() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Indicates wether or not the current MembraneModel has been edited again since last load or save
getMembraneHasBeenEditedAgain() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
Indicated wether or not the current MembraneModel has been edited again since last load or save
getMembraneModel() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
returns the Instance of the MembraneModel currently open
getMembraneSide() - Method in class org.cellmicrocosmos.cm2.dataobjects.Lipid_3D
 
getMembraneSide() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Lipid
Returns the assigned Side of the Membrane.
getMembraneSize() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the size of the membrane
getMessageString() - Method in exception org.cellmicrocosmos.cm2.io.InvalidEntriesException
concatenates all error Messages to one String, seperated by the new Line indicator "\n"
getMicroDomain(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getMicroDomain(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the microdomain object that has the specified id
getMicroDomainAt(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the microdomain object at the specified index
getMicroDomainAtPoint(Point, int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
getMicroDomainAtPoint(Point2f, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Tests if the passed point is inside the area of a microdomain of the given membrane layer and returns the Domain_ID for it
getMicroDomainAtPoint(Point2f) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Tests if the passed point is inside the area of a microdomain of the active membrane layer and returns the Domain_ID for it
getMicroDomainAtXZ(float, float) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
Returns the microdomain at the given x/z coordinates.
getMicroDomainCount() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the count of microdomains in the membrane
getMicroDomainManager() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
getMifHandler() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
Gets the MIFHandler needed for the PDB_TM alignment.
getMinAtomDistance() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the desired distance between atoms that has been set in the settings dialog of the applycation
getMinRadius() - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Returns the minimum orbit radius.
getMode() - Method in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
Returns the currently active cameramode
getModel() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.ParameterMatrixPanel
Returns the model of the table in this panel
getModelcount() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getModelSet() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns the index of the model this molecule is constructed from.
getMoleculesInRadius(Molecule, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns all molecules within the given radius of the molecule mol.
getMoleculesInRadiusExcept(Molecule, int, Vector<Molecule>) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns all molecules within the given radius of the molecule mol.
getMoleculesInRadiusOnMySide(Point3f, int, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns all molecules within the given radius of the Point3f on given membrane side.
getMoleculesInRadiusOnMySide(Molecule, int, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns all molecules within the given radius of the molecule mol on the given membrane side.
getMoleculesInRadiusOnMySideExcept(Molecule, int, int, Vector<Molecule>) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns all molecules within the given radius of the molecule mol on the given membrane side.
getMouseBehavior() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getMRNA() - Static method in class org.cellmicrocosmos.cm2.engine.Engine
 
getName() - Method in interface org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmInterface
 
getName() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.AdvancedRandomPlacing
 
getName() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
 
getName() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
 
getName() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.IntersectionDeleter
 
getName() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.LinearPlacing
 
getName() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.MembraneShifter
 
getName() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
 
getName() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
returns the name of this algorithm.
getName() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
 
getName() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
 
getName() - Method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.ToolkitMembranePackingAlgorithm
 
getName() - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
getNearestLipidOnMySide(Molecule, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the nearest lipid to the given molecule mol on the determined membrane side.
getNearestMolecule(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the closest molecule to the passed one.
getNearestMoleculeExcept(Molecule, Vector<Molecule>) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the nearest molecule to the given molecule mol.
getNearestMoleculeExceptDetailed(Molecule, Vector<Molecule>, boolean) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the nearest molecule to the given molecule mol.
getNearestMoleculeExceptOnMySide(Molecule, Vector<Molecule>, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the nearest molecule to the given molecule mol on the determined membrane side.
getNearestMoleculeExceptOnMySideDetailed(Molecule, Vector<Molecule>, int, boolean) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the nearest molecule to the given molecule mol on the determined membrane side.
getNearestMoleculeOnMySide(Molecule, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the nearest molecule to the given molecule mol on the determined membrane side.
getNearestMoleculeOnMySideDetailed(Molecule, int, boolean) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the nearest molecule to the given molecule mol on the determined membrane side.
getNearestProtein(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the nearest protein.
getNearestProteinDetailed(Molecule, boolean) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the nearest protein.
getNearestProteinExcept(Molecule, Vector<Protein>) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the nearest protein.
getNearestProteinExceptDetailed(Molecule, Vector<Protein>, boolean) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the nearest protein.
getNewMatrix() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.EnterMatrixDialog
 
getNewYTranslation() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.EnterMatrixDialog
 
getNextFreeProteinId() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
Returns the next Protein ID number that should be used for a new instance.
getOccupancy() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns the field occupancy as specifed in the pdb-file entry
getOriginalAllAtomConstraintLenghts() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Deprecated.
getOriginalAllAtomConstraintLengths() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getOriginalAtoms() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
Returns the list of all actual Atom instances.
getOriginalConstraintLenghts(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Deprecated.
getOriginalConstraintLengths(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
NOT MEANT TO BE USED BY PLUGIN DEVELOPERS!
getOriginalFile() - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
getOriginalHeight() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getOriginalLenght() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Bond
Deprecated.
getOriginalLength() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Bond
Returns the ideal length of this bond, as determined by the pdb-file or the profile applied to the molecule
getOriginalMolecule() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
returns the original Molecule_3D of this wrapper molecule.
getOriginalTrianglePoints() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
returns the original, unaligned trianglepoints
getOwnThread() - Static method in class org.cellmicrocosmos.cm2.engine.Engine
 
getParameterKey() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns the string that serves as a possible key for parameters.
getParentalMolecule() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns the molecule instance that hosts this atom
getParticleID() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns the particle identifier of this particle
getPDBcode() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getPDBFile() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns the pdb file this molecule was created from
getPDBTMRotation() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns the molecule's PDBTM rotation matrix.

Returns a identity matrix by default.
getPDBTMTranslation() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns the y-coordinate of the molecule's bounding center after transforming by the PPE.

Value 0 by default.
getPercent() - Method in class org.cellmicrocosmos.cm2.dataobjects.Lipid_3D
Returns the percentage of this lipid
getPercentages_ExtraCellular(int, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Get the percentages of the defined layer and domainID on the extracellular side.
getPercentages_IntraCellular(int, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Get the percentages of the defined layer and domainID on the intracellular side.
getPickNDragManager() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Returns the PND manager
getPluginManager() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
 
getPluginManager() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
getPluginManager() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
 
getPluginManager() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
getPosition() - Method in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
The (anstrom) position of this Atom
getPosition() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns the Position of this instance in the membrane All values are anstroms
getPosition() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Gets a copy of the atom's current position inside the molecule
getPosition() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
returns the position of the molecule in the membrane
getProteinAt(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
gets the protein at the specifed index
getProteinCount() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns the current number of Proteins in the model
getProteins() - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
getProteinsByPDBCode(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns all Protein individues which are of the specified type.
getProteinTypeAlreadyInside(String) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Tests if a Protein with the passed PdbCode is already inside the Membrane
getRandom() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.SimpleRandom
Returns the used Random object.
getRandomLipid(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
Returns a randomly chosen lipid from all lipids placed on the chosen membrane side.
getRandomLipidColor() - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
Get a randomly created Color for Lipids
getRandomNumber(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
 
getRandomProteinColor() - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
Get a randomly created Color for Proteins
getRandomRotationInMode(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
Returns a random integer for the roation in the given mode.
getRawPdbData(String) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
 
getRealtiveComponent() - Method in class org.cellmicrocosmos.cm2.engine.Engine.J3DOperations
 
getRecordName() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns the record name of this atom's pdb-file entry
getRemark() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns the comment String
getRenderMode() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getResidueName() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns the name of the atom's residue as specifed in its pdb-file entry
getResultingMembraneModel() - Method in class org.cellmicrocosmos.cm2.io.MembraneXmlReader
Returns the MembraneModel that should have been filled before
getResultingRowdata() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.EditDBEntryDialog
Returns the rowdata that was passed to the dialog
getRotateEnable() - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Retrieves the state of rotate enabled
getRotationCenter(Point3d) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Places the value of the center around which the View rotates into the Point3d.
getRotationMatrix() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
returns the current rotation matrix of this molecule relative to the coordinates of the pdb file this instance uses
getRotationMatrix() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
returns the current rotation matrix of this molecule.
getRotXFactor() - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Returns the x rotation movement multiplier
getRotYFactor() - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Returns the y rotation movement multiplier
getRuntimeControlPanel() - Method in interface org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmInterface
 
getRuntimeControlPanel() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.AdvancedRandomPlacing
 
getRuntimeControlPanel() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
 
getRuntimeControlPanel() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
 
getRuntimeControlPanel() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.IntersectionDeleter
 
getRuntimeControlPanel() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.LinearPlacing
 
getRuntimeControlPanel() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.MembraneShifter
 
getRuntimeControlPanel() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
 
getRuntimeControlPanel() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
 
getRuntimeControlPanel() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
 
getRuntimeControlPanel() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
 
getRuntimeControlPanel() - Method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.ToolkitMembranePackingAlgorithm
 
getSampleLipid_Extracellular(int, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the extracellular lipid template at the specified index.
getSampleLipid_ExtraCellular(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MicroDomain
Returns a copy of the extracellular lipid template at the specified index.
getSampleLipid_Intracellular(int, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the intracellular lipid template at the specified index.
getSampleLipid_IntraCellular(int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MicroDomain
Returns a copy of the intracellular lipid template at the specified index
getScaleFactor() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.EnergyFunction
Return a scale factor for your Energy Values.
getSeed() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.UniqueRandom
Get the actual used seed.
getSelected() - Method in class org.cellmicrocosmos.cm2.functionality3d.PickNDragManager
Returns the currently selected proteins
getSelectedArea() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the ID of the microdomain that has been highlighted at startup.
getSelectedMolecules() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Returns the selected Proteins from the PNDmanager
getSelectedType() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.EditDBEntryDialog
Returns which type of Molecule was selected
getShape() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getShape(Component, int, int, int, int) - Method in class org.cellmicrocosmos.cm2.gui.MainGui.TabComponentNoBorder
 
getShortInformation() - Method in interface org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmInterface
 
getShortInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.AdvancedRandomPlacing
 
getShortInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
 
getShortInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
 
getShortInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.IntersectionDeleter
 
getShortInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.LinearPlacing
 
getShortInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.MembraneShifter
 
getShortInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
 
getShortInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
returns the short information about this algorithm
getShortInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
 
getShortInformation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
returns short information about this algorithm
getShortInformation() - Method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.ToolkitMembranePackingAlgorithm
 
getSimpleName(File) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
Returns the simple name without the file extension
getSize() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Returns the size of the membrane
getSOURCE() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
returns a list of entered species
getSOURCE() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getSpecies() - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D.PdbAttributes
Returns the Species that was found under SOURCE or null
getSpecifiedIcon(String) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_IconDepot
Returns the Icon that has the passed name.
getSpinnerValues() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.ChangeSizeDialog
Returns the Value the Spinners are set to
getSpinnerValues() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.NewMembraneDialog
Returns the Value the Spinners are set to
getStartingTime() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Gets the starting time of the algorithm.
getState() - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
getStereoAvailable() - Static method in class org.cellmicrocosmos.cm2.engine.Engine
 
getStereoEnable() - Method in class org.cellmicrocosmos.cm2.gui.MainGui
 
getStereoSlider() - Method in class org.cellmicrocosmos.cm2.gui.MainGui
 
getStereoSliderPosition() - Method in class org.cellmicrocosmos.cm2.gui.MainGui
 
getStereoValue() - Method in class org.cellmicrocosmos.cm2.engine.Engine.J3DOperations
 
getStereoValueString() - Method in class org.cellmicrocosmos.cm2.engine.Engine.J3DOperations
 
getStereoViewAutoFocusMode() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
getStereoViewAutoFocusMode() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Get the actual Stereo View Auto Focus Mode.
getStereoViewAutoFocusMode() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
getStereoViewMode() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
getStereoViewMode() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Get the actual Stereo View Mode.
getStereoViewMode() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
getStereoViewScalingMode() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
getStereoViewScalingMode() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Get the actual Stereo View Scaling Mode.
getStereoViewScalingMode() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
getStringRepresentationOfSetupParameters() - Method in interface org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmInterface
 
getStringRepresentationOfSetupParameters() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.AdvancedRandomPlacing
 
getStringRepresentationOfSetupParameters() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
 
getStringRepresentationOfSetupParameters() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
 
getStringRepresentationOfSetupParameters() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.IntersectionDeleter
 
getStringRepresentationOfSetupParameters() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.LinearPlacing
 
getStringRepresentationOfSetupParameters() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.MembraneShifter
 
getStringRepresentationOfSetupParameters() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
 
getStringRepresentationOfSetupParameters() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
returns string representation of the chosen settings.
getStringRepresentationOfSetupParameters() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
 
getStringRepresentationOfSetupParameters() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
returns a string representation of users GUI settings
getStringRepresentationOfSetupParameters() - Method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.ToolkitMembranePackingAlgorithm
 
getSystemCovalentRadius(String) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the covalent radius that is stored by this application under the specified key.
getSystemVanDerWaalsRadius(String) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns the Van-der-Waals-radius that is stored by this application under the specified key.
getTable() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.ParameterMatrixPanel
Returns the table displayed in this panel.
getTableOnFrontIndex() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Returns which table is currently on Front
getTableOnFrontIndex() - Method in interface org.cellmicrocosmos.cm2.interfaces.EditDBEntryDialogListener
 
getTempFactor() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns the field tempfactor as specifed in the pdb-file entry
getTempJar() - Static method in class org.cellmicrocosmos.cm2.io.FileIOHandler
 
getTerminationTime() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Gets the termination time of the algorithm.
getText() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyNumberTextField
 
getTitle() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Returns the title String
getTitle() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getTitle() - Method in class org.cellmicrocosmos.cm2.engine.Engine
 
getTitles() - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D.PdbAttributes
Returns the Title that was found or null Multiple titles in the pdb will be concatenated to the returnvalue
getToolText(String, int, int, boolean, boolean, boolean, boolean, boolean, boolean, int, int, boolean, boolean) - Method in class org.cellmicrocosmos.cm2.gui.CompatibilityPanel
 
getTooltip(int) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
For a better overview, the Tooltips are defined in this method and they can be accessed by their index
getTooltip() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.EnergyFunction
Return a tooltip for this algorithm's Button
getTotalHeight(Molecule_3D) - Static method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
NOT MEANT TO BE USED BY PLUGIN DEVELOPERS!
getTotalHeight(Lipid) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
NOT MEANT TO BE USED BY PLUGIN DEVELOPERS!
getTotalMoleculeCount(int) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Returns the total molecule count.
getTransformGroup() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getTransformMatrixOf(String) - Method in class org.cellmicrocosmos.cm2.io.ppe.toolbox.MIFHandler
Obtains the transform matrix of a given PDB-Id.
getTransformVectorOf(String) - Method in class org.cellmicrocosmos.cm2.io.ppe.toolbox.MIFHandler
Obtains the transformation vector of a given PDB-Id.
getTranslateEnable() - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Retrieves the state of translate enabled
getTransXFactor() - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Returns the x translation movement multiplier
getTransYFactor() - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Returns the y translation movement multiplier
getTrianglePoints() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
returns the scaled points of the triangles that build up the shape of the molecule.
getType() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
returns the PDB code of the molecule
getType() - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
getTypes() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.ParameterMatrixPanel
Return this names for each row / column that was passed inside the constructor
getUniverse() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
returns the 3D universe
getUnrotatedBounds() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getUpper(boolean) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns the upper corner of the current boundingbox.
getUrl() - Method in class org.cellmicrocosmos.cm2.io.ppe.network.http.Connection
 
getUserData() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns the object that has been stored by setUserData()
getValue(String) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.ConfigIO
returns the value(s) under the given key/tagname as a String-Array.
getValue(String) - Static method in class org.cellmicrocosmos.cm2.misc.ConfigParser
returns the value(s) under the given key/tagname as a String-Array.
getVanDerWaalsRadius(String) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.AtomValues
 
getVanDerWaalsRadiusInAngstrom() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Returns the determined Van-der-Waals-radius of this atom
getWholeDocument() - Method in class org.cellmicrocosmos.cm2.io.ppe.network.http.OPMConnection
 
getX() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getXZBounds() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
Determines the BoundingBox of the molecule and returns a rectangle that represents the bounds on the x/z plane
getY() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getYHeight() - Method in class org.cellmicrocosmos.cm2.dataobjects.Layer
 
getYTranslation() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns the current Y-height of this molecule in angstrom
getYTranslation() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
returns the translation on the y-axis.
getZ() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
getZoomEnable() - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Retrieves the state of zoom enabled
getZoomFactor() - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Returns the zoom movement multiplier
GlobalDatabaseBrowser - Class in org.cellmicrocosmos.cm2.gui
A Gui that allows the User to search and to download Pdb Files via the RCSB Database
GlobalDatabaseBrowser(String, String) - Constructor for class org.cellmicrocosmos.cm2.gui.GlobalDatabaseBrowser
Constructs and shows the Gui
GranularityPanel - Class in org.cellmicrocosmos.cm2.coarsegrainsupport
This class represents the controlpanel used in the Coarse-Grain-mode of the molecule editor
GranularityPanel(MoleculeEditor) - Constructor for class org.cellmicrocosmos.cm2.coarsegrainsupport.GranularityPanel
 
graphics2DDeactivator - Static variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
GraphPanel - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
This panel displays multiple graphs that can be updated frequently
GraphPanel(String, String, String, String[], Color[]) - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.GraphPanel
Construcs a new Graphpanel
Gui - Class in org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer
This class displays and handles all components of the graphical user interface of the algorithm
Gui(Atom_Level_Minimizer) - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Gui
 
GUI_MODE_ALIGN_PROTEIN - Static variable in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
GUI_MODE_ALIGN_PROTEIN_PLUS - Static variable in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
GUI_MODE_ALIGN_SAMPPLELIPID - Static variable in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
GUI_MODE_MODEL_CHANGE - Static variable in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
GUI_SETTINGS_AND_CONTROLS() - Constructor for class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GUI_SETTINGS_AND_CONTROLS
 
guiListener - Variable in class org.cellmicrocosmos.cm2.gui.MainGui
 
GuiListener - Interface in org.cellmicrocosmos.cm2.interfaces
This interface provides all relevant events occured in the Gui
guiMode - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Gui
 
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