- 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
-
- 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
-