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R

radii - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.AtomValues
 
radiusCov - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
 
radiusVDW - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
 
random - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
The random that may be used
RandomPlacing - Class in org.cellmicrocosmos.cm2.membranepackingalgorithms
Places the lipids randomly within membrane bounds and may try to approach proteins or the membrane center and twisting and shaking the lipids.
RandomPlacing() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
 
Raster - Class in org.cellmicrocosmos.cm2.functionality3d
The Raster that is painted on the plane in the 3d view.
Raster() - Constructor for class org.cellmicrocosmos.cm2.functionality3d.Raster
 
rasterVisible - Variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
RAWDATA_SEPERATOR - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
rawPdbData - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool
 
rb1 - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
 
rb2 - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
 
rcsbdownloadLink - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
 
rcsbentriesLink - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
 
rcsbimageLink - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
 
rcsbLink - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
 
read() - Static method in class org.cellmicrocosmos.cm2.pluginmanager.PluginIO
 
READ_HELPFILES_DIRECTLY_FROM_MAIN_FOLDER - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.DEBUG
 
readAttributes(File) - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D
Reads in some attributes of the passed Pdb File.
readAttributes(String[]) - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D
Reads in some attributes of the passed pdb file contents (must be the lines from an Pdb File in Strings).
readDataFromDisc() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.ConfigIO
restores the Hasttable from the cfg_file.
readDataFromDisc() - Static method in class org.cellmicrocosmos.cm2.misc.ConfigParser
restores the Hasttable from the cfg_file.
readDefaultProfile(Molecule_3D) - Static method in class org.cellmicrocosmos.cm2.coarsegrainsupport.Molecule_Profile_IO
 
readFile(File) - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D
Just reads the passed pdb File
readIcons() - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_IconDepot
Initializes all icons
readLipid(File, int, Vector<String>) - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D
Constructs a Lipid_3D according to the file
readMembrane(File) - Method in class org.cellmicrocosmos.cm2.io.MembraneXmlReader
Reads in the passed file and fills the MembraneModel with Data
readModel(String[], int) - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D
Reads all ATOM/HETATM/TER lines for the specified model
readPreview(File) - Static method in class org.cellmicrocosmos.cm2.io.DatabaseIO
Read the data from a file and return a preview
readPreview(File) - Static method in class org.cellmicrocosmos.cm2.io.MembraneXmlReader
Reads in the passed file and returns Info
readProfile(Molecule_3D, String, String) - Static method in class org.cellmicrocosmos.cm2.coarsegrainsupport.Molecule_Profile_IO
 
readProtein(File, int, Vector<String>) - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D
Constructs a Protein_3D according to the file
readSection(File, String) - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D
Reads (only!) the lines of a section in a pdb file that uses the passed tag as recordname
readToPlugin(File) - Method in class org.cellmicrocosmos.cm2.pluginmanager.PluginManager
 
recalculatePoints() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Allows to realign the trianglePoints and the boundingbox manually.
recombineEditedMembers(boolean) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
recordName - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
 
RECTANGULAR - Static variable in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
REDIRECT_ERRORS_TO_LOGFILE - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.DEBUG
if true, all Errors will be printed into a file instead of the System Tray
redoAtomsShiftedToOtherSide - Variable in class org.cellmicrocosmos.cm2.io.ReversePDBParser
 
redoMesh(Vector<Point3f>, Point3f) - Method in class org.cellmicrocosmos.cm2.io.PdbReader_3D
 
refreshMembranesInCm1(String, String) - Method in class org.cellmicrocosmos.cmX.mrna.MRNA
 
refreshViews(boolean, boolean, boolean, boolean, boolean, boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.J3DOperations
 
refreshViews(boolean, boolean, boolean, boolean, boolean, boolean, boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
refreshViews(boolean, boolean, boolean, boolean, boolean, boolean, boolean) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
refreshViews(boolean, boolean, boolean, boolean, boolean, boolean) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Use this method if you changed some values relevant for the GUI of CmME.
reloadGeometry() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
Called, when its necessary to rebuild all shapes in the mebrane, for instance when another detail level is chosen.
reloadGeometry() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
reloadGeometry() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
 
reloadGeometry() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
remark() - Method in class org.cellmicrocosmos.cm2.io.Compatibility
 
removeExtracellularLipid(Lipid) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Deprecated.
use removeLipidsFromMembrane(Lipid[] lipid) instead
removeInnerAtomsFactor - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
removeIntersectingEarthOrSkyLipids(HashSet<Lipid>) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
Remove all lost wanderers from the intra- and extracellular side.
removeIntracellularLipid(Lipid) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Deprecated.
use removeLipidsFromMembrane(Lipid[] lipid) instead
removeLayer(Layer) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
removeLipidExtra(Lipid_3D) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
removeLipidExtra(Lipid_3D) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
removeLipidIntra(Lipid_3D) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
removeLipidIntra(Lipid_3D) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
removeLipidsFrom3D(Lipid_3D[]) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
removeLipidsFrom3D(Lipid_3D[]) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
removeLipidsFromMembrane(Lipid[]) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Removes the passed list of lipids from the membrane
removeMicroDomain(MicroDomain_3D) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
removeMicroDomain(MicroDomain_3D) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
removeMicroDomain(MicroDomain_3D) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
removeMoleculesFrom3D(Molecule_3D[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
removes given proteins from the 3D model
removeProteinsFrom3D(Protein_3D[]) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
removeProteinsFrom3D(Protein_3D[]) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
RENDER_MODE_BALLS_N_STICKS - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.RENDERMODE
 
RENDER_MODE_BALLS_N_STICKS - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
 
RENDER_MODE_COLORED_STICKS - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.RENDERMODE
 
RENDER_MODE_COLORED_STICKS - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
 
RENDER_MODE_COVALENT - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.RENDERMODE
 
RENDER_MODE_COVALENT - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
 
RENDER_MODE_POLYGON - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.RENDERMODE
 
RENDER_MODE_POLYGON - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
 
RENDER_MODE_VAN_DER_WAALS - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.RENDERMODE
 
RENDER_MODE_VAN_DER_WAALS - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
 
RENDERMODE() - Constructor for class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.RENDERMODE
 
repaintByMembraneModel(MembraneModel) - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
repaints the 3D model by using the informations from the model.
repainted(Graphics) - Method in interface org.cellmicrocosmos.cm2.interfaces.CM2AdditionalListener
 
replaceLastLog(String, int) - Method in class org.cellmicrocosmos.cm2.coarsegrainsupport.ControlPanel
 
replaceMembraneModel(MembraneModel) - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
replaces the current Membrane completely
reportDBLoadingException(Exception) - Method in class org.cellmicrocosmos.cm2.io.FileIOHandler
Report an Exception that occured during loading the DB here and the User will be informed regarding to the type of exception
reportDBSavingException(IOException) - Method in class org.cellmicrocosmos.cm2.io.FileIOHandler
Report an Exception occured during saving the DB here to inform the User
reportImageSavingException(Exception) - Method in class org.cellmicrocosmos.cm2.io.FileIOHandler
Report an Exception occured during saving here to inform the User
reportMembraneGeneratingException(Exception) - Method in class org.cellmicrocosmos.cm2.io.FileIOHandler
Report an Exception occured during Generating the Membrane into a pdb file
reportMembraneLoadingException(Exception) - Method in class org.cellmicrocosmos.cm2.io.FileIOHandler
Report an Exception that occured during loading here and the User will be informed regarding to the type of exception
reportMembraneSavingException(Exception) - Method in class org.cellmicrocosmos.cm2.io.FileIOHandler
Report an Exception occured during saving here to inform the User
reportProtocolSavingException(Exception) - Method in class org.cellmicrocosmos.cm2.io.FileIOHandler
Report an Exception occured during saving here to inform the User
REQUEST_KEY_AUTHORIZATION - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.CONNECTION
 
requestChangeOfRenderMode() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
NOT MEANT TO BE USED BY PLUGIN DEVELOPERS!
requestFocusOnView(int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
requestFocusOnView(int) - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
requestRenderModeChange() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
requestRenderModeChange() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
requestUsertoChooseFile(int) - Method in class org.cellmicrocosmos.cm2.io.FileIOHandler
Initializes the specified file Choosing operation.
requestUsertoChooseFileForGeneratingMembrane() - Method in class org.cellmicrocosmos.cm2.io.FileIOHandler
Initializes the specified file Choosing operation for the pdb File the generated Membran will have.
requiredAtomserials() - Method in class org.cellmicrocosmos.cm2.io.Compatibility
 
requiredChains() - Method in class org.cellmicrocosmos.cm2.io.Compatibility
 
resetModels() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
sets new Models on the tables which means that they get completely cleared
reshapeDomains() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
 
residueName - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
 
restartNumberingWith0 - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.LimitationSettings
 
restoreFromCoarseGrain(Particle) - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
restoreLayout() - Method in class org.cellmicrocosmos.cm2.gui.MainGui
trying to retrieve the layout here from the layout file.
restoreMembraneFromPDB(String, String, CoordinateTransformationHints, boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
Restore a membrane from a PDB file with the following options and wait until the reverse parsing status is returned.
restoreMembraneFromPDB(String, String, CoordinateTransformationHints, boolean, boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
Restore a membrane from a PDB file with the following options (Set optional parameters to null if not needed):
restoreMembraneFromPDB(String, String, CoordinateTransformationHints, boolean) - Method in class org.cellmicrocosmos.cm2.engine.Engine
This method loads a PDB-Membrane into the running MembraneEditor.
restoreMembraneFromPDB(String, String, CoordinateTransformationHints, boolean) - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
 
restoreMembraneFromPDB(String, String, CoordinateTransformationHints, boolean) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Restore a membrane from a PDB file with the following options (Set optional parameters to null if not needed):
restoreMembraneFromPDBPressed() - Method in class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
Show the dialog to restore a membrane from a PDB file.
restoreMembraneFromPDBPressed() - Method in interface org.cellmicrocosmos.cm2.interfaces.GuiListener
 
restoreMembraneModelFromPdbFile(File) - Method in class org.cellmicrocosmos.cm2.io.ReversePDBParser
 
restoreMembraneModelFromPdbFile(File, File, CoordinateTransformationHints) - Method in class org.cellmicrocosmos.cm2.io.ReversePDBParser
 
restoreSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.AlgorithmSettings
Restores the settings from the config file
restoreSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.APLVoroSettings
 
restoreSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.CoordinateTransformationSettings
Restores the settings from the config file
restoreSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
 
restoreSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
Restores settings from configParser
restoreSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.JmolSettings
 
restoreSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.LimitationSettings
Restores the settings from the config file
restoreSettings() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.PPESettings
Restores the settings from the config file
restoreView(int) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
Restores the specified view
RETRIES_AT_RANDOM_PROTEIN_PLACING - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.MISC
number of retries when a Protein gets randomly added
retrieveUserCommentFromDB(File, int) - Method in class org.cellmicrocosmos.cm2.engine.Engine.DatabaseOperations
 
retrieveUserCommentFromDB(File, int) - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
 
retrieveUserCommentFromDB(File, int) - Method in interface org.cellmicrocosmos.cm2.interfaces.DatabaseViewListener
 
returnFromSystemTray() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
returnFromSystemTray() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
This method returns a CmME instance which has been sent to the SystemTray back to the screen.
returnFromSystemTray() - Method in class org.cellmicrocosmos.cm2.pluginmanager.CalculationManager
 
REVERSE_ALL - Static variable in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Constructor flag to reverse all the behaviors
REVERSE_ROTATE - Static variable in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Constructor flag to reverse the rotate behavior
REVERSE_TRANSLATE - Static variable in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Constructor flag to reverse the translate behavior
REVERSE_ZOOM - Static variable in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Constructor flag to reverse the zoom behavior
reverseParsing - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.LimitationSettings
 
ReversePDBParser - Class in org.cellmicrocosmos.cm2.io
This class is used to parse a once saved PDB file against the original Cm2 file.
ReversePDBParser(File, boolean) - Constructor for class org.cellmicrocosmos.cm2.io.ReversePDBParser
 
ReverseRotate(Object[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Property which sets reverse rotate behavior.
ReverseTranslate(Object[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Property which sets reverse translate behavior.
ReverseZoom(Object[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Property which sets reverse zoom behavior.
RIGHT_BUTTON_MODIFIER - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GUI_SETTINGS_AND_CONTROLS
modifiers for the right Mouse Button for Systems that only have one button (like Mac)
ROOTELEMENTNAME_DB - Static variable in class org.cellmicrocosmos.cm2.io.DatabaseIO
 
ROOTELEMENTNAME_MEMBRANE - Static variable in class org.cellmicrocosmos.cm2.io.MembraneXmlReader
 
rotate_X_Axis_Matrix(Matrix3f, float) - Static method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.RotationToolkit
Simply rotates a matrix around its X Axis.
rotate_X_Axis_Matrix(Matrix3f, float) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
 
rotate_X_Axis_Of_CoordinateSystem(Matrix3f, float) - Static method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.RotationToolkit
Rotates a matrix around the X Axis of the MembraneEditor's coordinate space.
rotate_X_Axis_Of_CoordinateSystem(Matrix3f, float) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
 
rotate_Y_Axis_Matrix(Matrix3f, float) - Static method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.RotationToolkit
Simply rotates a matrix around its Y Axis.
rotate_Y_Axis_Matrix(Matrix3f, float) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
 
rotate_Y_Axis_Of_CoordinateSystem(Matrix3f, float) - Static method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.RotationToolkit
Rotates a matrix around the Y Axis of the MembraneEditor's coordinate space.
rotate_Y_Axis_Of_CoordinateSystem(Matrix3f, float) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
 
rotate_Z_Axis_Matrix(Matrix3f, float) - Static method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.RotationToolkit
Simply rotates a matrix around its Z Axis.
rotate_Z_Axis_Matrix(Matrix3f, float) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
 
rotate_Z_Axis_Of_CoordinateSystem(Matrix3f, float) - Static method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.RotationToolkit
Rotates a matrix around the Z Axis of the MembraneEditor's coordinate space.
rotate_Z_Axis_Of_CoordinateSystem(Matrix3f, float) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
 
rotateCoarseGrainMembers() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
RotateEnable(Object[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Property which enables or disables rotation.
rotateImage90(BufferedImage) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
 
RotationCenter(Object[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Property which sets the center around which the View rotates.
RotationToolkit - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
This toolkit offers some useful static methods concerning calculations with matrices
RotationToolkit() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.RotationToolkit
 
RotFactors(Object[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Property which sets the rotation x and y factors.
rotX(float) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
rotates the molecule around the x-axis
RotXFactor(Object[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Property which sets the rotation x factor.
rotY(float) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
rotates the molecule around the y-axis
RotYFactor(Object[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.OrbitBehaviorAdvanced
Property which sets the rotation y factor.
rotZ(float) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Molecule
rotates the molecule around the z-axis
rowFinished(int) - Method in interface org.cellmicrocosmos.cm2.interfaces.SearchListener
 
ROWX_ENTRY - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.MIFILE
 
ROWY_ENTRY - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.MIFILE
 
ROWZ_ENTRY - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.MIFILE
 
run() - Method in class org.cellmicrocosmos.cm2.pluginmanager.CalculationManager.CalculationThread
 
RUN_MODE - Static variable in class org.cellmicrocosmos.cm2.gui.dialogs.AlgorithmWizzard
 
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