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I

iAmWebstart - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool
 
ICONS_PARENT - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IMAGES_AND_ICONS
Directory where the Icons are located
ICONS_PARENT_CM2_1 - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IMAGES_AND_ICONS
 
id - Variable in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
IllegalOperationException - Exception in org.cellmicrocosmos.cm2.membranepackingalgorithm
 
IllegalOperationException(String) - Constructor for exception org.cellmicrocosmos.cm2.membranepackingalgorithm.IllegalOperationException
 
IMAGES_AND_ICONS() - Constructor for class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IMAGES_AND_ICONS
 
INCLUDED - Static variable in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
INCLUDED_ALGORITHMS - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.ALGORITHMS
 
INCLUDED_COMPATIBILITIES - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
includedAtoms - Variable in class org.cellmicrocosmos.cm2.dataobjects.Particle
 
includes(Atom_3D) - Method in class org.cellmicrocosmos.cm2.dataobjects.Particle
 
indexForPDBWriter - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
 
init() - Static method in class org.cellmicrocosmos.cm2.io.Installer
 
init() - Method in class org.cellmicrocosmos.cm2.pluginmanager.PluginManager
 
initFilePaths() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool.IO
 
initialPoints - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.MoleculeEditor
 
initialRotationMatrix - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.Display
 
initilizeBorderlessLayout() - Method in class org.cellmicrocosmos.cm2.gui.MainGui
Initialize the borderless Layout, required especially for the StereoView.
initMIFHandler() - Static method in class org.cellmicrocosmos.cm2.engine.DataPool
Initializes the MIFHandler needed for the PDB_TM Settings.
initWorkspace() - Static method in class org.cellmicrocosmos.cm2.io.Installer
 
insertString(int, String, AttributeSet) - Method in class org.cellmicrocosmos.cm2.gui.dialogs.LimitedDocument
 
Installer - Class in org.cellmicrocosmos.cm2.io
The Installer installs the images, the external Jmol library, the help files, the settings and the workspace during the first start.
Installer() - Constructor for class org.cellmicrocosmos.cm2.io.Installer
 
installHelpfiles() - Static method in class org.cellmicrocosmos.cm2.io.Installer
 
installImages() - Static method in class org.cellmicrocosmos.cm2.io.Installer
 
installJmol() - Static method in class org.cellmicrocosmos.cm2.io.Installer
 
installSettings() - Static method in class org.cellmicrocosmos.cm2.io.Installer
 
INTEGER - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyNumberTextField
 
intercects_Molecule_Border(Molecule_3D, Dimension) - Method in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
Tests, if a molecule is completely inside the defined membrane bounds Returns false if not, no matter if the molecule intersects with the border or if it is completely outside the range
intercects_Molecule_Border_In_Detail(Molecule_3D, Dimension) - Method in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
An enhanced version of the molecule_border-test.
intercects_Molecule_Earth(Molecule_3D) - Method in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
Tests, if a molecule is inside the lower limit.
intercects_Molecule_Sky(Molecule_3D) - Method in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
Tests, if a molecule is inside the upper limit.
intercectsBorderOrAnyMolecule(Molecule_3D, boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
 
intercectsBorderOrAnyMolecule(Molecule_3D, int, boolean, HashSet<String>) - Method in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
 
intercectsWithBorderOrAnyProtein(Molecule_3D, boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
Tests, if a molecule collides with either the border or any Protein that is already added to the membrane.
InternetSettings() - Constructor for class org.cellmicrocosmos.cm2.engine.DataPool.InternetSettings
 
IntersectionDeleter - Class in org.cellmicrocosmos.cm2.membranepackingalgorithms
This tool algorithm deletes selected intersecting lipids from the bilayer.
IntersectionDeleter() - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithms.IntersectionDeleter
 
IntersectionPanel() - Constructor for class org.cellmicrocosmos.cm2.gui.elements.MembraneView.IntersectionPanel
 
IntersectionsDisplayer - Class in org.cellmicrocosmos.cm2.functionality3d
This class is used to display intersecting lipids.
IntersectionsDisplayer(MembraneView) - Constructor for class org.cellmicrocosmos.cm2.functionality3d.IntersectionsDisplayer
 
IntersectManager - Class in org.cellmicrocosmos.cm2.functionality3d
Offers various Methods to check Objects for Intersections.
IntersectManager() - Constructor for class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
 
intersector - Variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
intersectPanel - Variable in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
intersects(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns true if the passed lipid or protein intersects with any other molecule in the membrane.
intersectsAnyMicroDomain(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Tests if the center of the passed molecule is located inside a microdomain
intersectsBorderEast(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns true if the lipid intersects with the eastern border.
intersectsBorderNorth(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns true if the lipid intersects with the northern border.
intersectsBorders(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns true if the passed lipid intersects with the border or is located completely outside the membrane.
intersectsBorderSouth(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns true if the lipid intersects with the southern border.
intersectsBorderWest(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns true if the lipid intersects with the western border.
intersectsEarth(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns true if the passed lipid intersects with the the lower limit.
intersectsEarthOrSky(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns true if the passed lipid intersects with the the lower or upper limit.
intersectsMoleculeAnyMolecules(Molecule_3D, boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
Tests, if a molecule collides with any Molecule that is already added to the membrane, inclusive lipids.
intersectsMoleculeAnyMolecules(Molecule_3D, int, boolean, HashSet<String>) - Method in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
Tests, if a molecule collides with any Molecule that is already added to the membrane, inclusive lipids.
intersectsMoleculeAnyProtein(Molecule_3D, boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
Tests, if a molecule collides with any Protein that is already added to the membrane.
intersectsMoleculeMoleculesVector(Molecule_3D, Vector<?>, boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
Tests, if a molecule collides with any molecule in a list that also has to be passed.
intersectsMoleculeMoleculesVector(Molecule_3D, int, Vector<?>, boolean, HashSet<String>) - Method in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
Tests, if a molecule collides with any molecule in a list that also has to be passed.
intersectsMoleculeWithMolecule(Molecule, Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns true if the first argument's molecule intersects with the molecule in the second argument Intersection tests do not require passed molecule objects to be added to the membrane already! It will refer to the position and rotation that have been set
intersectsMoleculeWithMolecules(Molecule, Vector<Molecule>) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns true if the first argument's molecule intersects with one of the second argument's molecules.
intersectsSky(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns true if the passed lipid intersects with the the upper limit.
intersectsWithLipid(Molecule, int) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns true if the molecule intersects with any lipid on the specified membrane side.
intersectsWithLipids(Lipid) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
Returns true is the given Lipid intersects with a Lipid on both sides of the membrane.
intersectsWithProteins(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Returns true if the passed lipid intersects with any protein in the membrane.
INTRA - Static variable in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
 
INTRA - Static variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
INTRA - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Used to specify the intracellular membrane side
INVALID_POSITION - Static variable in class org.cellmicrocosmos.cm2.functionality3d.SelectionBox
 
InvalidEntriesException - Exception in org.cellmicrocosmos.cm2.io
This special Exception will be thrown by the MembraneIO if at least one of the membrane xml's Entries is invalid.
InvalidEntriesException() - Constructor for exception org.cellmicrocosmos.cm2.io.InvalidEntriesException
 
IO() - Constructor for class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
IO() - Constructor for class org.cellmicrocosmos.cm2.engine.DataPool.IO
 
IO() - Constructor for class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.IO
 
isActive() - Method in class org.cellmicrocosmos.cm2.engine.Engine
 
isActive - Static variable in class org.cellmicrocosmos.cm2.engine.TestArea
Has to be true in order to have access to the test button in the menu.
isAlreadyIn(String, File) - Method in class org.cellmicrocosmos.cm2.pluginmanager.PluginManager
 
isAlreadyIn(String, File, Plugin) - Method in class org.cellmicrocosmos.cm2.pluginmanager.PluginManager
 
isAtomCollisionOn() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Determines wether or not atom collision is activated in the options-dialog of the MembraneEditor
isAtomDistanceAbsolute() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Determines wether or not the atom distance values for the atom collision is absolute.
isBorderOpaque() - Method in class org.cellmicrocosmos.cm2.gui.MainGui.TabComponentNoBorder
 
isClosedPressed() - Method in class org.cellmicrocosmos.cm2.gui.dialogs.StatusDialog
Check if the user pressed the close button.
isCoarseGrainParticle() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
Determines, wether this atom is actually a coarse-grain-particle
isCompletelyInside(Point3d, float[]) - Method in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
 
isComputeAbsoluteValuesSelected() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Determines wether or not the use of absolute values is selected in the component view MembraneEditor
isCorrectlyInitialized() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.ConfigIO
Checks if the data has already been loaded properly from the file.
isCorrectlyInitialized() - Static method in class org.cellmicrocosmos.cm2.misc.ConfigParser
Checks if the data has already been loaded properly from the file.
isCurrentlyEmpty() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
 
isDark() - Static method in class org.cellmicrocosmos.cm2.gui.MainGui
 
isElementOfMIF(String) - Method in class org.cellmicrocosmos.cm2.io.ppe.toolbox.MIFHandler
Checks whether the given PDB-Id in the MIFile exists.
isElementOfOPM(String) - Method in class org.cellmicrocosmos.cm2.io.ppe.toolbox.MIFHandler
Checks whether the given PDB-Id in the OPM entry of the MIFile exists.
isElementOfPDBTM(String) - Method in class org.cellmicrocosmos.cm2.io.ppe.toolbox.MIFHandler
Checks whether the given PDB-Id in the PDBTM entry of the MIFile exists.
isEmpty() - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Tests, wether the Membrane is completely Empty or not
isEnabled() - Method in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
isEnabled() - Method in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
 
isEnabled() - Method in class org.cellmicrocosmos.cm2.gui.MainGui
 
isExtendedPlugin() - Method in class org.cellmicrocosmos.cm2.pluginmanager.Plugin
 
isHigh - Variable in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
isInsideArea(Molecule) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MicroDomain
Tests wether a molecule's center is located inside the defined area of this microdomain.
isInSpecialMode() - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
isInSystemTray - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
isInSystemTray() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Determines, wether the MembraneEditor is currently visible or minimized into the system-tray.
isMaximized(int) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
Tests whether the passed view is maximized or not
isMembraneAttrsShowing() - Method in class org.cellmicrocosmos.cm2.gui.elements.PropertiesView
 
isMoleculeStillIn(Molecule_3D) - Method in class org.cellmicrocosmos.cm2.dataobjects.MembraneModel
Tests, if the passed protein is currently in the model
isOnAir() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Deprecated.
use isInSystemTray() instead Determines, wether the MembraneEditor is currently visible or minimized into the system-tray
isPicked() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns wether this protein is currently picked or not
isPositionInAValidSpace() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns wether this protein has the valid position flag set or not
isPositionisinavalidspace() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Deprecated.
isProperties_Membrane_Atrribus_Showing() - Method in class org.cellmicrocosmos.cm2.engine.Engine.MembraneOperations
 
isProperties_Membrane_Atrribus_Showing() - Method in interface org.cellmicrocosmos.cm2.interfaces.MembraneViewListener
 
isRasterVisible() - Method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
Returns if the raster is visible currently
isScreenDocked - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
isStartInBackgroundAllowed() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
Is true if the algorithm can be started in the background.
isStartInBackgroundSelected() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
This is true if the user selected to start the algorithm immediately in background after the calculation was started.
isStereoViewActive() - Static method in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
isTransparent() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
isUsingAtomColors() - Method in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
Returns if the Molecule is displaying atom colors in Covalent or Van Der Waals Mode.
isValid - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyNumberTextField
 
itemStateChanged(ItemEvent) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
item state changed method.
itemStateChanged(ItemEvent) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
handles users GUI settings
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