- 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
-
- 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