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F

FAST_TRANSITIONS - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
 
feedWithRadii(Hashtable<String, Vector2f>) - Static method in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.ATOMVALUES
 
FileIOHandler - Class in org.cellmicrocosmos.cm2.io
This class provides the filechoosing processes.
FileIOHandler() - Constructor for class org.cellmicrocosmos.cm2.io.FileIOHandler
Creates a new XmlIOManager.
FileIOHandler(Component) - Constructor for class org.cellmicrocosmos.cm2.io.FileIOHandler
Creates a new XmlIOManager.
fillWithAnotherLipid() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
 
fillWithLipids() - Method in interface org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmInterface
 
fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.AdvancedRandomPlacing
The runtime of this algorithm is: g*(s*(A+b*B)) = g*s*n, where g = sectors of the membrane grid s = salary, generated by the user-defined and the membrane size A = side A (newlipid) placing attempt b = number of side B retries B = side B (otherlipid) placing attempt n = (T+o*O) = each lipid
fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
 
fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
The runtime of this algorithm is: r*((n*M || RP) + n*D), where r = repetitions until the user stopped the algorithm or the defined values are reached n = number of actual lipids in the membrane M = mix up attempt (repositioning of already placed lipid) D = distribute procedure The runtime of RandomPlacing (RP) is: RP = (l*A+n*P+l*S), where l = limit = membrane width + membrane depth A = lipid random placing attempt n = number of actual lipids in the membrane P = protein or membrane center approaching S = shaking and/or twisting
fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.IntersectionDeleter
 
fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.LinearPlacing
 
fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.MembraneShifter
 
fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
The runtime of this algorithm is: r*(l*A+n*P+l*S), where r = repetitions until the user stopped the algorithm l = limit = membrane width + membrane depth A = lipid random placing attempt n = number of actual lipids in the membrane P = protein or membrane center approaching S = shaking and/or twisting
fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
calls methods to fill membrane with lipids.
fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
 
fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
The runtime of this algorithm is: n*([F+]D[+C]), where n = number of attempts to place new lipids F = place first lipid in row, with: FreeEast, FreeSouth, [FellowWest, FellowNorth, [RotateNorthWest]] D = place a follow-up lipid directly, with: FreeEast, FreeSouth, [FellowWest, FellowNorth, [RotateNorthWest]] C = place a correcting follow-up lipid if the first attempt did not succed, with: ([FellowNorth,] FreedomSouth, FreedomEast, [FellowNorth, FellowWest]) || (FreedomEast, FreedomSouth, [FellowWest, FellowNorth, [RotateNorthWest]])
fillWithLipids() - Method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.ToolkitMembranePackingAlgorithm
 
finishDomainMode(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.MicroDomainManager
 
finishSpecialMode(boolean) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
 
fireUpdateTablesOnMembraneModel() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
Just performs an update on the two tables.
fixLinuxJavaLibraryBug() - Static method in class org.cellmicrocosmos.cm2.engine.StartMain
This fix is required for new Java versions on Linux which do not find the libjawt.so library anymore.
focusGained(FocusEvent) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyNumberTextField
 
focusLost(FocusEvent) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyNumberTextField
 
focusView(int) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
Focus the view specified by its index and brings it on top if covered.
FONT_PDB_TEXTFIELDS - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.GUI_SETTINGS_AND_CONTROLS
 
forbidDraggingInFreeLookMode - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
forwardButton(int, Molecule_3D) - Method in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
 
forwardMouseEvent(MouseEvent) - Method in class org.cellmicrocosmos.cm2.functionality3d.Hud
 
FREE - Static variable in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
 
FREE - Static variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
freeSpace() - Method in class org.cellmicrocosmos.cm2.io.ppe.toolbox.ConfParser
Closes the open streams and frees the space.
fromArrayToVector(Object[]) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
Copies the array into a new Vector
FTP_TEST_LINK - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.IO
 
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