- FAST_TRANSITIONS - Static variable in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.J3D
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- feedWithRadii(Hashtable<String, Vector2f>) - Static method in class org.cellmicrocosmos.cm2.constants.CM2_CONSTANTS.ATOMVALUES
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- FileIOHandler - Class in org.cellmicrocosmos.cm2.io
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This class provides the filechoosing processes.
- FileIOHandler() - Constructor for class org.cellmicrocosmos.cm2.io.FileIOHandler
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Creates a new XmlIOManager.
- FileIOHandler(Component) - Constructor for class org.cellmicrocosmos.cm2.io.FileIOHandler
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Creates a new XmlIOManager.
- fillWithAnotherLipid() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
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- fillWithLipids() - Method in interface org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmInterface
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- fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.AdvancedRandomPlacing
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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
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- fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
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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
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- fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.LinearPlacing
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- fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.MembraneShifter
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- fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
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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
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calls methods to fill membrane with lipids.
- fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
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- fillWithLipids() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
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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
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- finishDomainMode(boolean) - Method in class org.cellmicrocosmos.cm2.functionality3d.MicroDomainManager
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- finishSpecialMode(boolean) - Method in class org.cellmicrocosmos.cm2.gui.elements.MembraneView
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- fireUpdateTablesOnMembraneModel() - Method in class org.cellmicrocosmos.cm2.gui.elements.DatabaseView
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Just performs an update on the two tables.
- fixLinuxJavaLibraryBug() - Static method in class org.cellmicrocosmos.cm2.engine.StartMain
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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
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- focusLost(FocusEvent) - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.MyNumberTextField
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- focusView(int) - Method in class org.cellmicrocosmos.cm2.gui.MainGui
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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
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- forbidDraggingInFreeLookMode - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
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- forwardButton(int, Molecule_3D) - Method in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
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- forwardMouseEvent(MouseEvent) - Method in class org.cellmicrocosmos.cm2.functionality3d.Hud
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- FREE - Static variable in class org.cellmicrocosmos.cm2.functionality3d.CameraMode
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- FREE - Static variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
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- freeSpace() - Method in class org.cellmicrocosmos.cm2.io.ppe.toolbox.ConfParser
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Closes the open streams and frees the space.
- fromArrayToVector(Object[]) - Static method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit
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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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