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B

background - Variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
BACKUP_FILENAME_ADDON - Static variable in class org.cellmicrocosmos.cm2.io.ppe.toolbox.PPE_CONSTANTS.IO
 
BasicOperations() - Constructor for class org.cellmicrocosmos.cm2.engine.Engine.BasicOperations
 
basicOperations - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
 
behavior - Variable in class org.cellmicrocosmos.cm2.dataobjects.Molecule_3D
 
BIbright - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.Display
 
BIbright - Variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
BIbrightUni - Variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
BIdark - Variable in class org.cellmicrocosmos.cm2.coarsegrainsupport.Display
 
BIdark - Variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
BIdarkUni - Variable in class org.cellmicrocosmos.cm2.functionality3d.Membrane3D
 
biggestCovalentRadius - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.AtomValues
 
biggestVanDerWaalsRadius - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.AtomValues
 
Bond - Class in org.cellmicrocosmos.cm2.membranepackingalgorithm
This class is used in order to represent a bonded neighbor of an atom.
Bond(Atom, Atom, float) - Constructor for class org.cellmicrocosmos.cm2.membranepackingalgorithm.Bond
Constructs a new Object !NOT TO BE USED BY AUTHORS!
bonds - Variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.Atom
 
BORDER_EAST - Static variable in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
 
BORDER_EAST - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
 
BORDER_MAX_Y - Static variable in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
 
BORDER_MAX_Y - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
 
BORDER_MIN_Y - Static variable in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
 
BORDER_MIN_Y - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
 
BORDER_NORTH - Static variable in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
 
BORDER_NORTH - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
 
BORDER_SOUTH - Static variable in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
 
BORDER_SOUTH - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
 
BORDER_WEST - Static variable in class org.cellmicrocosmos.cm2.functionality3d.IntersectManager
 
BORDER_WEST - Static variable in class org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithm
 
branch - Variable in class org.cellmicrocosmos.cm2.dataobjects.MicroDomain_3D
 
branchGroup - Variable in class org.cellmicrocosmos.cm2.dataobjects.Atom_3D
 
bright_appearance - Static variable in class org.cellmicrocosmos.cm2.engine.DataPool.J3DSettings
 
buildAndShowGui() - Method in interface org.cellmicrocosmos.cm2.membranepackingalgorithm.MembranePackingAlgorithmInterface
 
buildAndShowGui() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.AdvancedRandomPlacing
 
buildAndShowGui() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer.Atom_Level_Minimizer
 
buildAndShowGui() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Distributor
 
buildAndShowGui() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.IntersectionDeleter
 
buildAndShowGui() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.LinearPlacing
 
buildAndShowGui() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.MembraneShifter
 
buildAndShowGui() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.RandomPlacing
 
buildAndShowGui() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.SimulatedAnnealing
Sets up the GUI for the settings
buildAndShowGui() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.Tetris
 
buildAndShowGui() - Method in class org.cellmicrocosmos.cm2.membranepackingalgorithms.TheWandererRookie
Generates the GUI with different options.
buildAndShowGui() - Method in class org.cellmicrocosmos.cm2.misc.Cm2_Toolkit.ToolkitMembranePackingAlgorithm
 
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