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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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