Modifier and Type | Method and Description |
---|---|
Lipid |
MembraneModel.createNextLipid(int membraneside,
Lipid_3D[] sampleLipids,
int domainID,
int layerID,
MembranePackingAlgorithm algo) |
void |
MembraneModel.prepare(MembranePackingAlgorithm memb) |
Modifier and Type | Method and Description |
---|---|
void |
Engine.MembraneOperations.calculate(MembranePackingAlgorithm algo) |
Modifier and Type | Method and Description |
---|---|
void |
MembraneViewListener.calculate(MembranePackingAlgorithm memb) |
Modifier and Type | Method and Description |
---|---|
void |
MembranePackingAlgorithm.setListenerAndPrepare(MembranePackingAlgorithm algorithmToGetListeners)
Use this method to inherit listeners from one algorithm to the next one.
|
abstract void |
EnergyFunction.setMembranePackingAlgorithm(MembranePackingAlgorithm algo)
Gets called at startup and passes a reference to the underLying
MembraneAlgortihm
|
Constructor and Description |
---|
Atom(Atom_3D originalAtom,
Molecule parentMolecule,
int index,
MembranePackingAlgorithm algo)
!NOT MEANT TO BE USED BY ALGORITHM DEVELOPERS!
|
Lipid(Lipid_3D original,
MembranePackingAlgorithm algo) |
MicroDomain(MicroDomain_3D microDomain,
MembranePackingAlgorithm algo)
Contructs a new MicroDomain object
! NOT MEANT TO BE USED BY PLUGIN DEVELOPERS !
|
Molecule(Molecule_3D original,
MembranePackingAlgorithm algo)
Creates a new wrapper object of the given Molecule_3D
! NOT MEANT TO BE USED BY PLUGIN DEVELOPERS !
|
Protein(Protein_3D original,
MembranePackingAlgorithm algo) |
Modifier and Type | Class and Description |
---|---|
class |
AdvancedRandomPlacing
This algorithm places lipids at randomly picked positions.
|
class |
Distributor
Distributes lipids onto a membrane trying to reach the pre-defined absolute
lipid numbers.
|
class |
IntersectionDeleter
This tool algorithm deletes selected intersecting lipids
from the bilayer.
|
class |
LinearPlacing
Places the lipids in rows for each Domain\n\n"
--> Works best with only one single type of\n"
lipid used on each membrane side and\n"
without any random rotation"
|
class |
MembraneShifter
This tool algorihtm can be used to shift all membrane components
of one type (lipids of the inner and/or outer layer and/or proteins)
at once.
|
class |
RandomPlacing
Places the lipids randomly within membrane bounds and may
try to approach proteins or the membrane center and
twisting and shaking the lipids.
|
class |
SimulatedAnnealing
This algorithm represents the power of geometrical based membrane simulations.
|
class |
Tetris
See algorithm description...
|
class |
TheWandererRookie
The Wanderer is an algorithm looking for an opportunity to rest.
|
Modifier and Type | Class and Description |
---|---|
class |
Atom_Level_Minimizer
This is the base-class of the Atom-Level-Minimizer, described by my Diploma-Thesis.
|
Modifier and Type | Class and Description |
---|---|
static class |
Cm2_Toolkit.ToolkitMembranePackingAlgorithm
This class is only used for direct access to the different methods
of the MembranePackingAlgorithm interface.
|
Modifier and Type | Method and Description |
---|---|
MembranePackingAlgorithm |
PluginManager.createMembranePackingAlgorithm(Plugin newPlugin,
java.io.File originalFile) |
static MembranePackingAlgorithm |
CalculationManager.getAlgo() |
Modifier and Type | Method and Description |
---|---|
void |
PluginManager.writeAlgorithmSettings(Plugin plugin,
MembranePackingAlgorithm algo) |
Constructor and Description |
---|
CalculationManager(Engine.MembraneOperations membraneOperations,
MembranePackingAlgorithm memb,
MembraneView membraneview,
Engine.BasicOperations basicOperations,
Engine.DatabaseOperations databaseOperations,
StatisticsView stats,
PropertiesView props) |