Package | Description |
---|---|
org.cellmicrocosmos.cm2.dataobjects | |
org.cellmicrocosmos.cm2.membranepackingalgorithm | |
org.cellmicrocosmos.cm2.membranepackingalgorithms |
Modifier and Type | Method and Description |
---|---|
Lipid |
MembraneModel.createNextLipid(int membraneside,
Lipid_3D[] sampleLipids,
int domainID,
int layerID,
MembranePackingAlgorithm algo) |
Modifier and Type | Method and Description |
---|---|
Lipid |
MicroDomain.createNextExtracellularLipid()
Creates a new Lipid that can be placed in the membrane.
|
Lipid |
MembranePackingAlgorithm.createNextExtracellularLipid()
Creates a new Lipid that can be placed in the membrane.
|
Lipid |
MembranePackingAlgorithm.createNextExtracellularLipid(int layerID)
Creates a new Lipid that can be placed in the membrane.
|
Lipid |
MicroDomain.createNextIntracellularLipid()
Creates a new Lipid that can be placed in the membrane.
|
Lipid |
MembranePackingAlgorithm.createNextIntracellularLipid()
Creates a new Lipid that can be placed in the membrane.
|
Lipid |
MembranePackingAlgorithm.createNextIntracellularLipid(int layerID)
Creates a new Lipid that can be placed in the membrane.
|
Lipid[] |
MicroDomain.getAllSampleLipids_ExtraCellular()
Returns a copy of all lipid templates of the extracellular side of this
microdomain
|
Lipid[] |
MembranePackingAlgorithm.getAllSampleLipids_ExtraCellular(int layerID)
Returns all lipid templates of the extracellular side of this microdomain
|
Lipid[] |
MembranePackingAlgorithm.getAllSampleLipids_ExtraCellular(int layerID,
int domainID)
Returns all lipid templates of the extracellular side of this microdomain
|
Lipid[] |
MicroDomain.getAllSampleLipids_IntraCellular()
Returns a copy of all lipid templates of the intracellular side of this
microdomain
|
Lipid[] |
MembranePackingAlgorithm.getAllSampleLipids_IntraCellular(int layerID)
Returns all lipid templates of the intracellular side of this microdomain
|
Lipid[] |
MembranePackingAlgorithm.getAllSampleLipids_IntraCellular(int layerID,
int domainID)
Returns all lipid templates of the intracellular side of this microdomain
|
Lipid[] |
MembranePackingAlgorithm.getAllSampleLipidsInModel()
Returns a list of all (!) lipid templates in the model
|
Lipid |
MembranePackingAlgorithm.getExtracellularLipidByPDBCode(java.lang.String pdbcode)
Returns a new extracellular lipid by given PDB-Code.
|
Lipid |
MembranePackingAlgorithm.getIntracellularLipidByPDBCode(java.lang.String pdbcode)
Returns a newintracellular lipid by given PDB-Code.
|
Lipid |
MembranePackingAlgorithm.getNearestLipidOnMySide(Molecule mol,
int membraneside)
Returns the nearest lipid to the given molecule mol on the determined
membrane side.
|
Lipid |
MicroDomain.getSampleLipid_ExtraCellular(int index)
Returns a copy of the extracellular lipid template at the specified
index.
|
Lipid |
MembranePackingAlgorithm.getSampleLipid_Extracellular(int index,
int layerID)
Returns the extracellular lipid template at the specified index.
|
Lipid |
MicroDomain.getSampleLipid_IntraCellular(int index)
Returns a copy of the intracellular lipid template at the specified index
|
Lipid |
MembranePackingAlgorithm.getSampleLipid_Intracellular(int index,
int layerID)
Returns the intracellular lipid template at the specified index.
|
Modifier and Type | Method and Description |
---|---|
java.util.Vector<Lipid> |
MembranePackingAlgorithm.getAllLipids(int mode)
Returns a Vector with all lipids in the membrane of one side.
|
java.util.Vector<Lipid> |
MembranePackingAlgorithm.getAllLipidsInDomain(int domainID,
int mode)
Returns a Vector with all lipids in the membrane of one domain and one side.
|
Modifier and Type | Method and Description |
---|---|
void |
MembranePackingAlgorithm.addExtracellularLipid(Lipid lipidToAdd)
adds the given extracellular lipid to the extracellular side of the
membrane.
|
void |
MembranePackingAlgorithm.addIntracellularLipid(Lipid lipidToAdd)
Adds the given intracellular lipid to the intracellular side of the
membrane.
|
float |
MembranePackingAlgorithm.getLipidInMembraneHeight(Lipid lip)
Returns the scaled height in the membrane of the given lipid.
|
float |
MembranePackingAlgorithm.getTotalHeight(Lipid lip)
NOT MEANT TO BE USED BY PLUGIN DEVELOPERS!
|
void |
MembranePackingAlgorithm.removeExtracellularLipid(Lipid lipidToRemove)
Deprecated.
use removeLipidsFromMembrane(Lipid[] lipid) instead
|
void |
MembranePackingAlgorithm.removeIntracellularLipid(Lipid lipidToRemove)
Deprecated.
use removeLipidsFromMembrane(Lipid[] lipid) instead
|
void |
MembranePackingAlgorithm.removeLipidsFromMembrane(Lipid[] toremove)
Removes the passed list of lipids from the membrane
|
Modifier and Type | Method and Description |
---|---|
Lipid |
TheWandererRookie.createNewLipid(Lipid newLipidToAdd,
int newLipidDomainID,
int numberOfRuns)
Create a new lipid.
|
Lipid |
SimulatedAnnealing.getRandomLipid(int membraneside)
Returns a randomly chosen lipid from all lipids placed on the chosen
membrane side.
|
Lipid |
SimulatedAnnealing.testForBetterPositionInFirstState(Lipid lip,
int membraneside)
Tests if a new Random Position is better then the old Position.
|
Modifier and Type | Method and Description |
---|---|
void |
TheWandererRookie.addNewLipid(Lipid newLipidToAdd,
int numberOfRuns)
Add the given lipid to the membrane.
|
Lipid |
TheWandererRookie.createNewLipid(Lipid newLipidToAdd,
int newLipidDomainID,
int numberOfRuns)
Create a new lipid.
|
boolean |
TheWandererRookie.intersectsWithLipids(Lipid givenLipid)
Returns true is the given Lipid intersects with a Lipid on both sides of
the membrane.
|
void |
SimulatedAnnealing.moveMolecule(Lipid mol,
int membraneside)
Moves the molecule to a new position.
|
Lipid |
SimulatedAnnealing.testForBetterPositionInFirstState(Lipid lip,
int membraneside)
Tests if a new Random Position is better then the old Position.
|
javax.vecmath.Point3f |
TheWandererRookie.wanderForFellowEast(Lipid givenLipid,
int microDomainID,
float plusForExtraMinusForIntra)
Move the placed and free lipid to the east until it meeting a fellow or
the border.
|
javax.vecmath.Point3f |
TheWandererRookie.wanderForFellowNorth(Lipid givenLipid,
int microDomainID,
float plusForExtraMinusForIntra)
Move the placed and free lipid to the north until it meeting a fellow or
the border.
|
javax.vecmath.Point3f |
TheWandererRookie.wanderForFellowSouth(Lipid givenLipid,
int microDomainID,
float plusForExtraMinusForIntra)
Move the placed and free lipid to the south until it meeting a fellow or
the border.
|
javax.vecmath.Point3f |
TheWandererRookie.wanderForFellowVertical(Lipid givenLipid,
int microDomainID,
float plusForExtraMinusForIntra,
float[] directXZ)
Move the placed and free lipid to the east until it meeting a fellow or
the border.
|
javax.vecmath.Point3f |
TheWandererRookie.wanderForFellowWest(Lipid givenLipid,
int microDomainID,
float plusForExtraMinusForIntra)
Move the placed and free lipid to the west until it meeting a fellow or
the border.
|
javax.vecmath.Point3f |
TheWandererRookie.wanderForFreedomEast(Lipid givenLipid,
int microDomainID,
float plusForExtraMinusForIntra)
Move the placed and trapped lipid to the east until it is free.
|
javax.vecmath.Point3f |
TheWandererRookie.wanderForFreedomNorth(Lipid givenLipid,
int microDomainID,
float plusForExtraMinusForIntra)
Move the placed and trapped lipid to the north until it is free.
|
javax.vecmath.Point3f |
TheWandererRookie.wanderForFreedomSouth(Lipid givenLipid,
int microDomainID,
float plusForExtraMinusForIntra)
Move the placed and trapped lipid to the south until it is free.
|
javax.vecmath.Point3f |
TheWandererRookie.wanderForFreedomSouthEast(Lipid givenLipid,
int microDomainID,
float plusForExtraMinusForIntra)
Move the placed and trapped lipid to the south-east until it is free.
|
javax.vecmath.Point3f |
TheWandererRookie.wanderForFreedomWest(Lipid givenLipid,
int microDomainID,
float plusForExtraMinusForIntra)
Move the placed and trapped lipid to the west until it is free.
|
javax.vecmath.Point3f |
TheWandererRookie.wanderForOptimalRotationNorthWest(Lipid givenLipid,
int microDomainID,
float plusForExtraMinusForIntra,
int mode)
Wanders to the North and to the West for a Fellow and tries to find the
optimal y-Rotation, following the mode.
|
Modifier and Type | Method and Description |
---|---|
void |
TheWandererRookie.removeIntersectingEarthOrSkyLipids(java.util.HashSet<Lipid> lipidsOfActualRuns)
Remove all lost wanderers from the intra- and extracellular side.
|