Package | Description |
---|---|
org.cellmicrocosmos.cm2.dataobjects | |
org.cellmicrocosmos.cm2.membranepackingalgorithm | |
org.cellmicrocosmos.cm2.membranepackingalgorithms |
Modifier and Type | Field and Description |
---|---|
Molecule |
Molecule_3D.teporaryMolecule |
Modifier and Type | Class and Description |
---|---|
class |
Lipid
This is an extension of the molecule class and is used either for
representing a lipid in the membrane or a lipid template
|
class |
Protein
This is an extension of the molecule class and is representing a protein
|
Modifier and Type | Method and Description |
---|---|
Molecule[] |
MembranePackingAlgorithm.getAllMoleculesInCurrentModel()
Returns all Molecule Instances that are currently in the Membrane Model,
including all Layers and Microdomains.
|
Molecule[] |
MembranePackingAlgorithm.getIntersectedMolecules(Molecule mol)
Returns the molecules the passed lipid intersects with.
|
Molecule |
MembranePackingAlgorithm.getNearestMolecule(Molecule mol)
Returns the closest molecule to the passed one.
|
Molecule |
MembranePackingAlgorithm.getNearestMoleculeExcept(Molecule mol,
java.util.Vector<Molecule> except)
Returns the nearest molecule to the given molecule mol.
|
Molecule |
MembranePackingAlgorithm.getNearestMoleculeExceptDetailed(Molecule mol,
java.util.Vector<Molecule> except,
boolean detailed)
Returns the nearest molecule to the given molecule mol.
|
Molecule |
MembranePackingAlgorithm.getNearestMoleculeExceptOnMySide(Molecule mol,
java.util.Vector<Molecule> except,
int membraneside)
Returns the nearest molecule to the given molecule mol on the determined
membrane side.
|
Molecule |
MembranePackingAlgorithm.getNearestMoleculeExceptOnMySideDetailed(Molecule mol,
java.util.Vector<Molecule> except,
int membraneside,
boolean detailed)
Returns the nearest molecule to the given molecule mol on the determined
membrane side.
|
Molecule |
MembranePackingAlgorithm.getNearestMoleculeOnMySide(Molecule mol,
int membraneside)
Returns the nearest molecule to the given molecule mol on the determined
membrane side.
|
Molecule |
MembranePackingAlgorithm.getNearestMoleculeOnMySideDetailed(Molecule mol,
int membraneside,
boolean detailed)
Returns the nearest molecule to the given molecule mol on the determined
membrane side.
|
Molecule |
Atom.getParentalMolecule()
Returns the molecule instance that hosts this atom
|
Modifier and Type | Method and Description |
---|---|
java.util.Vector<Molecule> |
MembranePackingAlgorithm.getLipidsInRadiusExcept(Molecule mol,
int radius,
java.util.Vector<Molecule> except)
Returns all lipids within the given radius of the molecule mol.
|
java.util.Vector<Molecule> |
MembranePackingAlgorithm.getMoleculesInRadius(Molecule mol,
int radius)
Returns all molecules within the given radius of the molecule mol.
|
java.util.Vector<Molecule> |
MembranePackingAlgorithm.getMoleculesInRadiusExcept(Molecule mol,
int radius,
java.util.Vector<Molecule> except)
Returns all molecules within the given radius of the molecule mol.
|
java.util.Vector<Molecule> |
MembranePackingAlgorithm.getMoleculesInRadiusOnMySide(Molecule mol,
int radius,
int membraneside)
Returns all molecules within the given radius of the molecule mol on the
given membrane side.
|
java.util.Vector<Molecule> |
MembranePackingAlgorithm.getMoleculesInRadiusOnMySide(javax.vecmath.Point3f mol,
int radius,
int membraneside)
Returns all molecules within the given radius of the Point3f on given
membrane side.
|
java.util.Vector<Molecule> |
MembranePackingAlgorithm.getMoleculesInRadiusOnMySideExcept(Molecule mol,
int radius,
int membraneside,
java.util.Vector<Molecule> except)
Returns all molecules within the given radius of the molecule mol on the
given membrane side.
|
Modifier and Type | Method and Description |
---|---|
float |
MembranePackingAlgorithm.distance(Molecule mol1,
Molecule mol2,
boolean absval)
Returns the distance between mol1 and mol2.
|
int[] |
MembranePackingAlgorithm.getIntersectedBorders(Molecule mol)
Returns all borders the molecule intersects with.
|
Molecule[] |
MembranePackingAlgorithm.getIntersectedMolecules(Molecule mol)
Returns the molecules the passed lipid intersects with.
|
java.util.Vector<Molecule> |
MembranePackingAlgorithm.getLipidsInRadiusExcept(Molecule mol,
int radius,
java.util.Vector<Molecule> except)
Returns all lipids within the given radius of the molecule mol.
|
java.util.Vector<Molecule> |
MembranePackingAlgorithm.getMoleculesInRadius(Molecule mol,
int radius)
Returns all molecules within the given radius of the molecule mol.
|
java.util.Vector<Molecule> |
MembranePackingAlgorithm.getMoleculesInRadiusExcept(Molecule mol,
int radius,
java.util.Vector<Molecule> except)
Returns all molecules within the given radius of the molecule mol.
|
java.util.Vector<Molecule> |
MembranePackingAlgorithm.getMoleculesInRadiusOnMySide(Molecule mol,
int radius,
int membraneside)
Returns all molecules within the given radius of the molecule mol on the
given membrane side.
|
java.util.Vector<Molecule> |
MembranePackingAlgorithm.getMoleculesInRadiusOnMySideExcept(Molecule mol,
int radius,
int membraneside,
java.util.Vector<Molecule> except)
Returns all molecules within the given radius of the molecule mol on the
given membrane side.
|
Lipid |
MembranePackingAlgorithm.getNearestLipidOnMySide(Molecule mol,
int membraneside)
Returns the nearest lipid to the given molecule mol on the determined
membrane side.
|
Molecule |
MembranePackingAlgorithm.getNearestMolecule(Molecule mol)
Returns the closest molecule to the passed one.
|
Molecule |
MembranePackingAlgorithm.getNearestMoleculeExcept(Molecule mol,
java.util.Vector<Molecule> except)
Returns the nearest molecule to the given molecule mol.
|
Molecule |
MembranePackingAlgorithm.getNearestMoleculeExceptDetailed(Molecule mol,
java.util.Vector<Molecule> except,
boolean detailed)
Returns the nearest molecule to the given molecule mol.
|
Molecule |
MembranePackingAlgorithm.getNearestMoleculeExceptOnMySide(Molecule mol,
java.util.Vector<Molecule> except,
int membraneside)
Returns the nearest molecule to the given molecule mol on the determined
membrane side.
|
Molecule |
MembranePackingAlgorithm.getNearestMoleculeExceptOnMySideDetailed(Molecule mol,
java.util.Vector<Molecule> except,
int membraneside,
boolean detailed)
Returns the nearest molecule to the given molecule mol on the determined
membrane side.
|
Molecule |
MembranePackingAlgorithm.getNearestMoleculeOnMySide(Molecule mol,
int membraneside)
Returns the nearest molecule to the given molecule mol on the determined
membrane side.
|
Molecule |
MembranePackingAlgorithm.getNearestMoleculeOnMySideDetailed(Molecule mol,
int membraneside,
boolean detailed)
Returns the nearest molecule to the given molecule mol on the determined
membrane side.
|
Protein |
MembranePackingAlgorithm.getNearestProtein(Molecule mol)
Returns the nearest protein.
|
Protein |
MembranePackingAlgorithm.getNearestProteinDetailed(Molecule mol,
boolean detailed)
Returns the nearest protein.
|
Protein |
MembranePackingAlgorithm.getNearestProteinExcept(Molecule mol,
java.util.Vector<Protein> except)
Returns the nearest protein.
|
Protein |
MembranePackingAlgorithm.getNearestProteinExceptDetailed(Molecule mol,
java.util.Vector<Protein> except,
boolean detailed)
Returns the nearest protein.
|
float[] |
MembranePackingAlgorithm.getOriginalConstraintLenghts(Molecule molecule)
Deprecated.
|
float[] |
MembranePackingAlgorithm.getOriginalConstraintLengths(Molecule molecule)
NOT MEANT TO BE USED BY PLUGIN DEVELOPERS!
|
boolean |
MembranePackingAlgorithm.intersects(Molecule lip)
Returns true if the passed lipid or protein intersects with any other molecule in
the membrane.
|
boolean |
MembranePackingAlgorithm.intersectsAnyMicroDomain(Molecule mol)
Tests if the center of the passed molecule is located inside a
microdomain
|
boolean |
MembranePackingAlgorithm.intersectsBorderEast(Molecule mol)
Returns true if the lipid intersects with the eastern border.
|
boolean |
MembranePackingAlgorithm.intersectsBorderNorth(Molecule mol)
Returns true if the lipid intersects with the northern border.
|
boolean |
MembranePackingAlgorithm.intersectsBorders(Molecule lip)
Returns true if the passed lipid intersects with the border or is located
completely outside the membrane.
|
boolean |
MembranePackingAlgorithm.intersectsBorderSouth(Molecule mol)
Returns true if the lipid intersects with the southern border.
|
boolean |
MembranePackingAlgorithm.intersectsBorderWest(Molecule mol)
Returns true if the lipid intersects with the western border.
|
boolean |
MembranePackingAlgorithm.intersectsEarth(Molecule lip)
Returns true if the passed lipid intersects with the
the lower limit.
|
boolean |
MembranePackingAlgorithm.intersectsEarthOrSky(Molecule lip)
Returns true if the passed lipid intersects with the
the lower or upper limit.
|
boolean |
MembranePackingAlgorithm.intersectsMoleculeWithMolecule(Molecule mol,
Molecule mol2)
Returns true if the first argument's molecule intersects with the
molecule in the second argument
Intersection tests do not require passed molecule objects to be added to
the membrane already! It will refer to the position and rotation that
have been set
|
boolean |
MembranePackingAlgorithm.intersectsMoleculeWithMolecules(Molecule mol,
java.util.Vector<Molecule> others)
Returns true if the first argument's molecule intersects with one of the
second argument's molecules.
|
boolean |
MembranePackingAlgorithm.intersectsSky(Molecule lip)
Returns true if the passed lipid intersects with the
the upper limit.
|
boolean |
MembranePackingAlgorithm.intersectsWithLipid(Molecule mol,
int side)
Returns true if the molecule intersects with any lipid on the specified
membrane side.
|
boolean |
MembranePackingAlgorithm.intersectsWithProteins(Molecule mol)
Returns true if the passed lipid intersects with any protein in the
membrane.
|
boolean |
MicroDomain.isInsideArea(Molecule mol)
Tests wether a molecule's center is located inside the defined area of
this microdomain.
|
float |
MembranePackingAlgorithm.nearestAtomPoints(Molecule mol1,
Molecule mol2)
Determines the distance between two molecules about the nearest atoms of
each molecule to the other molecule.
|
float |
MembranePackingAlgorithm.nearestTrianglePoints(Molecule mol1,
Molecule mol2)
Determines the distance between two molecules about the nearest triangles
of each molecule to the other molecule.
|
Modifier and Type | Method and Description |
---|---|
java.util.Vector<Molecule> |
MembranePackingAlgorithm.getLipidsInRadiusExcept(Molecule mol,
int radius,
java.util.Vector<Molecule> except)
Returns all lipids within the given radius of the molecule mol.
|
java.util.Vector<Molecule> |
MembranePackingAlgorithm.getMoleculesInRadiusExcept(Molecule mol,
int radius,
java.util.Vector<Molecule> except)
Returns all molecules within the given radius of the molecule mol.
|
java.util.Vector<Molecule> |
MembranePackingAlgorithm.getMoleculesInRadiusOnMySideExcept(Molecule mol,
int radius,
int membraneside,
java.util.Vector<Molecule> except)
Returns all molecules within the given radius of the molecule mol on the
given membrane side.
|
Molecule |
MembranePackingAlgorithm.getNearestMoleculeExcept(Molecule mol,
java.util.Vector<Molecule> except)
Returns the nearest molecule to the given molecule mol.
|
Molecule |
MembranePackingAlgorithm.getNearestMoleculeExceptDetailed(Molecule mol,
java.util.Vector<Molecule> except,
boolean detailed)
Returns the nearest molecule to the given molecule mol.
|
Molecule |
MembranePackingAlgorithm.getNearestMoleculeExceptOnMySide(Molecule mol,
java.util.Vector<Molecule> except,
int membraneside)
Returns the nearest molecule to the given molecule mol on the determined
membrane side.
|
Molecule |
MembranePackingAlgorithm.getNearestMoleculeExceptOnMySideDetailed(Molecule mol,
java.util.Vector<Molecule> except,
int membraneside,
boolean detailed)
Returns the nearest molecule to the given molecule mol on the determined
membrane side.
|
boolean |
MembranePackingAlgorithm.intersectsMoleculeWithMolecules(Molecule mol,
java.util.Vector<Molecule> others)
Returns true if the first argument's molecule intersects with one of the
second argument's molecules.
|
Constructor and Description |
---|
Atom(Atom_3D originalAtom,
Molecule parentMolecule,
int index,
MembranePackingAlgorithm algo)
!NOT MEANT TO BE USED BY ALGORITHM DEVELOPERS!
|
Modifier and Type | Method and Description |
---|---|
float |
SimulatedAnnealing.energyFunction(Molecule mol,
int membraneside)
The energy function returns a value which specifies the average distance
to the neighbor molecules in the cutoff radius.
|
void |
SimulatedAnnealing.shakeMolecule(Molecule mol)
Simple method to change position and rotation of a molecule at random.
|