Package | Description |
---|---|
org.cellmicrocosmos.cm2.dataobjects | |
org.cellmicrocosmos.cm2.functionality3d | |
org.cellmicrocosmos.cm2.membranepackingalgorithm |
Modifier and Type | Class and Description |
---|---|
class |
Particle
The particles are extended atom models needed to represent
coarse grains.
|
Modifier and Type | Field and Description |
---|---|
Atom_3D[] |
Molecule_3D.allAtomsSorted |
Atom_3D |
Constraint_3D.atomA |
Atom_3D |
Constraint_3D.atomB |
Atom_3D[] |
Molecule_3D.atoms |
Atom_3D[] |
Molecule_3D.opmAtoms |
Modifier and Type | Field and Description |
---|---|
java.util.Vector<Atom_3D> |
Atom_3D.currentNeighbors |
java.util.Vector<Atom_3D> |
Particle.includedAtoms |
Modifier and Type | Method and Description |
---|---|
Atom_3D |
Atom_3D.copy()
Returns an exact clone of this instance
|
Atom_3D[] |
Molecule_3D.getAlignedAtoms() |
Atom_3D[] |
Molecule_3D.getAlignedOPMAtoms() |
Atom_3D[] |
Molecule_3D.getAtoms(boolean aligned,
boolean copy)
Returns a copy of all atoms for this instance in the right alignment.
|
Modifier and Type | Method and Description |
---|---|
void |
Molecule_3D.displayAdditionalInformation(Atom_3D atCursor,
float camDist) |
Particle |
Molecule_3D.getHostParticle(Atom_3D atom) |
boolean |
Particle.includes(Atom_3D a) |
void |
Particle.set(Atom_3D[] includedAtoms) |
Constructor and Description |
---|
Constraint_3D(Atom_3D a,
Atom_3D b) |
MyBounds(Atom_3D[] allPoints) |
Particle(Atom_3D[] includedAtoms) |
Constructor and Description |
---|
MyBounds(java.util.Vector<Atom_3D> allPoints) |
Modifier and Type | Method and Description |
---|---|
static void |
Atom_Creator_3D.addBalls(Molecule_3D mol,
Atom_3D[] atoms,
boolean fullSize,
java.awt.Color selectionColor,
int radiusMode,
boolean opmAtoms) |
Constructor and Description |
---|
Atom(Atom_3D originalAtom,
Molecule parentMolecule,
int index,
MembranePackingAlgorithm algo)
!NOT MEANT TO BE USED BY ALGORITHM DEVELOPERS!
|