Package | Description |
---|---|
org.cellmicrocosmos.cm2.membranepackingalgorithm | |
org.cellmicrocosmos.cm2.membranepackingalgorithms.atomlevelminimizer |
Modifier and Type | Field and Description |
---|---|
Atom |
Bond.neigbor |
Modifier and Type | Method and Description |
---|---|
Atom[] |
Molecule.getAlignedAtomCopies()
returns a copy of all atoms of the molecule.
|
Atom |
Bond.getBondedNeighbor()
Returns the instance of the bonded neighbor of the atom that contains
this bond
|
Atom[] |
Molecule.getOriginalAtoms()
Returns the list of all actual Atom instances.
|
Modifier and Type | Method and Description |
---|---|
abstract double |
EnergyFunction.calculateEnergy(Atom referenceAtom,
Atom otherAtom,
double bondFactor,
float distance,
float currentTemperature)
Return the Energy between the pair of passed Atoms.
|
abstract float |
EnergyFunction.getCutoff(Atom reference,
Atom other,
float defaultCutoff)
Used to get the cutoff between this pair of atoms if "Autocutoff" is
activated.
|
abstract void |
EnergyFunction.MembersUpdated(Atom[] allAtoms)
Gets called everytime when any atoms have been added, or removed from the
model during runtime
|
Constructor and Description |
---|
AutoBox(Atom[] allPoints)
Creates an AutoBox around the passed scatter-plot by the coordinates of
atoms
|
Bond(Atom source,
Atom neigbor,
float originalLength)
Constructs a new Object !NOT TO BE USED BY AUTHORS!
|
Modifier and Type | Method and Description |
---|---|
void |
Atom_Level_Minimizer.doBorderCutoff(Atom[] effectedAtoms) |
double |
Energies.totalEnergy(Atom atom) |
double |
Energies.totalInternalEnergy(Atom atom) |