gov.nasa.javaGenes.forceFields
Class ManyMoleculesEnergyFitness
java.lang.Object
gov.nasa.javaGenes.core.FitnessFunction
gov.nasa.javaGenes.forceFields.ManyMoleculesEnergyFitness
- All Implemented Interfaces:
- java.io.Serializable
- Direct Known Subclasses:
- ForceFitnessRMS, ManyMoleculesEnergyFitnessRatio, ManyMoleculesEnergyFitnessTanimotoDistance, MMEFreferenceRMS
- public class ManyMoleculesEnergyFitness
- extends FitnessFunction
- See Also:
- Serialized Form
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
potential
protected Potential potential
molecules
protected ManyMultiBodiesForOneEnergy molecules
energies
protected java.util.Vector energies
scaleTo
protected DoubleInterval scaleTo
originalEnergyInterval
protected DoubleInterval originalEnergyInterval
filename
protected java.lang.String filename
doPerAtomEnergies
protected boolean doPerAtomEnergies
ManyMoleculesEnergyFitness
protected ManyMoleculesEnergyFitness()
ManyMoleculesEnergyFitness
public ManyMoleculesEnergyFitness(Potential p,
ManyMultiBodiesForOneEnergy m,
boolean inDoPerAtomEnergies)
ManyMoleculesEnergyFitness
public ManyMoleculesEnergyFitness(Potential p,
ManyMultiBodiesForOneEnergy m)
setFilename
public void setFilename(java.lang.String f)
getFilename
public java.lang.String getFilename()
addEnergy
public void addEnergy(double energy)
setEnergy
public void setEnergy(int index,
double energy)
getEnergy
public double getEnergy(int index)
getMultiBodiesForOneEnergy
public MultiBodiesForOneEnergy getMultiBodiesForOneEnergy(int index)
add
public void add(MultiBodiesForOneEnergy m,
double energyOrWhatever)
evaluateFitness
public Fitness evaluateFitness(Evolvable evolvable)
- Specified by:
evaluateFitness
in class FitnessFunction
- Returns:
- the fitness. Low values are fitter than high values.
calculateEnergy
protected double calculateEnergy(MultiBodiesForOneEnergy test)
calculateDistance
protected double calculateDistance(double energy,
double targetEnergy)
scaleEnergiesTo
public void scaleEnergiesTo(DoubleInterval spread)
addToEnergies
public void addToEnergies(double value)
multiplyEnergiesBy
public void multiplyEnergiesBy(double value)
getEnergyInterval
public DoubleInterval getEnergyInterval()
report
public void report(Population population)
- Overrides:
report
in class FitnessFunction
toString
public java.lang.String toString()