org.wallerlab.yoink.adaptive.smooth

Class SmoothnerImpl

java.lang.Object

org.wallerlab.yoink.adaptive.smooth.SmoothnerImpl

All Implemented Interfaces:

Smoothner

Direct Known Subclasses:

DensitySmoothner, DistanceSmoothner

public abstract class SmoothnerImpl
extends java.lang.Object
implements Smoothner

this class is for smoothing the buffer region.

Nested Class Summary

Nested classes/interfaces inherited from interface org.wallerlab.yoink.api.service.adaptive.Smoothner

Smoothner.Type

Field Summary

Fields

Modifier and Type	Field and Description
protected Computer<Coord,java.util.Set<Molecule>>	centerOfMassComputer

Constructor Summary

Constructors

Constructor and Description
SmoothnerImpl(SmoothFunction smoothFunction) SmoothnerImpl constructor with specified smooth function.

Method Summary

Modifier and Type	Method and Description
protected abstract void	getOriginalMinAndMax(java.util.List<java.lang.Double> smoothParameters, java.util.Map<JobParameter,java.lang.Object> parameters)
protected abstract void	getProperSmoothParameters(java.util.Set<Molecule> qmCoreMolecules, java.util.List<java.lang.Double> smoothParameters, Molecule molecule)
protected java.util.List<java.lang.Double>	loopOverAllBufferMolecules(Job job)
void	smooth(Job job) calculate smooth factors for molecules in buffer region

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

centerOfMassComputer

protected Computer<Coord,java.util.Set<Molecule>> centerOfMassComputer

Constructor Detail

SmoothnerImpl

public SmoothnerImpl(SmoothFunction smoothFunction)

SmoothnerImpl constructor with specified smooth function.

Parameters:

smoothFunction - -the specified smooth function for a new object of SmoothnerImpl.

Method Detail

smooth

public void smooth(Job job)

calculate smooth factors for molecules in buffer region

Specified by:

smooth in interface Smoothner

Parameters:

job - Job

loopOverAllBufferMolecules

protected java.util.List<java.lang.Double> loopOverAllBufferMolecules(Job job)

getProperSmoothParameters

protected abstract void getProperSmoothParameters(java.util.Set<Molecule> qmCoreMolecules,
                                                  java.util.List<java.lang.Double> smoothParameters,
                                                  Molecule molecule)

getOriginalMinAndMax

protected abstract void getOriginalMinAndMax(java.util.List<java.lang.Double> smoothParameters,
                                             java.util.Map<JobParameter,java.lang.Object> parameters)