org.wallerlab.yoink.density.service.densityProperties

Class SilvaDensityComputer

java.lang.Object

org.wallerlab.yoink.density.service.densityProperties.SilvaDensityComputer

All Implemented Interfaces:

Computer<java.lang.Double,DensityPoint>

Direct Known Subclasses:

DensityOverlapRegionsIndicatorComputer, SingleExponentialDecayDetectorComputer

@Service
public class SilvaDensityComputer
extends java.lang.Object
implements Computer<java.lang.Double,DensityPoint>

This class is to do Silva density analysis calculation for a point. Silva developed two density analysis methods (DORI and SEDD). For DORI,see:De Silva, Piotr, and Clémence Corminboeuf. "Simultaneous Visualization of Covalent and Noncovalent Interactions Using Regions of Density Overlap." Journal of chemical theory and computation 10.9 (2014): 3745-3756. For SEDD, see:De Silva, Piotr, Jacek Korchowiec, and Tomasz A. Wesolowski. "Revealing the Bonding Pattern from the Molecular Electron Density Using Single Exponential Decay Detector: An Orbital‐Free Alternative to the Electron Localization Function." ChemPhysChem 13.15 (2012): 3462-3465.

Constructor Summary

Constructors

Constructor and Description
SilvaDensityComputer()

Method Summary

Modifier and Type	Method and Description
java.lang.Double	calculate(DensityPoint densityPoint) calculate Silva density analysis value for a density point
protected double	calculateSilvaValue(DensityPoint densityPoint, double silvaValue)
protected double	getSilvaValue(DensityPoint densityPoint, double silvaValue)
protected double	loopOverHessian(DensityPoint densityPoint, double silvaValue)

Methods inherited from class java.lang.Object

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

Constructor Detail

SilvaDensityComputer

public SilvaDensityComputer()

Method Detail

calculate

public java.lang.Double calculate(DensityPoint densityPoint)

calculate Silva density analysis value for a density point

Specified by:

calculate in interface Computer<java.lang.Double,DensityPoint>

Parameters:

densityPoint - -DensityPoint

Returns:

silvaValue of a density point

calculateSilvaValue

protected double calculateSilvaValue(DensityPoint densityPoint,
                                     double silvaValue)

getSilvaValue

protected double getSilvaValue(DensityPoint densityPoint,
                               double silvaValue)

loopOverHessian

protected double loopOverHessian(DensityPoint densityPoint,
                                 double silvaValue)