meshi.energy.sideChainModelingSolvate
Class SideChainSolvateHBAngle

java.lang.Object
  meshi.energy.sideChainModelingSolvate.SideChainSolvateHBAngle

public class SideChainSolvateHBAngle
extends java.lang.Object

This class is a truncated form of the corresponding class in the "meshi.energy.solvate" package. It was designed solely for accelerating the application SCMOD (concurrent sidechain modeling), and should not be used for other purposes. Please do not use it!

Field Summary

private DistanceMatrix	dm
private double	hbAngScore
private double	sigmCosAng1
private double	sigmCosAng2
private double	sigmoidBegins
private double	sigmoidBeginsNoH
private double	sigmoidBeginsWithH
private double	sigmoidEnds
private double	sigmoidEndsNoH
private double	sigmoidEndsWithH

Constructor Summary

SideChainSolvateHBAngle(DistanceMatrix dm, double sigmoidBeginsWithH, double sigmoidEndsWithH, double sigmoidBeginsNoH, double sigmoidEndsNoH)
The constructor parameters: dm - The distance matrix used in this object.

Method Summary

double	hbAngScore()
private void	updateAndEvaluateAtoms123(Atom a1, Atom a2, Atom a3)
void	updateAndEvaluateAtoms1234(Atom a1, Atom a2, Atom a3, Atom a4)
private void	updateAndEvaluateAtoms234(Atom a2, Atom a3, Atom a4)

Methods inherited from class java.lang.Object

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

Field Detail

dm

private DistanceMatrix dm

sigmoidBeginsWithH

private final double sigmoidBeginsWithH

sigmoidEndsWithH

private final double sigmoidEndsWithH

sigmoidBeginsNoH

private final double sigmoidBeginsNoH

sigmoidEndsNoH

private final double sigmoidEndsNoH

sigmoidBegins

private double sigmoidBegins

sigmoidEnds

private double sigmoidEnds

hbAngScore

private double hbAngScore

sigmCosAng1

private double sigmCosAng1

sigmCosAng2

private double sigmCosAng2

Constructor Detail

SideChainSolvateHBAngle

public SideChainSolvateHBAngle(DistanceMatrix dm,
                               double sigmoidBeginsWithH,
                               double sigmoidEndsWithH,
                               double sigmoidBeginsNoH,
                               double sigmoidEndsNoH)

The constructor parameters: dm - The distance matrix used in this object. All the atoms given as parameters to the 'updateAndEvaluateAtoms1234' method must be represented in this object. sigmoidBeginsWithH,sigmoidEndsWithH - The transition angles (in degrees) for the HB sigmoid when the hydrogen atom is known explicitly. Above sigmoidEndsWithH the sigmoid is given a value of 1.0 . Bellow sigmoidBeginsWithH the sigmoid is given a value of 0.0 . In between it raises smoothly by cubic spline. sigmoidBeginsNoH,sigmoidEndsNoH - The same as above, only for HB angle sigmoids when the hydrogen atom is not given explicitly.

Method Detail

hbAngScore

public final double hbAngScore()

updateAndEvaluateAtoms1234

public final void updateAndEvaluateAtoms1234(Atom a1,
                                             Atom a2,
                                             Atom a3,
                                             Atom a4)

updateAndEvaluateAtoms123

private final void updateAndEvaluateAtoms123(Atom a1,
                                             Atom a2,
                                             Atom a3)

updateAndEvaluateAtoms234

private final void updateAndEvaluateAtoms234(Atom a2,
                                             Atom a3,
                                             Atom a4)