meshi.energy.sideChainModelingSolvate
Class SideChainSolvateEnergy

java.lang.Object
  meshi.energy.AbstractEnergy
      meshi.energy.CooperativeEnergyTerm
          meshi.energy.sideChainModelingSolvate.SideChainSolvateEnergy

All Implemented Interfaces:

Attributable, Updateable

public final class SideChainSolvateEnergy
extends CooperativeEnergyTerm

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!

Nested Class Summary

Nested classes/interfaces inherited from class meshi.energy.AbstractEnergy

AbstractEnergy.UpdateableList

Field Summary

private int	atomListSize
private double[]	AtomSumSigmC These are fields for temporary array results that are needed in the evaluation stage.
private double[]	AtomSumSigmHB
private Atom[]	baseAtom
private double	hbEnergy
private boolean[]	inactive
private boolean[]	inactiveAtConstructor
private int[]	lut These fields are for general use in the class
private SideChainSolvateParametersList	parameters
private double	simpleHBweight
private SideChainSolvateHBAngle	solvateHBAngle
private Spline1D[]	splines

Fields inherited from class meshi.energy.CooperativeEnergyTerm

atomList, coordinates, dm, DX, relativeDiffTolerance, verySmall, XYZ

Fields inherited from class meshi.energy.AbstractEnergy

comment, filter, INFINITY, NaN, on, updateableResources, weight

Constructor Summary

SideChainSolvateEnergy()

SideChainSolvateEnergy(AtomList atomList, DistanceMatrix dm, SideChainSolvateParametersList parameters, double simpleHBweight, double sigmoidBeginsWithH, double sigmoidEndsWithH, double sigmoidBeginsNoH, double sigmoidEndsNoH, double weight)
The constructor parameters: atomList,dm,weight - standard CooperativeEnergyTerm inputs.

Method Summary

double	evaluate() Evaluates the energy term and update the derivatives.
double	evaluate(boolean updateAtoms, double cooperativeWeight, double simpleHBweight)
void	evaluateAtoms() Evaluates the energy term and devides the energy between the atoms.
double	getNonWeightedHBenergy()
void	inactivateFarFromAtom(Atom atom, double R)
private void	setBaseAtom() For any polar atom (O,N or S in Cys) we calculate the base atom that participate in the definition of the hydrogen bond angle.
void	setComment(java.lang.String str)
void	setSimpleHBweight(double newWeight)
private void	updateSigmVals(Distance dis) Here goes the processing of the various sigmoid functions concerning atom1 and atom2 in the Distance - dis.

Methods inherited from class meshi.energy.CooperativeEnergyTerm

test

Methods inherited from class meshi.energy.AbstractEnergy

addAttribute, comment, getAttribute, handleMissingParameters, isOn, off, on, toArray, toArray, toArray, toArray, toString, update

Methods inherited from class java.lang.Object

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

Field Detail

AtomSumSigmC

private double[] AtomSumSigmC

These are fields for temporary array results that are needed in the evaluation stage. They are declared as fields so that time will not be waisted on creating new instances of the arrays.

AtomSumSigmHB

private double[] AtomSumSigmHB

lut

private int[] lut

These fields are for general use in the class

atomListSize

private int atomListSize

parameters

private SideChainSolvateParametersList parameters

simpleHBweight

private double simpleHBweight

splines

private Spline1D[] splines

solvateHBAngle

private SideChainSolvateHBAngle solvateHBAngle

baseAtom

private Atom[] baseAtom

inactive

private boolean[] inactive

inactiveAtConstructor

private boolean[] inactiveAtConstructor

hbEnergy

private double hbEnergy

Constructor Detail

SideChainSolvateEnergy

public SideChainSolvateEnergy()

SideChainSolvateEnergy

public SideChainSolvateEnergy(AtomList atomList,
                              DistanceMatrix dm,
                              SideChainSolvateParametersList parameters,
                              double simpleHBweight,
                              double sigmoidBeginsWithH,
                              double sigmoidEndsWithH,
                              double sigmoidBeginsNoH,
                              double sigmoidEndsNoH,
                              double weight)

The constructor parameters: atomList,dm,weight - standard CooperativeEnergyTerm inputs. The 'weight' parameter is the parmeter of the cooperative part (Wcooperative). Note, that changing it will not affect the weight given to the HB part. simpleHBweight - The weight of the HB part. sigmoidBeginsWithH,sigmoidEndsWithH - The transition angles (in degrees) for the HB sigmoid when one of the base atoms (or both) is a hydrogen. 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 sigmoids where none of the base atoms is a hydrogen.

Method Detail

setComment

public void setComment(java.lang.String str)

setSimpleHBweight

public void setSimpleHBweight(double newWeight)

getNonWeightedHBenergy

public double getNonWeightedHBenergy()

inactivateFarFromAtom

public void inactivateFarFromAtom(Atom atom,
                                  double R)

evaluateAtoms

public void evaluateAtoms()

Description copied from class: AbstractEnergy

Evaluates the energy term and devides the energy between the atoms. The energy field of each atom is assigned a value - its contribution to the total energy sum.

Specified by:

evaluateAtoms in class AbstractEnergy

evaluate

public double evaluate()

Description copied from class: AbstractEnergy

Evaluates the energy term and update the derivatives.

Specified by:

evaluate in class AbstractEnergy

evaluate

public final double evaluate(boolean updateAtoms,
                             double cooperativeWeight,
                             double simpleHBweight)

updateSigmVals

private final void updateSigmVals(Distance dis)

Here goes the processing of the various sigmoid functions concerning atom1 and atom2 in the Distance - dis. The results are updated in the fields of the SolvateDistanceAttribute of dis - sigmaValues.

setBaseAtom

private final void setBaseAtom()

For any polar atom (O,N or S in Cys) we calculate the base atom that participate in the definition of the hydrogen bond angle. This base atom is the attached hydrogen (if present), or the heavy atom to which the polar atom is attached (when the hydrogen is not present).