Package ffx.xray

Class SolventGaussFormFactor

java.lang.Object

ffx.xray.SolventGaussFormFactor

All Implemented Interfaces:

FormFactor

public final class SolventGaussFormFactor
extends Object
implements FormFactor

SolventGaussFormFactor class.

Since:

1.0

Author:

Timothy D. Fenn

Constructor Summary

Constructors

Constructor	Description
SolventGaussFormFactor(Atom atom, double sd)	Constructor for SolventGaussFormFactor.
SolventGaussFormFactor(Atom atom, double sd, double[] xyz)	Constructor for SolventGaussFormFactor.

Method Summary

Modifier and Type	Method	Description
double	rho(double f, double lambda, double rsq)	rho
double	rho(double f, double lambda, double[] xyz)	Compute the real space density rho
void	rhoGrad(double[] xyz, double dfc, RefinementMinimize.RefinementMode refinementmode)	Compute the real space gradient
void	update(double[] xyz)	update the coordinates to the current position
void	update(double[] xyz, double badd)	update the coordinates to the current position and Badd

Methods inherited from class java.lang.Object

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

Constructor Details

SolventGaussFormFactor

public SolventGaussFormFactor(Atom atom,
 double sd)

Constructor for SolventGaussFormFactor.

Parameters:

atom - a Atom object.

sd - a double.

SolventGaussFormFactor

public SolventGaussFormFactor(Atom atom,
 double sd,
 double[] xyz)

Constructor for SolventGaussFormFactor.

Parameters:

atom - a Atom object.

sd - a double.

xyz - an array of double.

Method Details

rho

public double rho(double f,
 double lambda,
 double[] xyz)

Compute the real space density rho

Specified by:

rho in interface FormFactor

Parameters:

f - the current density to modify

lambda - the state variable

xyz - the requested point for evaluating density

Returns:

the real space density value at xyz

rho

public double rho(double f,
 double lambda,
 double rsq)

rho

Parameters:

f - a double.

lambda - a double.

rsq - a double.

Returns:

a double.

rhoGrad

public void rhoGrad(double[] xyz,
 double dfc,
 RefinementMinimize.RefinementMode refinementmode)

Compute the real space gradient

Specified by:

rhoGrad in interface FormFactor

Parameters:

xyz - the requested point for evaluating gradient

dfc - the multiplier to apply to the gradient

refinementmode - RefinementMinimize.RefinementMode determines which gradients will be computed

update

public void update(double[] xyz)

update the coordinates to the current position

Specified by:

update in interface FormFactor

Parameters:

xyz - an array of double.

update

public void update(double[] xyz,
 double badd)

update the coordinates to the current position and Badd

Specified by:

update in interface FormFactor

Parameters:

xyz - an array of double.

badd - a double.