Package ffx.xray.scatter

Class XRayFormFactor

java.lang.Object

ffx.xray.scatter.XRayFormFactor

All Implemented Interfaces:

FormFactor

public final class XRayFormFactor
extends Object
implements FormFactor

This implementation uses either coefficients from Su and Coppens or 3 coefficient parameters derived from CCTBX.

Since:

1.0

Author:

Timothy D. Fenn

See Also:

• R. W. Grosse-Kunstleve, N. K. Sauter and P. D. Adams. Newsletter of the IUCr Commission on Crystallographic Computing. (2004). 3, 22-31.
• M. J. Schnieders, T. D. Fenn, V. S. Pande and A. T. Brunger, Acta Cryst. (2009). D65 952-965.

Field Summary

Fields inherited from interface ffx.xray.scatter.FormFactor

dUdU11, dUdU12, dUdU13, dUdU22, dUdU23, dUdU33, inverseTwoPI32, oneThird, twoPI2, v0, vx, vy, vz

Constructor Summary

Constructors

Constructor	Description
XRayFormFactor(Atom atom, boolean use3G, double badd)	Constructor for XRayFormFactor.
XRayFormFactor(Atom atom, boolean use3G, double badd, double[] xyz)	Constructor for XRayFormFactor.

Method Summary

Modifier and Type	Method	Description
double	f(HKL hkl)	f
double	fN(HKL hkl, int nGaussians)	f_n
double	rho(double f, double lambda, double[] xyz)	Compute the real space density rho
void	rhoGrad(double[] xyz, double dfc, 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

XRayFormFactor

public XRayFormFactor(Atom atom,
 boolean use3G,
 double badd)

Constructor for XRayFormFactor.

Parameters:

atom - a Atom object.

use3G - a boolean.

badd - a double.

XRayFormFactor

public XRayFormFactor(Atom atom,
 boolean use3G,
 double badd,
 double[] xyz)

Constructor for XRayFormFactor.

Parameters:

atom - a Atom object.

use3G - a boolean.

badd - a double.

xyz - an array of double.

Method Details

f

public double f(HKL hkl)

f

Parameters:

hkl - a HKL object.

Returns:

a double.

fN

public double fN(HKL hkl,
 int nGaussians)

f_n

Parameters:

hkl - a HKL object.

nGaussians - a int.

Returns:

a double.

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

rhoGrad

public void rhoGrad(double[] xyz,
 double dfc,
 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 - 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.