Package ffx.xray

Class SolventPolyFormFactor

java.lang.Object
ffx.xray.SolventPolyFormFactor
All Implemented Interfaces:
FormFactor
public final class SolventPolyFormFactor extends Object implements FormFactor
SolventPolyFormFactor class.
Since:
1.0
Author:
Timothy D. Fenn

  • Constructor Summary

    Constructors
    Constructor
    Description
    SolventPolyFormFactor(Atom atom, double arad, double w)
    Constructor for SolventPolyFormFactor.
    SolventPolyFormFactor(Atom atom, double arad, double w, double[] xyz)
    Constructor for SolventPolyFormFactor.

  • Method Summary

    Modifier and Type
    Method
    Description
    double
    rho(double f, double lambda, double ri)
    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

    • SolventPolyFormFactor

      public SolventPolyFormFactor(Atom atom, double arad, double w)
      Constructor for SolventPolyFormFactor.
      Parameters:
      atom - a Atom object.
      arad - a double.
      w - a double.

    • SolventPolyFormFactor

      public SolventPolyFormFactor(Atom atom, double arad, double w, double[] xyz)
      Constructor for SolventPolyFormFactor.
      Parameters:
      atom - a Atom object.
      arad - a double.
      w - 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 ri)
      rho
      Parameters:
      f - a double.
      lambda - a double.
      ri - 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.