Package ffx.xray.refine

Enum Class RefinementMode

java.lang.Object
java.lang.Enum<RefinementMode>
ffx.xray.refine.RefinementMode
All Implemented Interfaces:
Serializable, Comparable<RefinementMode>, Constable
public enum RefinementMode extends Enum<RefinementMode>
Different refinement mode selection types.

  • Enum Constant Details

    • BFACTORS

      public static final RefinementMode BFACTORS
      refine B factors only (if anisotropic, refined as such)

    • BFACTORS_AND_OCCUPANCIES

      public static final RefinementMode BFACTORS_AND_OCCUPANCIES
      refine B factors and occupancies

    • COORDINATES

      public static final RefinementMode COORDINATES
      refine coordinates only

    • COORDINATES_AND_BFACTORS

      public static final RefinementMode COORDINATES_AND_BFACTORS
      refine coordinates and B factors (if anisotropic, refined as such)

    • COORDINATES_AND_BFACTORS_AND_OCCUPANCIES

      public static final RefinementMode COORDINATES_AND_BFACTORS_AND_OCCUPANCIES
      refine all

    • COORDINATES_AND_OCCUPANCIES

      public static final RefinementMode COORDINATES_AND_OCCUPANCIES
      refine coordinates and occupancies

    • OCCUPANCIES

      public static final RefinementMode OCCUPANCIES
      refine occupancies only (alternate conformers are constrained)

  • Method Details

    • values

      public static RefinementMode[] values()
      Returns an array containing the constants of this enum class, in the order they are declared.
      Returns:
      an array containing the constants of this enum class, in the order they are declared

    • valueOf

      public static RefinementMode valueOf(String name)
      Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)
      Parameters:
      name - the name of the enum constant to be returned.
      Returns:
      the enum constant with the specified name
      Throws:
      IllegalArgumentException - if this enum class has no constant with the specified name
      NullPointerException - if the argument is null

    • includesCoordinates

      public boolean includesCoordinates()
      Determines whether the refinement mode includes coordinates.
      Returns:
      true if the refinement mode involves coordinates, false otherwise.

    • includesBFactors

      public boolean includesBFactors()
      Determines whether the refinement mode includes B-factors.
      Returns:
      true if the refinement mode involves B-factors, false otherwise.

    • includesOccupancies

      public boolean includesOccupancies()
      Determines whether the refinement mode includes occupancies.
      Returns:
      true if the refinement mode involves occupancies, false otherwise.

    • toString

      public String toString()
      Overrides:
      toString in class Enum<RefinementMode>

    • getDefaultEps

      public double getDefaultEps()
      Returns the default epsilon value for the current refinement mode.
      Returns:
      The default epsilon value for the current refinement mode.

    • getDefaultEps

      public double getDefaultEps(boolean hasAnisou)
      Returns the default epsilon value for the current refinement mode. The returned value depends on whether the refinement mode includes anisotropic displacement parameters (ANISOU) and the specific refinement mode.
      Parameters:
      hasAnisou - Indicates whether the refinement mode includes anisotropic displacement parameters.
      Returns:
      The default epsilon value for the current refinement mode.

    • parseMode

      public static RefinementMode parseMode(String mode)
      Parse a string into a refinement mode.
      Parameters:
      mode - Refinement mode string.
      Returns:
      An instance of RefinementMode.