Package org.biojava.nbio.structure.io.density

Enum Class DensityMapKind

java.lang.Object
java.lang.Enum<DensityMapKind>
org.biojava.nbio.structure.io.density.DensityMapKind
All Implemented Interfaces:
Serializable, Comparable<DensityMapKind>, java.lang.constant.Constable
public enum DensityMapKind extends Enum<DensityMapKind>
The kind of density map being requested, i.e. what the values in the grid mean.
Since:
7.3.0
Author:
Amr ALHOSSARY

  • Nested Class Summary

    Nested classes/interfaces inherited from class java.lang.Enum

    Enum.EnumDesc<E extends Enum<E>>

  • Enum Constant Summary

    Enum Constants
    Enum Constant
    Description
    AUTO
    Not a map in itself: asks for whichever map the entry actually has.
    EM
    The primary map of a cryo-EM or cryo-ET reconstruction.
    FO_FC
    The mFo-DFc difference map, showing density that the model does not account for (positive) and model that has no density to support it (negative).
    TWO_FO_FC
    The 2mFo-DFc "best" map: the electron density itself, showing how the model fits the experimental data.

  • Method Summary

    Modifier and Type
    Method
    Description
    String
    getFileToken()
    The short token used to distinguish this kind in a cached file name.
    boolean
    isDifferenceMap()
    Whether this kind is conventionally displayed as a signed pair of surfaces, one positive and one negative.
    List<DensityMapKind>
    resolve()
    Expands this kind into the concrete kinds to try, in order.
    static DensityMapKind
    valueOf(String name)
    Returns the enum constant of this class with the specified name.
    static DensityMapKind[]
    values()
    Returns an array containing the constants of this enum class, in the order they are declared.

    Methods inherited from class java.lang.Enum

    clone, compareTo, describeConstable, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

    Methods inherited from class java.lang.Object

    getClass, notify, notifyAll, wait, wait, wait

  • Enum Constant Details

    • TWO_FO_FC

      public static final DensityMapKind TWO_FO_FC
      The 2mFo-DFc "best" map: the electron density itself, showing how the model fits the experimental data. This is what is normally meant by "the electron density" of an X-ray structure.

    • FO_FC

      public static final DensityMapKind FO_FC
      The mFo-DFc difference map, showing density that the model does not account for (positive) and model that has no density to support it (negative). It is conventionally displayed as a signed pair of surfaces.

    • EM

      public static final DensityMapKind EM
      The primary map of a cryo-EM or cryo-ET reconstruction. Strictly this is a Coulomb potential map rather than an electron density map, and it is conventionally contoured at an absolute author-recommended level rather than in multiples of sigma.

    • AUTO

      public static final DensityMapKind AUTO
      Not a map in itself: asks for whichever map the entry actually has. Resolves to TWO_FO_FC first and then EM, which covers X-ray and cryo-EM entries without the caller having to know which it is holding.

  • Method Details

    • values

      public static DensityMapKind[] 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 DensityMapKind 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

    • getFileToken

      public String getFileToken()
      The short token used to distinguish this kind in a cached file name.
      Returns:
      the token, or null for AUTO, which is never itself cached

    • resolve

      public List<DensityMapKind> resolve()
      Expands this kind into the concrete kinds to try, in order.
      Returns:
      a single-element list for a concrete kind, or the X-ray-then-EM order for AUTO

    • isDifferenceMap

      public boolean isDifferenceMap()
      Whether this kind is conventionally displayed as a signed pair of surfaces, one positive and one negative.
      Returns:
      true only for FO_FC