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

Enum Class DensityMapSource

java.lang.Object
java.lang.Enum<DensityMapSource>
org.biojava.nbio.structure.io.density.DensityMapSource
All Implemented Interfaces:
Serializable, Comparable<DensityMapSource>, java.lang.constant.Constable
public enum DensityMapSource extends Enum<DensityMapSource>
A remote service that density data can be fetched from.

These differ enormously in size for the same entry, which is why more than one is supported. For PDB entry 1cbs a density-server slice at the coarsest detail level is about 210 kB and contains both the 2Fo-Fc and Fo-Fc maps, where the two pre-computed CCP4 files come to about 2.1 MB together. For cryo-EM the gap is far wider: the primary map of EMD-0262 is about 106 MB, against roughly 480 kB for the equivalent density-server slice.

Note that RCSB's own edmaps.rcsb.org service, which used to serve DSN6 and MTZ files, was shut down in October 2024. The map coefficients published with the wwPDB validation reports replaced it, but those are structure factors rather than a sampled grid; see DensityFileFormat.MAP_COEFFICIENTS_CIF_GZ.

Since:
7.3.0
Author:
Amr ALHOSSARY

  • Enum Constant Details

    • RCSB_VOLUME_SERVER

      public static final DensityMapSource RCSB_VOLUME_SERVER
      RCSB's Mol* density server at maps.rcsb.org, which serves downsampled BinaryCIF volume slices for both X-ray and EM entries.

    • PDBE_VOLUME_SERVER

      public static final DensityMapSource PDBE_VOLUME_SERVER
      PDBe's Mol* density server, equivalent to RCSB_VOLUME_SERVER.

    • PDBE_CCP4

      public static final DensityMapSource PDBE_CCP4
      PDBe's pre-computed full CCP4 maps. This is the source Jmol itself uses for its built-in map-loading shortcuts.

    • EMDB_MAP

      public static final DensityMapSource EMDB_MAP
      The primary map of an EMDB entry, at full resolution. Can be very large.

    • WWPDB_MAP_COEFFICIENTS

      public static final DensityMapSource WWPDB_MAP_COEFFICIENTS
      Map coefficients from the wwPDB validation reports. Archival only: these cannot be displayed without an FFT.

  • Method Details

    • values

      public static DensityMapSource[] 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 DensityMapSource 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 source in a cached file name, so that maps of the same kind from different sources never collide.
      Returns:
      the token