Package de.unijena.cheminf.deglycosylation

Enum Class SugarRemovalUtility.PreservationModeOption

java.lang.Object
java.lang.Enum<SugarRemovalUtility.PreservationModeOption>
de.unijena.cheminf.deglycosylation.SugarRemovalUtility.PreservationModeOption
All Implemented Interfaces:
Serializable, Comparable<SugarRemovalUtility.PreservationModeOption>, Constable
Enclosing class:
SugarRemovalUtility
public static enum SugarRemovalUtility.PreservationModeOption extends Enum<SugarRemovalUtility.PreservationModeOption>
Enum with options for how to determine whether a substructure that gets disconnected from the molecule during the removal of a sugar moiety should be preserved or can get removed along with the sugar.
The set option plays a major role in discriminating terminal and non-terminal sugar moieties. If only terminal sugar moieties are removed from the molecule, any disconnected structure resulting from a removal step must be too small to keep according to the set preservation mode option and the set threshold and is cleared away. If all the sugar moieties are to be removed from the query molecule (including non-terminal ones), those disconnected structures that are too small are only cleared once at the end of the routine.
Also, the set preservation mode threshold interrelates with this option. It specifies at least how many heavy atoms or what minimum molecular weight a disconnected structure needs to have to be preserved (depending on the set option).

Important Note for further development: If an option is added here, it needs to have a treatment in the method isTooSmallToPreserve(IAtomContainer). Otherwise, an UnsupportedOperationException will be thrown.

  • Enum Constant Details

    • ALL

      public static final SugarRemovalUtility.PreservationModeOption ALL
      Specifies that all structures should be preserved. Note that if this option is combined with the removal of only terminal moieties, even the smallest attached structure will prevent the removal of a sugar. The most important consequence is that circular sugars with any hydroxy groups will not be removed because these are not considered as part of the sugar moiety.

    • HEAVY_ATOM_COUNT

      public static final SugarRemovalUtility.PreservationModeOption HEAVY_ATOM_COUNT
      Specifies that whether a structure is worth preserving will be judged by its heavy atom count. The default threshold to preserve a structure is set to 5 heavy atoms (inclusive).

    • MOLECULAR_WEIGHT

      public static final SugarRemovalUtility.PreservationModeOption MOLECULAR_WEIGHT
      Specifies that whether a structure is worth preserving will be judged by its molecular weight. The default threshold to preserve a structure is set to 60 Da (= 5 carbon atoms, inclusive).

  • Method Details

    • values

      public static SugarRemovalUtility.PreservationModeOption[] 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 SugarRemovalUtility.PreservationModeOption 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

    • getDefaultThreshold

      public int getDefaultThreshold()
      Returns the default threshold to preserve a structure (inclusive) for this option.
      Returns:
      the default threshold