Package org.openscience.cdk.smirks

Enum Class SmirksOption

java.lang.Object
java.lang.Enum<SmirksOption>
org.openscience.cdk.smirks.SmirksOption
All Implemented Interfaces:
Serializable, Comparable<SmirksOption>, Constable
public enum SmirksOption extends Enum<SmirksOption>

  • Enum Constant Details

    • PEDANTIC

      public static final SmirksOption PEDANTIC
      Additional check and warnings when parsing SMIRKS.

    • REVERSE

      public static final SmirksOption REVERSE
      Run the reaction backwards (retro synthesis). The right-hand-side is now matched as a query. Note that not all SMIRKS are reversible and good form is usually write separate forward/backwards transformations.

    • DIFF_PART

      public static final SmirksOption DIFF_PART
      Do not allow '[*:1].[*:2]' to match the same fragment. The preferred way to do this component grouping '([*:1]).([*:2])' but if you are only performing reactions it is reasonable that you expect the parts to be different and some toolkits only have this as an option.

    • IGNORE_SET_ELEM

      public static final SmirksOption IGNORE_SET_ELEM
      Do not allow the atomic number to be changed. [Pb:1]>>[Au:1] will do nothing.

    • IGNORE_IMPL_H

      public static final SmirksOption IGNORE_IMPL_H
      Do not allow the implicit hydrogen count to be set. [Ch4:1]>>[Ch3:1] does nothing.

    • IGNORE_TOTAL_H

      public static final SmirksOption IGNORE_TOTAL_H
      Do not allow the total hydrogen count to be set. [CH4:1]>>[CH3:1] does nothing.

    • IGNORE_TOTAL_H0

      public static final SmirksOption IGNORE_TOTAL_H0
      Do not allow the total hydrogen count to be set if it is 0. [CH4:1]>>[CH3:1] works but [CH4:1]>>[CH0:1] does not.

    • OVERWRITE_BOND

      public static final SmirksOption OVERWRITE_BOND
      If a bond already exists where a new one is to be created update the bond order as required.

    • REMOVE_UNMAPPED_FRAGMENTS

      public static final SmirksOption REMOVE_UNMAPPED_FRAGMENTS
      Postprocessing - Remove any disconnected fragments that were not matched by the transformed.

    • RECOMPUTE_HYDROGENS

      public static final SmirksOption RECOMPUTE_HYDROGENS
      Postprocessing - Recompute the implicit hydrogen count on changed atoms that has not had its hydrogen count explicitly set.

    • EXPAND_HYDROGENS

      public static final SmirksOption EXPAND_HYDROGENS
      Preprocessing - Automatically convert implicit hydrogens to explicit hydrogens when the pattern contains a '*'.

  • Field Details

    • RDKIT

      public static final Set<SmirksOption> RDKIT
      Align closer with RDKit's "Reaction SMARTS" semantics.

    • DAYLIGHT

      public static final Set<SmirksOption> DAYLIGHT

  • Method Details

    • values

      public static SmirksOption[] 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 SmirksOption 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