Enum SmirksOption

    • Enum Constant Detail

      • 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 Detail

      • RDKIT

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

      • values

        public static SmirksOption[] values()
        Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:
        for (SmirksOption c : SmirksOption.values())
            System.out.println(c);
        
        Returns:
        an array containing the constants of this enum type, in the order they are declared
      • valueOf

        public static SmirksOption valueOf​(String name)
        Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (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 type has no constant with the specified name
        NullPointerException - if the argument is null