Package com.chemaxon.search

Class MatchingOptions.Builder

    • Field Detail

      • atomTypeMatching

        protected boolean atomTypeMatching

      • bondTypeMatching

        protected boolean bondTypeMatching

      • chargeMatching

        protected boolean chargeMatching

      • isotopeMatching

        protected boolean isotopeMatching

      • radicalMatching

        protected boolean radicalMatching

      • atomMapMatching

        protected boolean atomMapMatching

      • exactQueryAtomMatching

        protected boolean exactQueryAtomMatching

      • exactQueryBondMatching

        protected boolean exactQueryBondMatching

      • orderSensitive

        protected boolean orderSensitive

    • Constructor Detail

      • Builder

        public Builder()
        Creates a Builder object with the default settings.

      • Builder

        public Builder​(MatchingOptions opts)
        Creates a Builder object containing the settings of the given search options object. Useful if only a few options need to be changed, compared to an existing search options object.
        Parameters:
        opts - the default values

    • Method Detail

      • atomTypeMatching

        public abstract MatchingOptions.Builder atomTypeMatching​(boolean value)
        Sets whether atom types should be considered in search. By default, the atom types are checked, i.e., a carbon atom does not match to an oxygen atom.
        Parameters:
        value - specifies whether atom types are checked (true) or ignored (false)
        Returns:
        this builder

      • bondTypeMatching

        public abstract MatchingOptions.Builder bondTypeMatching​(boolean value)
        Sets whether bond types should be considered in search. By default, the bond types are checked, i.e., "CC" does not match to "C=C".
        Parameters:
        value - specifies whether bond types are checked (true) or ignored (false)
        Returns:
        this builder

      • chargeMatching

        public abstract MatchingOptions.Builder chargeMatching​(boolean value)
        Sets whether formal charges of atoms should be considered in search. By default, charges are ignored.
        Parameters:
        value - specifies whether charges are checked (true) or ignored (false)
        Returns:
        this builder

      • isotopeMatching

        public abstract MatchingOptions.Builder isotopeMatching​(boolean value)
        Sets whether isotopes of atoms should be considered in search. By default, mass numbers are ignored, so isotopes of the same element match each other.

        If atom type matching is disabled, isotopes are also ignored, irrespective of this search option.

        Parameters:
        value - specifies whether mass numbers are checked (true) or ignored (false)
        Returns:
        this builder

      • radicalMatching

        public abstract MatchingOptions.Builder radicalMatching​(boolean value)
        Sets whether the radical information of atoms should be considered in search. By default, radicals are ignored.
        Parameters:
        value - specifies whether radicals are checked (true) or ignored (false)
        Returns:
        this builder

      • atomMapMatching

        public abstract MatchingOptions.Builder atomMapMatching​(boolean value)
        Sets whether atom map numbers should be considered in search. If set to true, two atoms with different map numbers do not match each other. By default, it is set to false.
        Parameters:
        value - specifies whether atom map numbers are checked (true) or ignored (false)
        Returns:
        this builder

      • exactQueryAtomMatching

        public abstract MatchingOptions.Builder exactQueryAtomMatching​(boolean value)
        Sets whether generic query atoms should be matched only to atoms of exactly the same type. If set to true, generic atoms are not considered as query features. For example, an "any" atom matches only to another "any" atom. By default, it is set to false.
        Parameters:
        value - true if generic query atoms should match only atoms of exactly the same type
        Returns:
        this builder

      • exactQueryBondMatching

        public abstract MatchingOptions.Builder exactQueryBondMatching​(boolean value)
        Sets whether generic query bonds should be matched only to bonds of exactly the same type. If set to true, generic bonds are not considered as query features. For example, an "any" bond matches only to another "any" bond. By default, it is set to false.
        Parameters:
        value - true if generic query bonds should match only bonds of exactly the same type
        Returns:
        this builder

      • customMatching

        public abstract MatchingOptions.Builder customMatching​(CustomMatcherFactory matcherFactory)
        Sets the factory to be used to create a custom matcher. During search, two atom or bonds may be matched only if they are accepted by the corresponding method of the CustomMatcher created by the given factory (in addition to the criteria specified by other search options).
        Parameters:
        matcherFactory - the factory for creating the custom matcher to be used
        Returns:
        this builder

      • orderSensitive

        public abstract MatchingOptions.Builder orderSensitive​(boolean value)
        Sets whether search is sensitive to the order of the matched atoms and bonds when searching for multiple results.

        By default, this option is set to false. It means that two search results are considered to be different only when they cover different atoms or bonds of the query or the target. In contrast, order sensitive search differentiates two results with the same set of mapped atoms and bonds in both molecules if the actual mappings are different.

        For example, if the query molecule is "CNC" and target molecule is "CNCNC", then order sensitive search provides four different mappings of the query to the target, while order insensitive (default) search provides only two of these hits (that cover different parts of the target molecule).

        Warning: Order sensitive search may produce orders of magnitude more hits as it also deals with the internal symmetry of the molecules.

        Parameters:
        value - true if the search should be order sensitive
        Returns:
        this builder

      • build

        public abstract MatchingOptions build()
        Creates a search options object with the settings specified by this builder instance.
        Returns:
        the search options object