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*   (Sub)Structure Search
You can make a structure or substructure query from the Structure Editor window, the Database Manager window, or a fragment copied from the Fragments & Mechanism window.
Structure and substructure searches are important features for retrieving library entries. The structure search is the most straightforward method for finding compounds in a library. Because the rules of systematic nomenclature do not necessarily lead to a unique name for each compound, a name search can be ineffective in many cases. Drawing or importing a structure query is easier than typing a complicated name or CAS number.
While a structure search (Identity search) provides an exact match of query and library structure, a substructure search retrieves compounds that contain a common structural subset, called a substructure. The exact substructure must be embedded in each molecule retrieved. The exact match in structure and substructure searches has a notable exception: it ignores stereo bonds because optical activity does not play a significant role in mass spectrometry. All other structural features such as bond multiplicity, atom state, and skeletal arrangement must match exactly. You have the option to ignore charges, radicals, and unspecified charge sites, and the option to disregard isotopes. See (Sub)Structure Search Rules.
A substructure search offers two additional search options: Substructure Best Match and Substructure Match Ring Bonds. A substructure can sometimes fit at several locations of a larger structure. When the Substructure Best Match option representing the closest match is found, it appears in red on the Structure page. See (Sub)Structure search results. Using this option lengthens calculation times. Because fragmentation mechanisms on rings significantly differ from acyclic moieties, searching substructures that exactly match the ring membership is useful for each bond. Using this option also lengthens calculation times.
Use a (sub)structure search for multiple purposes:
To positively identify an unknown or to interpret a mass spectrum. Compounds retrieved through a substructure search can provide analogies to the fragmentation processes in the spectrum under consideration.
When searching structures with an unspecified charge site or substituents, be aware of the search rules that apply. You can perform a structure similarity search using substituents.
The (Sub)Structure Search dialog box includes the following pages:
(Sub)Structure search results
Data page in the (Sub)Structure Search dialog box
The On option applies the search constraints defined in the Search Constraints dialog box. See Search Constraints.
The Off option ignores the search constraints defined in the Search Constraints dialog box.
When selected, the application displays the search results in the current Database Manager window and adds the search results to the Work spreadsheet.
Available when you have a copied substructure on the Clipboard. Lets you search for a substructure other than the currently selected substructure in the Database Manager window.
Advanced page in the (Sub)Structure Search dialog box
Locates a library spectrum that closely matches an unknown. Provides an exact match of query and library structure.
Ignore Charges, Radicals and Adducts
Available only with the Substructure option. A substructure can sometimes fit at several locations of a larger structure. When the Substructure Best Match option representing the closest match is found, it appears in red on the Structure page. Using this option lengthens calculation times.
Available only with the Substructure option. Because fragmentation mechanisms on rings significantly differ from acyclic moieties, searching substructures that exactly match the ring membership is useful for each bond. Using this option lengthens calculation times.
Search in Fragmentation Scheme
Available when you have a copied substructure on the Clipboard. Lets you search for a substructure other than the currently selected substructure in the Database Manager window.


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Related Topics:
  (Sub)Structure Search Rules
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