Specifying a Query Structure

Commercially available structure editors provide several tools that allow a query to be defined with specific or general components. The back-end software has to transfer this information to the substructure search module. Transferring the structure and special information is done via standardized molecule file formats that include or are enhanced by special code conventions for the additional information. The substructure search module interprets the special conventions and translates them into an internal substructure representation. Examples for special query information are as follows  

If the structure search retrieves too many results, then there are a number of ways to refine or limit the result  

Query atoms can be defined either as single atoms or as atom lists. Atom lists are represented in brackets, such as [C,N,0,P], In this case, the atoms in the list are allowed at the corresponding position. Query atom lists can be negated (NOT [N,0]) to exclude atom types at certain positions. It is possible to define multiple query atom lists at several positions. 

Several other options are provided by most of the commercially available structure editors  

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