Flexmatch search

Data storage and querying are the most fundamental requirements of all informatics systems. Thanks to the Oracle Extensibility Framework (a.k.a. Oracle Data Cartridge Technology), chemical structure data can be stored and queried using direct SQL and special query operators, such as substructure search, flexmatch search, similarity search, and formula search. Also, some indexing techniques make these otherwise slow searches fast. Detailed discussions about these databases and cartridges are beyond the scope of this book. Please refer to the vendor s website and product documentation for more information. 

Flexmatch Search. Term used in MDL structure searching to allow "relaxed" exact match searching of structures. One can specify, for instance, that everything must match except bond orders, or stereochemistry, or valence at atom centers, etc. By turning on or off various flags, one can for a given structure query, retrieve isomers of various types, salts of a the structure, or instances of the structure that may contain different values of certain types of attached data. 

The first interface of the Data Persistence Layer is the finder interface— the interface for querying the database. Two types of queries must be supported by a chemical information database one is numeric or text query, and the other is structure query. The first type is the same as any other type of database. The second type is where chemistry databases differ—search the database based on substructure, structure similarity, and structure flexmatch. As such, the finder interface has to support these two types of finder methods. The CompoundFinder interface is as follows ... 

Readers who are familiar with the MDL database should not be surprised to see MDL s structure query operators such as sss, molsim, and flexmatch. The CompoundMapper s StatementSource objects use ChemDBQueryBuilder to append these structure search operators to the structure search SQL statements. Take the substructure search as an example. In CompoundMapper, we have an inner class FindBySubstructure whose getSql() method is as follows ... 

---