Formula search

To seat ch for available starting materials, similarity searches, substructure searches, and some classical retrieval methods such as full structure searches, name searches, empirical formula searches, etc., have been integrated into the system. All searches can be applied to a number of catalogs of available fine chemicals (c.g, Fluka 154]. In addition, compound libraries such as in-housc catalogs can easily be integrated. 

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. 

Bibliographic data Substance identification data Molecular formula search Reaction data... 

Structure and data storage is shown on the right. A structure table contains the structures, their internal identifiers, and their external identifiers, if any. The structures are stored in a compact binary representation that includes the connection table, the coordinates, the ring information, and any stereochemical, valence, isomer, isotope, or bond information. Certain types of structure-specific information such as polymer or component designations are stored here, whereas other types of structure-specific information (atom- or bond-specific data, and more verbose text data) are stored in their own tables, referenced by the internal identifier, and the atom or bond numbers to which the data correspond. A formula table contains the molecular formula and various atom and atom-type indexes to enhance formula searching and sorting. 

WebMolecules Web visualization of molecules in 3D - in real-time - has now been achieved. Over 150,000 molecular models are available onsite, which may be searched by CAS number or exact form ula. In addition partial formula searching is permitted to look into the Top 2,000 molecules, which includes molecules of commercial value, educational importance, and of topical interest. Thousands of common molecules are organized into over 30 categories. http //www.webmolecules.com... 

Molecular formula search and molecular mass search. 

Substructure Match on all components Formula Search on all components Tautomer Search on all components... 

Formula Searches spectra corresponding to a chemical formula. Parentheses are resolved, e.g., CH3CH(C(CH3)3)2 is converted to C10H22-Constraints like name fragment or certain peaks can be selected. 

Fig. 5.17. Screenshot of NIST/EPA/NIH mass spectral database (V 2.0, 2005) after a formula search for spectra corresponding to QHjoCIN. The second of two rephcate spectra of 2-(p-chlorophenyl)-ethylamine has been selected.

The TRC THERMODYNAMIC TABLES Database contains the evaluated data published in the TRC Thermodynamic Tables - Hydrocarbons and Non-Hydrocarbons. The contents of this database are updated quarterly in conjunction with the publication of the hard-copy supplements. The database is accessible on-line through TRCTHERMO module on the STN international network. From 1994, a version of this database developed using B-tree index files will be available for IBM PC or compatible computers on a yearly lease basis with a subscription to the hard copy of the TRC Thermodynamic Tables. Multiple copies will be available with a single hard-copy subscription. Its features include search for compound by name, formula or CASRN, with flexible name and formula searching capabilities. Data for a selected series of compounds can be retrieved and saved to external files for later analysis. 

The major capabilities of chemical information retrieval today are formula searches, substructure searches, exact match searches, and sequence match, homology, and subsequence searches. (Name, textual, and data searches are ignored in this note, as essentially belonging to the realm of text and data retrieval.)... 

In the toolkit concept, a tool fulfils a specific function, can be used independently, may easily be replaced by another tool as necessary and is fully documented with respect to its function, implementation and use. A simple example of a tool is a molecular formula search module, which may be implemented for use within a DBMS, is easily replaceable by another molecular formula search module and whose molecular formula search capabilities and calls from any apphcation are fully documented. DARC tools are classified as simple tools and advanced tools. Examples of simple tools are ... 

The user must be able to store structures in a database and retrieve them. The user must be able to do various structural searching operations, such as exact match, substructure search, similarity search, and formula search. 

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