Search where structure

Today, fragment coding is still quite important in patent databases (sec Chapter 5, Section 5.11, e.g., Dei went) where Markush structures are also stored. There, the fragments can be applied to substructure or othei types of searches where the fragments arc defined, c.g., on the basis of chemical properties. 

To complete the specification of the algorithm, we require one additional decision parameter how to select the next problem Yix), which we will solve, or equivalently, which node in the branching structure to expand. We will define a search function, s, which allows us to select a node from the currently unexpanded nodes for expansion. In this chapter, as in Ibaraki (1978), we consider only best bound search, where we select the node with the minimum gix) value for expansion. Thus our branch-and-bound algorithm. A, is explicitly specified by... 

Approximately three decades ago, the U.S. government created the Registry of Toxic Effects of Chemicals (RTECS) database (www.ccohs.ca/education/asp/search rtecs.html). Initially available in book form only, it became later available on CD-ROM, from the National Institute of Occupational Safety and Health, USA, or affiliated vendors (e.g., the Canadian Center for Occupational Health and Safety [CCOHS] www.ccohs.ca). This database contains information on approximately 120,000 substances, including (where available) acute and chronic toxicity data for terrestrial organisms, primarily mammalian species, such as rats, mice, rabbits, monkeys, and humans. This database will be transferred to the private sector in the near future for maintenance. RTECS cannot be searched by structure, but by name, formula, CAS, and several other means. CCOHS provides also a website which allows limited searching of the RTECS database at ccin-foweb.ccohs.ca/rtecs/search.html, but access to data is for subscribers only. 

Inverted Keys. When substructure search keys are generated for a structure, they may be stored in normal order (where each record represents a structure, and the bits or fields for that structure represent the keys). Alternatively, they may be stored in inverted or pivoted order, where each record represents a given substructure key, and the bits represent structures that have that particular key set. This type of storage benefits key searching, where a user wants all the structures that have a particular key set. 

The ACD/NNMR version 8 content database contains >8300 chemical structures (>21,000 N chemical shifts). These data have been culled from the literature and checked for quality according to a number of stringent criteria prior to adding to the database. The chemical shift reference is homogenized during the process such that all shifts are relative to one reference. A record includes the chemical structure, the original literature reference, the N chemical shift(s) and, where available, associated heteronuclear coupling constants. These data can be searched by structure, substructure. 

One of the most useful features of the NIST WebBook we have found is the name search, where a large selection of alternative names for a particular compound are available and searchable, greatly increasing the chance of finding the information you want on a particular substance of you do not know the lUPAC or CAS name or the CAS registry number and are not reaUy too sure of the chemical structure. However it is possible to upload chemical structures for example (Fig. 24.5). 

Consider the case of a text search where we combine several keywords to form a specific query to meet our requirements, and so is the case here each fragment is like a keyword, which can be combined to perform a specific stracture search. When we use a particular fragment as our query or as a part of our query, the retrieved structure must contain that fragment. The list of retrieved stractures will include all those structures that contain the fragment in the specified manner in their stracture. 

Ultimately, a structure match can be determined only by resolving a node into its constituent partial structures, and performing an atom-by-atom search where these are represented by connection tables, or matching by parameters where one of the partial structures in a pair represents a generic rascal. 

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