Substructuring

The prime global authority is the International Maritime Organisation. The IMO sets the standards and guidelines for the removal of offshore installations. The guidelines specify that installations in less than 75 meters of water with substructures weighing less than 4,000 tons be completely removed from the site. Those in deeper water must be removed to a depth of 55 meters below the surface so that there is no hazard to navigation. In some countries the depth to which structures have to be removed has already been extended to 100m. 

SFIG or SFG from a medium that has a strong response in a separate detection anu. By this means, one may fiilly compensate for variations not only in pulse energy, but also in the temporal and spatial substructure of the laser pulses. Some experiments may require measurement of the phase of the nonlinear signal [57]. 

Edeison L H and Giaeser A M 1988 Roie of particie substructure in the sintering of monosized titania J. Am. Ceram. See. 71 225... 

The work by Hammett and Taft in the 1950s had been dedicated to the separation and quantification of steric and electronic influences on chemical reactivity. Building on this, from 1964 onwards Hansch started to quantify the steric, electrostatic, and hydrophobic effects and their influences on a variety of properties, not least on the biological activity of drugs. In 1964, the Free-Wilson analysis was introduced to relate biological activity to the presence or absence of certain substructures in a molecule. 

ROSDAL is used in the Beilstein-DIALOG system [17] as a data exchange format. The code can represent not only full structures and substructures but also some generic structures. 

Besides specifications on atoms, bonds, branches, and ring closure, SLN additionally provides information on attributes of atoms and bonds, such as charge or stereochemistry. These are also indicated in square [ ] or angle < > brackets behind the entity e.g., trans-butane CH3CH=[s=t]CHCH3). Furthermore, macro atoms allow the shorthand specification of groups of atoms such as amino adds, e.g., Ala, Protein2, etc. A detailed description of these specifications and also specifications for 2D substructure queries or combinatorial libraries can be found in the literature [26]. 

Lines 4—18 form the connection table (Ctah), containing the description of the collection of atoms constituting the given compound, which can be wholly or partially connected by bonds. Such a collection can represent molecules, molecular fragments, substructures, substituent groups, and so on. In case of a Molfile, the Ctah block describes a single molecule. 

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. 

Figure 2-65. This fingerprint was received by hashing, whereas only one part of all the substructures is specified in the illustration. The asterisk indicates the address of a collision in the bit string, generated by the algorithm.

The JME can also serve as a query input tool for structure databases by allowing creation of complex substructure queries (Figure 2-130), which are automatically translated into SMARTS [22]. With the help of simple HTML-format elements the creation of 3D structure queries is also possible, as were used in the 3D pharmacophore searches in the NCI database system [129]. Creation of reac-... 

Factual databases may provide the electronic version of printed catalogs on chemical compoimds. The catalogs of different suppliers of chemicals serve to identify chemical compounds with their appropriate synonyms, molecular formulas, molecular weight, structure diagrams, and - of course - the price. Sometimes the data are linked to other databases that contain additional information. Structure and substructure search possibihties have now been included in most of the databases of chemical suppliers. 

Once the query has been entered, the search for the compound can be executed with an exact match or a substructure search. All resulting matches, up to 10 000,... 

Besides structure and substructure searches, Gmclin provides a special search strategy for coordiuation compouuds which is found in no other database the ligand search system, This superior search method gives access to coordination compounds from a completely different point of view it is possible to retrieve all coordination compounds with the same ligand environment, independently of the central atom or the empirical formula of the compound. 

As already mentioned (Section 5.3), the stored structure information in this type of database makes it possible to search for chemical structures in several ways. One method is to draw a structure (via a molecule editor) and to perform either a precise structure search (full structure search) or a search containing part of the input structure (substructure search) (see Sections 6.2-6.4). The databases also allow the searching of chemical names and molecular formulas (see Section 6.1). The search results are in most cases displayed in a graphical manner. 

The Web-based graphical user interface permits a choice from numerous criteria and the performance of rapid searches. This service, based on the chemistry information toolkit CACTVS, provides complex Boolean searches. Flexible substructure searches have also been implemented. Users can conduct 3D pharmacophore queries in up to 25 conformations pre-calculated for each compound. Numerous output formats as well as 2D and 3D visuaHzation options are supplied. It is possible to export search results in various forms and with choices for data contents in the exported files, for structure sets ranging in size from a single compound to the entire database. Additional information and down-loadable files (in various formats) can be obtained from this service. 

The next abstraction level of reaction retrieval is a so-called reaction substructure search in which both query structures arc considered as substructures. In the case of a reaction substructure search, no hydrogen atoms arc added internally during the execution of the search. Atoms which have their valencies not completely saturated are considered as open sites, where any hind ofelement could be bonded. 

Figure 5-25. First record of the hit list of the reaction substructure search (MDC number RXCI91107130).

To obtain the required product yield, the reaction substructure search is combined with a textual search using the queiy builder" of the MDL" ISIS program. 

To learn a more thorough approach to the solution of the substructure search problem. 

The search for structural fragments (substructures) is very important in medicinal chemistry, QSAR, spectroscopy, and many other fields in the process of perception of pharmacophore, chromophore, or other -phores. 

Mathematical theory of labeled colored graphs is exclusively used to formalize the structure and substructure search problem. There is almost a one-to-one correspondence between the terms used in graph theory and the ones used in chemical structure theory. Formally a graph G can be given by Eq. (1), where V is the set of graph vertices and H the set of edges. 

Gq is a substructure of Gp (i.e., Gq is isomorphic with a subgraph of Gp) if and only if all the atoms of Gq can be mapped onto a subset of atoms of Gp in such a way that the bonds of Gq map the corresponding bonds which connect the mapped atoms fi om Gp Each mapping between Gq and Gxcan be considered as a function... 

To obtain an effective algorithm for substructure searching the factorial degree of the brute force algorithm has to be drastically deaeased. In the next sections we discuss several approaches where combination leads to a much more effective and apphcable approach for substructure searching. In the process of searching the isomorphism between Gq and a substructure of Gx, the partial mappings Gq —> Gj can be used as well. In these cases, not all atoms from Gq are mapped and, for those which are not, the array value Mj is set to 0. 

There are several basic strategies for the improvement of the performance of substructure search algorithms ... 

The pre-processing concepts have been a more recent development of substructure searching systems. These approaches have become popular since the mid-1980s, when the cost of the storage devices (hard disks and CD-ROMs) decreased. 

The next sections deal exclusively with the second and the third approaches to the optimization of substructure search algorithms. 

---