Fragment Coding

In contrast to canonical linear notations and connection tables (see Sections 2.3 and 2.4), fragment codes arc ambiguous. Several different structures could all possess an identical fragment code, because the code docs not describe how the fragments arc interconnected. Moreover, it is not always evident to the user whether all possible fi aginents of the stmetures ai e at all accessible. Thus, the fragments more or less characterise a class of molecules this is also important in generic structures that arise in chemical patents (sec Section 2.7.1) 

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. 

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Over and beyond the representations of chemical structures presented so far, there are others for specific applications. Some of the representations discussed in this section, e.g., fragment coding or hash coding, can also be seen as structure descriptors, but this is a more philosophical question. Structure descriptors are introduced in Chapter 8. 

A particularly good selection of physical properties may be spectra, because they are known to depend strongly on the chemical structure. In fact, different types of spectra carry different kinds of structural information, NMR spectra characterize individual carbon atoms in their molecular environment. They therefore correspond quite closely to fragment-based descriptors, as underlined by the success of approaches to predict NMR spectra by fragment codes (see Section 10.2.3). 

Four main approaches have been suggested for the representation of chemical structures in machine-readable form fragment codes, systematic nomenclature, linear notations, and connection tables. 

Duineveld BM, Kowalchuk GA, Keijzer A, van Elsas JD, van Veen JA (2001) Analysis of Bacterial Communities in the Rhizosphere of Chrysanthemum via Denaturing Gradient Gel Electrophoresis of PCR-Amplified 16S rRNA as Well as DNA Fragments Coding for 16S rRNA. Appl Environ Micrbiol 67 172-178... 

The representation is unambiguous since it corresponds to one and only one substance, but it is not unique because alternative numberings of the connection table would result in different representations for the same chemical substance (the connection table representation is discussed in more detail below). In addition to being categorized according to their uniqueness and ambiguity, chemical substance representations commonly used within computer-based systems can be further classified as systematic nomenclature, fragment codes, linear notations, connection tables, and coordinate representations. 

With the variety of chemical substance representations, i.e., fragment codes, systematic nomenclature, linear notations, and connection tables, a diversity of approaches and techniques are used for substructure searching. Whereas unique, unambiguous representations are essential for some registration processes, it is important to note that this often cannot be used to advantage in substructure searching. With connection tables, there is no assurance that the atoms cited in the substructure will be cited in the same order as the corresponding atoms in the structure. With nomenclature or notation representation systems, a substructural unit may be described by different terms or... 

Programs now exist to convert Wiswesser Line Notation [29], Hayward [30], and IUPAC [18] linear notations to connection tables. Because fragment codes alone do not provide the complete description of all structural detail, conversion to other representations is typically not possible. 

Craig, P. N. and N. M. Ebert, "Eleven Years of Structure Retrieval Using the SK F Fragment Codes," Journal of Chemical Documentation, J .(3), 141-146 (1969). 

The described fragment code can be modified according to the users needs. With larger strings, larger fragments can be encoded or the atoms more specifically determined. 

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