Fragments, definition

Add-catalyzed dehydration, lignin model compounds, 130-131 Activating fragments, definition, 54... 

Table A.3 Fragments Definitions and Partial Surface Areas ...

The flexibility permitted in fragment definition is necessary in order to make full use of the encoded 2 D chemistry in the CSD. However, this flexibility, together with certain specific conventions used in the database, can lead to apparent misconceptions of the search process. Some of these problem areas are discussed in detail in Section 3.7.4 below. 

In the preceding chapters we have seen how to define and describe the structure of a molecule or molecular fragment (Chapters 1 and 2), how to retrieve the relevant information from electronic databases (Chapter 3) and how to analyze this information with a variety of statistical methods (Chapter 4). Fragment definition, data retrieval and statistical analysis in structure correlation have their analogs in ordinary chemical experiments First a problem is identified, then the data are acquired from an appropriate experiment, filtered to distinguish the relevant from the irrelevant, and processed into a clear summary form. However, this is not the final step. The data still need to be understood. 

Whatever the precise fragment definition that is used, the resulting molecular representations are input to dictionary-or fingerprint-based procedures analogous to those described previously for 2D similarity searching, with the final global similarity measure being obtained by means of a Tanimoto-like calculation. 

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