Connection tables Translator

The conversion from a connection table to other unambiguous representations is substantially more difficult. The connection table is the least structured representation and incorporates no concepts of chemical significance beyond the list of atoms, bonds, and connections. A complex set of rules must be applied in order to derive nomenclature and linear notation representations. To translate from these more structured representations to a connection table requires primarily the interpretation of symbols and syntax. The opposite conversion, from the connection table to linear notation, nomenclature, or coordinate representation first requires the detailed analysis of the connection table to identify appropriate substructural units. The complex ordering rules of the nomenclature or notation system or the esthetic rules for graphic display are then applied to derive the desired representation. 

The three-dimensional structure is the most unique description of a chemical compound. That is why chemical entities should be compared on the basis of their structure as represented in a connection table, not on their common or nomenclature name. Comparison of structures, however, requires that mentions of chemical entities in text are translated into connection tables this is typically done by name-to-structure (N2S) tools. On a conference on chemical information in Sitges (International Chemistry Information Conference [ICIC]) 2007), preliminary data on attempts at benchmarking N2S tools were reported 46 Although this analysis is preliminary and care should be taken to avoid drawing conclusions that are not supported by the analysis, these data suggest that the N2S tools currently available are correctly converting only between 30% and 50% of all named entities. 

Nomenclatures can be divided into three classes, i.e., systematic, semisystematic, and nonsystematic or Hrivial (see Figure 2). Systematic nomenclature, like notations and connection tables, provides a direct translation between name and structure, trivial (nonsystematic) nomenclature does not, and semisystematic nomenclature is a mixture of the two. 

Sort the rows of the connection table and the stereorelation table according to the precedence determined first by the initial canonical values and in case where the initial canonical values are equal, by the final canonical values. In this process prepare a translation table such that the ith entry of the table is the new number of old atom number i. 

D. I. Cooke-Fox, G. H. Kirby, M. R. Lord, and J. D. Rayner, J. Chem. Inf. Comput. Sci., 30, 122 (1990). Computer Translation of lUPAC Systematic Organic Chemical Nomenclature. 4. Concise Connection Tables to Structure Diagrams. 

This paper derives from experience gained in using the Hull Chemical Nomenclature Translator as a front-end to various structure-based software packages. The benefits of nomenclature input facilities for chemical structure software present a need to link stand-alone packages into multiprocess systems running on PCs under MS-DOS, using connection tables for data exchange. 

The computer translation of systematic chemical nomenclature into chemical structures is now possible. At least three groups have software which demonstrates this. Chemical Abstracts Service has for a long time used software running on mainframe computers to translate names in its style of nomenclature into connection tables. More recently, the Beilstein Institute has developed the VICA name interpreter for an IBM 3090 mainframe. This translates with a high success rate a wide range of names into a connection table using a dictionary of some 3000 name fragments. ... 

Given then that computer translation of organic nomenclature into structural information is now a practical proposition, what use is it We see nomenclature translation widening access to a variety of information systems that deal with chemical structures, their properties and reactions. Many of these systems are structure-based, requiring structure input to be provided either graphically or by a notation such as a connection table or WLN. However, in some circumstances, nomenclature input has advantages. 

The availability of software providing translation of nomenclature input into connection tables serves to illustrate the problems caused by the insular design of much structure-based software, and the limitations of the MS-DOS operating system on what has been the standard PC used in the chemical information field. We would echo the comments made here three years ago on the need for open software architectures. Software developers should consider more fully the wider consequences of their systems interface designs, to encourage greater flexibility for users in building software systems from modules tailored to their individual needs. 

The CTF description language appears to be flexible enough to describe the vast majority of connection table formats in use today, and extensible enough to be adapted to those likely to arise in the future. A practical limitation of the language as described here is the inability to handle binary data conveniently. If interpretation of binary connection table formats becomes important, binary-oriented translation operators could be added to the language. 

Development of computer methods for the interconversion of chemical nomenclatures to and from molecular formulae, connection tables, and structural diagrams followed and seems to continue to follow two separate paths. On the one hand there are a great many reports, mainly from university sources, dealing with translation of systematic names into structural diagrams, and on the other hand there is relatively limited literature on translation of structural diagrams directly into systematic chemical names. Although these are two opposite directions of the same conversion, they have in practice very little in common as far as algorithms and applicable methods are concerned. 

Table IX contains the results for the various metals. One value of

Table 4.3. Determination of translational and rotational diffusion coefficients for connective tissue macromolecules from quasi-elastic light scattering reproduced from Silver, 1987...

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