Connection tables file conversion

Substantial attention and progress has been made in the development of procedures to effect conversion between chemical substance representations. Zamora and Davis [26] describe an algorithm to convert a coordinate representation of a chemical substance (derived from input by a chemical typewriter) to a connection table. An approach for interactive input of a structure diagram and conversion of this representation to a connection table suitable for substructure searching is discussed by Feldmann [27]. The conversion of systematic nomenclature to connection tables offers a powerful editing tool as well as a potential mechanism for conversion of name files to connection tables this type of conversion is described by Vander Stouw [28]. 

A search facility was provided using the CROSSBOW Bit and String search program, which is sufficient for small files but clumsy to use. However our primary aim was to obtain clean and useful WLN files, ready for conversion to a graphics system in due course, so the extra expense of connection table based searching seemed unjustified. 

Lease negotiations were concluded and MACCS was installed on the MSDRL VAX in November, 1984. A few project files were generated from CSIS. These provided opportunities to refine the CSIS conversion programmes and develop quality control procedures. Four chemists were hired and trained for the quality control work, and the database conversion began in the second quarter of 1985. CSIS records were converted in blocks of 6,000 records each and in L-number order. The L-numbers from each batch that failed to generate a connection table were saved in a separate file. A CSIS structure print and the corresponding MACCS plot were manually compared by the quality control staff for each record that was converted. Approximately 30% of these required some correction to the structure diagram and/or the text data. 

The last few years have seen substantial interest in the development of database-searching systems for files of 3D structures. The atom coordinate information in such databases is obtained either experimentally, usually from the Cambridge Structural Database, which contains X-ray structures that have been reported in the published literature,or by the use of a struaure-builder, which is a computer program that calculates an approximate 3D structure from a 2D connection table. - The best known of such programs is CONCORD, which uses a knowledge base of rules that describe preferred molecular conformational patterns and a simplified force-field. CONCORD has been widely used for the conversion of both in-house and public databases of 2D structures to 3D form. 

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