Structure diagram, connection table

Clearly, there is a pressing need for an equivalent to optical character recognition, optical chemical structure recognition, that can automatically turn bitmapped structural diagrams into structure descriptions—connection tables or equivalent structural strings—that are suitable for input into chemical structure databases. 

Figure 2-20. A connection table the structure diagram of ethanal, with the atoms arbitrarily labeled, is defined by a list of atoms and a list of bonds.

Structure databases are databases that contain information on chemical structures and compounds. The compounds or structure diagrams are not stored as graphics but are represented as connection tables (see Section 2.4). The information about the structure includes the topological arrangement of atoms and the connection between these atoms. This strategy of storage is different from text files and allows one to search chemical structures in several ways. 

Figure 10.3-16. Graphical representation of the chemical structure of the reactants and products of a chemical reaction a) as a 2D image b) with structure diagrams showing all atoms and bonds of the reactants and products to indicate how this information is stored in a connection table.

Figure 8.1 Example of (a) a structure diagram, (b) systematic nomenclature, (c) connection table in MDL format (see URL http //www.mdli.com), and (d) SMILES for a molecule.

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]. 

With any of the systems discussed, it is very likely that an incorrect connection table will be built if there are no specific rules to detect that a structure diagram contains a feature that is unusual or conveys an ambiguous situation. Some of these difficult features that have been identified are discussed below. 

Mapping a set of metabolites from one species onto a pathway created with another species, would allow one to see which metabolites are identical and which are missing. A diagram template may also be used to create a default pathway. As mentioned before, each pathway keeps its own information about the position of metabolites, and each created pathway may serve as basis for a template. A pathway diagram needs to be printable and easily transferred to a report container, such as a document. Finally, a pathway diagram may be exported either as image or in XML format including the structure (connection tables) and connectivity information of the molecules. 

The advantage of such a system was that the chemist was able to use the structural diagram input, which was convenient for the human, and at the same time the computer used the connection table, which was convenient for it. In practice, chemists were able to enter complex molecules after only a 3-minute introduction, and molecules could be entered essentially as fast as the chemist could draw. Yet another advantage was that the output was in a form imme-... 

The ready communication of structural information is fundamental to the development of chemistry. The most universally understood form of such information is the chemical structure diagram, such as that illustrated in Figure 1. However, it is frequently Inconvenient to convey structural information directly (e.g., in conversation), so a number of other methods of representing chemical structures have been developed to satisfy a variety of needs. These methods include nomenclatures, notations, connection tables, adjacency matrices, molecular fonnulas, and fragment codes [1 2]. 

The first step in the development of a supporting theory was the introduction, by Dalton in 1803, of symbols representing single atoms rather than any amount of an element. This led to the first attempts to represent chemical structures by structure diagrams (Figure 3). The structure diagrams provided the needed theoretical basis for the recently-proposed systematic nomenclature and laid the foundation for the continued development of systematic nomenclature and for the eventual introduction and devdopment of notations and connection tables. 

The ability to produce a printed copy of both the structural diagram and the corresponding connection table. 

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. 

A second objective is to build accurate models rapidly given only a description of connectivity (connection table or user drawn structural diagram) and do this symbolically, avoiding any use of molecular mechanics. After all, chemists build very good models manually and mentally without minimisation. 

For many computer tasks and for the transfer of structiural information from one computer program to another, a linear representation of the chemical structure may be more suitable. " A popular linear representation is the SMILES notation. Part of its appeal is that for acyclic structures the SMILES is similar to the traditional linear diagram. For example, ethane is denoted by CC and ethylene C=C. Examples of additional SMILES are given in Figure 4. SMILES is the basis of a chemical information system, and this notation provides a convenient framework for more sophisticated computer coding of chemistry described below. For some internal computer functions, structures encoded in a linear notation may be converted to connection tables. 

Many difEerent approaches have been, and continue to be, described for the representation of the 2D structures of chemical compounds. i> Of these approaches, the connection table is now by hr the most important. A connection table contains a list of all of the (typically nonhydrogen) atoms within a structure, together with bond information that describes the exact manner in which the individual atoms are linked together. An example of a 2D structure diagram and the corresponding connection table are shown in Figure 1. 

Figure 1 Example 2D structure diagram and connection table, r refers to ring c to acyclic s to single and d to double. Nbr refers to neighboring atom.

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