Input and Output of Chemical Structures

As was said in the introduction (Section 2.1), chemical structures are the universal and the most natural language of chemists, but not for computers. Computers woi k with bits packed into words or bytes, and they perceive neither atoms noi bonds. On the other hand, human beings do not cope with bits very well. Instead of thinking in terms of 0 and 1, chemists try to build models of the world of molecules. The models ai e conceptually quite simple 2D plots of molecular sti uctures or projections of 3D structures onto a plane. The problem is how to transfer these models to computers and how to make computers understand them. This communication must somehow be handled by widely understood input and output processes. The chemists way of thinking about structures must be translated into computers internal, machine representation through one or more intermediate steps or representations (sec figure 2-23, The input/output processes defined 

Interconvevsions of these representations are also usually possible. 

At the moment, most scientists and students, both in companies and at universities, use similar tools for the encoding processes described. But this was not the case in the past, when research was much more differentiated and fascinating with regard to the chemist-computer interaction. Some of these old-fashioned results are still impressive or some are still used, even now, as the following examples illustrate. 

In the ancient times the 1950s), data were transferred to computers by using punched cards. But already in 1959 Ascher Opier from Dow Chemical Company reported the use of a light pen for graphical entiy of chemical structures into a computer. Light pens were also used in the Chemical Abstracts Service in the 1970s. 

In 1962 special formula reading machines [41] were constructed and used at BASF Lridwigshafcn. They scanned formulas drawn on transparent grid sheets 

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The different internal and external file formats make it necessary to have programs which convert one format into another. One of the first conversion programs for chemical structure information was Babel (around 1992). It supports almost 50 data formats for input and output of chemical structure information [61]. CLIFF is another file format converter based on the CACTVS technology and which supports nearly the same number of file formats [29]. In contrast to Babel, the program is more comprehensive it is able to convert chemical reaction information, and can calculate missing atom coordinates [29]. 

Chapter 7 introduces ways in which RDBMS can be used to handle chemical structural information using SMILES and SMARTS representations. It shows how extensions to relational databases allow chemical structural information to be stored and searched efficiently. In this way, chemical structures themselves can be stored in data columns. Once chemical structures become proper data types, many search and computational options become available. Conversion between different chemical structure formats is also discussed, along with input and output of chemical structures. 

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