Internal representation molfile

Another choice for the internal representation of molecular structure is a molfile. It would be possible to construct SQL functions like those described in this chapter that would operate on this type of data. One disadvantage of molfiles is their greater size compared with SMILES. One advantage is that it is possible to store atomic coordinates, which is not possible with SMILES. There are other molecular file formats, but these are substantially the same as a molfile, except perhaps for specific atom types that may be of use in some database applications. 

The external representation of molecular structure is a less rigorous definition. For example, there are many programs available that can convert to and from SMILES and molfiles. These can be used when a molfile (the external representation) needs to be imported as a SMILES (the internal representation) into the database. Similarly, a SMILES can be easily exported as a SMILES or converted to a molfile or other file format. It is useful to have these conversion functions as SQL extensions. 

The internal representation of molecules is accomplished using the technique developed by Wipke and Dyott (3), and later used by Molecular Design Limited (MDL) in several of their commercial programs. An MDL program, MACCS, is used to graphically input the molecular structure of the compound of interest, then save that structure into a file (molfile). The importation of this file provides CHESS with information such as the number and type of atoms and bonds, as well as stereochemical information. 

Structure registration is the process of entering structural information in a centralized repository, usually a structure database. These repositories serve as a pool for providing structure information that has been created in other departments of a company. Structure databases are set up according to the individual needs of a department or company. They consist of a common representation of a structure in a standardized file format, such as MolFile, SDF, reaction (RXN) (MDL), JCAMP (International Union of Pure and Applied Chemistry), or simplified molecular input line entry specification. Any additional data can be stored with the structure depending on the context typical examples are structure properties, reaction conditions, and literature references. 

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