Molecular description file, development

B. A., Laufer, J. Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited. J. Chem. Inf. Comput. Sci. 1992, 32, 244-255. 

Rule scripts operate on substances defined in a data file in either SMILES (simplified molecular input line entry specification) or CMP (compound) format. The conventional SMILES notation as developed by Weininger [28] provides a basic description of molecules in terms of two-dimensional chemical graphs. The CMP file format developed with the OASIS system [29] provides separate logical records for information about connectivity, three-dimensional structure, electronic structure from quantum-chemical molecular-orbital computations, as well as physicochemical and experimental toxicological data. 

Another approach to the introduction of molecular mechanics into the curriculum is described in a paper by Biali. The stereochemical exercise discussed here involves the calculation of relative energies of the six possible isomers/conformers of [3.3]metacyclophanes. Even in this case, however, the input coordinates are calculated laboriously from framework molecular models and the calculations performed on a VAX 11/750 computer. An important development, however, described in this paper, is the transfer of coordinate data files to a visualization program (Ball and Stick) on the Macintosh microcomputer for simple visualization. This is one of the first descriptions of the use of file transfer on simple microcomputer programs to produce visually attractive structural representations. 

A. Dalby, J. Nourse, W. D. Hounshell, A. Gushurst, D. Grier, B. Leland, and J. Laufer, /. Chetn. Inf. Comput. Set., 32, 244 (1992). Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited. 

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