Molecular description file formats

The Effort To Define a Standard Molecular Description File Format... 

Figure 1. Writing a program for each possible transformation between N incompatible molecular description file formats requires - N programs.

Figure 3. With a standard molecular description file format modelers would not have to write conversion programs.

There are two molecular description file formats which can be read by many public domain and commercial programs. The Cambridge Crystallographic Data Base... 

The features which a standard molecular description file format must have in order to be useful and enduring largely depend on the research areas in which the file is to be used. But certainly, it would be helpful if the standard were versatile and extensible so that emerging areas of research could be accommodated without frequent major revisions being necessary. However, the scale of detail in the models employed in some research areas differs so greatly that it may be better to have different but related standards for each area. Specifically, perhaps there should be a standard for molecular descriptions at the atomic level and a separate standard for biopolymer descriptions at the residue level. The two standards must be related so that a molecular model at the atomic level could be generated for conformation studies when only a sequence is known and sequence homologies in a sequence data bank could be rapidly searched for a biopolymer of known conformation. 

A Proposal for a Standard Format for Molecular Description Files. ... 

Dalby A, J G Nourse, W D Hounshell, A K I Gushurst, D L Grier, B A Leland and J Laufer 1991 Description of Several Chemical Structure File Formats Used by Computer Programs Developei at Molecular Design Limited, journal of Chemical Information and Computer Science 32 244-255. 

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. 

Chemical representation can be rule-based or descriptive. Here we will give a short description of two popular file formats for molecular structures, MOLfiles (9) and SMILES (10-13), to illustrate how molecules are represented in computer. SMILES is a rule-based format while MOLfile is a more descriptive one. 

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. 

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. 

A consideration of the whole bulk of the CSD is both impractical and unnecessary. At the same time, the Cif file format in which the CSD entries are stored requires extensive manipulation of alphabetic data and is impractical for use with computer programs written in the most widely used languages for scientific calculation. For the examples shown in this chapter, some reduced databases have therefore been prepared from the CSD, containing molecular data in numerical form. A full description of the retrieval procedure is given in the Supplementary material (see OPiX manual, Retcif-Coor procedures). 

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