Standard Molecular Data format

J. S. Garavelli, Chem. Design Automation News, S(8), 2 (1990). Issues in the Development of a Standard Molecular Data Format. 

This operates at three levels import and export of reaction data in SMD (Standard Molecular Data) format, interactive communication with other devices and processes via an ASCII datastream (not yet implemented), and a callable level. 

J. Schilling, P. Woost, B. Zirz, C. The Standard Molecular Data Format (SMD... 

Description by rotational lists was introduced by Cook and Rohde [110] in the specification of the Standard Molecular Data (SMD) format [111]. In this stereochemical approach, the basic geometrical arrangements around a stcrcoccntcr arc defined in a list (c.g., square, tetrahedron, etc.). The atoms in those stcrcoclcmcnts are also labeled with numbers in a pre-defined way (Figure 2-72),... 

J. M, Barnard, /. Chem. Inf. Comput. Sci., 30, 81 (1990). Draft Specification for Revised Version of the Standard Molecular Data (SMD) Format. 

The attention of software developers and users is drawn to current problems in redirecting all data input to be read from files and in allowing alternative entry points which avoid repeated initialisation. They are urged to make more use of the Standard Molecular Data (SMD) format for transfer of structure data. 

During the past few years interest has grown in the development of standard formats for the machine-readable presentation of chemical structures, and a few proposals have been published. One of these is the Standard Molecular Data (SMD) format, developed by a group of European chemical companies. Under the auspices of the Chemical Structure Association, a series of technical working groups have examined the original version of SMD format and proposed a number of revisions and extensions. This poster paper describes the revised version of the format using annotated examples, and discusses the areas where further extension is required. 

John Barnard s poster on the Standard Molecular Data (SMD) File is mainly of historic interest because SMD has since progressed fast under his leadership as Technical Secretary. The Weiningers poster also involved a connection table format. The chapter describes Daylight Chemical Information Systems GEMINI language and interpreter. 

AIA = Analytical Instruments Association AFFN = ASCII free format numeric API = application programming interface ASDF = ASCII squeezed difference form ASMS = American Society of Mass Spectrometry ASTM = American Society for Testing and Materials CCDB = Committee on Chemical Databases CDF = common data form CPEP = Committee on Printed and Electronic Publications CS = chemical structure EPA = United States Environmental Protection Agency lUPAC = International Union of Pure and Applied Chemistry JCAMP-DX = Joint Committee on Atomic and Molecular Physical Data - Data Exchange LDR = labeled data record netCDF = network common data form SMD = standardized molecular data UCAR = University Corporation for Atmospheric Research XDR = external data representation. 

The molecular information file (MIF), developed from extensions to the earlier standard molecular data (SMD) format, designed to be compatible with CIF and mmCIF and, at present at least, used primarily by the crystallographic community. 

Some standard ways of storing and transferring chemical structures are proprietary (e.g., MDL s Molfile) others such as the JCAMP-CS format, published by the Joint Committee on Atomic and Molecular Physics, are in the public domain. Barnard (36) refers to some of them in a paper that deals with recent developments in improving the Standard Molecular Data (SMD) file format and work towards establishing it as the one standard for transfer of chemical structure information between systems. In Chapter 11 of this book, Donner et al. describe the SMD format in more detail. Garavelli, in Chapter 12, also discusses SMD, but concentrates on existing standards for molecular modeling systems. 

The Standard Molecular Data (SMD) format is described providing a powerful tool for data exchange between chemically oriented programs. 

The Standard Molecular Data (SMD) format is designed to provide such an integration tool on the basis of a file format. It has been developed in the course of the CASP project (Computer Assisted Synthesis Planning) which is run by a consortium of seven German and Swiss Chemical Companies (BASF, Bayer, Ciba-Geigy, Hoechst, E Merck, Hoffmann La Roche and Sandoz). The basis of this development was the Molfile format of the earlier SECS program (4) (Simulation and Evaluation of Chemical Synthesis). 

Orchard, S., Sarkans, U., vonMering, C., et al, (2004) The HUPO PSI s Molecular Interaction Format[mdash]a Community Standard for the Representation of Protein Interaction Data. Nat Biotech, 22, 177. 

Selected Physical Property Data (molecular weights, specific gravities of solids and liquids, melting and boiling points, heats of fusion and vaporization, critical temperature and pressure, standard heats of formation and combustion)... 

Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R. The HUPO PSI s molecular interaction format— A community standard for the representation of protein interaction data. Nat Biotechnol 2004 22(2) 177-83. 

Thermodynamic Data of Formation. The standard enthalpy of formation of gaseous PH3, fH298 = 5.4 1.7 kJ/mol, was calculated from the heats of the explosive decomposition of PH3/SbH3 mixtures with white phosphorus as the reference state and is the recommended value different experimental values are given in Phosphor C, 1965, pp. 10/1. The experimentally determined value yields AfG29s=13.4 and AfHo=13.39 kJ/mol [27]. Calculations from molecular constants with standard methods yielded thermodynamic data of formation and the equilibrium constant for the formation of PH3 as an ideal gas the reference states used were crystalline a white phosphorus (0 to 195 K), crystalline p white phosphorus (195 to 317 K), the melt (317 to 1180 K), and an ideal P2 gas at higher temperatures. Selected results are as follows [28] ... 

A notable hybrid between representation by geometrical objects and structure data is the Molecular Inventor (MI) system from Silicon Graphics. MI is based on the standard Inventor file format, which is very similar to VRML 1,0, In addition to normal Inventor nodes, a MI file contains additional nodes which describe a chemical structure and attached physicochemical data. Because both arbitrary visualizations and structure-oriented data for potential extraction and further processing are stored together in one file, the best features from both approaches are combined. The major problem is portability MI viewers are available for free, only for Silicon Graphics platforms. Commercial versions for PCs can now be purchased. Compared to the much easier and generally free availability of viewers both for pure VRML and for chemical MIME data, this severely reduces the general acceptance of this product. 

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