Standard molecular data

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. 

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. 

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. 

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

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. 

FIZ Chemie = Fachinformation.szentrum Cheniie ISl = institute for Scientific Information IRDAS = ISIS reaction database access system ISIS = integrated scientific information system JSM = Journal of Synthetic Methods MACCS = molecule access system MOS = Metlwd.s in Organic Synthesis, ORAC = Organic Reaction Acce.ss by Computer REACCS = Reaction Access System SMD = standard molecular data SPORE = Solid Phase Organic Reactions, STN = Scientific and Technical Information Network SYNLIB = Synthesis Library. 

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. 

CAS = Chemical Abstracts Service CIP = Cahn-Ingold-Prelog system of labeling stereogenic atoms and bonds MDLI = Molecular Design Limited, Inc. MIF = molecular information file MOLFile = molecule file SEMA = stereo-chemically extended Morgan algorithm SMD = Standard Molecular Data SMILES = simplified molecular input line entry specification. 

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. 

Data transfer between software systems created by a single vendor is usually fairly straightforward. Where more than one vendor is involved, the absence of any agreed standard can make the development of software to accomplish such transfers a needlessly time-consuming process. For this reason we strongly support the development of an interchange standard and indeed have recently developed software utilities which permit the transfer of data either from an ORAC/OSAC data base to a Standard Molecular Data (SMD) file (SMD EXPORT) or from an SMD file to an ORAC/OSAC data base (SMD IMPORT). 

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). 

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