SMD Format

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),... 

Thus, each stereochemical stnicttirc can be described and recognised with this rotational list if the structure is designated, c.g., in the STEREO block of the SMD format. The compact and extensible representation of the rotational list can include additional information, such as the name specification of the geometiy or whether the configuration is absohtte, relative, or racemic (Eigitre 2-73). 

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. 

SMD format " is a computer file format which is being proposed as a standard for the exchange of chemical structure information between different organisations and computer programs. 

SMD Format has been developed by a series of technical working groups which have included participants from a wide range of chemical companies and chemical information providers in the United States and Europe. The format is structured as a series of independent blocks, different types of information being shown in different blocks only those blocks which are actually needed in a particular case need be included in the file. 

The use of independent blocks in SMD format allows a program to skip over blocks which it does not require, or is unable to process. This should faciUtate exchange of structures between tot y different programs, such as systems for chemical structure database management, molecular modelling, chemical synthesis planning, QSAR and spectroscopy-based structure elucidation. 

There is httle point in arbitrarily extending SMD Format to compete with existing standard formats in fields where these are already estabhshed. However, there is an urgent need to unite the efforts behind standard formats currently being developed for particular purposes, in order to prevent the emergence of a series of incompatible and competing standards, used by different groups of users. It is possible that SMD format may be able to become a sort of umbrella for more specialised formats. 

The American Society for Testing and Materials (ASTM) has recently begun an activity in the area of standard interchange formats for computerised chemical information, and meetings took place in Philadelphia in November 1989 and in Boston in April 1990, and were attended by a number of individuals who have been concerned with the development of SMD format. It is hoped that it may be possible to integrate these parallel activities. 

A draft formal specification for the revised Version of SMD Format has recently been published for comment in the Journal of Chemical Information and Computer Sciences. The format is defined by means of a set of syntax diagrams, similar to those used in the definition of programming languages such as Pascal. 

The blocks available for description of molecules in SMD format, as defined in the draft specification, are as follows ... 

Special records are also used to specify defaults and audit data (date/time written etc). Each Section, Block, Sub-block etc. starts with a header line with a distinctive tag character, and ends with an explicit terminator hne. Some examples of SMD Format structure descriptions are given in the published draft specification. ... 

Mid-1980s SMD Format developed by the GASP group of European... 

Open workshop to discuss SMD Format at ACS National Meeting, Los Angeles, CA. 

Description of Version 4.3 of SMD format published in Journal of Chemical Information and Computer Sciences,... 

A mailing list is being maintained of those interested in the development of SMD Format. Anyone wishing to be included on it should contact the Secretary of the Chemical Structure Association. 

The following individuals participated in all or some of the technical working groups, which proposed the draft specification for Version 5.0 of SMD format. Affiliations shown are those which were current at the time the person concerned attended working group meetings. 

Financial support for the development of SMD Format during 1988 and 1989 has been provided by the following organisations ... 

Most in-house systems permit links to other database management software, in particular to relational database systems such as ORACLE, in order to integrate large amounts of textual or numeric data that already exist there with reaction databases. As many of the reaction retrieval systems mentioned here are able to import and export files in MolFile or RxnFile formats (originally proprietary file formats of MDL, later published), or in the SMD format, even exchange of reaction databases between different retrieval systems is often possible. ... 

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. 

Two examples will serve to illustrate the value of the SMD IMPORT utility. The Hampden Data Services PsiORAC software permits a complete reaction data card to be treated on a PC in SMD format. We have now used SMD IMPORT to load some 10,000 such cards into an OR AC data base (held on a DEC VAX computer). The second example involves the automatic generation of an ORAC database of 40,000 reactions from raw data contained in (1) a file of starting material and product structures held in a DARC-SMS data base, and (2) an ASCII file containing pointers to these structures plus additional data. With a modest amount of effort, a conversion program was written which, as shown in Figure 2, made use of an existing DARC to SMD utility and also merged the structures with the other data to create a reaction data base in SMD format. This was then loaded into an ORAC data base in the usual way. 

Our work on these problems has enabled us to identify some of the drawbacks of the current SMD format and we will certainly work with other interested parties to try to improve this standard. 

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