2.4. Specification of the Molecular Information File (MIF)
F. H. Allen, J. M. Barnard, A. P. F. Cook and S. R. Hall
Abstract
The Molecular Information File (MIF) is a data-exchange format for chemical structure utilizing the STAR File format described elsewhere in this volume. The current implementation addresses the core requirements for representing a two-dimensional molecular structure, with limited facilities for describing stereochemistry and the molecular geometry at stereogenic centres. The approach is complementary to that of the crystallographic information file (CIF) but the two formats use different subsets of the full STAR syntax and are therefore not fully compatible.
A brief historical review is given of the evolution of MIF from the concepts of the Standard Molecular Data format of the late 1980s. After an account of the file structure and syntax, examples are given of: representing atoms, bonds and molecules; the ability of the format to accommodate a variety of bond-type assignments (including the simultaneous description of bonding by different schemes); the mechanism for describing and managing structural templates (e.g. ligands, functional groups, amino-acid units etc.); and stereochemical descriptors. There is also an account of the use of MIF as a database query language.
Links
Dictionaries
The following dictionary is referenced in this chapter:
Specifications
Chapter 2.4 of this volume should be considered the definitive specification for the Molecular Information File (MIF) as of 2005, revising and updating the J. Chem. Inf. Comput. Sci. paper of Allen, Barnard, Cook & Hall (1995), and should be cited as:
Allen, F. H., Barnard, J. M., Cook, A. P. F. & Hall, S. R. (2005). International Tables for Crystallography, Volume G, Definition and exchange of crystallographic data, edited by S. R. Hall & B. McMahon, Chapter 2.4, Specification of the Molecular Information File. Heidelberg: Springer.
Supplementary documents
- Backus-Naur form of the STAR syntax and grammar (HTML format)
- Backus-Naur form of the STAR syntax and grammar (plain text file with Unix-style line endings)
References
Allen, F. H. (2002). The Cambridge Structural
Database: a quarter of a million crystal structures and rising.
Acta Cryst. B58, 380-388.
Allen, F. H., Barnard, J. M.,
Cook, A. P. F. & Hall, S. R. (1995). The Molecular
Information File (MIF): core specifications of a new standard format
for chemical data. J. Chem. Inf. Comput. Sci. 35,
412-427.
Allen, F. H., Davies, J. E., Galloy,
J. J., Johnson, O., Kennard, O., Macrae, C. F., Mitchell,
E. M., Mitchell, G. F., Smith, J. M. & Watson,
D. G. (1991). The development of versions 3 and 4 of the
Cambridge Structural Database System.
J. Chem. Inf. Comput. Sci. 31, 187-204.
Allen, F. H. & Glusker, J. P. (2002).
Preface. Acta Cryst. B58, Part 3.
Allen, F. H. & Rogers, D. (1970). X-ray studies of terpenoid derivatives, Part III. A re-determination of the crystal structure of (+)-3-bromocamphor : the absolute configuration of (+)-camphor. J. Chem. Soc. B, pp. 632-636.
ASTM (1994). Standard specification for the content of computerized chemical structural information files or data sets. ASTM Standard E 1586-93. American Society for Testing and Materials, Philadelphia, PA, USA.
Barnard, J. M. (1990). Draft specification
for revised version of the Standard Molecular Data (SMD) format.
J. Chem. Inf. Comput. Sci. 30, 81-96.
Barnard, J. M. & Cook, A. P. F. (1992). The Molecular Information File (MIF): a standard format for molecular information. Report. Chemical Structure Association, London, UK.
Barnard, J. M., Cook, A. P. F. & Rohde, B. (1990). Beyond the structure diagram, edited by D. Bawden & E. Mitchell, pp. 29-41. Chichester: Ellis Horwood.
Bebak, H., Buse, C., Donner, W. T., Hoever, P.,
Jacob, H., Klaus, H., Pesch, J., Roemelt, J., Schilling, P., Woost, B.
& Zirz, C. (1989). The Standard Molecular Data format (SMD
format) as an integration tool in computer chemistry.
J. Chem. Inf. Comput. Sci. 29, 1-5.
Brown, I. D. (1988). Standard
Crystallographic File Structure-87. Acta Cryst. A44,
232.
Cahn, R. S., Ingold, C. K. &
Prelog, V. (1966). Specification of molecular chirality.
Angew. Chem. Int. Ed. Engl. 5, 385-415.
Dalby, A., Nourse, J. G., Hounshell,
W. D., Gushurst, A. K. I., Grier, D. L., Leland,
B. A. & Laufer, J. (1992).
Description of several chemical structure file formats used by
computer programs developed at Molecular Design Limited.
J. Chem. Inf. Comput. Sci. 32, 244-255.
Feldmann, R. J., Milne, G. W. A.,
Heller, S. R., Fein, A., Miller, J. A. & Koch, B. (1977).
An interactive substructure search system.
J. Chem. Inf. Comput. Sci. 17, 157-163.
Hall, S. R. (1991). The STAR File: a new
format for electronic data transfer and archiving.
J. Chem. Inf. Comput. Sci. 31, 326-333.
Hall, S. R., Allen, F. H. &
Brown, I. D. (1991). The Crystallographic Information File
(CIF): a new standard archive file for crystallography.
Acta Cryst. A47, 655-685.
See also
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![[cdrom]](../graphics/cd.gif){kind=small}
HTML version
(http://www.iucr.org/iucr-top/cif/standard/cifstd1.html).
Hall, S. R. & Cook, A. P. F.
(1995). STAR Dictionary Definition Language: initial
specification. J. Chem. Inf. Comput. Sci. 35,
819-825.
Hall, S. R. & Spadaccini, N. (1994).
The STAR File: detailed specifications. J. Chem. Inf. Comput.
Sci. 34, 505-508.
Harary, F. (1972). Graph Theory, 3rd ed. London: Addison-Wesley.
ISO (2002a). ISO/IEC 8824-1.
Abstract Syntax
Notation One (ASN.1). Specification of basic notation.
Geneva: International Organization for Standardization.
See also
http://asn1.elibel.tm.fr/en/index.htm.
ISO (2002b). ISO/IEC 8825-1. ASN.1
encoding rules. Specification of Basic Encoding Rules (BER), Canonical
Encoding Rules (CER) and Distinguished Encoding Rules (DER).
Geneva: International Organization for Standardization.
See also
http://asn1.elibel.tm.fr/en/index.htm.
Mockus, J. & Stobaugh, R. E. (1980).
The Chemical Abstracts Service Chemical Registry System. VII.
Tautomerism and alternating bonds. J. Chem. Inf. Comput. Sci.
20, 18-22.
Prelog, V. & Helmchen, G. (1982). Basic
principles of the CIP-system and proposals for a revision.
Angew. Chem. Int. Ed. Engl. 21, 567-583.
Wippke, W. T. & Dyott, T. M. (1975).
Use of ring assemblies in ring perception algorithm. J. Chem. Inf.
Comput. Sci. 15, 140-147.