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CIF applications. II. CIFIO : for CIF input/output in the Xtal system
Journal of Applied Crystallography
Abstract
CIFIO is the primary CIF input and output program in the Xtal System and provides for global data exchange and machine-readible publication submission. CIFIO also creates and reads an Xtal archive file which is a CIF-like ASCII replica of an Xtal binary file. CIFIO is written in Ratmac and may be implemented, along with the other 94 calculations in the Xtal3.2 package, on any computer.
... This paper is part of a series on CIF applications. Other programs in this series are QUASAR (Hall & Sievers, 1993) for generating a requested CIF from existing CIF data; CIFIO (Hall, 1993a) for reading and writing CIFs in a custom application and CYCLOPS (Hall, 1993b) for validating CIF data names in an ASCII file. The purpose of the CIFtbx software is similar to CIFIO, i.e. it may be used to convert ASCII CIF data into an internal binary representation and the reverse. ...
... In addition to data access commands, CIFtbx will validate data against one or more CIF dictionaries. This feature is useful for checking data conformance (using standard dictionaries such as eifdic.C91) or for local customized applications such as CIFIO (Hall, 1993a). ...
CIFtbx is a subroutine library which provides simple commands for reading and writing CIF data. This library is referred to as the CIF (software) tool box. CIFtbx routines may be applied to any Fortran program. The library is written in Fortran77 and may be installed without modification on most computers. CIFtbx is public-domain software.
... Most programmers had little or no experience in parsing freeformat data, all data then being in fixed format files. This gap was closed with the circulation of several STAR-compliant data checking routines (Hall & Sievers 1993;Hall 1993a;Hall 1993b;Hall 1993c) coded in Fortran 77. This code provided tools and examples for programmers who needed them. ...
The global application of the Crystallographic Information Framework (CIF) to the molecular structure domain has been successful over the past 20 years. It is used widely by molecular science journals and databases for submission, validation and deposition. This paper will give an overview of the CIF implementation, highlighting its particular successes and occasional failures. It will also recommend criteria for the application of an ontology-based data management system to any information domain. The paper will conclude with some details of the latest STAR data definition language and the importance of methods to the preservation of derivative data items.
The specification of a new standard Crystallographic Information File (CIF) is described. Its development is based on the Self-Defining Text Archive and Retrieval (STAR) procedure [Hall (1991). J. Chem. Inf. Comput. Sci. 31, 326-333]. The CIF is a general, flexible and easily extensible free-format archive file; it is human and machine readable and can be edited by a simple text editor. The CIF is designed for the electronic transmission of crystallographic data between individual laboratories, journals and databases: it has been adopted by the International Union of Crystallography as the recommended medium for this purpose. The file consists of data names and data items, together with a loop facility for repeated items. The data names, constructed hierarchically so as to form data categories, are self-descriptive within a 32-character limit. The sorted list of data names, together with their precise definitions, constitutes the CIF Dictionary (Core Version 1991). The CIF Core Dictionary is presented in full and covers the fundamental and most commonly used data items relevant to crystal structure analysis. The Dictionary is also available as an electronic file suitable for CIF computer applications. Future extensions to the Dictionary will include data items used in more specialized areas of crystallography.
The program QUASAR performs two basic functions. It extracts specific data items from an input CIF and places them into an output CIF format and it tests the input CIF for logical integrity (i.e. that the file conforms to the STAR File syntax). QUASAR is written in Fortran77 and has been implemented on a wide range of computers. It is available as public domain software.
Editors. Xtal3.2 Users Manual. Univs
- S R Hall
- H D Flack
- J M Stewart
- Australia
- Australia
- Usa Maryland
- S R Hall
- J M Stewart
HALL, S. R., FLACK, H. D. & STEWART, J. M. (1992). Editors. Xtal3.2 Users Manual. Univs. of Western Australia, Australia, and Maryland, USA. HALL, S. R. & STEWART, J. M. (1990). Editors. Xtal3.0 Users Manual. Univs. of Western Australia, Australia, and Maryland, USA.
- S R Sievers
HALL, S. R. ~ SIEVERS, R. (1993). J. Appl. Cryst. 26, 469-
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- F H Brown
HALL, S. R., ALLEN, F. H. & BROWN, I. D. (1991]. Acta C~st.
A47, 655-685.
- S R Allen
- F H Brown
HALL, S. R., ALLEN, F. H. & BROWN, I. D. (1991]. Acta C~st.
A47, 655-685.