International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G. ch. 5.3, p. 522

Section 5.3.8.1.  CIFOBJ and related libraries

B. McMahona*

a International Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England
Correspondence e-mail: bm@iucr.org

5.3.8.1. CIFOBJ and related libraries

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Early in the development of the mmCIF dictionary, the Nucleic Acid Database at Rutgers University (Berman et al., 1992[link]) created a number of CIF libraries and utilities to underpin data-processing activities. Much of this development work was carried across when the curatorship of the Protein Data Bank was transferred to the Research Collaboratory for Structural Bioinformatics (RCSB; Berman et al., 2002[link]), and the software provides the engine for many of the robust and industrial-strength database operations of these organizations.

CIFLIB (Westbrook et al., 1997[link]) was an early class library, no longer supported, that was developed to provide an API to macromolecular CIF data files and to the associated dictionaries (Chapters 3.6[link] and 4.5[link] ) and underlying dictionary definition language (DDL2) files (Chapter 2.6[link] ).

The RCSB Protein Data Bank now distributes object-oriented parsing tools (CIFPARSE_OBJ; Tosic & Westbrook, 2000[link]) which fully support CIF data files and their underlying metadata descriptions in dictionaries and DDL2 attribute sets, and a comprehensive library of access methods for data and dictionary objects at category and item level.

The information infrastructure of the Protein Data Bank, built upon these tools, is discussed in Chapter 5.5[link] . All the software produced for this purpose is distributed with full source under an open-source licence, to promote the development of mmCIF tools and to encourage interoperability with other software environments.

References

First citation Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Feng, Z., Gilliland, G. L., Iype, L., Jain, S., Fagan, P., Marvin, J., Padilla, D., Ravichandran, V., Schneider, B., Thanki, N., Weissig, H., Westbrook, J. D. & Zardecki, C. (2002). The Protein Data Bank. Acta Cryst. D58, 899–907.Google Scholar
First citation Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.-H., Srinivasan, A. R. & Schneider, B. (1992). The Nucleic Acid Database: a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63, 751–759.Google Scholar
First citation Tosic, O. & Westbrook, J. D. (2000). CIFParse. A library of access tools for mmCIF. Reference guide. http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/cifparse/index.html .Google Scholar
First citation Westbrook, J. D., Hsieh, S.-H. & Fitzgerald, P. M. D. (1997). CIF applications. VI. CIFLIB: an application program interface to CIF dictionaries and data files. J. Appl. Cryst. 30, 79–83.Google Scholar








































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