|
INTERNATIONAL TABLES for CRYSTALLOGRAPHY |
Volume G |
Definition and Exchange of Crystallographic Data |
This chapter is an introduction, for programmers new to CIF, to ways of creating new 'CIF-aware' applications and of adapting existing applications to make them CIF-aware. We review general considerations in programming CIF-aware applications, ranging from leaving an application CIF-unaware and relying on external filter utilities to do the job, through engineering an existing application to directly read and write CIFs, to writing a new CIF-aware application from scratch.
The following programs are referenced in this chapter:
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., Kennard, O., Motherwell,
W. D. S., Town, W. G. & Watson, D. G. (1973).
Cambridge Crystallographic Data Centre. II. Structural Data File.
J. Chem. Doc. 13, 119-123.
Andrews, N. (1987). Rich Text Format standard makes transferring text easier. Microsoft Syst. J., 2, 63-67.
Berners-Lee, T. (1989). Information management: a proposal. Internal Report. Geneva: CERN. http://www.w3.org/History/1989/proposal-msw.html.
Bernstein, F. C. & Bernstein,
H. J. (1996). Translating mmCIF data into PDB entries.
Acta Cryst. A52 (Suppl.), C-576.
Bernstein, F. C., Koetzle, T. F.,
Williams, G. J. B., Meyer, E. F. Jr, Brice, M. D.,
Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M.
(1977). The Protein Data Bank: a computer-based archival file for
macromolecular structures.
J. Mol. Biol. 112, 535-542.
Bernstein, H. J. (1997). cif2cif - CIF copy program. Bernstein + Sons, Bellport, NY, USA. Included in http://www.bernstein-plus-sons.com/software/ciftbx.
Bernstein, H. J. & Bernstein,
F. C. (2002). YAXDF and the interaction between CIF and XML.
Acta Cryst. A58 (Suppl.), C257.
Bernstein, H. J., Bernstein, F. C.
& Bourne, P. E. (1998). CIF applications. VIII.
pdb2cif: translating PDB entries into mmCIF format.
J. Appl. Cryst. 31, 282-295.
Software available from
http://www.bernstein-plus-sons.com/software/pdb2cif.
Bray, T., Paoli, J. & Sperberg-McQueen, C. (1998). Extensible Markup Language (XML). W3C Recommendation 10-February-1998. http://www.w3.org/TR/1998/REC-xml-19980210.
Cambridge Structural Database (1978). Cambridge Crystallographic Database User Manual. Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge, England.
Chang, W. & Bourne, P. E. (1998).
CIF applications. IX. A new approach for representing and manipulating
STAR files. J. Appl. Cryst. 31, 505-509.
Diamond, R. (1971). A real-space
refinement procedure for proteins.
Acta Cryst. A27, 436-452.
Dubuisson, O. (2000). ASN.1 - communication between heterogeneous systems. San Francisco, CA: Morgan Kaufmann. (Translated from the French by P. Fouquart). See also http://www.oss.com/asn1/dubuisson.html.
Flack, H. D., Blanc, E. &
Schwarzenbach, D. (1992). DIFRAC, single-crystal
diffractometer output-conversion software.
J. Appl. Cryst. 25, 455-459.
Hall, S. R. (1993). CIF applications.
IV. CIFtbx: a tool box for manipulating CIFs.
J. Appl. Cryst. 26, 482-494.
Hall, S. R. & Bernstein, H. J.
(1996). CIF applications. V. CIFtbx2: extended tool box for manipulating
CIFs.
J. Appl. Cryst. 29, 598-603.
Hall, S. R. & Sievers, R. (1993).
CIF applications. I. QUASAR: for extracting data from a CIF.
J. Appl. Cryst. 26, 469-473.
Hammersley, A. P. (1997). FIT2D: an introduction and overview. ESRF Internal Report ESRF97HA02T. Grenoble: ESRF.
Heller, S. R., Milne, G. W. A. & Feldmann, R. J. (1977). A computer-based chemical information system. Science, 195, 253-259.
Hester, J. R. & Okamura, F. P.
(1998). CIF applications. X. Automatic construction of CIF input
functions: CifSieve.
J. Appl. Cryst. 31, 965-968.
ISO (1986). ISO 8879. Information processing
- Text and office systems - Standard Generalized Markup Language
(SGML). Geneva: International Organization for Standardization.
ISO (2002). 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.
Johnson, S. C. (1975). YACC: Yet another Compiler-Compiler. Bell Laboratories Computing Science Technical Report No. 32. Bell Laboratories, Murray Hill, New Jersey, USA. (Also in UNIX Programmer's Manual, Supplementary Documents, 4.2 Berkeley Software Distribution, Virtual VAX-11 Version, March 1984.)
Keller, P. A. (1996). A mmCIF toolbox
for CCP4 applications.
Acta Cryst. A52 (Suppl.), C-576.
Klosowski, P., Koennecke, M., Tischler, J. Z. & Osborn, R. (1997). NeXus: a common format for the exchange of neutron and synchrotron data. Physica B Condens. Matter, B241-243, 151-153.
Knuth, D. E. (1986). The TeXbook. Computers and Typesetting, Vol. A. Reading, MA: Addison-Wesley.
Lesk, M. E. & Schmidt, E. (1975). Lex - a lexical analyzer generator. Bell Laboratories Computing Science Technical Report No. 39. Bell Laboratories, Murray Hill, New Jersey, USA. (Also in UNIX Programmer's Manual, Supplementary Documents, 4.2 Berkeley Software Distribution, Virtual VAX-11 Version, March 1984.)
Lykos, P. (1975). Editor. Computer networking and chemistry. ACS Symposium Series, Vol. 19. Washington, DC: American Chemical Society.
Murray-Rust, P. & Rzepa, H. (1999).
Chemical markup, XML and the WWW, Part I: Basic principles.
J. Chem. Inf. Comput. Sci. 39, 928-942.
NCSA (1993). NCSA HDF: specification and developer's guide. Version 3.2. University of Illinois at Urbana-Champaign, USA.
Ohkawa, H., Ostell, J. & Bryant, S. (1995). MMDB: an ASN.1 specification for macromolecular structure. In Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, Cambridge, England, 16-19 July 1995, pp. 259-267. Menlo Park, CA: American Association for Artificial Intelligence.
PDB (1974). PDB Newsletter 1. Brookhaven National Laboratory, USA. Available from ftp://ftp.rcsb.org/pub/pdb/doc/newsletters/old_bnl/.
PDB (1976a). PDB Newsletter 2. Brookhaven National Laboratory, USA. Available from ftp://ftp.rcsb.org/pub/pdb/doc/newsletters/old_bnl/.
PDB (1976b). PDB Newsletter 3. Brookhaven National Laboratory, USA. Available from ftp://ftp.rcsb.org/pub/pdb/doc/newsletters/old_bnl/.
PDB (1977). PDB Newsletter 4. Brookhaven National Laboratory, USA. Available from ftp://ftp.rcsb.org/pub/pdb/doc/newsletters/old_bnl/.
Spadaccini, N. & Hall, S. R.
(1994). Star_Base: accessing STAR File data.
J. Chem. Inf. Comput. Sci. 34, 509-516.
Stampf, D. R. (1994). ZINC - galvanizing CIF to work with UNIX. Manual. Protein Data Bank, Brookhaven National Laboratory, USA.
Tosic, O. & Westbrook, J. D. (1998). CIFPARSE: a library of access tools for mmCIF. Reference guide. Version 3.1. Nucleic Acid Database Project, Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, USA. http://sw-tools.pdb.org/apps/CIFPARSE/cifparse/index.html.
Walters, P. & Stahl, M. (1994). BABEL reference manual. Version 1.06. Dolata Research Group, Department of Chemistry, University of Arizona, USA.
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.
Copyright © 2005 International Union of Crystallography