5.3. Syntactic utilities for CIF

B. McMahon

Abstract

This chapter reviews the general-purpose software tools available for managing CIF data that rely solely or largely on the syntactic structure of the CIF. That is, they allow the checking, extraction, editing or manipulation of arbitrary data items without regard to any specifically crystallographic computation. Some lightweight libraries are also described.

The programs reviewed fall within the categories:

syntax checkers
editors with graphical user interfaces
software for data-name validation
file-transformation programs
libraries callable from scripting languages
rapid development tools
tools particularly useful for macromolecular applications using mmCIF

Links

Figures

The figures in this chapter representing screenshots of computer applications are reproduced here at full size and in colour.

	Fig. 5.3.3.1. The enCIFer graphical user interface.
	Fig. 5.3.3.2. The enCIFer loop editor.
	Fig. 5.3.3.3. The enCIFer publication data wizard. Information about the title and authors of an article to be submitted for publication is requested through a sequence of linked dialogue boxes.
	Fig. 5.3.3.4. The enCIFer chemical and crystal data wizard.
	Fig. 5.3.3.5. Visualization of a molecular and crystal three-dimensional structure with enCIFer.
	Fig. 5.3.3.6. The use of CIFEDIT to display and alter the contents of a CIF; here a non-looped data item is shown.
	Fig. 5.3.3.7. Row-based loop editing with CIFEDIT; here loop_2 (comprising the ATOM_SITE category) has been selected by the user; the editing cursor begins at row 1 of the loop.
	Fig. 5.3.3.8. Control window of the HICCuP application.
	Fig. 5.3.3.9. HICCuP edit window and error description.
	Fig. 5.3.3.10. HICCuP dictionary browser window.
	Fig. 5.3.3.11. A category view in the beCIF editor of a CIF with navigation by tabs.
	Fig. 5.3.3.12. Representation by the beCIF editor of looped data within a category (here ATOM_SITE) in spreadsheet style.
	Fig. 5.3.3.13. The dual RTF/CIF editing windows in the printCIF for Word application. In this example, the author has selected the word 'Monoclinic' in the read-only table of crystal data; the corresponding CIF data item `_symmetry_cell_setting` is highlighted in the CIF window, where it may be edited.

Software

The following programs are referenced in this chapter:

Supporting materials

The following example applications may be of interest. Both require the Perl modules of the STAR::Parser family

makedict.pl The complete source code of the dictionary formatting application used in simplified form as the example of Fig. 5.3.6.1.
makedicthtml.pl A similar dictionary formatting application used to generate the HTML representations of the CIF dictionaries on this CD-ROM.

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