Section 5.3.7.1.1. Description of the ZINC format

The ZINC format (Stampf, 1994) was developed to transform CIF data into an isomorphous format suitable for manipulation by standard Unix utilities.

The manner in which Unix textual utilities work suggests that an appropriate working format is one in which every individual CIF data value is available within a single-line textual record. The record must also contain information about the context of the value, conveyed through: the name of the data block in which the data value occurs; its associated data name (from which the meaning of the data value is inferred); and for recurrent data (i.e. values in a looped list) an indication of the list in which the data value occurs and a counter of its current occurrence in that list. In practice, each record is structured as a data line containing five TAB-separated fields in the order

blockcode name index value list-id

where blockcode is the name of the CIF data block (the leading data_ string is omitted); name is the data name; index is a zero-based index of the number of occurrences of the data name within a loop (with a null value if the data occur outside a loop); value is the data value itself; text strings extending over several lines are collapsed into a single line with the replacement of the end-of-line character by the sequence \n; and list-id is a list identifier, stored as the data name within the list that sorts earliest (because it is a purely syntactic transformation, the utility does not consult a dictionary file for the correct _list_reference identifying token).

Comments in the CIF are also stored, to permit regeneration of the original file by an inverse transformation; and because it is often convenient to read such interpolations, especially in interactive activities with CIFs of which the user has no prior knowledge. Comments are stored with a value of ` (' in the data-name field. They are also numbered (starting from zero) in the index field of the ZINC record.

Most details of the ZINC transformation are illustrated by the simple example in CIF format shown in Fig. 5.3.7.1(a). This file transformed to ZINC format would appear on a display terminal as illustrated in Fig. 5.3.7.1(b). However, the spacing is deceptive, since typical display terminals convert TAB characters to a variable number of spaces. A more accurate (albeit less legible) representation of the output is given in Fig. 5.3.7.1(c).

Figure 5.3.7.1 | top | pdf | ZINC transformation of CIF. (a) is a sample file in CIF format. (b) shows the output to a display terminal when this file is transformed by cifZinc. (c) The same output as (b), but with TAB characters represented by special graphical characters.

Note the following points: the data-block name is initially null; each comment line is numbered in sequence from zero; the index field is null for data names that are not within looped lists.