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. 2.2, pp. 21-22

Section 2.2.3. The syntax of a CIF

S. R. Halla* and J. D. Westbrookb

2.2.3. The syntax of a CIF

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The essential syntax rules for a CIF data file are discussed alongside an example (Fig. 2.2.3.1[link]), which is an extract from a file used to exemplify the reporting of a small-molecule crystal structure to Acta Crystallographica Section C. The following discussion is tutorial in nature and is intended to give an overview of the syntactic features of CIF to the general reader. The special use of save frames in dictionary files is not discussed in this summary. Software developers will find the full specification at the end of the chapter. If there are any real or apparent discrepancies between the two treatments, the full specification is to be taken as definitive.

[Figure 2.2.3.1]

Figure 2.2.3.1 | top | pdf |

Typical small-molecule CIF.

A CIF contains only ASCII characters, organized as lines of text.

Tokens (the discrete components of the file) are separated by white space; layout is not significant. Thus, in the list of atom-site coordinates in Fig. 2.2.3.1[link], the hydrogen-atom entries are cosmetically aligned in columns, but the non-aligned entries for the other atoms are equally valid. Indeed, there is no requirement that each cluster of looped data values be confined to a separate row; contrast the cosmetic ordering of the atom-sites loop with the loop of symmetry-equivalent positions, where entries run on the same or following lines indiscriminately.

A comment is a token introduced by a hash character # and extending to the end of the line. Comments are considered to have no portable information content and may freely be discarded by a parser. However, revision 1.1 of the CIF specification introduces a recommendation that a CIF begin with a comment taking the form [Scheme scheme1] where the 1.1 is a version identifier of the reference CIF specification. This is primarily for the benefit of general file-handling software on current operating systems (e.g. graphical file managers that associate software applications with files of specific type), and its presence or absence does not guarantee the integrity of the file with respect to any particular revision of the CIF specification.

The first non-comment token of a CIF must be a data-block header, which is a character string that does not include white space and begins with the case-insensitive characters data_.

The file may be partitioned into multiple data blocks by the insertion of further data-block headers. Data-block headers are case-insensitive (that is, two headers differing only in whether corresponding letter characters are upper or lower case are considered identical). Within a single data file identical data-block headers are not permitted.

Data names are character strings that begin with an underscore character _ and do not contain white-space characters. Data names serve to index data values and are case-insensitive.

Where a data name indexes a single data value, that value follows the data name separated by white space.

Where a data name indexes a set of data values (conceptually a vector or table column), the relevant data items are preceded by the case-insensitive string loop_ separated by white space.

The examples of Fig. 2.2.3.1[link] show the use of loop_ to specify a vector or one-dimensional list of values (the symmetry-equivalent positions) and a tabular or matrix list (the atom-site positions). Again it should be emphasized that the rows and columns of the table are identified by parsing each value and referring back to the sequence in the header of its identifying tag, and not by a conventional layout of items. It is usual for CIF writers to lay out two-dimensional data arrays as well formatted tables for ease of inspection in text editors or other viewers, but CIF readers must never rely on layout alone to identify a tabulated value.

A corollary of this is that the number of values in a looped list must be an exact integer multiple of the number of data names declared in the loop header.

Within a single data block the same data name may not be repeated. Thus if a data item may have multiple values, these items must be collected together within a looped list, the data name itself being given once only in the loop header.

A data value is a string of characters. CIF distinguishes between numerical and character data in a broad sense (see Section 2.2.5.2[link] below). Numerical values may not contain white space (and indeed are constrained to a limited character set and ordering, essentially encompassing a small range of ways in which numbers are characteristically represented in printed form). Because tokens are separated by white space, character data that include white-space characters must be quoted. If the data value does not extend beyond the end of a line of text, it may be quoted by matching single-quote (apostrophe, ') or double-quote (quotation mark, ") characters. If the data value does extend beyond the end of a line of text, then paired semicolon characters ; as the first character of a line may be used as delimiters. The closing semicolon is the first character of a line immediately following the close of the data-value string. Fig. 2.2.3.1[link] shows examples of all three types of delimited character values that include white space.

Character strings that begin with certain other characters must also be quoted. These leading characters are those which introduce tokens with special roles in a STAR File (such as underscore _ at the start of a data name, hash # at the start of a comment and dollar $ identifying a save-frame reference pointer). Likewise, the STAR File reserved words loop_, stop_ and global_ must be quoted if they represent data values, as must any character string beginning with data_ or save_.

Lines of text are restricted to 2048 characters in length and data names are restricted to 75 characters in length. These are increases over the original values of 80 and 32 characters, respectively.








































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