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. 23-24

Section 2.2.5.2. Data typing

S. R. Halla* and J. D. Westbrookb

2.2.5.2. Data typing

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In the STAR File grammar, all data values are represented as character strings. CIF applications may define data types, and in the macromolecular (mmCIF) dictionary (see Chapter 3.6[link] ) a range of types has been assigned corresponding to certain contemporary computer data-storage practices (e.g. single characters, case-insensitive single characters, integers, floating-point numbers and even dates). This dynamic type assignment is supported by the relational dictionary definition language (DDL2; see Chapter 2.6[link] ) used for the mmCIF dictionary and is not available for all CIF applications.

However, a more restricted set of four primary or base data types is common to all CIF applications.

The type numb encompasses all data values that are interpretable as numeric values. It includes without distinction integers and non-integer reals, and the values may be expressed if desired in scientific notation. At this revision of the specification it does not include imaginary numbers. All numeric representations are understood to be in the number base 10.

It is, however, a complex type in that the standard uncertainty in a measured physical value may be carried along as part of the value. This is denoted by a trailing integer in parentheses, representing the integer multiple of the uncertainty in the last place of decimals in the numeric representation. That is, a value of `1085.3(3)' corresponds to a measurement of 1085.3 with a standard uncertainty of 0.3. Likewise, the value 34.5(12) indicates a standard uncertainty of 1.2 in the measured value.

Care should be taken in the placement of the parentheses when a number is expressed in scientific notation. The second example above may also be presented as 3.45E1(12); that is, the standard uncertainty is applied to the mantissa and not the exponent of the value.

Note that existing DDL2 applications itemize standard uncertainties as separate data items. Nevertheless, since the DDL2 dictionary includes the attribute _item_type_conditions.code with an allowed value of `esd', future conformant DDL2 parsers might be expected to handle the parenthesized standard uncertainty representation.

The preferred behaviour of a CIF application is to determine the type of a data value by looking up the corresponding dictionary definition. However, some CIF-reading software may not be designed with the ability to parse dictionaries; and indeed any CIF reader may encounter data names that are not defined in a public or accompanying dictionary. It is therefore appropriate to adopt a strategy of interpreting as a number any data value that looks like one, i.e. adopts any of the permitted ways to represent a numeric value. Therefore, in the absence of a specific counter-indication (from a dictionary definition), the data value in the following example may be taken as the numeric (integer) value 1: [Scheme scheme4] On the other hand, if _unknown_data_name were explicitly defined in a dictionary with a data type of `char', then the value should be stored as the literal character 1.

This is a subtle point, perhaps of interest only to software authors. Nevertheless, the consistent behaviour of CIF applications will depend on correct implementation of this behaviour.

The data type char covers single characters or extended character strings. Since CIF tokens are separated by white space, any character string that includes white-space characters (including line-terminating characters) must be delimited by one or other of a set of special characters used for this purpose. The detailed rules for quoting such strings are given in Section 2.2.7.1.4[link] and comprise the standard CIF syntax rules for this case. No semantic distinction is made in general between short character strings and text strings that extend over several lines, described in the specification document as `text fields', although again particular CIF applications may choose to impose distinctions. Note that numbers within a quoted string or a text block (bounded by semicolons in column 1) are not interpreted as type `numb' but as type `char'.

The data type uchar was introduced explicitly at revision 1.1 of the CIF specification, and is intended to formalize the description and automated handling of certain strings in CIFs that are case-insensitive (such as data names and data-block headers).

The data type null is a special type that has two uses. It is applied to items for which no definite value may be stored in computer memory. As such it is a formal device for allowing the introduction of data names into dictionary files that do not represent data values permissible within a data file instance. The usual example is that of the special data names introduced in DDL1 dictionaries (such as the core dictionary) to discuss categories.

The more important use of the null data type is its application to the meta characters ` ?' (query) and ` .' (full point) that may occur as values associated with any data name and therefore have no specific type. (Arguably, for this case `any' might be a better type descriptor than `null'.)

The substitution of the query character ` ?' in place of a data value is an explicit signal that an expected value is missing from a CIF. This `missing-value signal' may be used instead of omitting an item (i.e. its tag and value) entirely from the file, and serves as a reminder that the item would normally be present.

The substitution of the full-point character ` .' in place of a CIF data value serves two similar, but not identical, purposes. If it is used in looped lists of data it is normally a signal that a value in a particular packet (i.e. a value in the row of the table) is `inapplicable' or `inappropriate'. In some CIF applications involving access to a data dictionary it is used to signal that the default value of the item is defined in its definition in the dictionary. Consequently, the interpretation of this signal is an application-specific matter and its use must be determined according to the application. For example, in a CIF submitted for publication in Acta Crystallographica the presence of a ` .' value for the item _geom_bond_site_symmetry_1 is predetermined as the default value 1_555 (as per the dictionary definition). Note that, in this instance, it is also equivalent to `no additional symmetry' or `inapplicable'.








































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