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. 2.6, p. 68

Section 2.6.6.1.17. ITEM_TYPE_LIST

J. D. Westbrook,a* H. M. Bermana and S. R. Hallb

a Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, NJ 08854-8087, USA, and bSchool of Biomedical and Chemical Sciences, University of Western Australia, Crawley, Perth, WA 6009, Australia
Correspondence e-mail:  jwest@rcsb.rutgers.edu

2.6.6.1.17. ITEM_TYPE_LIST

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The ITEM_TYPE_LIST category holds the list of item data-type definitions. The key item in this category is _item_type_list.code. Data types are associated with data items by references to this key from the ITEM_TYPE category. One of the data-type codes defined in this category must be assigned to each data item.

The definition of a data type consists of the specification of the item's primitive type and a regular expression that defines the pattern that must be matched by any occurrence of the item. The primitive type code, _item_type_list.primitive_code, can assume values of char, uchar, numb and null. This code is provided for backward compatibility with STAR and CIF applications that employ loose data typing. The data item _item_type_list.construct holds the regular expression that must be matched by the data type. Simple regular expressions can be used to define character fields of restricted width, floating-point and integer formats.

Molecular Information File (MIF) applications (Allen et al., 1995[link]) have extended the notion of the regular expression to include data-item components. This permits the construction of complex data items from one or more component data items using regular expression algebra. These extended regular expressions are defined in the category ITEM_TYPE_CONDITIONS.

Example 2.6.6.1[link] illustrates the data types that are defined within this DDL. The DDL uses a number of character data types which have subtly different definitions. For instance, the data type identified as code defines a single-word character string; char extends the code type with the addition of a white-space character; and text extends the char type with the addition of a newline character. Two special character data types name and idname are used to define the full STAR data name and the STAR name components, respectively. The data type any is used to match any potential data type. This type is used for data items that may hold a variety of data types. The data type int is defined as one or more decimal digits and the yyyy-mm-dd type defines a date string.

Example 2.6.6.1. The description of permitted data types in the DDL2 dictionary.

[Scheme scheme6]

References

First citation Allen, F. H., Barnard, J. M., Cook, A. F. P. & Hall, S. R. (1995). The Molecular Information File (MIF): core specifications of a new standard format for chemical data. J. Chem. Inf. Comput. Sci. 35, 412–427.Google Scholar








































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