International
Tables for Crystallography Volume G Definition and exchange of crystallographic data Edited by S. R. Hall and B. McMahon © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. G. ch. 2.6, pp. 65-66
Section 2.6.6.1.1. ITEM
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 |
The category named ITEM is used to assign membership of data items to categories. This category forms the bridge between the category and data-item levels of abstraction. The key data item in this category is the full data-item name, _item.name. This name contains both the category and data-item identifiers, and is thus a unique identifier for the data item. The category identifier, _item.category_id, is included in this category as a separate mandatory data item. This has been done to provide an explicit reference to those categories that use the category identifier as a unique identifier.
One could alternatively use the category and item identifiers as the basis for this category rather than the concatenated form of the item name, and thus eliminate the redundant specification of the category identifier. The full name has been used here in order to provide compatibility with existing applications.
The item category also includes a code to indicate whether a data item is mandatory in a category and therefore must be included in any tuple of items in the category. This code, _item.mandatory_code, may have three values: yes, no and implicit. This last named value indicates that the item is mandatory, but that the value of this item may be derived from the context. In the case of an item name or a category identifier, these values can be obtained from the current save-frame name. Implicit specification dramatically simplifies the appearance of each dictionary definition because it avoids the repeated declaration of item names and category identifiers that are basis components or the unique identifiers for most categories.
Although the data item _item.name is the basis for all of the item-level categories, its definition and properties need only be specified at a single point. Here, the data items that occur in multiple categories are defined only in the parent category. In certain situations, a child data item may be used in a manner which requires a description distinct from the parent data item. For instance, _item_linked.parent_name and _item_linked.child_name are both data-item names as well as children of _item.name, but clearly the manner in which these items are used in the ITEM_LINKED category requires additional description. It is important to note that although the design of this DDL supports the definition of data items in multiple categories within the parent category, it is also possible to provide separate complete definitions within each category.