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. 5.3, p. 511

Section 5.3.5.1.4. Output from QUASAR

B. McMahona*

a International Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England
Correspondence e-mail: bm@iucr.org

5.3.5.1.4. Output from QUASAR

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The body of the request list is a series of data names. Where a data name appears in the CIF, it will be extracted with its associated data value or values. The user need not have prior knowledge of whether a data item occurs in a looped list or not: QUASAR will automatically retrieve the matching values and construct a loop header if necessary. However, because the requests are served in the exact order in which they occur in the file, data items in the same list in the input CIF may be extracted into different lists upon output. Although this breaks the semantic association between items grouped in the same list (especially for CIFs described by the DDL2 relational scheme), it is a syntactically valid construction and may be a valuable feature for some processes.

5.3.5.1.4.1. Treatment of missing data

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When a requested data item is absent from the CIF, QUASAR will nevertheless emit a data name with a corresponding value of ` ?', the conventional CIF value of null type for `unknown quantity'. A CIF comment is also generated by QUASAR to indicate that the entry was missing from the input CIF. If the missing data name is found between data names that have multiple values and that occur in the same looped list, it is assumed that the missing data name should be associated with the same looped list, and it will be emitted in the loop header; the integrity of the list is then satisfied by emitting a column of unknown values. Note how this behaviour differs from that of the generic STAR File extraction utility Star_Base (Spadaccini & Hall, 1994[link]), which silently ignores missing data items. However, it is a useful behaviour for applications that depend on finding a specific data item in their processing stream, even where its value is unknown.

5.3.5.1.4.2. Matching data names

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As with the specification of data-block names, the data names in the request list may have a trailing underscore. Where this is the case, QUASAR will retrieve all data items where the data name starts with the specified string. For example, a request for ` _atom_site_' will extract all data names starting with ` _atom_site_'. The special case of an isolated underscore character ` _' matches all data names present in the current data block.

5.3.5.1.4.3. Case sensitivity

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The example demonstrates the way in which the application handles the case insensitivity of a requested data item. Data names are converted internally to a lower-case representation, both from the request list and the input CIF. Matches are therefore determined in a case-insensitive manner. However, if a data name is present in the CIF, its original case is retained on output. This permits the computationally irrelevant but cosmetically useful retention of capitalization as used in canonical CIF dictionary definitions. Where the requested data name is absent, the output is all lower-case.

References

First citation Spadaccini, N. & Hall, S. R. (1994). Star_Base: accessing STAR File data. J. Chem. Inf. Comput. Sci. 34, 509–516.Google Scholar








































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