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. 3.1, p. 89

Section 3.1.9.2. Protocol implementation

B. McMahona*

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

3.1.9.2. Protocol implementation

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At the time of publication (2005), there is no reference implementation for this protocol, and so the proper treatment of the fine details of merging and overlay operations is not available. The following guidelines outline the first steps in an implementation under DDL1.4.

The description assumes that a composite dictionary is to be assembled from two public dictionaries, a.dic and b.dic, and a local dictionary mod.dic that includes some modifications to the definitions in one or both of the public dictionaries (and is therefore processed in OVERLAY mode). It is assumed that the composite dictionary will be written to disk as a separate file, virtual.dic, although in practice applications may simply construct the image of the composite dictionary in memory.

(1) Each contributing dictionary fragment should have at most one data block containing the data names _dictionary_name and _dictionary_version (with, optionally, _dictionary_update and _dictionary_history). The *_name and *_version together identify the dictionary file uniquely and should match the corresponding entries in the IUCr register if this is a public dictionary. This information is conventionally stored in a data block named data_on_this_dictionary.

In DDL1.4, all four of the items _dictionary_name, *_version, *_update and *_history are scalars, i.e. may not be looped. Hence a new dictionary identifier section in virtual.dic may be constructed as follows.

(i) Create a data block data_on_this_dictionary at the beginning of virtual.dic.

(ii) If a name for the composite dictionary is supplied (via a command-line switch, for example), write this as the value of _dictionary_name; otherwise generate a pseudo-unique string (e.g. concatenate the computer identifier string, process number and current date string).

(iii) If a dictionary version number is supplied (via a command-line switch, for example), write this as the value of _dictionary_version; otherwise supply the value `1.0'.

(iv) Supply the current date in the format yyyy-mm-dd as the value of _dictionary_update.

(v) Create a composite _dictionary_history by concatenation of the individual _dictionary_history fragments. The application may add details of the current merge operation to the history field.

(2) There is no significance to the ordering of data blocks containing definitions in dictionaries, although they are conventionally sorted alphabetically. For convenience, data blocks should be written out in the order in which they are encountered in the input primitive dictionary files, except that definitions modified by subsequent entries remain in their initial location.

(3) In STRICT mode, if the same value of _name is present in two or more data blocks, the composite dictionary is invalid and the application should raise a fatal error. Otherwise the composite dictionary simply contains the aggregate definitions from multiple input dictionaries.

(4) In REPLACE mode, a stored definition block is discarded and replaced by a new definition of the item referenced by _name.

(5) For the OVERLAY mode (assumed in the present discussion), the following procedure is proposed. Load a data block from the first dictionary file. Locate the _name tag. (Because _name may be looped, a data block may contain definitions for more than one data name. For convenience, we consider only the case of a data block containing a single value of _name. In any event, it is possible to separate a set of looped definitions into individual data blocks, each defining only one of the data names in the initial _name loop.) Search the next dictionary file for a data block containing the same value of _name. Load the contents of that data block.

(i) If the new data block contains only data items that do not appear in the first data block, they are simply concatenated with those already present.

(ii) If the new data block contains a scalar data item already present in the first data block (i.e. with _list no), discard the stored attributes.

(iii) If the new data block contains data items that may be looped and that occur in the first data block, build a new composite table of values in the following way: (a) construct a valid loop header if necessary; (b) do not repeat identical sets of values (i.e. collapse identical table rows); (c) if it is possible to identify the category key, then raise a fatal error if there are identical instances of a key value [after the normalization of step (b) has occurred]; (d) else append new rows to the table.

When the new composite data block has been built according to these principles, search the next dictionary file specified and repeat.








































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