Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

RE: _atom_site_aniso_label is broken

May I suggest that, when there is serious concern that
the strict rule of one loop per category be adhered to,
that DDL2 dictionaries be used.  -- Herbert

At 11:31 AM -0500 6/20/05, Bollinger, John Clayton wrote:
>Nick Spadaccini wrote:
>>  On Mon, 20 Jun 2005, James Hester wrote:
>>  > I state that a (any?) reading of the DDL1.4 spec implies that
>>  > _atom_site_aniso_label is broken.
>>  >
>>  > Nick explains that the parent/child relationship between
>>  > _atom_site_aniso_label and _atom_site_label means that they can be
>>  > used as keys to join/split loops even during validation,
>>  consequently
>>  > solving the list_mandatory and _list_reference problem.
>>  Operationally whether your validator does any joining or
>>  splitting is an application level decision. What it must do
>>  is accept either joined or split lists as valid alternatives
>>  provided they meet the syntactic and structure requirements.
>Your position, then, is that all the items in a particular category that
>appear in lists should be considered to be in a single logical list,
>regardless of whether they are in the same physical list?  Is this a
>practical suggestion, or an interpretation of the DDL?  The DDL is
>ambiguous on the point, for although it says "[...] there may be more
>than one looped list of the same category provided that each loop has
>its own independent reference item (see _list_reference)" (_category
>definition), it also says "Signals if the defined item must be present
>in *the* loop structure containing other items of the designated
>_category" (_list_mandatory definition; emphasis mine).  Frankly,
>although the "one list" position is convenient from a practical
>standpoint, I don't think it's the most straightforward reading of the
>>  As far as I can recall
>>  CIF/DDL were originally syntactic constructs and semantics
>>  were argued on the fly. Whether or not they were ever agreed
>>  on is another matter. However much of CIF/DDL1.4 is simple
>>  and obvious, but there are the occasional contradictions like
>  > the "quick fix"
>  > construction of _atom_site_aniso_label to meet rapidly
>  > evolving requirements (at the time).
>All the more reason to look critically at the definition.  I assert that
>it _is_ broken, if only because having attribute list_mandatory means
>that it MUST appear among the list data for the atom_site category, even
>if there was no anisotropic refinement.  I suppose you could argue that
>the value can be assumed based on the parent link to _atom_site_label,
>but if you waved your arms that fast I'd feel the breeze here.
>Even the validity of splitting the atom_site_aniso_* stuff into a
>separate physical list depends on this idea of an implied join unifying
>multiple physical lists into one logical one for validation purposes.  I
>agree that the joins themselves are implied by parent/child
>relationships, but as far as I can tell, the best support for
>interpreting the DDL in terms of one logical list per category is the
>fact that splitting out the aniso stuff into its own list and putting it
>in the same list with the other atom_site stuff are both supposed to be
>valid.  Is it unreasonable to decide instead that the dictionary just
>didn't succeed in accomplishing that?  How much cruft should CIF be
>allowed to acquire simply to make an acknowledged "quick fix" correct?
>John Bollinger
>cif-developers mailing list

  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

               Office:  +1-631-244-3035
            Lab (KSC 020): +1-631-244-3451
cif-developers mailing list

Reply to: [list | sender only]
International Union of Crystallography

Scientific Union Member of the International Science Council (admitted 1947). Member of CODATA, the ISC Committee on Data. Partner with UNESCO, the United Nations Educational, Scientific and Cultural Organization in the International Year of Crystallography 2014.

International Science Council Scientific Freedom Policy

The IUCr observes the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science.