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Re: [ddlm-group] Draft EBNF for CIF2

I completely agree.   Nesting has not been used in the macromolecular applications.

Regards,

John

On 8/26/14, 9:30 PM, James Hester wrote:
> Dear DDLm group:
>
> My understanding of nested save frames is as follows:
> (1) In a dictionary, they structurally mirror the definition hierarchy, that is, they contain no additional information.  There is
> no scoping function given that the dREL definitions are able to refer to any dataname in any save frame.
> (2) In a data file, there appears to be no difference between using nested save frames as compared to a simple sequence of save
> frames. The save frame references introduced in the STAR2 paper require all save frame names to be unique within a datablock,
> regardless of nesting.
>
> In both cases it seems that nested save frames are an organisational tool only.
>
> So I don't believe that we lose anything by dropping nested save frames.
>
> James.
>
>
> On Mon, Aug 25, 2014 at 10:48 PM, Bollinger, John C <John.Bollinger@stjude.org <mailto:John.Bollinger@stjude.org>> wrote:
>
>     Hi John,
>
>     The EBNF James distributed does require save frames to be named, as in previous versions of CIF.  Here is the relevant production:
>
>          save-heading = save-token, container-name;
>
>
>     Regards,
>
>     John
>
>     --
>     John C. Bollinger, Ph.D.
>     Computing and X-Ray Scientist
>     Department of Structural Biology
>     St. Jude Children's Research Hospital
>     John.Bollinger@StJude.org
>     (901) 595-3166 <tel:%28901%29%20595-3166> [office]
>     www.stjude.org <http://www.stjude.org>
>
>
>
>     -----Original Message-----
>     From: ddlm-group-bounces@iucr.org <mailto:ddlm-group-bounces@iucr.org> [mailto:ddlm-group-bounces@iucr.org
>     <mailto:ddlm-group-bounces@iucr.org>] On Behalf Of John Westbrook
>     Sent: Thursday, August 21, 2014 7:36 PM
>     To: Group finalising DDLm and associated dictionaries
>     Subject: Re: [ddlm-group] Draft EBNF for CIF2. .
>
>     Hi James,
>
>     I would prefer that there be no self nesting of either save or data sections and that save sections should be named.
>
>     Regards,
>
>     John
>
>
>     On 8/21/14, 8:26 PM, James Hester wrote:
>      > Dear DDLm group,
>      >
>      > John Bollinger has reminded by of a further change: nested save
>      > frames, which were introduced in the STAR2 and DDLm papers, are
>      > included in the EBNF.  CIF1.1 only envisioned a single level of save frames, and only in dictionary files.  Absent a decision
>     by this group or COMCIFS, the restriction of save frames to dictionary files (nested or otherwise) would continue.
>      >
>      > James.
>      >
>      >
>      >
>      > On Wed, Aug 20, 2014 at 4:33 PM, James Hester <jamesrhester@gmail.com <mailto:jamesrhester@gmail.com>
>     <mailto:jamesrhester@gmail.com <mailto:jamesrhester@gmail.com>>> wrote:
>      >
>      >     Dear DDLm group,
>      >
>      >     John Bollinger and myself have put our heads together and produced an ISO 14977 EBNF specification of CIF2.0 syntax.  We were
>      >     working from the 10 August 2011 "CIF Changes" document agreed by this group and approved in Madrid, available in the
>     archives of
>      >     this list at http://www.iucr.org/__data/iucr/lists/ddlm-group/pdf00001.pdf, with the following change:
>      >
>      >     (1) triple-quoted strings were returned to the specification as agreed in Montreal, in the form contained in the draft
>     posted at
>      >
>      > http://www.iucr.org/__data/assets/pdf_file/0020/59420/cif2_syntax_chan
>      > ges-jcb20110728.pdf
>      >
>      >     Please study the attached EBNF (plain text format) and advise of any errors, omissions or ambiguities.  Note that EBNF is
>      >     clearly not the best format for machine-generation of parsers, but it should be sufficiently precise and understandable
>     to serve
>      >     as a foundation document for CIF2.
>      >
>      >     For those, such as myself, who have not seen the ENBF '-' operator before, the meaning of "A-B" is: all character sequences
>      >     satisfying A, except those that satisfy B.
>      >
>      >     My intention is to start producing documentation for CIF2 on the basis of this EBNF, so your earliest comments would be most
>      >     appreciated.
>      >
>      >     all the best,
>      >     James.
>      >
>      >     --
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>      >
>      >
>      >
>      >
>      > --
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>      >
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>
>     --
>
>     John Westbrook, Ph.D.
>     RCSB, Protein Data Bank
>     Rutgers, The State University of New Jersey Department of Chemistry and Chemical Biology
>     174 Frelinghuysen Rd
>     Piscataway, NJ 08854-8087
>     e-mail: jwest@rcsb.rutgers.edu <mailto:jwest@rcsb.rutgers.edu>
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-- 

John Westbrook, Ph.D.
RCSB, Protein Data Bank
Rutgers, The State University of New Jersey
Department of Chemistry and Chemical Biology
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
e-mail: jwest@rcsb.rutgers.edu
Ph: (848) 445-4290 Fax: (732) 445-4320
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