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Re: [ddlm-group] Draft EBNF for CIF2


I'm having trouble seeing the down side of providing for save frame nesting in the CIF2 syntax specifications.  Doing so would enable *but not require* nested frames to be used in DDLm and DDLm dictionaries, but any way around they are irrelevant to DDL1 and DDL2 dictionaries (whether written in CIF1 or CIF2 syntax) and to all CIF data files currently envisioned.  To a parser that does not understand them, nested frames will look like a combination of a missing frame terminator between adjacent frames plus an extraneous frame terminator at some later point, and such a parser must be prepared to handle those errors in some way anyway (that is exactly the CIF1 situation).  A parser specialized for a domain to which nested save frames are not relevant can be such a parser, since nested frames would be erroneous in its target domain anyway.

On the other hand, allowing nested frames in the syntax would maximize our leverage from the Perth group's existing tools and recent work. 


Regards,

John

-- 
John C. Bollinger, Ph.D.
Computing and X-Ray Scientist
Department of Structural Biology
St. Jude Children's Research Hospital


-----Original Message-----
From: ddlm-group-bounces@iucr.org [mailto:ddlm-group-bounces@iucr.org] On Behalf Of John Westbrook
Sent: Wednesday, August 27, 2014 5:37 AM
To: ddlm-group@iucr.org
Subject: 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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>     --
>
>     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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