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Re: [ddlm-group] Draft EBNF for CIF2
- To: ddlm-group@iucr.org
- Subject: Re: [ddlm-group] Draft EBNF for CIF2
- From: John Westbrook <jwest@rcsb.rutgers.edu>
- Date: Wed, 27 Aug 2014 06:37:22 -0400
- In-Reply-To: <CAM+dB2dFBEVAhVo+rdJkJP+KzLXwvjUpsCxRK=8j=XcRZ3N94A@mail.gmail.com>
- References: <CAM+dB2eWm0m2qYTB1O7L2St-RUOJM5FRimFCozhwqWLEC0UR-Q@mail.gmail.com> <CAM+dB2eR1cHPGFUyEYbdiTVCSDpGYfpSZa_MhfAGs+7FBDfUaQ@mail.gmail.com> <53F69074.8040000@rcsb.rutgers.edu> <8F77913624F7524AACD2A92EAF3BFA54756EB8E8D8@11.stjude.org><CAM+dB2dFBEVAhVo+rdJkJP+KzLXwvjUpsCxRK=8j=XcRZ3N94A@mail.gmail.com>
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. > > > > -- > > T +61 (02) 9717 9907 <tel:%2B61%20%2802%29%209717%209907> <tel:%2B61%20%2802%29%209717%209907> > > F +61 (02) 9717 3145 <tel:%2B61%20%2802%29%209717%203145> > > M +61 (04) 0249 4148 > > > > > > > > > > -- > > T +61 (02) 9717 9907 > > F +61 (02) 9717 3145 > > M +61 (04) 0249 4148 > > > > > > _______________________________________________ > > ddlm-group mailing list > > ddlm-group@iucr.org <mailto:ddlm-group@iucr.org> > > http://mailman.iucr.org/mailman/listinfo/ddlm-group > > > > -- > > 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> > Ph: (848) 445-4290 <tel:%28848%29%20445-4290> Fax: (732) 445-4320 <tel:%28732%29%20445-4320> > _______________________________________________ > ddlm-group mailing list > ddlm-group@iucr.org <mailto:ddlm-group@iucr.org> > http://mailman.iucr.org/mailman/listinfo/ddlm-group > > > Email Disclaimer: www.stjude.org/emaildisclaimer <http://www.stjude.org/emaildisclaimer> > Consultation Disclaimer: www.stjude.org/consultationdisclaimer <http://www.stjude.org/consultationdisclaimer> > > _______________________________________________ > ddlm-group mailing list > ddlm-group@iucr.org <mailto:ddlm-group@iucr.org> > http://mailman.iucr.org/mailman/listinfo/ddlm-group > > > > > -- > T +61 (02) 9717 9907 > F +61 (02) 9717 3145 > M +61 (04) 0249 4148 > > > _______________________________________________ > ddlm-group mailing list > ddlm-group@iucr.org > http://mailman.iucr.org/mailman/listinfo/ddlm-group > -- 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 _______________________________________________ ddlm-group mailing list ddlm-group@iucr.org http://mailman.iucr.org/mailman/listinfo/ddlm-group
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