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Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and Python. .
- To: Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org>
- Subject: Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and Python. .
- From: James Hester <jamesrhester@gmail.com>
- Date: Fri, 14 Jan 2011 15:31:07 +1100
- In-Reply-To: <85782.48834.qm@web87007.mail.ird.yahoo.com>
- References: <AANLkTimdAavg2KCjPZTj1xDYXDQ1JLiQCkQb4snyBErZ@mail.gmail.com><alpine.BSF.2.00.1101120536370.71134@epsilon.pair.com><AANLkTimA8+YXbJ8yS0AtKgFjq9221oMFjR6habn6DsXR@mail.gmail.com><alpine.BSF.2.00.1101120834010.42232@epsilon.pair.com><8F77913624F7524AACD2A92EAF3BFA54166D7D1EA8@SJMEMXMBS11.stjude.sjcrh.local><alpine.BSF.2.00.1101121400400.85750@epsilon.pair.com><alpine.BSF.2.00.1101121556380.31518@epsilon.pair.com><698308.91583.qm@web87015.mail.ird.yahoo.com><alpine.BSF.2.00.1101121845060.90622@epsilon.pair.com><alpine.BSF.2.00.1101131202050.27153@epsilon.pair.com><8F77913624F7524AACD2A92EAF3BFA54166D7D1EB8@SJMEMXMBS11.stjude.sjcrh.local><85782.48834.qm@web87007.mail.ird.yahoo.com>
I'm frankly not entirely sure why people are exercised about STAR compatibility. Perhaps Simon and Herbert could explain why small syntactical differences are such a big deal? While I am in favour of keeping the essential STAR philosophy ("a syntactical container for data") and maintaining compatibility in abstract datastructures, I don't see why CIF can't stand on its own legs. Why is anybody spooked by the thought that CIF might parse certain vanishingly rare strings in a different way to STAR? I note that none of my objections to the Python elide proposal have anything to do with STAR. On Fri, Jan 14, 2011 at 11:15 AM, SIMON WESTRIP <simonwestrip@btinternet.com> wrote: >> that the CIF2 syntax we had been discussing was a compatible subset of an >> as-yet unpublished updated version of STAR > > This was my assumption. > >>I now find that this is not exactly the case... > > This is disappointing to say the least. > > > > ________________________________ > From: "Bollinger, John C" <John.Bollinger@STJUDE.ORG> > To: Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org> > Sent: Thursday, 13 January, 2011 23:35:21 > Subject: Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and Python. . > > > On Thursday, January 13, 2011 11:18 AM, Herbert J. Bernstein wrote: >>[...] it has become clear to me that I was >>making false assumptions about the relationship between >>CIF2 and STAR. I believe that a zero-based discussion is >>now needed on what the relationship should be among CIF2, >>STAR, CIF1 and Python to best serve the interests >>of the crystallographic community. I do not know what >>is best and do not know how long such a discussion may take. >>I leave it to James, Nick and Brian to decide if Nick's and >>Brian's messages should be posted on this list for the record. > > Indeed, I find that I, too, was making false assumptions about the > relationship between CIF2 and STAR. In particular, I mistakenly believed > that the CIF2 syntax we had been discussing was a compatible subset of an > as-yet unpublished updated version of STAR. I now find that this is not > exactly the case, at least in that the STAR update now being prepared for > publication includes a minimal set of string delimiter elides that CIF2 does > not contain, thus rendering the two incompatible (some well-formed CIF2 > files would not be well-formed STAR files). As I understand it, these > elides apply to single-quoted strings and to one form of triple-quoted > string, using approximately \<delimiter> as the elide. > > I'm not entirely sure what would be a "zero-based discussion [...] on what > the relationship should be among CIF2, STAR, CIF1 and Python to best serve > the interests of the crystallographic community." As for what the > relationship *is*, though, my analysis of CIF1.1 and STAR1, as published in > ITG, is that all documents conforming to the CIF1.1 syntax also conform to > the STAR1 syntax, EXCEPT those that contain at least one data block without > any data in it. (Empty data blocks are allowed in CIF, but not in STAR1.) > > As for what the relationships should be, all we can influence is the > relationships between CIF2 and the others. I think they should be something > like this: > > CIF2 <=> CIF1: > To the greatest extent feasible, well-formed CIF1 documents should be > well-formed CIF2 documents (modulo a CIF version identification signature) > having the same meaning. > > CIF2 <=> STAR: > Inasmuch as CIF1 is derived from STAR, I think it appropriate for CIF2 to > look first to STAR, including its post-CIF1 development, for new features it > may need. Even if CIF2 is not 100% compatible with STAR, it is worthwhile > to avoid diverging without compelling reason. > > CIF2 <=> Python: > I see no particular reason for any formal relationship here beyond Python's > role as the indirect inspiration for CIF2's new triple-quote syntax. I am > wary of the idea of tying CIF tightly to a particular language. CIF2 > documents are not and never will be Python programs. I could imagine > embedding Python in CIF or vise versa, but I have seen no evidence to > suggest that greater similarity between the two languages' syntax and > semantics would benefit efforts such as those. > > > Regards, > > John > > -- > John C. Bollinger, Ph.D. > Department of Structural Biology > St. Jude Children's Research Hospital > > > Email Disclaimer: www.stjude.org/emaildisclaimer > > _______________________________________________ > ddlm-group mailing list > ddlm-group@iucr.org > http://scripts.iucr.org/mailman/listinfo/ddlm-group > > _______________________________________________ > ddlm-group mailing list > ddlm-group@iucr.org > http://scripts.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://scripts.iucr.org/mailman/listinfo/ddlm-group
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- Re: [ddlm-group] Simon's elide proposal (Herbert J. Bernstein)
- Re: [ddlm-group] Simon's elide proposal (James Hester)
- Re: [ddlm-group] Simon's elide proposal (Herbert J. Bernstein)
- Re: [ddlm-group] Simon's elide proposal (Bollinger, John C)
- Re: [ddlm-group] Simon's elide proposal (Herbert J. Bernstein)
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- Re: [ddlm-group] Simon's elide proposal (Herbert J. Bernstein)
- [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and Python (Herbert J. Bernstein)
- Re: [ddlm-group] Relationship asmong CIF2, STAR,CIF1 and Python. . (Bollinger, John C)
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