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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: "Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>
- Date: Fri, 14 Jan 2011 05:32:44 -0500 (EST)
- In-Reply-To: <AANLkTik2X=SKJyCKKqYJ7_g=hHCcPAOKYbiiJujKCz5s@mail.gmail.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><AANLkTik2X=SKJyCKKqYJ7_g=hHCcPAOKYbiiJujKCz5s@mail.gmail.com>
I think we need to rethink, because for issue after issue that was resolved to get us to where we are now the supposed need to "STAR compatibility" was raised as a way to stop further discussion of alternatives. That turns out not to have been a relevant consideration. Maybe the final answers would have turned out the same, maybe they would not have, but I personally find it a useful exercise to rethink my own positions issue by issue in light of this changed constraint. This being the case, the first issue I think we need to resolve is, once we know what STAR is, is there value to CIF in achieving compatibility with it. James seem to think not. I simply don't know, because I don't know what really is or is not in STAR. ===================================================== Herbert J. Bernstein, Professor of Computer Science Dowling College, Kramer Science Center, KSC 121 Idle Hour Blvd, Oakdale, NY, 11769 +1-631-244-3035 yaya@dowling.edu ===================================================== On Fri, 14 Jan 2011, James Hester wrote: > 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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