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Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and Python. .

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 as-yet unpublished updated version of STAR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
>>
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>
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>
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