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

Dear James,

   For me there were many more issues for which the
argument of STAR compatibility persuaded me to
accept the majority decision, rather than to keep
persuing my own views, especially to ensure continued
support for imgCIF.  I am not sure that the final
conclusions would have been, or should have been
different, but I am sure that I need to work through
it all again from the beginning to make a rational
decision.  I don't know how long it will take, but
hearing what others think on the current version
of CIF2 feature by feature would help.

   Regards,
     Herbert
=====================================================
  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:

> OK, fair enough.  None of my decisions were based on STAR
> compatibility (except to the extent that CIF1 compatibility means STAR
> compatibility), thus my puzzlement at the level of concern that the
> "discovery" of STAR incompatibility produced.
>
> A review of the document that was voted on suggests to me that the
> only area where STAR may have had an influence on the outcome is in
> the exclusion of quote and double quote from the list of allowed
> characters within quote or double quote delimited strings.  I support
> this on general grounds, not by reference to STAR.
>
> All other changes are either enhancements to Nick and Syd's original
> ideas (addition of  Unicode), adopted without argument (list syntax)
> or else adjustments, ie not perfectly in alignment with STAR2.  Thus
> my assertion that STAR compatibility or lack of it has not been a
> dominant concern in our discussions.  I likewise consider it of little
> significance to the elide discussion, and have not put it forward as
> an objection to the Python proposal.
>
> I would therefore be strongly against reopening any non-elide
> discussions on the basis that the relationship of CIF2 to STAR has
> changed.
>
> On Fri, Jan 14, 2011 at 9:32 PM, Herbert J. Bernstein
> <yaya@bernstein-plus-sons.com> wrote:
>> 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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>
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> M +61 (04) 0249 4148
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