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

Hi John

Just as I've just appologised to Herbert for my lack of clarity, I appologise to you
for my comments about 'pyREL'. I was guilty of 'chatting' rather than presented arguments;
I had already stated that I do not wish to contest the nature of dREL without having actually
worked with it.

Cheers

Simon


From: John Westbrook <jwest@rcsb.rutgers.edu>
To: Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org>
Sent: Sunday, 16 January, 2011 14:29:20
Subject: Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and Python. .


Hi Simon,

I strongly differ on this point.  I think that the methods support will have
far greater impact if it is NOT limited to a discipline specific language implementation.
I think building a framework that can support Python and potentially other scripting languages on
the horizon would be the preferred approach.    As Herbert points out, if we were in the
short term to focus on a Python implementation, the list of domain specific libraries
and tools that could be leveraged is long.  The accumulated expertise and experience
of members of this committee in Python development is quite exceptional.  To me it
seems like this option that should be strongly considered/reconsidered.

John



On 1/15/11 6:08 PM, SIMON WESTRIP wrote:
> True - but I can't see dREL becoming pyREL at this stage?
>
> ------------------------------------------------------------------------------------------------------------------------------------
> *From:* Herbert J. Bernstein <yaya@bernstein-plus-sons.com>
> *To:* Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org>
> *Sent:* Saturday, 15 January, 2011 22:57:17
> *Subject:* Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and Python. .
>
> Dear Simon,
>
> But dREL already shares much of Python syntax and data structures,
> but, being significantly mutated, lacks the software support and
> documentation that Python has. Anyone who has to work with the
> methods in a DDLm dictionary would be much better off if we
> simply made Python work with DDLm. We would gain large libraries
> of pre-written utilities, tools to test code fragments interactively,
> and a lot more time to do science or whatever we are actually
> funded to do.
>
> Regards,
> Herbert
>
>
>
> At 10:35 PM +0000 1/15/11, SIMON WESTRIP wrote:
>  >As far as I can see, parsing DDLm into an object stucture is fairly
>  >uncomplicated;
>  >the hurdle is parsing the dREL script as a method of the object.
>  >Unless working with python, I'm not sure that adopting python syntax
>  >for DDLm/CIF
>  >is of any great benefit; likewise for dREL.
>  >
>  >That said, I have yet to actually do anything with DDLm, let alone
>  >dREL, so I may be
>  >well off the mark. But even if this is the case, I suspect there
>  >will be non-python programmers out
>  >there that have cause to work with CIF and similarly will see no
>  >obvious benefit in
>  >CIF sharing python syntax (especially if it only adopts it for one
>  >set of delimiters at the
>  >data-source level).
>  >
>  >Cheers
>  >
>  >Simon
>  >
>  >
>  >
>  >From: Herbert J. Bernstein <yaya@bernstein-plus-sons.com <mailto:yaya@bernstein-plus-sons.com>>
>  >To: Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org <mailto:ddlm-group@iucr.org>>
>  >Sent: Saturday, 15 January, 2011 21:16:59
>  >Subject: Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and Python. .
>  >
>  >At 12:43 PM +0000 1/15/11, Brian McMahon wrote:
>  >>It might be worth remarking (again) that dREL is being developed as a
>  >>canonical methods description language, and not necessarily the runtime
>  >>methods evaluator of choice for future applications. It may be that in
>  >>practice future methods are initially developed and most frequently
>  >>executed directly in Python or some other language. As I see it, the
>  >>goal of CIF and DDL evolution is not to exclude such a possibility.
>  >
>  >If we are trying to be Python friendly and much of dREL is derived
>  >from a Jython implementation, I don't understand why we are not
>  >conforming dREL, DDLm and CIF2 to Python conventions as closely as
>  >possible.
>  >
>  >
>  >
>  >
>  >
>  >
>  >
>  >At 12:43 PM +0000 1/15/11, Brian McMahon wrote:
>  >>On Thu, Jan 13, 2011 at 05:35:21PM -0600, Bollinger, John C wrote:
>  >>>
>  >>> (snip)
>  >>>
>  >>> 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.
>  >>
>  >>Agreed.
>  >>
>  >>> 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.
>  >>
>  >>Agreed
>  >>
>  >>> 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.
>  >>
>  >>Agreed. As I mention elsewhere, there is a greater influence on the
>  >>prototype dREL (arising from the initial Jython implementation), and
>  >>the list and table data types doubtless arise from that also.
>  >>
>  >>It might be worth remarking (again) that dREL is being developed as a
>  >>canonical methods description language, and not necessarily the runtime
>  >>methods evaluator of choice for future applications. It may be that in
>  > >practice future methods are initially developed and most frequently
>  >>executed directly in Python or some other language. As I see it, the
>  >>goal of CIF and DDL evolution is not to exclude such a possibility.
>  >>
>  >>Regards
>  >>Brian
>  >>_______________________________________________
>  >>ddlm-group mailing list
>  >><mailto:ddlm-group@iucr.org <mailto:ddlm-group@iucr.org>>ddlm-group@iucr.org <mailto:ddlm-group@iucr.org>
>  >><http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iucr.org/mailman/listinfo/ddlm-group
>  >
>  >
>  >--
>  >=====================================================
>  > Herbert J. Bernstein, Professor of Computer Science
>  > Dowling College, Kramer Science Center, KSC 121
>  > Idle Hour Blvd, Oakdale, NY, 11769
>  >
>  > +1-631-244-3035
>  > <mailto:yaya@dowling.edu <mailto:yaya@dowling.edu>>yaya@dowling.edu <mailto:yaya@dowling.edu>
>  >=====================================================
>  >_______________________________________________
>  >ddlm-group mailing list
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>  >
>  >
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>
>
> --
> =====================================================
> 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 <mailto:yaya@dowling.edu>
> =====================================================
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--
******************************************************************
  John Westbrook, Ph.D.
  Rutgers, The State University of New Jersey
  Department of Chemistry and Chemical Biology
  610 Taylor Road
  Piscataway, NJ 08854-8087
  e-mail: jwest@rcsb.rutgers.edu
  Ph:  (732) 445-4290  Fax: (732) 445-4320
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