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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: Sun, 16 Jan 2011 07:26:28 -0500 (EST)
- In-Reply-To: <917746.19637.qm@web87007.mail.ird.yahoo.com>
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Dear Simon, If I read your message correctly, you seem to be saying that the design objectives of CIF2 are: 1. enchance CIF as a data source 2. accomodate DDLm 3. do 1 and 2 in a way that does not complicate CIF as a data source I don't understand what you mean by "enhance CIF as a data source". This is the first time I recall hearing that objective. Please clarify. In terms of present practice, I had thought that the major current uses of CIF to be: 1. As a language for publication of papers in IUCr journals; 2. As a language for submission of data to CCDC; 3. As a language for submission of data to the PDB; 4. As a data harvest language for CCP4; and 5. As a language for formatting image data from Dectris detectors, with some emerging use for data management of synchrotron data ( Please fill in uses I have missed ...) which would seem to me to represent a large current investment in data management software that depends critically on stability and reliability of CIF representation of both numeric data and text. As I understand it, DDLm and dREL can contribute to these current uses by enhancing the reliabiity of validation of data in these contexts, especially in uses 1, 2 and 3, above. To me, that would seem to change the objectives to: 1. Accomodate DDLm and dREL; and 2. Do this in a way that keeps required changes to existing archives to a minimum; and 3. Do this in a way that allows as much existing CIF software as possible to continue to operate reliably; and 4. To the extent that changes will be needed in archives and software, provide a clearly understood mechanism for making those changes, with as much support software as possible; and 5. Subordinate to the above, add new features to CIF that may encourage broader use and more software support Please tell me what I have misunderstood in this. 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 Sun, 16 Jan 2011, SIMON WESTRIP wrote: > I believe that the CIF2 syntax changes enhance CIF as data source, > even with the restriction to the contents of ' and " delimited values, > which > I suspect will be the main source of incompatability between archived CIFs > and CIF2. What we havent acheived is 100% compatability of CIF1 with CIF2, > but having agreed that CIF2 is distinct from CIF1 and minimized the > incompatability, > I do not see the changes as disruptive or retrograde. > > DDLm methods will not be applicable to a significant percentage of a CIF > data source > (those 'free text' fields used to report experimental details etc.). I > believe other approaches > will be needed to enhance their content (referencing other data items from > an item etc). > Unicode support in CIF2 is beneficial in this area, and the new alternative > delimiters may > prove convenient. The list and table structures may also be exploited. > > So from my point of view, though I understood the aim of CIF2 was to > accommodate DDLm, > it turns out that it does offer a little bit more. I would still like the > problem of including all delimiters > in a value to be solved, and line-folding to be included. On my 'wish list' > are value concatenation > and a value-referencing mechanism for use with CIF as a data source. > > I know this doesnt really answer your question. What we are *not* trying to > do is complicate > CIF as a data source? > > Cheers > > Simon > > ____________________________________________________________________________ > From: Herbert J. Bernstein <yaya@bernstein-plus-sons.com> > To: Group finalising DDLm and associated dictionaries <ddlm-group@iucr.org> > Sent: Sunday, 16 January, 2011 2:05:59 > Subject: Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and Python. . > > Dear Simon, > > I have reviewed the record on this, and I have trouble finding > a strong basis for most of the decisions made other than arguments > from the authority of established past practice in STAR and dREL. > Now that those arguments have turned out not to have been what they > seemed, I have trouble accepting the resulting conclusions without > new, clearly stated arguments based in the functionality we are > trying to achieve, but it is now not even clear what functionality we > are > trying to achieve. > > Perhaps you can help me -- what are we trying to do in defining > CIF2? > > Regards, > Herbert > > > At 11:55 PM +0000 1/15/11, SIMON WESTRIP wrote: > >That's a question I asked myself when I first joined this discussion group > :-) > > > >To be honest Herbert, I do not feal qualified to contest anything to do > with > >dREL, nor DDLm, given that I havent worked on them and respecting the > >years of effort that went into development thus far. The same is > >true with respect to some of > >the changes to CIF syntax that invalidate CIF1: I have accepted that > >they are necessary > >to facilitate implementation of dREL methods. > > > >Cheers > > > >Simon > > > > > > > >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 23:14:36 > >Subject: Re: [ddlm-group] Relationship asmong CIF2, STAR, CIF1 and Python. > . > > > >Why not? It is almost that right now. > > > > > >At 11:08 PM +0000 1/15/11, SIMON WESTRIP wrote: > >>True - but I can't see dREL becoming pyREL at this stage? > >> > >> > >> > >>From: Herbert J. Bernstein > >><<mailto:yaya@bernstein-plus-sons.com>yaya@bernstein-plus-sons.com> > >>To: Group finalising DDLm and associated dictionaries > >><<mailto:ddlm-group@iucr.org>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 > >>><<mailto:<mailto:yaya@bernstein-plus-sons.com>yaya@bernstein-plus-sons.c > om><mailto:yaya@bernstein-plus-sons.com>yaya@bernstein-plus-sons.com> > >>>To: Group finalising DDLm and associated dictionaries > >>><<mailto:<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org><mailto:ddlm-gr > oup@iucr.org>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:<mailto:<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org><mailto > :ddlm-group@iucr.org>ddlm-group@iucr.org><mailto:<mailto:ddlm-group@iucr.or > g>ddlm-group@iucr.org><mailto:ddlm-group@iucr.org>ddlm-group@iucr.org > >>>><<<http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.i > ucr.org/mailman/listinfo/ddlm-group><http://scripts.iucr.org/mailman/listin > fo/ddlm-group>http://scripts.iucr.org/mailman/listinfo/ddlm-group><<http:// > scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iucr.org/mailma > n/listinfo/ddlm-group><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:<mailto:<mailto:yaya@dowling.edu>yaya@dowling.edu><mailto:yaya@d > owling.edu>yaya@dowling.edu><mailto:<mailto:yaya@dowling.edu>yaya@dowling.e > du><mailto:yaya@dowling.edu>yaya@dowling.edu > >>>===================================================== > >>>_______________________________________________ > >>>ddlm-group mailing list > >>><mailto:<mailto:<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org><mailto: > ddlm-group@iucr.org>ddlm-group@iucr.org><mailto:<mailto:ddlm-group@iucr.org > >ddlm-group@iucr.org><mailto:ddlm-group@iucr.org>ddlm-group@iucr.org > >>><<<http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iu > cr.org/mailman/listinfo/ddlm-group><http://scripts.iucr.org/mailman/listinf > o/ddlm-group>http://scripts.iucr.org/mailman/listinfo/ddlm-group><<http://s > cripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iucr.org/mailman > /listinfo/ddlm-group><http://scripts.iucr.org/mailman/listinfo/ddlm-group>h > ttp://scripts.iucr.org/mailman/listinfo/ddlm-group > > >> > >>> > >>>_______________________________________________ > >>>ddlm-group mailing list > >>><mailto:<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org><mailto:ddlm-gro > up@iucr.org>ddlm-group@iucr.org > >>><<http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iuc > r.org/mailman/listinfo/ddlm-group><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:<mailto:yaya@dowling.edu>yaya@dowling.edu><mailto:yaya@dowling.ed > u>yaya@dowling.edu > >>===================================================== > >>_______________________________________________ > >>ddlm-group mailing list > >><mailto:<mailto:ddlm-group@iucr.org>ddlm-group@iucr.org><mailto:ddlm-grou > p@iucr.org>ddlm-group@iucr.org > >><<http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iucr > .org/mailman/listinfo/ddlm-group><http://scripts.iucr.org/mailman/listinfo/ > ddlm-group>http://scripts.iucr.org/mailman/listinfo/ddlm-group > >> > >> > >>_______________________________________________ > >>ddlm-group mailing list > >><mailto:ddlm-group@iucr.org>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>yaya@dowling.edu > >===================================================== > >_______________________________________________ > >ddlm-group mailing list > ><mailto:ddlm-group@iucr.org>ddlm-group@iucr.org > ><http://scripts.iucr.org/mailman/listinfo/ddlm-group>http://scripts.iucr.o > rg/mailman/listinfo/ddlm-group > > > > > >_______________________________________________ > >ddlm-group mailing list > >ddlm-group@iucr.org > >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 > yaya@dowling.edu > ===================================================== > _______________________________________________ > ddlm-group mailing list > ddlm-group@iucr.org > http://scripts.iucr.org/mailman/listinfo/ddlm-group > >
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