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Re: [ddlm-group] CIF-2 changes

Dear Coleagues,

   To make sure we are all on the same page, let's review the various 
containers in 2007, 2008, and 2008

   2007:
       Single 'a single value'
       Multiple 'values related by boolean ',|&!*' or range ":" ops'
       List 'list of values bounded by []; separated by commas'
       Array 'list of fixed length and dimension'
       Tuple 'immutable List bounded by (); nested tuples allowed'
       Table 'key:value elements bounded by {}; separated by commas'
       Implied 'implied by type.container of associated value

       imports are given as a list
             _import_list.id ['att','atom_site_label','com_att.dic']
       or as separate tags


   2008:

       Single 'a single value'
       Multiple 'values related by boolean ',|&!*' or range ":" ops'
       List 'list of values bounded by []; separated by commas'
       Array 'list of fixed length and dimension'
       Tuple 'immutable List bounded by (); nested tuples allowed'
       Table 'key:value elements bounded by {}; separated by commas'
       Implied 'implied by type.container of associated value'

       imports are given as a tuple
             _import_list.id (('Sta','units_code','com_val.dic'))

If I understand correctly, the new list will be

   2009:

       Single 'a single value'
       Multiple 'values related by boolean ',|&!*' or range ":" ops'
       List 'list of values bounded by {}; separated by commas'
       Array 'list of fixed length and dimension'
       Table 'list of key:value elements bounded by {};
          separated by commas'
       Implied 'implied by type.container of associated value'
       Tuple 'immutable List bounded by {}; nested

removing the term "Tuple", instead just referring to a list with
nesting as in

            _import_list.id {{'Sta','units_code','com_val.dic'}}

In other words -- everthing uses the list syntax.

Is this right?

   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, 30 Oct 2009, James Hester wrote:

> As the syntax that we have been developing now stands, the only reason
> for not using square brackets is so that it will be possible to
> correctly parse a CIF in which a space is accidentally missing between
> a dataname and a bracketed list.  This seems to me to be a pretty
> minor reason to fiddle with the bracket syntax, but having got that
> off my chest I don't have any objections to the revised syntax.
>
> NB I believe Nick would like to drop the concept of tuples in DDLm and
> dREL altogether, with which I also agree.
>
> On Thu, Oct 29, 2009 at 10:31 PM, Herbert J. Bernstein
> <yaya@bernstein-plus-sons.com> wrote:
>> I have no objection to Nick's approach.  I would suggest a straw vote as
>> soon as possible, so that we can have move forward on coding.  So to be as
>> specific as possible, here is what I think Nick is proposing:
>>
>>   1.  All the bracketed constructs in a CIF be delimited by {}:
>>        Lists:  { ..., ... }
>>        Tuples: { ..., ... }
>>        Arrays: { ..., ... }
>>        Tables: { key:value, key:value } with the distinctions among them
>> made primarily by the type specifications. Note that the key in a table
>> should be a quoted string.
>>
>>   2.  That array dimensions in a CIF also be delimited by {} as in
>> {3} or {3,4}
>>
>>   3.  That the same changes be made in dREL
>>
>> (Nick, did I get that right?)
>>
>> I can work with all of the above, and I suspect Nick is right about the
>> long-term value of consistency here, and reasonably strong typing does
>> tend to reduce coding errors.  What do other people think?
>>
>> 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 Wed, 28 Oct 2009, Nick Spadaccini wrote:
>>
>>> The move away from [] lists to {} lists (thus overlapping with {}
>>> associative arrays) had to do with cleaning up the syntax under CIF-2.
>>>
>>> There are legacy issues with existing CIF data names with embedded [] which
>>> meant that using [ to initiate a list would come unstuck.
>>>
>>> Accordingly to simplify matters and to move forward, I proposed using {} to
>>> define lists or associative arrays. The complication to the parser is that
>>> you must start to look inside the object to determine which it is.
>>>
>>> That is CIF. dREL is a different matter but consistency is a good thing, so
>>> that it makes sense to keep the syntax the same as a CIF data file. Hence
>>> your transcription of the dREL code is correct. It makes my work a lot more
>>> difficult of course because until now I just called up a Python parser to
>>> handle almost all of dREL.
>>>
>>> Such is life.
>>>
>>>
>>> On 25/10/09 10:24 PM, "Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>
>>> wrote:
>>>
>>>> Dear Colleagues,
>>>>
>>>>    Please take a look at the dictionaries I have drafted at
>>>>
>>>>    http://vcif.sf.net/cif2_dicts
>>>>
>>>> and tell me if I am on the right track in trying to convert to CIF-2
>>>> format dictionaries.  I have taken all the August 2008 () style tuples in
>>>> the upper level and converted them to October 2009 CIF-2 {} style lists.
>>>> I have not changed any array dimension specifications, e.g. [*], nor the
>>>> innards of any methods.
>>>>
>>>>    Questions:
>>>>
>>>>    1.  Should the dimensions be changed, e.g. from [3] to {3}?
>>>>    2.  Should there be any changes in dREL methods themselves?
>>>>
>>>> For example consider:
>>>>
>>>> ======
>>>> save_function.SymEquiv
>>>>      _definition.id              'function.SymEquiv'
>>>>      _definition.update           2007-10-11
>>>>      _description.text
>>>> ;
>>>>       The function
>>>>                       xyz' =  SymEquiv( symop, symcat, xyz )
>>>>
>>>>       returns a fractional coordinate vector xyz' which is input vector
>>>>       xyz transformed by the input symop 'n_pqr' applied to the symmetry
>>>>       equivalent matrix extracted from the category symcat.
>>>> ;
>>>>      _name.category_id            function
>>>>      _name.object_id              SymEquiv
>>>>      _type.purpose                Assigned
>>>>      _type.container              Array
>>>>      _type.contents               Real
>>>>      _type.dimension              [3]
>>>>       loop_
>>>>      _method.purpose
>>>>      _method.expression
>>>>       Evaluation
>>>> ;
>>>>       Function SymEquiv( c :[Single, Symop],    # symop string n_pqr
>>>>                          l :[Category, Tag],    # loop of symmetry matrices
>>>>                          x :[Array, Real]    )  # fract coordinate vector
>>>>       {
>>>>               s = l [ SymKey( c ) ]
>>>>
>>>>               SymEquiv = s.R * x + s.T + SymLat( c )
>>>>       }
>>>> ;
>>>>      save_
>>>> ======
>>>>
>>>> Should that remain the same, or should it be as follows
>>>>
>>>> ======
>>>> save_function.SymEquiv
>>>>      _definition.id              'function.SymEquiv'
>>>>      _definition.update           2007-10-11
>>>>      _description.text
>>>> ;
>>>>       The function
>>>>                       xyz' =  SymEquiv( symop, symcat, xyz )
>>>>
>>>>       returns a fractional coordinate vector xyz' which is input vector
>>>>       xyz transformed by the input symop 'n_pqr' applied to the symmetry
>>>>       equivalent matrix extracted from the category symcat.
>>>> ;
>>>>      _name.category_id            function
>>>>      _name.object_id              SymEquiv
>>>>      _type.purpose                Assigned
>>>>      _type.container              Array
>>>>      _type.contents               Real
>>>>      _type.dimension              {3}
>>>>       loop_
>>>>      _method.purpose
>>>>      _method.expression
>>>>       Evaluation
>>>> ;
>>>>       Function SymEquiv( c :{Single, Symop},    # symop string n_pqr
>>>>                          l :{Category, Tag},    # loop of symmetry matrices
>>>>                          x :{Array, Real}    )  # fract coordinate vector
>>>>       {
>>>>               s = l { SymKey( c ) }
>>>>
>>>>               SymEquiv = s.R * x + s.T + SymLat( c )
>>>>       }
>>>> ;
>>>>      save_
>>>> ======
>>>>
>>>> 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
>>>> =====================================================
>>>>
>>>> _______________________________________________
>>>> ddlm-group mailing list
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>>>
>>> cheers
>>>
>>> Nick
>>>
>>> --------------------------------
>>> Associate Professor N. Spadaccini, PhD
>>> School of Computer Science & Software Engineering
>>>
>>> The University of Western Australia    t: +61 (0)8 6488 3452
>>> 35 Stirling Highway                    f: +61 (0)8 6488 1089
>>> CRAWLEY, Perth,  WA  6009 AUSTRALIA   w3: www.csse.uwa.edu.au/~nick
>>> MBDP  M002
>>>
>>> CRICOS Provider Code: 00126G
>>>
>>> e: Nick.Spadaccini@uwa.edu.au
>>>
>>>
>>>
>>>
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>
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