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Re: [ddlm-group] CIF-2 changes

The question is one of what we gain from having both [] and {}.  I think
Nick is right to consolidate them. -- 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
                  [email protected]
=====================================================

On Thu, 29 Oct 2009, Joe Krahn wrote:

> I agree with James here. I don't see how brackets interfere with parsing
> at all. A list bracket can only be misinterpreted if it follows a data
> name with no intervening space, but that should be invalid anyhow,
> right? Switching to parenthesis is reasonable, but it should not be done
> just because brackets are part of the new STAR/CIF syntax.
>
> As for the list examples below, why use commas instead of just quoting
> and whitespace delimiters, as in the current STAR syntax? If commas are
> used, commas would become a reserved character and need quoting or escaping.
>
> I don't have strong opinions either way. My main interest is just to aim
> for a well-defined syntax without any parsing ambiguities.
>
> Joe
>
> 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
>> <[email protected]> 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
>>>                  [email protected]
>>> =====================================================
>>>
>>> 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" <[email protected]>
>>>> 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
>>>>>                   [email protected]
>>>>> =====================================================
>>>>>
>>>>> _______________________________________________
>>>>> ddlm-group mailing list
>>>>> [email protected]
>>>>> http://scripts.iucr.org/mailman/listinfo/ddlm-group
>>>> 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: [email protected]
>>>>
>>>>
>>>>
>>>>
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>>
>>
>>
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