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Re: [ddlm-group] Finalizing DDLm

I really don't understand why

_atom_site_label Cu
_atom_site.fract_x 0.0
_atom_site.fract_y 0.0
_atom_site.fract_z 0.0

is a problem.  It looks very clear and is easily coerced to

loop_
_atom_site_label
_atom_site.fract_x
_atom_site.fract_y
_atom_site.fract_z
  Cu 0.0 0.0 0.0

when a dictionary is available to tell you that this is supposed to be a 
looped list.

And, while

_atom_site_label Cu
_atom_site.fract_x 0.0

loop_
_atom_site.fract_y 0.0
_atom_site.fract_z 0.0

is a little strange it is just as clear.  The more interesting case is 
related to what David suggested, of mixing a single tag value pair with a 
loop with more than one row.  That seems very useful and echoes some of 
what was already done in the mmCIF dictionary.

If a sensible coercion is clear from the dictionary, why not just do it?

=====================================================
  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, 31 Mar 2010, Nick Spadaccini wrote:

>
>
>
> On 31/03/10 12:23 AM, "Herbert J. Bernstein" <[email protected]>
> wrote:
>
>> 1.  Existing DDL2 style dictionaries have many looped categories with
>> subcategories.
>
> As do the dictionaries written in the DDLm.
>
>> 2.  I do not understand why there is any special need to forbid the
>> presentation of a single row list category as separate tags and
>> values, nor why there is any special need to forbid the presentation
>> of an unlooped catagory as a single row loop.  Any necessary coercion
>> is easily done in either case, and deserves at most a warning, if even
>> that.
>
> The reasoning is that you are enforcing its "type" specification. It is a
> List category object. ALL List category objects MUST be syntactically
> presented by the loop_ keyword, followed by a sequence of tags, followed by
> a list of values whose type then matches the tag type. Anybody reading the
> data in the absence of a dictionary will immediately know it is a List
> object.
>
> I must say Syd and my reasoning is pretty clear as to why we enforce it the
> way we do. However I can't see the reasoning behind your and David's desire
> to allow for,
>
> _atom_site_label Cu
> _atom_site.fract_x 0.0
>
> loop_
> _atom_site.fract_y 0.0
>
> _atom_site.fract_z 0.0
>
> The above is a logical consequence of what is being suggested. You may not
> intend it, but "when you'se open the can, you'se eat the worms".
>
> Again (and again and again) I repeat IF the IUCr wishes this to be an
> extension in its implementation of DDLm that is for it to decide.
>
>
>>
>>
>> =====================================================
>>   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 Tue, 30 Mar 2010, David Brown wrote:
>>
>>> James seems to have summarized matters pretty well.� The implication is that
>>> a list category must be the end of the line - it cannot have a subcategory.�
>>> My real questions was whether a list category must explicitly included as a
>>> loop, or whether the loop structure is unnecessary if it only contained a
>>> single row.� It is easy enough to be safe by always inculding the loop, and
>>> I will probably arrange to do this in the dictionaries.� There are likely to
>>> be several places with single fow loops appear, e.g., in examples or
>>> aliases.
>>>
>>> David
>>>
>>>
>>>
>>> James Hester wrote:
>>>       Thanks Nick for clarifying this.� We then return to David's
>>>       question.� If we assume that a 'Set' category cannot be a child
>>>       of a 'List' category (I hope this is written down somewhere if
>>>       it is the case) then my originally proposed solution would be
>>>       impossible.� Therefore, what David should do is to put the
>>>       invariant items into a *parent* 'Set' category and state that
>>>       the child 'List' category.� That would solve the immediate issue
>>>       of separating out looped and unlooped datanames.� If some
>>>       convenience is desired for dREL processing, the child 'List'
>>>       category could be made joinable to that parent category, thereby
>>>       making both invariant and looped items available in shorthand
>>>       form by looping over the parent category.� Of course, even if
>>>       the child 'List' category is not explicitly joined to the parent
>>>       'Set' category, the parent category can be explicitly referenced
>>>       in any dREL method using the full dataname.
>>>
>>>       Nick may wish to confirm that I have correctly understood the
>>>       proposed behaviour of DDLm.
>>>
>>>       James.
>>>
>>>       On Thu, Mar 25, 2010 at 3:18 PM, Nick Spadaccini
>>>       <[email protected]> wrote:
>>>             I have not had any time to respond to David?s
>>>             original email or the
>>>             subsequent discussions. However I have discussed it
>>>             with Syd.
>>>
>>>             DDLm defines loopable categories strictly and
>>>             sub-categories of those have
>>>             strictly enforced outer joins (given we have ONLY
>>>             considered sub-categories
>>>             that are List). This is how we overcome the split
>>>             versus non-split versions
>>>             of atom_site and atom_site_aniso loops. List is
>>>             strictly looped, Set is
>>>             strictly non-looped - contrary to your reading, and
>>>             possibly Syd?s original
>>>             text. He has since re-read what he wrote and
>>>             clarified the ambiguity. I will
>>>             send you that re-write shortly.
>>>
>>>             We had not considered a SET category being a
>>>             sub-category of a List
>>>             category, but if it is allowed then it would not be
>>>             an outer-join as you
>>>             suggested in your previous contribution but a
>>>             relational Cartesian product
>>>             (which is very different).
>>>
>>>             The DDLm specification has that List category data
>>>             MUST appear in a loop
>>>             (irrespective of how many rows there are), and SET
>>>             categories are strictly
>>>             singular (non-looped data). The formal specification
>>>             will formally remain
>>>             that way.
>>>
>>>             HOWEVER the IUCr is free to ?extend? the
>>>             specification of the DDLm for its
>>>             own internal and private use, so long as you
>>>             appreciate that the FORMAL
>>>             published specification of what Syd and I have
>>>             created can?t include it.
>>>
>>>             You might explain as to why you feel you have
>>>             trouble with
>>>
>>>             loop_
>>>             �_atom_site.label
>>>             �_atom_site.frac_x
>>>             �_atom_site.frac_y
>>>             �_atom_site.frac_z
>>>             �Cu 0 0 0
>>>
>>>             And yet
>>>
>>>             �_atom_site.label �Cu
>>>             �_atom_site.frac_x �0.
>>>             �_atom_site.frac_y �0.
>>>             �_atom_site.frac_z �0.
>>>
>>>             Is so much more obvious? Given that people
>>>             understand what the loop is, I
>>>             can't see what they would gain from the unrolled
>>>             version (apart from
>>>             confusion). The real danger is those less
>>>             experienced who DON'T read a
>>>             dictionary and read the latter form may be
>>>             encouraged to replicate it when
>>>             there is more that 1 atom (thus corrupting the CIF
>>>             structure).
>>>
>>>             However these are just personal observations, and if
>>>             the IUCr wants to
>>>             qualify the use of DDLm with its own tweaks there is
>>>             nothing stopping them
>>>             from doing so.
>>>
>>>
>>>
>>>>>>>
>>>>>>> At 10:35 AM -0500 3/11/10, David Brown wrote:
>>>>>>>>
>>>>>>>> Dear Colleagues,
>>>>>>>>
>>>>>>>> I assume that we are essentially finished in
>>>             resolving syntax
>>>>>>>> problems, but in that discussion some items
>>>             were identified as being
>>>>>>>> related to DDLm rather than syntax, so before
>>>             we settle into serious
>>>>>>>> dictionary writing we need to understand the
>>>             DDLm rules.
>>>>>>>>
>>>>>>>> One item that I believe was raised under this
>>>             heading was whether,
>>>>>>>> if a loop contained a single set of items, it
>>>             was necessary to
>>>>>>>> formally include this in a loop structure. �If
>>>             this is deemed to be
>>>>>>>> necessary, then there has to be some way of
>>>             identifying the items
>>>>>>>> that must appear in a loop. �The presence in
>>>             the dictionary of a
>>>>>>>> _category_key.* item would seem to flag this,
>>>             but it is applied at
>>>>>>>> the level of the category rather than at the
>>>             level of an individual
>>>>>>>> item. �If the requirement that the loop
>>>             structure must always be
>>>>>>>> used, then all the items in the category must
>>>             be loopable, i.e., the
>>>>>>>> category cannot include items that would not
>>>             normally be included in
>>>>>>>> the loop, items for example that apply equally
>>>             to all the listed
>>>>>>>> items such as a scale factor that is the same
>>>             for all the structure
>>>>>>>> factors in a loop. �This seems to be workable,
>>>             but I am not sure how
>>>>>>>> the legacy CIFs would fit in, since categories
>>>             may include some
>>>>>>>> listable item and some non-listable items, and
>>>             I am sure the
>>>>>>>> listable items do not always appear in a loop
>>>             if there is only one
>>>>>>>> set of such items reported in the CIF.
>>>>>>>>
>>>>>>>> Is this something that can be clarified fairly
>>>             easily? �It has an
>>>>>>>> important bearing on how the CIF dictionaries
>>>             are written.
>>>>>>>>
>>>>>>>> David
>>>>>>>>
>>>>>>>> Attachment converted: Macintosh HD:idbrown
>>>             55.vcf (TEXT/ttxt) (0046DFC7)
>>>>>>>>
>>>             _______________________________________________
>>>>>>>> ddlm-group mailing list
>>>>>>>> [email protected]
>>>>>>>>
>>>             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
>>>>>>> � � � � � � � � �[email protected]
>>>>>>>
>>>             =====================================================
>>>>>>> _______________________________________________
>>>>>>> ddlm-group mailing list
>>>>>>> [email protected]
>>>>>>>
>>>             http://scripts.iucr.org/mailman/listinfo/ddlm-group
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> T +61 (02) 9717 9907
>>>>>> F +61 (02) 9717 3145
>>>>>> M +61 (04) 0249 4148
>>>>>> _______________________________________________
>>>>>> ddlm-group mailing list
>>>>>> [email protected]
>>>>>>
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>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>
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>>>
>>>
>>>
>>>
>>> _______________________________________________
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>>>
>>>
>>>
>>>
>>> --
>>> T +61 (02) 9717 9907
>>> F +61 (02) 9717 3145
>>> M +61 (04) 0249 4148
>>>
>>>     ____________________________________________________________________
>>>
>>> _______________________________________________
>>> ddlm-group mailing list
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>>> http://scripts.iucr.org/mailman/listinfo/ddlm-group
>>>
>>>
>>>
>>>
>>>
>> _______________________________________________
>> ddlm-group mailing list
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>> 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]
>
>
>
>
> _______________________________________________
> ddlm-group mailing list
> [email protected]
> http://scripts.iucr.org/mailman/listinfo/ddlm-group
>
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