I was not aware that there was a default indexing of arrays. The only
place where this arises in DDL1 is in the list of symmetry opertations
where we originally failed to define a key for the symop loop. But
there, as far as I am aware, the assumed indexing always starts at 1
for the first item. This is strictly a fix since CIF1 specificly
states that the order within a loop has no significance. Later
additions to the dictionary have corrected this oversight by adding an
explicit key, but it is not yet often used. Otherwise, in DDL1 (and
DDL2?) the elements of an array have explicit data names that start at
1, not 0. The assumption that arrays are numbered from zero
must be an imgCIF
convention. It would always be better to include explicit indexing to
avoid these problems.
The DDLm dictionaries have methods for constructing arrays
from their elements, and methods for the reverse process could be
added. In this case it would not be necessary to decompose (or
assemble) an array on first resding as the necessary action would be
taken as soon as the array or its elements are invoked by a method or
by a list of items to output.
This raises another concern. Herbert, if you are writing DDLm
dictionaries for imgCIF and I am writing them for coreCIF, we need to
keep in contact to make sure we are not introducing conficting
conventions.
David
Herbert J. Bernstein wrote:
Dear Colleagues,
One very neat resolution to this problem would be to allow a
list or array-typed CIF2 tag to be referenced in a data file either
as a whole or element by element.
Thus
_a.vec
being defined as an array or list in CIF2 would automatically make
the tags
_a.vec[1]
_a.vec[2]
...
defined CIF2 tags. If the array or list were nested, the
_a.vec[1][1]
_a.vec[1][2]
etc. would be valid tags
I would propose that this be general and automatic, applying to
all tags defined as list or arrays. In view of past practice in
CIF1, there is a slight conflict with respect to the default starting
index in dREL versus the common CIF1 practice in indexing arrays
from 0, but that can (and should be solved) with explicit specification
of a starting index, so we can carry over the tag name usage from
CIF1 without confusing people with an index shift. So, if _a.vec
were an array of dimension 5, starting from index 0, _a.vec[0]
through _a.vec[4] would be valid, but if the starting index were
specified as 1, _a.vec[1] through _a.vec[5] would be valid, matching
CIF1 conventions.
The aliasing mechanism might have to be extended or clarified to
handle the mapping against CIF1 tags in bulk for _a.vec as a whole,
but, to me, this has a very intuitive feel.
Regards,
Herbert
At 3:29 PM -0500 12/9/09, John Westbrook wrote:
Hi all -
On the issue of reserved characters in mmCIF/PDBx data items, these
generally have been inherited from the style of items from the core. The
majority of items in this class are data items related to short
matrices/tensors
and vectors (e.g. items including []). Virtually all have a syntax which
could reasonably be interpreted as a programmatic reference. For instance,
_atom_sites.fract_transf_matrix[1][1] 0.007738
_atom_sites.fract_transf_matrix[1][2] 0.000000
_atom_sites.fract_transf_matrix[1][3] 0.004298
_atom_sites.fract_transf_matrix[2][1] 0.000000
_atom_sites.fract_transf_matrix[2][2] 0.016545
_atom_sites.fract_transf_matrix[2][3] 0.000000
_atom_sites.fract_transf_matrix[3][1] 0.000000
_atom_sites.fract_transf_matrix[3][2] 0.000000
_atom_sites.fract_transf_matrix[3][3] 0.020200
_atom_sites.fract_transf_vector[1] 0.00000
_atom_sites.fract_transf_vector[2] 0.00000
_atom_sites.fract_transf_vector[3] 0.00000
Are we close to being able to treat these as legal in the context of
CIF2/DDL+?
I suppose I am asking what will constitute a legal assignment for an element
of a matrix/array -
Only this -
_a.vec [1,2,3]
or also expanded assignment by element such as -
_a.vec[1] 1
_a.vec[2] 2
_a.vec[3] 3
If the latter is to be considered, then this will solve most of the data name
issues for our data.
Regards,
John
Joe Krahn wrote:
In practice, CIF2 parsers should allow CIF1 data names within a CIF2
formatted file. The question is whether these files should be allowed as
valid CIF2, or just for convenience as a non-standard CIF2.
When CIF files are used as working data files, the restrictions should
be relaxed. For long-term archival files, it makes sense to be more
restrictive. I would just make the CIF1 names inaccessible to dREL.
Alternatively, an implementation could allow CIF1 names only on reading,
and require dictionary alias mappings to CIF2 names.
One argument in favor of allowing them would be that someone wants to
convert all data files to CIF2 format, but they want to preserve the
original data as-is, without alias mapping.
I think that the current CIF2 syntax makes it possible to use CIF1 names
without any ambiguities. The question is whether they should be
considered valid CIF2, or just a non-standard version that will be
useful for the transitional period.
>
Joe
Herbert J. Bernstein wrote:
Personally, I would greatly prefer to allow all data names that do not
create a major lexer/parser conflict to appear in a data CIF and
only apply the strong restrictions to data names that appear in CIF2
dictionaries as defined data names (not as aliases). -- Herbert
At 2:40 PM +0000 12/9/09, Brian McMahon wrote:
I have one remaining niggle that I'd like to revisit before we put
this finally to bed. As has been mentioned a couple of times
recently, restricting the data-name character set does invalidate
syntactically many existing CIF 1 files (e.g. _refine_ls_shift/esd_max ).
We have discussed strategies for handling this, and I think these
are workable strategies, but will involve investment and hence expense
in workflow management in CIF archives.
I understand the rationale behind this restriction is to simplify
future processing of data names in areas such as dREL
applications. The question really is whether we're choosing the right
trade-off in making things cleaner at that end of the processing
chain. I would suppose that a dREL or other application could ingest a
data name with dangerous characters, convert it internally into a
"safe" identifier that's used for all processing, and then restore the
original form upon output; but writing that intermediate layer of
processing is of course expensive (especially if there aren't readily
available libraries that will do this transparently).
I suspect that some of the original proposed syntactic changes also
had the effect (whether by design or collaterally) of simplifying i/o,
data structure management, symbol table processing etc., but those may
have suffered in the subsequent revision exercise we've just been
practising. Given the consensus we are now approaching, would the code
builders now be prepared to incur the addition expense of handling
"dangerous" data names?
I really don't want to spark off a long discussion on this - if a
quick round of response shows that there's no appetite to allow
the additional punctuation characters in data names, I'll accept that
gracefully.
***
One last comment while I have the floor, though it is related in part
to the above question. A concern raised in the editorial office was
that there would be circumstances where users didn't know if they were
dealing with a CIF 1 or 2 ("users" meaning authors, perhaps resorting
to the vi editor - and we're imagining most of them are dealing with
small-molecule/inorganic CIFs). My supposition is that the IUCr
editorial offices would only want to use CIF2 seriously in association
with DDLm dictionaries, and that we would expect the revised core
dictionaries to use the dot component in data names to signal this
further evolution. So even a superficial glimpse of the middle of a
CIF would make it clear whether it was CIF1 or CIF2.
Does that fit in with how others see this progressing?
Cheers
Brian
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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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