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Re: Self-described CIF proposal

OK, I think I understand now how to include extra "non-standardized"
items, so that a regular user can write out some extra data not defined
in the normal dictionary: just include a minimal extension dictionary
for those extra items.

The one thing that still seems to be missing is how to define which CIF
dictionary a given data block and/or add-on dictionary depends on. Is
there a mechanism for a data block to specify a dictionary, or is it
just up to the user to know which dictionary to use?

Thanks,
Joe Krahn

Herbert J. Bernstein wrote:
> Yes, CIF dictionaries are layered, so you can have a local
> dictionary that just add the few terms that you need, but
> because they are layered, it is important to avoid namespace
> conflicts and use unique prefixes for local dictionaries.
> 
> =====================================================
>   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 Thu, 29 May 2008, Joe Krahn wrote:
> 
>> Often it is useful to write out data that does not make sense to
>> standardize, and is not intended for a database. For example, maybe I
>> want to calculate and write out a derived value for each atom, like
>> "distance from Tryptophan 217", or "number of waters within 3.0A". I
>> suppose one could use a dictionary with a few generic values like
>> "user1", "user2" for temporary working values.
>>
>> Alternatively, is it possible to write a dictionary that describes just
>> the additional entries and inherit the standard dictionary for
>> everything else?
>>
>> Joe Krahn
>>
...
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