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RE: Tidying up DDL1 (last time?)

  • Subject: RE: Tidying up DDL1 (last time?)
  • From: "Bollinger, John Clayton" <jobollin@xxxxxxxxxxx>
  • Date: Thu, 14 Jul 2005 09:41:28 -0500
 
Matthew Towler wrote:

> If the way to properly fix DDL1 is to make it very similar to 
> DDL2, this begs the question why not leave DDL1 alone and 
> simply move to DDL2?

It seems to me that the type of similarity sought is along the lines of
internal consistency, machine-readability, and referential integrity.
To the extent that DDL 2 provides these things better than does DDL 1,
yes, I think we should bring DDL 1 closer to DDL 2 in these respects.
We cannot simply "move to DDL2" because we want to be able to work with
CIFs written against dictionaries expressed in DDL 1 (most notably the
CIF Core dictionary).

>  From a programming perspective it may be simpler to enhance 
> programs to support DDL2 separately from DDL1, rather than to 
> have to simulaneously support both DDL1-old and DDL1-new.  Or 
> as in practice often happens with enhancements to formats 
> written by users, a mixture of the two.

Don't lose sight of the fact that we're talking mainly about the two
generations of DDL, not about the CIF dictionaries expressed _via_ one
or another DDL.  To the limited extent that the (DDL1-based) CIF Core
dictionary enters the discussion, the issues are primarily that that
dictionary is not fully compliant with the DDL, and that the DDL /
Dictionary combination fails in its attempts to codify and permit some
widespread practices of CIF creators (most notably, placing anisotropic
thermal parameters into a list separate from the one containing atomic
coordinates).  The proposition has been raised that little, if any,
existing software for DDL 1 dictionaries even makes use of the
properties that James proposes be modified.  Perhaps the existence of
the very DDL / dictionary flaws under discussion has contributed to
that.

As to "enhancements [...] written by users", although CIF users may
sometimes define their own data names, either ad hoc or via their own
supplementary dictionary, I have trouble imagining a user defining and
using DDL extensions.  Such extensions could in any case only be
leveraged by the user's own local dictionaries and software, so they
would be of limited use to most CIF users.  I don't think I see how
supporting two different versions of DDL 1 would be any more difficult
than supporting both DDL 1 and DDL 2; could you expand on that?  Any way
around, I would expect most new software to support just the
(hypothetical) DDL 1.5, not both 1.4 (or earlier) and 1.5.

Considering the great number of CIFs now in existence (and still being
created) that are based on CIF dictionaries defined via DDL 1, it is
highly desirable to be able to write programs that work with the
relevant dictionaries.  It is also desirable that any DDL changes should
not require substantial modification to existing dictionaries or render
CIFs invalid that are valid under the dictionaries as they stand today.
Considering, however, that very many of the CIFs written against the
core dictionary are *not* valid *because* of some of the dictionary and
DDL flaws that James has been pointing out, the question is moot.
Indeed, it may be that the proposed changes will be able to make many of
these currently-invalid CIFs valid against the revised dictionary / DDL
combination.


Regards,

John Bollinger

-- 

John C. Bollinger, Ph.D.
Indiana University
Molecular Structure Center

jobollin@indiana.edu 
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