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Re: CIF parser / dialects

  • Subject: Re: CIF parser / dialects
  • From: "Herbert J. Bernstein" <yaya@xxxxxxxxxxxxxxxxxxxxxxx>
  • Date: Tue, 15 Oct 2002 17:37:47 +0100 (BST)
Dear Alex and other Developers,

  Alex's message is surprising.  If anyone is having difficulty with
the Fortran-based parser in CIFtbx or the C-based CIF parsers in CBFlib
and RasMol, please send email and I will look at your problem.  I am
certain that many other's with CIF software would also be ready and
willing to discuss problems with the existing tools, so that we can all
end up with a better base of tools.


 Herbert J. Bernstein, Professor of Computer Science
   Dowling College, Kramer Science Center, KSC 020
        Idle Hour Blvd, Oakdale, NY, 11769


On Tue, 15 Oct 2002, alex avriette wrote:

> > Indeed, what is required is an extensive set of trip tests that could
> > be
> > used as the basis for self-certification of a parser. It turns out that
> > no two existing CIF parsers agree completely on the handling of some
> > of the
> > more subtle syntax features. For some time a working group within
> > has been trying to nail down the ambiguities and subtleties, and I
> > shall in
> > a separate message introduce to the list the current draft of the
> > specification for community review.
> This really irritates me. The CIF standard is very well defined. When I
> originally wrote my parser for CIF files, I did it because we didn't
> want to use FORTRAN, and the people we talked to all wanted to charge
> us money and consulting fees to make their broken software work.
> When I began to parse them, I found that many submitting authors (I'm
> in publications, the parser was for supporting information) were
> *hand-modifying* CIF files, and the software being used to generate
> them was *also* producing nonconformant files. As a publisher, we were
> (and are) in a bind parsing these files. On the one hand, we have
> trained chemists producing incorrect files, and on the other, we have
> programmers trying to tell chemists how to do their jobs. It really is
> a no-win situation.
> The best solution (in my opinion) is to get the *authors of the
> software* together (as they are on this very mailing list), and beat
> into their heads that they need to make their software play nicely. I
> spoke to somebody (at the IUCr I believe... I could dredge up the email
> if necessary) who lamented that CIF was not as useful or flexible as
> XML. I do not necessarily believe this. What I do appreciate about XML
> versus CIF is the *very strict* rules for parsing XML. You either parse
> it correctly because the file is correct, or you DIE LOUDLY WITH
> ERRORS. (sorry for the emphasis)
> I achieved about a 25% success rate contacting the software authors
> personally and asking them to correct their software. Most of them
> never even replied, and others gave me grief about "not being a
> chemist" or using perl.
> Sorry to jump on a six month old thread like this. I was cleaning out
> my mailboxes, and when I read this thread, I simply had to reply.
> Alex

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