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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.

  Regards,
    Herbert

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

                 +1-631-244-3035
                 [email protected]
=====================================================

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
> > COMCIFS
> > 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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