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Re: CIF parser / dialects

  • Subject: Re: CIF parser / dialects
  • From: alex avriette <a_avriette@xxxxxxx>
  • Date: Tue, 15 Oct 2002 16:10:22 +0100 (BST)

> 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.


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