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CONFORMANCE [was Re: Survey of available CIF software and

  • To: Multiple recipients of list <[email protected]>
  • Subject: CONFORMANCE [was Re: Survey of available CIF software and
  • From: Peter Murray-Rust <[email protected]>
  • Date: Fri, 1 Dec 2000 11:13:07 GMT
At 14:22 20/09/00 +0100, BrianMcM wrote:

>There has been a private discussion among some members over the
>last few days about how to direct the development of software to
>advance the use of CIF. I'd like to take that discussion onto the whole
>COMCIFS list for two reasons : (1) to survey what is needed, and
>(2) to canvass opinions on how to secure development effort and funding. It
>will be best to split these two threads, so I'll start here by trying to
>categorise the types of tools we need to consider, and reviewing what I know
>about the ones that exist.

I have been hacking CIF recently and find this would benefit from having 
some tools to help test conformance of software. I know this is a boring 
subject (!) but it is a necessary part of developing software. The key 
thing is to have a selection of CIF files, some correct, some incorrect, so 
that software can be run against them. These should include some 
quasi-pathological examples. For example, which of the following are valid 
CIFs (syntax only)

<empty file>

data_

data _X _ ""

data_foo _foo O5'

data_foo _foo 'O5''

data_A data_B

data_A data_a

data_A loop_ _a _b

data_A loop_ a_ b_ 1 2 3

(I got one of these wrong in my parser and I may have got others wrong. My 
parser also flags some CIFs currently on the web as incorrect, but I don't 
want to bugreport if it's my fault!

In testing XML parsers NIST used 1000 tests (produced, I believe by SUN). I 
don't think we can and should run to this scale, but a few cases would be 
useful.

I also think it's valuable to have some CIFs which exercise all of the core 
dictionary. Thus I want to implement _chemical_ and _chemical_conn_ but I 
can't find any examples of CIFs under COMCIFs or IUCr that I can use as 
reference.

         P.

Peter Murray-Rust, Director Virtual School of Molecular Sciences
Pharmaceutical Sciences, University of Nottingham, NG7 2RD, UK
Tel: +44-(0)-115-951-5087 Fax: +44-(0)-115-951-5110
http://www.vsms.nottingham.ac.uk