Dear all,
At Global Phasing, we have seen that there are still issues with the way
that different applications deal with mmCIF-format data, and this continues
to cause problems for users. I believe that part of the reason for this is
that the underlying syntax (the STAR format) is not universally understood,
and that a common and complete understanding of the full STAR syntax amongst
programmers who deal with the format will help with some of the existing
problems.
I wrote some code for low-level handling of the STAR format a while ago that
I have been meaning to release for over a year. Garry Battle's announcement
on 23 August about the mmCIF/PDBx workshop at the EBI has prompted me into
action: I have written a short article that discusses some examples of the
issues that we have encountered, and made my code available for download.
The references in the article are given primarily as web links: more
conventional citations can usually be found in the pages that I link to.
This code has not been used in any released products, but it has had some
internal use at Global Phasing. There is an MX bias in the article's
discussion, but the issues are not restricted to MX.
As I explain in the article, the handling of the input data is based on an
enourmous regular expression that matches STAR data, with only a little
logic in the code itself. The regular expression should be usable with a
variety of other languages, not only in Java (which I have used in this
case). The code, or the regular expression on its own, may be freely used in
other projects: see the included licencing for details, but basically you
should: (i) give credit for using it, and (ii) if you choose to modify the
regular expression, state that you have done so in that credit.
The article, which contains links to a tar file containing the code, and the
documentation, is here:
<http://www.globalphasing.com/startools/>
Hoping that others will find this useful and/or help to resolve or clarify
outstanding questions,
Peter.
--
Peter Keller Tel.: +44 (0)1223 353033
Global Phasing Ltd., Fax.: +44 (0)1223 366889
Sheraton House,
Castle Park,
Cambridge CB3 0AX
United Kingdom
