Hi Ed,
Here is what my colleague Jürgen (in CC) just sent me concerning the xml
parsing problem:
==========
==========
> conglomerate results
Entity: line 8: parser error : Attribute xml:lang redefined
<description xml:lang="en_CA" xml:lang="en">This is a document type
associated
^
** (conglomerate:7470): WARNING **: Problem parsing xds file: readme.xds.
** Message: coverage of Conglomerate Release Notes = 0.000000
** Message: coverage of Apache Documentation DTD v1.2 = 0.028571
** Message: coverage of XHTML 1.0 (strict) = 0.000000
** Message: coverage of DocBook = 0.028571
** Message: coverage of Website Layout = 0.000000
** Message: coverage of TEI Lite = 0.000000
** Message: coverage of Webpage = 0.000000
** Message: coverage of "Kernel Traffic" Newsletter = 0.000000
** Message: coverage of Conglomerate Display Specification = 0.000000
** Message: coverage of Experimental "cnxml" format = 0.028571
** Message: coverage of RELAX NG = 0.000000
** Message: coverage of Experimental "opml" format = 0.000000
** Message: coverage of XSL stylesheet = 0.000000
but it may be a special problem with 'conglomerate', now I tried
'xmlcopyeditor' and this one didn't complain.
==========
==========
I checked a bit and found a discussion of this problem on the web at:
http://lists.copyleft.no/pipermail/conglomerate-devel/2005-June/003682.html
All the best,
Séb :)
On 11-08-15 10:39 AM, Edward d'Auvergne wrote:
Hi,
Would you have any information about which part he cannot parse?
relax is using the standard python XML module 'xml'
(http://docs.python.org/library/xml.dom.minidom.html). This should
produce valid XML. Do you know what he's using to parse the XML? In
any case, if he can do a little programming, all the spin data is
reachable with something along the lines of:
from generic_fns.mol_res_spin import spin_loop
for spin in spin_loop():
print spin.s2
Regards,
Edward
On 15 August 2011 10:20, Sébastien Morin<sebastien.morin@xxxxxxxxx> wrote:
Hi Edward,
One colleague of mine has recently started using relax and told me he was
unable to read the xml output of relax using an xml reader...
I haven't verified this myself as I am really lacking time currently, but I
thought you might know a bit about this. ;)
Cheers,
Séb :)
P.S. As a compromise to using an external xml reader, I told him he could
start from the "final_data_extraction.py" script and modify it to fit his
needs...
--
Sébastien Morin, Ph.D.
Postdoctoral Fellow, S. Grzesiek NMR Laboratory
Department of Structural Biology
Biozentrum, Universität Basel
Klingelbergstrasse 70
4056 Basel
Switzerland
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--
Sébastien Morin, Ph.D.
Postdoctoral Fellow, S. Grzesiek NMR Laboratory
Department of Structural Biology
Biozentrum, Universität Basel
Klingelbergstrasse 70
4056 Basel
Switzerland
Re: XML parsing