Egon, I solved my issue thanks to your clue.

It turns out: by calling the getElementText() method in StaX:

String smarts = eventReader.getElementText();

All characters of a tag will be concatenated until the end tag is found.
This is not the case if you call event.asCharacters().getData()...
Thanks for the help. I appreciate it.

Nick 

-----Original Message-----
From: Egon Willighagen [mailto:[email protected]] 
Sent: Saturday, February 04, 2012 3:18 PM
To: Nick Vandewiele
Cc: [email protected]; [email protected]
Subject: Re: [Cdk-user] SMARTS [#1] in xml parsing?

On Sat, Feb 4, 2012 at 1:57 PM, Nick Vandewiele <[email protected]>
wrote:
> The SMARTS string would not contain the entire SMARTS string and be 
> cut-off after [#1] sequence, probably due to the .asCharacters() method.

Another aspect to keep in mind is that in the XML parser world character
events do not require a single event for all character content of a single
element. You have to concatenate *all* char events between the start and end
tag (see the CMLHandler and 'convention'
classes it uses)... did you try that?

Egon


--
Dr E.L. Willighagen
Postdoctoral Researcher
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers


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