[Biojava-l] Bad PDB files and batch processing with PDBFileReader

Andreas Prlic andreas at sdsc.edu
Wed Oct 27 04:11:28 UTC 2010

Hi Daniel,

can you explain a bit more what you are doing, in particular what
errors you would like to deal with on your end?  You should not need
to worry too much about exception handling. Are there any special
cases you are interested in?  In this case we should support you with
a clean interface rather than exception handling from your end...


On Tue, Oct 26, 2010 at 8:54 PM, Daniel Asarnow <dasarnow at gmail.com> wrote:
> Hi all,
> Let me first say thanks to all the BioJava community members for
> delivering such a useful set of libraries, and that I'm still a newbie
> when it comes to BioJava (and Java) so forgive me if my question is
> too trivial.
> I am doing work on lots (at least thousands) of PDB files from RCSB.
> As is commonly known, these are often rife with errors which can lead
> to exceptions during parsing with PDBFileParser.  Because
> PDBFileParser's methods contain their own try-catch blocks, exception
> propagation stops there and my code proceeds blindly along regardless
> of any error checking I do.  I would like to catch the exceptions up
> in my code where the parser is called, so that I can branch to a
> continue statement and have my batch processing loops move on to the
> next file.
> Should I edit out the try-catch blocks and compile my own version of
> the library?  Or should I test the returned StructureImpl objects for
> possession of the fields in question?  In that case, I'm not sure
> which properties will give the most general success information...and
> I'd rather not have to check for /every/ property being correct.
> If there is some great way to check if an exception was caught down a
> series of nested method calls, please hit me over the head with it.
> Thanks!
> -da
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526

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