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

Daniel Asarnow dasarnow at gmail.com
Wed Oct 27 03:54:43 UTC 2010

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.



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