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

[Andreas Prlic]

Hi Daniel,

PDB files are better nowadays, due to remediation, however there are
still issues..

it sounds like you just want to figure out how to do the try/catch
block properly. You could do something like that:
		
		boolean splitFileOrganisation = true;
		AtomCache cache = new
AtomCache("/path/to/your/installation/",splitFileOrganisation);
		
		String[] pdbIDs = new String[]{"4hhb", "1cdg","5pti","1gav", "WRONGID" };
		
		for (String pdbID : pdbIDs){
			
			try {
				Structure s = cache.getStructure(pdbID);
				if ( s == null) {
					System.out.println("could not find structure " + pdbID);
					continue;
				}
				// do something with the structure - your inner loop
				System.out.println(s);
				
			} catch (Exception e){
				// something crazy happened...
				System.err.println("Can't load structure " + pdbID + " reason: " +
e.getMessage());
				e.printStackTrace();
			}
		}
		



On Tue, Oct 26, 2010 at 9:59 PM, Daniel Asarnow <dasarnow at gmail.com> wrote:
> Glad to hear it, who doesn't like support or clean interfaces?.  No
> offense intended, by the way, with respect to PDB errors - obviously
> the PDB is an indispensable resource for all protein scientists.
>
> I am looking at many (fixed-length) pieces of protein chains and doin'
> stuff with 'em.  My current code has a pair of nested while loops; the
> outer iterates over PDB entries (locally rsync'd copy), parsing them
> and the inner iterates over the pieces from each.  When
> StructureExceptions come out of my PDBFileReader object I want to
> continue the outer loop, moving on to the next set of files without
> executing any of the code that depends on correct StructureImpl
> objects from the reader (database updates, the inner loop).
> Since the reader's methods have their own try-catch blocks, a thrown
> StructureException is stopped there and never reaches my own error
> handling.  I just need to know when those errors occur so I can skip
> those proteins - I am presuming that the correct entries will outweigh
> the problem ones by a significant factor and the overall data wont be
> seriously impacted.
>
> -da
>
> On Tue, Oct 26, 2010 at 21:11, Andreas Prlic <andreas at sdsc.edu> wrote:
>> 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...
>>
>> Andreas
>>
>>
>>
>> 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
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
>>
>>