[Biojava-dev] [Bug 3132] SITE records in PDBFileReader

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3132


darnells at dnastar.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|RESOLVED                    |REOPENED
         Resolution|FIXED                       |




------- Comment #2 from darnells at dnastar.com  2010-09-01 13:59 EST -------
I have applied the patch Amr sent over the weekend and tested it.  It's looking
pretty good.  I tested structures 3CYT, 4HHB, 3AFA, 1MR1, and 2OHX and the
following functions work as advertised:

Structure: getSites()
PDBSite: getSiteID(), getResidues()
PDBSite.Residue: getResidueName(), getResidueNumber()

I didn't directly test the set* methods, assuming they are working fine since
the get* methods work.

I noticed that PDBSite implements PDBRecord (similarly as SSBond).  The method
PDBSite.toPDB() ends in error:

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
        at java.util.Arrays.copyOf(Arrays.java:2882)
        at
java.lang.AbstractStringBuilder.expandCapacity(AbstractStringBuilder.java:100)
        at
java.lang.AbstractStringBuilder.append(AbstractStringBuilder.java:390)
        at java.lang.StringBuffer.append(StringBuffer.java:224)
        at org.biojava.bio.structure.PDBSite.toPDB(PDBSite.java:39)
        at org.biojava.bio.structure.PDBSite.toPDB(PDBSite.java:25)
        at com.dnastar.structureTest.Cookbook.printSiteIDs(Cookbook.java:36)
        at com.dnastar.structureTest.Cookbook.main(Cookbook.java:24)

That should be corrected so that it is consistent with the SSBond class.

I also agree with Jules Jacobsen's comments (via email): "We still need to
hook-up the REMARK 800 parser and make some unit tests for this."


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