[Biojava-dev] [Bug 3174] New: Inconsistency in behavior when reading JRNL section in pdb files between OSX and WIN7

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

http://bugzilla.open-bio.org/show_bug.cgi?id=3174

           Summary: Inconsistency in behavior when reading JRNL section in
                    pdb files between OSX and WIN7
           Product: BioJava
           Version: unspecified
          Platform: PC
        OS/Version: Windows
            Status: NEW
          Severity: normal
          Priority: P3
         Component: structure
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: schallers at dnastar.com
                CC: schallers at dnastar.com


I've found after using biojava for a project an inconsistency between OSX (Snow
Leopard) and Windows (Windows 7). While running the same
code under OSX it results in a warning but in windows using the same library it
throws a NumberFormatException.
It seems that the problem is caused by inconsistencies
in the "JRNL" section of the following pdb files: 1gpb.pdb and 3pfk.pdb.
Using the following code: 

                String path =
"/Users/schallers/Desktop/pdbNew/3pfk.pdb";
                File filename = new File(path);
                PDBFileReader parser = new PDBFileReader();
                Structure structure = parser.getStructure(filename);
                System.out.println(structure);

JRNL section of 1gpb.pdb: works only if you delete rows REF 2 and REF 3.

JRNL        AUTH   K.R.ACHARYA,D.I.STUART,K.M.VARVILL,L.N.JOHNSON
JRNL        TITL   GLYCOGEN PHOSPHORYLASE B: DESCRIPTION OF THE
JRNL        TITL 2 PROTEIN STRUCTURE
JRNL        REF    GLYCOGEN PHOSPHORYLASE B:                1 1991
JRNL        REF  2 DESCRIPTION OF THE PROTEIN
JRNL        REF  3 STRUCTURE
JRNL        PUBL   WORLD SCIENTIFIC PUBLISHING CO.,SINGAPORE
JRNL        REFN


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