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

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

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

           Summary: SITE records in PDBFileReader
           Product: BioJava
           Version: unspecified
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: structure
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: darnells at dnastar.com


Feature request from the BioJava community:

http://lists.open-bio.org/pipermail/biojava-l/2010-August/007254.html
I am interested in parsing SITE records from a PDB file. Â [...] would it be
possible to add this capability to PDBFileReader and the Structure class?

http://lists.open-bio.org/pipermail/biojava-l/2010-August/007260.html
REMARK 800 provides a very useful SITE_DESCRIPTION for each SITE_IDENTIFIER
code in use in the SITE records.  Could the site name also be associated with
the site identifier and residues?  There is precedence for parsing REMARK
records in BioJava (e.g. experiment type, resolution), but this is a special
case where REMARK 800 and SITE records are dependent on one another and
physically separated in the header.

Reply from Andreas Prlic:
http://lists.open-bio.org/pipermail/biojava-l/2010-August/007257.html
- Take a look at PDBFileParser.java and at
http://www.wwpdb.org/documentation/format32/sect7.html
- It needs a new Handler method for the Site records that builds up the data
containers.
- Create a new bean that will contain the data for the SITE record
- Instead of having fields for insertion code residue nr and chain IDs, you
can use the new PDBResidueNumber.java class to group this together.
- Add a get/set method for the Site beans to the Structure class
- Create a junit test that make sure the parsing works ok.


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