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

[Jules Jacobsen]

Hi Guys,

OK, please don't hack about with this - I'm adding it into the main 
branch of biojava 3, but things are changing a little.

PDBSite has been renamed to Site ('PDB' is a redundant)

The Residue inner class in PDBSite I have removed so as to use the Group 
interface which we have already defined.

As Steve says, Site.toPDB() throws an OutOfMemoryError - I'm fixing this 
and adding tests to Site, the PDBFileParser and other classes which have 
been touched.

Also I'm adding the Remark800 parser and minor cosmetic tweaks for 
consistent coding style.

This should be good to go for Mon/Tues next week.

Jules


On 01/09/2010 18:57, Steve Darnell wrote:
> Amr,
>
> I have applied the patch you 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.jav
> a: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'll update the bug in Bugzilla with this information.
>
> Regards,
> Steve
>
> CC: Jules Jacobsen (also looking at SITE patch)
>
> -----Original Message-----
> From: Steve Darnell
> Sent: Tuesday, August 31, 2010 5:52 PM
> To: 'Amr AL-Hossary'
> Subject: RE: Bug 3132: "SITE records in PDBFileReader"???
>
> Amr,
>
>> The configuration is related to the PROJECT PROPERTIES, not to Your
> system.
>
> My project/application is using JDK 1.6.0_20 (Windows/Mac).
>
>
>> so all you need is SITE_IDENTIFIER, you don't need EVIDENCE_CODE, right
> ?
>
> I need the SITE_DESCRIPTION from REMARK 800.  SITE_IDENTIFIER, which is
> the same as the siteID from the SITE record, is not meaningful.
> Correct, I do not need the EVIDENCE_CODE.
>
>
>> Sorry? Isn't it already there in the PDBSite bean?
>> or what is the difference between site name&  site ID?
>
> For example, PDBID: 3CYT
>
> SITE, siteID or REMARK 800, SITE_IDENTIFIER: "AC1"
> REMARK 800, SITE_DESCRIPTION: "BINDING SITE FOR RESIDUE HEM O 104"
>
> The description is meaningful, the identifier is not.
>
>
>> please recheck the date.
>
> My mistake.  Wednesday, September 8th, two days after Labor Day (Monday,
> September 6th).
>
> I hope I addressed your questions.  Let me know if I can clarify
> anything else.
>
> Regards,
> Steve