[Biojava-dev] Why is the Residue Number a String?

[tallpaulinjax at yahoo.com]

Andreas, that is actually confusing on my part, not James' part (I assume). That might be perfectly clear to everyone else! I'm not asking that you change on my account. :-) However, if it stays the same perhaps you could add your explanation on the chain, residueNumber, and insertion code into the javaddocs? As well as what the getPDBCode() and getPDBName return?
 
James, sorry I had a typo in my original email on the field name, getter and setter.

--- On Fri, 3/27/09, Andreas Prlic <andreas.prlic at gmail.com> wrote:


From: Andreas Prlic <andreas.prlic at gmail.com>
Subject: Re: [Biojava-dev] Why is the Residue Number a String?
To: "James Carman" <james at carmanconsulting.com>
Cc: tallpaulinjax at yahoo.com, biojava-dev at lists.open-bio.org
Date: Friday, March 27, 2009, 12:31 PM


Hi James,

Just to clarify, the names for the methods currently used in BJ are:

group.getPDBCode() gives you the number + insertion code
group.getPDBName() gives you the 3-letter name of the group, e.g. "ALA"

If people think that these names are not clear, we can of course
deprecate them and come up with more descriptive ones...

Andreas



On Fri, Mar 27, 2009 at 9:05 AM, James Carman
<james at carmanconsulting.com> wrote:
> Why would residueName's getter/setter be named getResidueNumber() and
> setResidueNumber()?  Wouldn't it be better to have the getter/setter
> as getResidueName() and setResidueName() or change the field to
> residueNumber?
>
> On Fri, Mar 27, 2009 at 11:52 AM,  <tallpaulinjax at yahoo.com> wrote:
>>
>> Hi,
>>
>> I was wondering why BioJava treats the ResidueNumber as a String while the PDB format specifies it as an Integer throughout the 3.2 specification? Perhaps it was a string in previous specs? The pertinent code in PDBFileParser is:
>> String residueNumber = line.substring(22,27).trim();
>> which is then later retrieved by a user as getPDBCode and setPDBCode within a Group, both as strings. BTW, it would seem a more obvious name would be residueName with getters and settors getResidueNumber and setResidueNumber... I always confuse the getPDBCode with returning the 4-character PDB code string!! :-).
>>
>> Thanks!
>>
>> Paul
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