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

[Andreas Prlic]

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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>
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