[Biojava-l] Structure.getChains()

[Andreas Prlic]

Hi Dmitry,

Yes you are right. The compound object just contains pointers to the
Chains if the info is available from the COMPND records in the PDB
headers. If you want to be sure to have a full set of chains, please
access them via the
structure.getChains() or structure.getChains(modelNr) methods. If you
think that is helpful, I can add a note for this into the javadoc for
the compound class. It is not having much javadoc anyway, feel free to
provide a patch! ;-)

Andreas




On Thu, Aug 28, 2008 at 8:26 AM, Dmitry Repchevsky
<dmitry.repchevski at bsc.es> wrote:
> Hello,
>
> Yeah, but you have:
>
> Structure
>  |
>  +-Model(s)
>  |    |
>  |    Chain(s) // ALL chains (ATOM/HETATM...)
>  |
>  +-Compound(s)
>       |
>       Chain(s) // Only those that are in "COMPND"
>
> Nothing wrong here. I just thought that Structure.getChains() returns chains
> from COMPND (Aminoacids)
> Cheers,
>
> Dmitry
>
> Andreas Prlic wrote:
>>
>> not sure if I understand you correctly. If you look at
>> http://biojava.org/wiki/BioJava:CookBook:PDB:atoms
>> you will see how the object model hierarchy looks like.
>> Groups are below chain.
>>
>> A
>>
>> On Thu, Aug 28, 2008 at 7:50 AM, Dmitry Repchevsky
>> <dmitry.repchevski at bsc.es> wrote:
>>
>>>
>>> Hello Andreas,
>>>
>>> I thought that chains are part of Compound (COMPND) so calling
>>> Structure.getChains() would get them from Compound and not from "groups".
>>> I was wrong. :-)
>>>
>>> It would be nice to put this in javadoc of the getChains() method...
>>>
>>> Thank you very much,
>>>
>>> Dmitry
>>>
>>> Andreas Prlic wrote:
>>>
>>>>
>>>> Hi Dmitry,
>>>>
>>>> The object model reflects the organization of data in PDB files
>>>> http://www.wwpdb.org/docs.html.
>>>>
>>>> Chains can contain a mix of different groups of atoms.  As such the
>>>> BioJava object model allows you to distinguish between amino acids
>>>> nucleotides and hetatoms on the Group level, rather than on the chain
>>>> level.
>>>>
>>>> Andreas
>>>>
>>>>
>>>>
>>>> On Thu, Aug 28, 2008 at 2:14 AM, Dmitry Repchevsky
>>>> <dmitry.repchevski at bsc.es> wrote:
>>>>
>>>>
>>>>>
>>>>> Hello!
>>>>>
>>>>> I have a PDB (1pio) with 2 chains and 1 HETATM solvent (water).
>>>>> A Structure object contains "models" and "compounds".
>>>>> "models" contains ALL elements (aminoacid chains AND solvents) and
>>>>> "compaunds" only aminoacids.
>>>>> The method Structure.getChains() returns me ALL elements... is it ok? I
>>>>> mean
>>>>> that when I'm asking for a "chain" I do not expect to get a solvent...
>>>>>
>>>>> Just a curiosity,
>>>>>
>>>>> Dmitry
>>>>> _______________________________________________
>>>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
>