[Owl-devel] Interface change in owl

[Jose M. Duarte]

Yes you are right. I was thinking also in having the option to pass only one
chain (or a subset of chains). That's easy to do, we could implement
constructors for that.

But, keep in mind that the treating of models remains as before: we only
load one model at a time. If one wants several models then you need to
instantiate several PdbAsymUnit objects each with all chains for each model.

Jose



On 30 March 2011 10:18, Henning Stehr <h.stehr at gmail.com> wrote:

> Hi Jose,
>
> That's very cool. Much better than before. Cheers for that!
>
> One question: For proteins with many chains, this may increase the memory
> consumption quite a bit, won't it? Would it be possible to (optionally) do
> 'lazy loading' of chains, i.e. Only load them to memory when they are
> needed? This way we could also load multi-model pdbs 'lazily' without eating
> up all memory.
>
> Cheers,
> Henning
>
> ------------------------------
> From: Jose M. Duarte <jose.m.duarte at gmail.com>
> Sent: Mittwoch, 30. März 2011 09:42
> To: owl-devel at bioinformatics.org
> Subject: [Owl-devel] Interface change in owl
>
> Good morning all
>
> I am about to commit some important changes to owl. Basically the main way
> of loading PDB data is changing to make things more consistent. Together
> with that I've done some refactoring hoping to aid consistency again.
>
> We used to load PDB data one chain at a time with this kind of
> construction:
>
> - for pdb file
>
> Pdb pdb = new PdbfilePdb("/path/mypdbfile.pdb");
> pdb.load("A");
>
> - for cif file
>
> Pdb pdb = new CiffilePdb("/path/myciffile.cif");
> pdb.load("A");
>
> - for pdbase
>
> Pdb pdb = new PdbasePdb("1abc",new MySQLConnection(),"pdbase");
> pdb.load("A");
>
>
> Now this changes to a hopefully less cumbersome approach. The recently
> added PdbAsymUnit class will be able to load full PDBs at once with all
> their chains. One can then use that or simply take a chain from it. At the
> same time Pdb is now called PdbChain. So this is how you would do the above
> now:
>
> - for pdb file or cif file
>
> PdbAsymUnit pdb = new PdbAsymUnit("/path/myfile.pdb-or-.cif");
> PdbChain chain = pdb.getChain("A");
>
> - for pdbase
>
> PdbAsymUnit pdb = new PdbAsymUnit("1abc",new MySQLConnection(),"pdbase");
> PdbChain chain = pdb.getChain("A");
>
> With this the PdbfilePdb, CiffilePdb and PdbasePdb classes that were
> subclasses of Pdb are now standalone parser classes and are hidden from the
> user. One needs to use only PdbAsymUnit for a whole asymmetric unit (i.e. a
> whole PDB structure) and then PdbChain for single chains within it.
>
> Hope this makes things easier. All code we had in owl and cmview has been
> changed accordingly. If you want to access the code before this change then
> you'll need to check out the last tag owl-1.9.3 instead of the trunk.
>
> Cheers
>
> Jose
>
>
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