[Biojava-l] atomcache with a file

[JAX]

Ok cool... Maybe it we be good to make the atom cache java doc should explicitly state that it is only for PDB files, and not any other structures. 

Jay Vyas 
MMSB
UCHC

On Sep 16, 2011, at 6:57 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi,
> 
> had a quick offline discussion with Spencer about this: The AtomCache
> provides a local mirror for public data, expects a specific
> organisation of files and only supports one toplevel-path under which
> all data is stored. If we would add support for private files to it,
> public and personal files would end mixed up in the same location,
> which in all likelihood would cause confusion. As such it makes more
> sense to access your personal files with the PDBFileReader and manage
> private files yourself. It is a one-liner in both classes anyways...
> 
> Andreas
> 
> 
> 
> 
> On Fri, Sep 16, 2011 at 11:13 AM, Spencer Bliven <sbliven at ucsd.edu> wrote:
>> I think that AtomCache is the wrong tool for this job. If you have private
>> PDB files you should just use a PDBFileReader to get each one (see
>> http://biojava.org/wiki/BioJava:CookBook:PDB:read3.0#Getting_more_control).
>> I don't think AtomCache should be modified to support this.
>> 
>> -Spencer
>> 
>> On Fri, Sep 16, 2011 at 07:43, Andreas Prlic <andreas at sdsc.edu> wrote:
>>> 
>>> If you
>>> think it is useful we can add something like a pre-fix which would
>>> tell the cache to load local files with a nonstandard name. Something
>>> like : private:a1 could be the name to describe your own file.
>> 
>>