[Biojava-l] atomcache with a file

[Andreas Prlic]

The AtomCache is built around naming conventions and supports more
than just loading PDB files. It can also load the representation of a
SCOP domain as a Structure object (and some other things). 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.

Andreas

On Thu, Sep 15, 2011 at 9:28 PM, Jay Vyas <jayunit100 at gmail.com> wrote:
> Thanks... but I have a directory of pdb files
>
> /Users/jay/pdb/a1.pdb
>
> Is it possible for atom cache to initially load the file from this directory
> ?
>
> I don't care where it caches the data ...  Its just that my pdb file is not
> at RCSB, and it appears that atomcache
> is set up to go to RCSB by default to find a pdb file.
>
> On Thu, Sep 15, 2011 at 11:52 PM, Andreas Prlic <andreas at sdsc.edu> wrote:
>>
>> Hi Jay,
>>
>> you can use it like this:
>>
>>                // by default PDB files will be stored in a temporary
>> directory
>>                // there are two ways of configuring a directory, that can
>> get
>> re-used multiple times:
>>                // A) set the environment variable PDB_DIR
>>                // B) call cache.setPath(path)
>>                AtomCache cache = new AtomCache();
>>
>>                try {
>>                        // alternative: try d4hhba_ 4hhb.A 4hhb.A:1-100
>>                        Structure s = cache.getStructure("4hhb");
>>                        System.out.println(s);
>>                }  catch (Exception e) {
>>
>>                        e.printStackTrace();
>>
>>                }
>>
>> Hope that helps,
>>
>> Andreas
>>
>>
>>
>> On Thu, Sep 15, 2011 at 8:32 PM, Jay Vyas <jayunit100 at gmail.com> wrote:
>> > Hi guys : Anyone want to share a code snippet to use AtomCache to load a
>> > PDB
>> > File from disk ?
>> >
>> > --
>> > Jay Vyas
>> > MMSB/UCHC
>> > _______________________________________________
>> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/biojava-l
>> >
>
>
>
> --
> Jay Vyas
> MMSB/UCHC
>