[Biojava-l] atomcache with a file

[Amr AL-Hossary]

AtomCache searches for files in a standard naming format
currently, you can imitate that standard format, by renaming your local 
files, and then they will be loaded just like normally.

Amr

--------------------------------------------------
From: "Andreas Prlic" <andreas at sdsc.edu>
Sent: Friday, September 16, 2011 4:43 PM
To: "Jay Vyas" <jayunit100 at gmail.com>
Cc: <biojava-l at lists.open-bio.org>
Subject: Re: [Biojava-l] atomcache with a file

> 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
>>
>
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