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" <[email protected]>
Sent: Friday, September 16, 2011 4:43 PM
To: "Jay Vyas" <[email protected]>
Cc: <[email protected]>
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 <[email protected]> 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 <[email protected]> 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 <[email protected]> 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 - [email protected]
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>
--
Jay Vyas
MMSB/UCHC
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