Re: atomcache with a file
Andreas Prlic <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <CALthepyWgTQqayUYZ7YW0NsjNSgGQN2ok__fS00ozJkA+2AWmQ@mail.gmail.com> |
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 > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l