[Biojava-l] atomcache with a file

[Daniel Asarnow]

Jay,
The AtomCache also gives a performance boost when re-reading PDB files by
using a cached IO mode.  I believe you can manually activate this mode for
your PDBFileReader; see line 115 of
AtomCache<http://www.biojava.org/docs/api/src-html/org/biojava/bio/structure/align/util/AtomCache.html#line.115>
class
for the example.

I'm not completely sure on this, but I think any time you are re-reading the
same structure within the same JVM instance there is an advantage.

-da

On Fri, Sep 16, 2011 at 17:15, JAX <jayunit100 at gmail.com> wrote:

> 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.
> >>
> >>
>
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