[Biojava-dev] default AtomCache constructor

[Spencer Bliven]

I've noticed a lot of hard-coded paths in the structure module from creating
AtomCaches. For instance, very common in main() functions:

    AtomCache cache = new AtomCache("/tmp",true);

This is not cross-platform compatible. I believe the proper way of doing
this is

    AtomCache cache = new AtomCache(new UserConfiguration());

which chooses the save location intelligently (java.io.tmpdir or PDB_DIR
system properties). Would anyone object if I made this the default AtomCache
constructor and removed all the existing hard paths?

-Spencer