Implementing #181
Now handling obsolete paths too #181
- some improvements for #111, #155 and #185
allowing better backwards compatibility by assuming that cachePath equals pdbFilePath if not specified otherwise
now has a new toString method
cleanup
Merge pull request #187 from josemduarte/master

Making PDB_DIR use the official ftp layout
Merge branch 'master' of github.com:biojava/biojava
trying to catch PDB ID 1A34 where the code fails to detect a short RNA sequence.
need to change integer definition of bio assembly to string to support "PAU" and "XAU" biological units (e.g. 1A34). Also smarter logging.
fixing a bug with mapping Transformations labeled with P or X instead of an integer to the correct assembly.
another fix for parsong PAU and XAU bio assemblies