Merge pull request #3 from biojava/master

Catch back up with biojava/master
Merge pull request #4 from biojava/master

Catch back up with biojava/master
Merge pull request #5 from biojava/master

Catch back up with biojava/master
Fix a NullPointer in createAFPChain

Ignore errors when trying to set the structure names
Fix ScopFactory bug

The current version was being returned sometimes,
even when an older version was requested.
updating example to latest API
Merge pull request #6 from biojava/master

Catch back up with biojava/master
some cleanup
Merge pull request #73 from andreasprlic/master

some cleanup
Checking for empty SCOP files

SCOP files can occationally be empty (eg if the server was down
at time of access). Future calls will now attempt to redownload them.
Merge branch 'master' of https://github.com/biojava/biojava
Initialize list of bonds lazily. The bond list in an Atom is now
initialized with Collections.emptyList(), rather than an ArrayList. This
doubles the speed of allocating Atoms, since the bond list is not
created.
Cleanup and minor bug fixes
RotationAxis: better handling of translational movements
Removing ScopDatabase from AtomCache

Always fetch the active Scop from the ScopFactory
Merge branch 'master' of https://github.com/biojava/biojava
Merge pull request #7 from biojava/master

Catch back up with biojava/master
Merge pull request #79 from pwrose/master

Initialize list of bonds lazily. The bond list in an Atom is now
Add a test case based on Daniel Cameron's example of failing FeatureList
code.  Modified FeatureList code to properly support adding indices both
before and after adding features.  Adding indicies between adds of
features are still not supported.  Ensure both adding index before
features and adding features before index are both tested.
Update method comment to indicate legal calling sequences for using
attribute features.