0. reorganize example scripts

1. HackaMol::PeriodicTable needs to be reengineered 
  - the data should be of higher quality
  - access needs to be fast
  - some datastructures such as KNOWN_NAMES accessible, and such mappings can be mutable.

2. need the FileHandleRole... even though it isn't perfect. add it... 
use Path::Class there is a moosex::role for it.
>>>>>>>>>> DMR 04-22-2014  
#  ScratchRole and FileRole have been added, minimally using 
#  MooseX::Types::Path::Class.  Potential for cool stuff became apparent
#  while building the tests, but should be encapsulated more within extensions.
#  ExeRole has been added, again with minimal capabilities. 

2a. or should i switch over to Path::Tiny???!  Argh!
>>>>>>>>> DMR 04-23-2014
# switched over to MooseX::Types::Path::Tiny, because documentation is a little better
# 
# 
2c. Combine FileRole and ScratchRole into PathRole.   
#DONE!

3. basic pdbqt reading support  ------>  DONE! DMR 04-01-2014
  3a. pull the tree of rotatable bonds groups

4. pdbqt writing support (3 should be easier)

5. refactor test suite

6. damn the pdb.. many programs do not write out the chemical symbol in the ~80 col.  Thus, the only
obvious way to determine the atom type is via the name, which are not always standard.  Need to have
a sloppier pdb reading method that will carp a warning or maybe dump a log file with all the unknown 
names. We will use the is_dirty parameter To make more robust and to put the responsibility on the user...
>>>>>>>>>> DMR 04-01-2014
#   made the reader set the is_dirty flag for unknown elements.
#   carping of the number of dirty atoms happens at the end so warning isn't as annoying


  6b. add an attribute that allows a map from names to symbols/Zs to be built

 
7. improve examples; add more
  - one with an extended class

8. storage, persistance, and use of MongoDB!

9. remove the QmMolRol attributes from being loaded.  That should be added through extensions that
actually manage QM.  it seems a bit excessive to include even if it they are lazy.

10. based on reading PDBQT may be able to simplify/rethink atom rotations about a bond.


11. document tmax, what_time, print_xyz_ts, print_pdb_ts([], fname) 
  -check tests for inspiration and add more tests if inspired
>>>>>>>>>>>>>DONE!  DMR 04-02-2014


12. improve the binning in AtomGroupRole.  there is bin_this and then atom_bin 
stuff etc.

13. improve use of hush_read attribute in MolReadRole.  Currently, only used for the dirty carp in PDB reading.

14. figure out how to get Dist::Zilla to automate version numbers with some sanity
