Update setup.py

Add new version number '0.1a2' to indicate start of work on Bug #1.
In addition, add lines with project website and license information.
Wrap cif_read and cif_parse methods in class

As VaspCat continues to grow, its  modules must be independent of
one another and adaptable to future feature additions.  In this
spirit, the cif_read and cif_parse methods were placed in a new
class Cif inside of posext.py.

Before, if new file formats were added in posext.py, poscar.py
had to be changed before it recognized the new file types.
Now, poscar.py scans posext for the classes contained in posext.
These names coorespond to file extensions, information which
poscar uses when scanning for files to convert.

To accommodate these changes, poscar.py was modified as well,
adding a new attribute 'supported' in main.  This is a list
containing the classes present in posext.py.
Wrap pdb_read and pdb_parse in class Pdb

Enable read and parse methods in pdb class to be searched for by
parent class name Pdb.
Fix Bug #1: Atoms not Appearing

This commit updates poscar.py to properly convert cif files to POSCAR
files if the cif file has extra atoms specified by the
_geom_bond_site_symmetry variable.

Before, the _geom_bond variable was ignored, but it turns out to be
very important.  The variable contains equations specifying how the
fractional positions of extra atoms in the unit cell should be found.
The modifications to poscar.py allow the program to use these
equations.  Before being merged with the master branch, this bugfix will
have to be tested with additional cif files.
Add duplicate coordinate finder to posext.py

In instances where duplicate coordinates are added by the space group
equations, the program now has the capability to remove the duplicates.
Also, the program is able to turn negative fractional
coordinates to positive ones.

A minor bug was also fixed with this commit, in which running VaspCat
in an empty folder crashed the program.  This was accomplished by
changing a line of code in poscar.py having to do with how the program
indicated to the user what file types were supported.