Remove commented out code; PEP8 tweaks
PEP8 tweaks; update copyright line
autopep8 E261 - Fix spacing after comment hash

$ autopep8 --version
autopep8 1.0.4
$ autopep8 -r -i --select E261 ...
autopep8 E265 - Format block comments.

$ autopep8 --version
autopep8 1.0.4
$ autopep8 -r -i --select E265 ...
autopep8 E203 - Remove extraneous whitespace (colon related)

$ autopep8 -r -i --select E203 ...

Note did not apply changes to e.g. Tests/test_Crystal.py and
Bio/SCOP/Raf.py where colon used for numpy array access, nor
auto-generated files like Bio/SubsMat/MatrixInfo.py
PEP8 tweaks to BioSQL, mostly using autopep8