Added transform and copy method to Entity in biopython.PDB

[benreynwar]

Minor changes to biopython.PDB to allow transforms to be applied to entities and copies of entities to be made. Also fixed a bug in the transform method of Atom. Tests are included.
The changes are from a few months ago but they still merge cleanly into the current master.

[etal]

Thanks for the patches, Ben, and sorry for the lag. The last commit causes the test_transform unit test to fail (naturally):

FAIL: test_transform (main.TransformTests)

Transform entities (rotation and translation).

Traceback (most recent call last):
File "test_PDB.py", line 864, in test_transform
self.assertAlmostEqual(newpos[i], newpos_check[i])
AssertionError: 26.538192549044155 != -19.705159487698754 within 7 places

I'm surprised nobody noticed the bug in Atom.transform during the nearly 8 years it's been around.

[etal]

Merged, except for the last commit:
ed4ca9c

Thanks again!