[Biopython-dev] Features of the GSOC branch ready to be merged

[João Rodrigues]

Following Peter's comments I changed some stuff.

I also noticed one thing: metal ions like CA and CL have their names
starting one character before regular C and N atoms. That allows some
discrimination between CA (alpha carbon) and CA (calcium) for example. I'd
never noticed this before, thus relying on the hetero_flag to try and
exclude metal ions (HETATM) because they would likely be wrong if such an
ambiguous case existed. I thus removed the hetero_flag I'd added to Atom
objects and expanded the element guessing logic to all atoms.

I also changed the tests in test_PDB.py to reflect this.

Best! And thanks Peter for the comments!