Update read and write

[CunliangGeng]

Updates:

1. added element column
2. update exportpdb to output properly formatted atom name and xyz values
3. remove no_extra
4. add read_pdb function
5. add get_rot_axis_angle function
6. update some functions to align with DeepRank needs
7. update docstrings

[NicoRenaud]

It looks nice but it breaks all the tests. So we have to fix that before merging !

[NicoRenaud]

That's nice and controlled but is it needed to read the data ? But at least to write it I think it's really useful

[CunliangGeng]

I assume the input PDB has strict format, so we don't it that for reading. But we do need some code to preprocess PDB files, I'll write it later.

[CunliangGeng]

only the test_pdb2sqlAlchemy.py failed, it should be fine. I did not change anything of pdb2sqlAlchemy.py file in the PR. We can have a look at the updates together.

[NicoRenaud]

we should fix the sqlalchemy test before merging
Maybe it's as easy as using a proper pdb ...

[CunliangGeng]

Actually there are two bugs in pdb2sqlAlchemy.py. Fixed.