Added a step to ensure unique atom names using pdb-tools

[amjjbonvin]

As obabel generates overlapping atom names (e.g. all carbons are call simply C) this is giving problems downstream when using the generated PDB file.

To solve this problem I added a step using pdb_uniqname from pdb-tools to ensure unique atom names.

[gbayarri]

Hi, I think the environment.yml is incorrect, pdb-tools does not exist in anaconda, so this package should be loaded via pip:

- pip:
    - pdb-tools

Anyway, we have recently launched biobb_pdb_tools, so maybe this step could be implemented via BioBB:

https://anaconda.org/bioconda/biobb_pdb_tools

Best.

[amjjbonvin]

I leave it to you to sort it out :-)