Correction of the usage of DSSP in the topocg module

[rversin]

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Checklist

• Tests added for the new code
• Documentation added for the code changes
• Does not break licensing
• Does not add any dependencies, if it does please add a thorough explanation

Summary of the Pull Request

Here, I adapt the code to produce DSSP usable pdb files and remove the usage of the DSSP function from the BioPython library, instead using the command line version.

Related Issue

Not related to an issue

Additional Info

The warning "No SS definition found for residue: ..." was removed, since if DSSP is installed and works, a secondary structure will be applied.
I will look into the Codacy reports issues with the aa2cg.py script for a following pull request.

[rvhonorato]

still somethings to be improved but good enough for now

[rversin]

should I merge the pool request ?

[amjjbonvin]

Go for it!

[rversin]

Thanks :D