Ensure an itp generated w/ dssp when using the --bias_auto flag

[sebtha]

There is no check if the itp was generated using dssp or another secondary structure assignment. If neither was used, line 5 contains the Martini 3 citation which contains a few "C" and "H", where then additional interactions are added to the respective BB beads.

It should be reasonable to check the usage of dssp in get_ss.

[Lp0lp]

Excellent point! I did not think of this! I can have a look!
In this case, would it also be interesting/of use to have an option to allow the user to enter a secondary structure assignment string manually?

[sebtha]

In my opinion, this (i.e., the manually added secondary structure assignment) is not necessary from a physical point of view. The manually supplied string for the secondary structure assignment is noted in the same line as the dssp assignment in the protein.itp file by martinize2, which makes our lifes here easy.

In terms of flexibility, testing and fine-tuning, however, it might be a good option. But not urgent for now in my view.