Improve proteins script

[paobtorres]

I created the PR but there are a few points to discuss before the merge:

• I adapted the script to add the radius of each beach (If im not mistaked sigma = 2*radius right?). However the results have a wider difference compared to Torres2017 and Torres2022 in some of the pH values. (I checked running in test and short-run mode). Also I get the warning the I'm overwritting the sigma of a previous defined aminoacid I checked a few but It seems to be ok.
• In globular_protein.py I added to the time_series output the charge of each aminoacid but I'm not sure how is the correct way. Currently: for label in net_charge_amino_save.keys (): charge_amino = sum(net_charge_amino_save[label]) time_series[label].append(charge_amino) I'm not sure if it should be sum or mean, I tried both but non of them seem to be correct. -While doing this I notice that In charge_dict ['residues'] there were several CA that had 1 positive charge. I don't know why and if it only happens in the proteins.
• create_paper_data.py its working for the protein If you would like to check
• testsuite\globular_protein_tests.py Its also working but I would like to fix the bugs that I mentioned before uploading the test data

[paobtorres]

@pm-blanco I finished with all the changes related to the radius. I run a simulation on test mode an the plots looks much much better. Also, I already merge this branch with the lastest changes from Seba PR. I think the only thing missing is the AA net charge that I didn't have the time to check (maybe tomorrow morning if you don't do it first).

PS: Related to the CI failed test, I don't understand why it fails on cph_ideal_tests.py because in the two previous commits the CI test was passed succesfully.