added value error if pka not provided for acidic or basic particles

[mariusaarsten]

Fixes #6

[mariusaarsten]

@pm-blanco I have added a very simple unit test now. I see there are some conflicting files with the parameters, I don't think I have touched them, but should I just change them to what they are in the main fork?

[pm-blanco]

@mariusaarsten yes, you will need to address the merge conflict:

• for Blanco2020.txt and Lunkad2021.txt just keep the version in the main fork
• for Makefile you need to merge it so it also includes the new test you added.

[pm-blanco]

@mariusaarsten I think the CI is now breaking actually due to a broken setup in the peptide files, for example in Lunkad2020.txt:

{"object_type":"particle", "name": "D", "acidity": "acidic", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}

an acidity is given but no pKa value is provided because it is later loaded from the pKa set, which now raises a ValueError with your new implementation. I think the solution is simple: just remove the acidity from all particles in the peptide files.

[pm-blanco]

@mariusaarsten I think the problem is that you need to change diameter to sigma in Blanco2020.txt

[pm-blanco]

It looks good to me now. Thank you for your work @mariusaarsten