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

pyMBE-dev / pyMBE

pyMBE provides tools to facilitate building up molecules with complex architectures in the Molecular Dynamics software ESPResSo. For an up-to-date API documention please check our website:

https://pymbe-dev.github.io/pyMBE/pyMBE.html

GNU General Public License v3.0

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added value error if pka not provided for acidic or basic particles #24

Closed mariusaarsten closed 4 months ago

mariusaarsten commented 5 months ago

Fixes #6

mariusaarsten commented 4 months ago

@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 commented 4 months ago

@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 commented 4 months ago

@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 commented 4 months ago

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