Closed pm-blanco closed 4 months ago
@davidbbeyer will you have time to take a look early next week? Otherwise I will simply proceed to merge this PR, this commit has been used by my students for the last two weeks and reviwed by @paobtorres so it seems quite stable 🙂
@pm-blanco Yes, on Monday.
Quite dense PR, I would appreciate at least two reviewers. Thank you @mariusaarsten for the help while addressing this PR. Partially solves #58.
Bug fixes:
diameter
bysigma
, but we did not correct the setup for the sample scripts with particles with different sizes. I have added a properoffset
to keep the intended previous behaviur.pmb.load_pka_set
andpmb.load_interaction_parameters
were called. Now one gets consistent behavior independently of the order.pmb.read_protein_vtf_in_df
returned the estimated diametertopology_dict["radius"]
instead than the radiuslib/create_cg_from_pdb.py
Code improvements:
pymbe_library.define_AA_particles_in_sequence()
pymbe_library.define_epsilon_value_of_particles()
pymbe_library.define_particles_parameter_from_dict()
pymbe_library.setup_particle_sigma()
pymbe_library.write_output_vtf_file()
pymbe_library.define_particles()
pymbe_library.write_output_vtf_file()
was not really necesary since there already exists a built-in function in espresso that does the same job and furthermore the output vtf were not compatible withvisualization/vmd-traj.py
.samples/Beyer2024/globular_protein.py
. Now the setup of the metal ions is done automatically insidedefine_protein
. I have also defined new functionspymbe_library.get_metal_ions_charge_map()
andpymbe_library.check_if_metal_ion()
to deal with the metal ions to make easier later the perspective generalization that we discussed @paobtorres @jngradNew CI tests for the following functions (some of them very much needed):
pymbe_library.calculate_net_charge()
pymbe_library.create_added_salt()
pymbe_library.create_counterions()
pymbe_library.load_interaction_parameters()
pymbe_library.check_aminoacid_key()
pymbe_library.check_if_metal_ion()
pymbe_library.get_metal_ions_charge_map()
pymbe_library.define_particles()
pymbe_library.define_particle()
pymbe_library.define_residue()
pymbe_library.define_molecule()
pymbe_library.create_particle()
pymbe_library.create_residue()
pymbe_library.create_molecule()
I ran the functional tests and they all pass. I also ran longer tests and the results seem pretty similar to the results in our publication.
Current coverage: 77% total, 70% in pymbe.py