Refactor how bonds are defined in pyMBE

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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Refactor how bonds are defined in pyMBE #20

Closed pm-blanco closed 4 months ago

pm-blanco commented 5 months ago

Currently, define_bond follows a different logic than the rest of functions to define objects on pyMBE. define_bond should:

[x] get name, bond_parameters, bond_type and bonded_particle_names as keyword arguments.
[x] Define the curresponding espresso object internally
[ ] Then, pmb.add_bonds_to_es should create bond objects in espresso

Request by @kosovan.