Add support for all bonded potentials

[pm-blanco]

Currently only harmonic and FENE bond interactions are supported in pyMBE. That limits our capabilities as a tool to setup advanced force fields in ESPResSo. Tasks to be done to make progress in this project:

• Implement define_angular_potential and define_dihedral_potential functions in analogy to our current setup for bonds, done with define_bond.
• Implement bookkeeping tool (map) of the connectivity between pairs, triplets and quadriplets of particles within molecules either using the pyMBE dataframe (one would need to create two more columns for particle ids) or with a dedicated data structure.
• When creating a molecule, pyMBE should check for the conectivity of the particle and add bending and dihedral potentials (if defined).

[pm-blanco]

Draft of define_angular_potential , after online discussion with @1234somesh

• We add support for "Harmonic angle", "Cosine angle" and "Harmonic cosine" potentials, given by the angle_potential_type
• particle_triplets = [ [name0, name1, name2 ], ], where we hard-code that the name in the center of the inner list is always the central particle. This should be clearly documented.
• We also define a create_angular_potential_in_espresso(self, angle_potential_type, angle_parameters) that checks the parameters and creates the espresso angular potential object (cf. create_bond_in_espresso)
• the angle_key of a particle triplet ["A", "B", "C"] should be "A-B-C"

 def define_angular_potential(self, angle_potential_type, angle_parameters, particle_triplets):
        # Add docs here
        angular_potential_object=self.create_angular_potential_in_espresso(angle_potential_type, angle_parameters)
        for side_particle0, central_particle, side_particle1 in particle_triplets :
            index = len(self.df)
            # Adapt this to the label for angular potential A-B-C
            for label in [f'{particle_name1}-{particle_name2}', f'{particle_name2}-{particle_name1}']:
                self._check_if_multiple_pmb_types_for_name(name=label, pmb_type_to_be_defined="angle_potential")
            name=f'{particle_name1}-{particle_name2}'
            self._check_if_multiple_pmb_types_for_name(name=name, pmb_type_to_be_defined="angle_potential")    
            self.df.at [index,'name']= name
            self.df.at [index,'bond_object'] = bond_object      
            self.add_value_to_df(index=index,
                                    key=('pmb_type',''),
                                    new_value='angle_potential')
            self.add_value_to_df(index=index,
                                    key=('parameters_of_the_potential',''),
                                    new_value=bond_object.get_params(),
                                    non_standard_value=True)
        self.df.fillna(pd.NA, inplace=True)
        return