BrokenBond module

[ryanmrichard]

I have added a property type to GhostFragment called BrokenBond. This issue is for writing, testing, and documenting a module which satisfies BrokenBond.

The BrokenBond API takes a FragmentedNuclei object and returns a std::vector<bond_set> object.

The return is a nested container such that:

• The i-th element of the result is a bond_set object which contains the set of bonds broken in forming fragment i.
• The set of bonds contains bond_type objects. One for each bond that was broken.
• Each bond_type object is a pair of integers. The first integer is the index of the atom which is in the fragment, the second index is the index of the atom
• Order of atoms is determined by the supersystem() method of the FragmentedNuclei object.

As a note the module will need to call a submodule of property type MolecularGraph (defined in include/ghostfragment/property_types/molecular_graph.hpp) to convert the the FragmentedNuclei object to a MolecularGraph object.

Tutorials on how to write modules are here. Also take a look at the files in src/connectivity in GhostFragment).

[ryanmrichard]

FWIW, the BrokenBond property type lives at include/ghostfragment/property_types/broken_bond.hpp