moves the NaiveAlign class from ts.py to conformer_generation/align.py
introduces a new function reset_pmol which resets the coordinates of the product to best match the reactant to better success when using double-ended TS generation methods (by unifying non-reacting internal coordinates)
introduces a new function align_reactant_fragments which calls the NaiveAlign method to create an aligned reactant complex
introduces a new function realistic_mol_prep to unify both functions above into a single function that can be used externally for preparing mols for reaction path computation
We could probably merge the function of these functions within a parent class. The key function realistic_mol_prep is all we need to adapt this preparation workflow for many different methods, so this is satisfactory for the time being.
This PR accomplishes the following:
We could probably merge the function of these functions within a parent class. The key function realistic_mol_prep is all we need to adapt this preparation workflow for many different methods, so this is satisfactory for the time being.