The linking of two unconnected compounds happens in Fragmenstein class's _join_neighboring.py methods.
The method join_neighboring_mols does the joining.
fragmenstein.join_neighboring_mols(mol_A, mol_B) # -> mol_combined
The closest atoms are chosen by the private method _find_closest.
This method depends on the closeness_weights class-attribute, a list of tuples of function(Chem.Atom) -> bool and float penalty.
Namely, if the passed atom is True the penalty is added to the distance.
- warhead atom: NaN (don't touch them)
- fully bonded: +1.0
- ring atom: +0.5
The joining is done by the private method _join_atoms, which will add atoms in a line.
The distance between two atoms added is 1.22 as when minimised they will be in a zip-zap.
Currently, the added linker is a hydrocarbon.