Improve PolyConf split_pol() error handling

[recombinatrix]

The algorithm used by PolyConf to generate conformations requires that the J-K atom pairs used in rotate() and dist() (and hence shuffler() and dihedral_solver() ) be chosen such that if the polymer is split by breaking the bond J-K, the resulting molecule will have exactly two completely disconnected groups of atoms (see polyconf manuscript figures S1 and S2.

This is not an error or a bug, it's a fundamental requirement of the approach; the geometric processes cannot be defined if this is not true.

Identifying the two disconnected groups of atoms is implemented in split_pol().

If a user chooses a bond such that the there will not be two disconnected groups of atoms (eg, one of the C-C bonds in an aromatic ring), split_pol() will fail with an unclear error message.

Example:

(polyconstruct-env) emilycameron@aibn-3k1tw14:~/polyconstruct$ python3 P5Tx_PolyConf.py 
 50%|█████████████████████▌                     | 25/50 [00:00<00:00, 84.34it/s]
Traceback (most recent call last):
  File "/home/emilycameron/polyconstruct/P5Tx_PolyConf.py", line 92, in <module>
    P5Tx.shuffler(NC_dihedrals)
    ~~~~~~~~~~~~~^^^^^^^^^^^^^^
  File "/home/emilycameron/polyconstruct/polyconf/polyconf/Polymer.py", line 475, in shuffler
    self.shuffle(J=dh['J'],J_resid=dh['J_resid'],K=dh['K'],K_resid=dh['K_resid'],mult=dh['mult'],dummies=dummies,clashcheck=clashcheck,cutoff=cutoff)
    ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/emilycameron/polyconstruct/polyconf/polyconf/Polymer.py", line 383, in shuffle
    self.rotate(J,J_resid,K,K_resid,mult,step)
    ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/emilycameron/polyconstruct/polyconf/polyconf/Polymer.py", line 300, in rotate
    fore,_=self._split_pol(J,J_resid,K,K_resid)
           ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
  File "/home/emilycameron/polyconstruct/polyconf/polyconf/Polymer.py", line 270, in _split_pol
    bond = self.polymer.atoms.bonds.atomgroup_intersection(pair,strict=True)[0]
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^
  File "/home/emilycameron/miniconda3/envs/polyconstruct-env/lib/python3.13/site-packages/MDAnalysis/core/topologyobjects.py", line 823, in __getitem__
    return outclass(self._bix[item],
                    ~~~~~~~~~^^^^^^
IndexError: index 0 is out of bounds for axis 0 with size 0

To do: I need to either build in some kind of checking to validate the chosen bond, and/or build in a more graceful error message to explain that the chosen bond was not sensible.