from_RDKMol can remove atoms from other configurations

[paulsaxe]

In from_RDKMol, this code:

            self.clear()
            try:
                ids = self.atoms.append(x=Xs, y=Ys, z=Zs, atno=atnos)
            except Exception:

causes problems because self.clear() deletes the atoms by calling self.atoms.delete("all"). In atom.py the code is this:

        # velocities, and gradients                                                                                                                                                       
        if atoms == "all" or atoms == "*":
            sql = """                                                                                                                                                                     
            DELETE FROM atom                                                                                                                                                              
             WHERE id IN (SELECT atom FROM atomset_atom WHERE atomset = ?)                                                                                                                
            """
            parameters = (self.atomset,)
            self.db.execute(sql, parameters)

The problem is that configurations usually share atoms by having the same atom set. The solution is to check for other configurations sharing the atoms whenever atoms are added, deleted, or have e.g. the element changed. If the atom set is shared, create new atom set and the appropriate atoms.