Bond can be created of an atom to itself

[padix-key]

Currently you can add a bond to BondList, that connects an atom with itself. This should never be possible.

Tangentially, pdbx.set_structure() does not check atom uniqueness when writing the chem_comp_bond category: If an AtomArray connects two atoms that are equal in all annotations relevant for chem_comp_bond, The resulting chem_comp_bond category will contain a self-bond for these two atoms.

[Linford24]

I would like to work on this issue @padix-key please is there any more thing I need to know

[padix-key]

Thanks for implementing this. I think this can also be tackled it two PRs. So you can decide if you want to solve both or only one of these problems.

For the problem in BondList: This check for self-bonds would need to be added in the constructor and add_bond()

For the problem in pdbx.set_structure(): I would think the easiest was to check this is if the atom name pairs written to chem_comp_bond are equal.