Refactor #guess_bonds implementation

[franciscoadasme]

The Structure#guess_bonds method is a complex method that does a ton of stuff, which was merged from several methods. We should split this into simpler methods, and keep #guess_bonds as the convenient helper:

class Chem::Structure
  def guess_bonds : Nil
    reset_bonds
    guess_connectivity
    guess_bond_orders
    guess_formal_charges
  end
end

Even more, this could be potentially moved to the Chem namespace.