The Backbone type could probably be improved by not including the oxygen slice in the coordinate matrix, since that's not really part of the main backbone. The heavy lifting could be given to the Chain type. Defining the Backbone type to represent only a contiguous chain of atoms has the advantage that you can easily flatten out the coordinates.
AssigningSecondaryStructure.jl still uses a 3x4xL array of coordinates, so the 3x3xL backbone with have to be concatenated along dimension 3 with the 3xL oxygen atom matrix reshaped to be a 3x1xL array.
The Backbone type could probably be improved by not including the oxygen slice in the coordinate matrix, since that's not really part of the main backbone. The heavy lifting could be given to the Chain type. Defining the Backbone type to represent only a contiguous chain of atoms has the advantage that you can easily flatten out the coordinates. AssigningSecondaryStructure.jl still uses a 3x4xL array of coordinates, so the 3x3xL backbone with have to be concatenated along dimension 3 with the 3xL oxygen atom matrix reshaped to be a 3x1xL array.