assign_secondary_structure(chain_backbones::Vector{Array{T,3}}) where T<:Real

Given a vector of chain backbones, each represented as a 3-dimensional array of size 3x3xL, this function assigns the secondary structure to each residue.

Returns a vector of vectors of integers, each of which is the secondary structure assignment for the corresponding chain and their respective residues. The integers are encoded as follows:

• 1: loop; neither helix nor strand.
• 2: helix; α, 3_10, or π.
• 3: strand; part of a β-sheet.