System: support multiple secondary structures per fragment

[tkemmer]

Breaking changes:

• The private column/field secondary_structure_idx has been removed from FragmentTable/Fragment
• Instead, SecondaryStructureTable/SecondaryStructure has now two additional private columns/fields first_fragment_idx and last_fragment_idx
• SecondaryStructure(...) requires an initial fragment as well as an terminal fragment instead of a chain, similar to its representation in PDB files:

# old behavior
SecondaryStructure(chain, ...)

# new behavior
SecondaryStructure(first_fragment, last_fragment, ...)

• Fragment(...)/Residue(...)/Nucleotide(...) no longer accept a secondary structure as their first argument
• parent_secondary_structure(...) has been removed (and incorporated into secondary_structures(...))

# old behavior
parent_secondary_structure(fragment)

# new behavior
secondary_structures(fragment)

• push!(chain, secondary_structure) has been removed without replacement