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tkemmer merged 2 commits into from
Apr 16, 2026
Merged

System: support multiple secondary structures per fragment #279

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18b57cf
System: support multiple secondary structures per fragment
tkemmer Mar 17, 2026
21fb327
Docs: update tutorials
tkemmer Mar 17, 2026
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3 changes: 0 additions & 3 deletions docs/src/public/system.md
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Original file line number Diff line number Diff line change
Expand Up @@ -114,10 +114,8 @@ SecondaryStructureTable
secondary_structure_by_idx
secondary_structures
nsecondary_structures
parent_secondary_structure
sort_secondary_structures!
Base.delete!(::SecondaryStructure)
Base.push!(::Chain{T}, ::SecondaryStructure{T}) where T
```

## Fragments
Expand Down Expand Up @@ -145,7 +143,6 @@ nfragments
parent_fragment
sort_fragments!
Base.delete!(::Fragment)
Base.push!(::SecondaryStructure{T}, ::Fragment{T}) where T
Base.push!(::Chain{T}, ::Fragment{T}) where T
```

Expand Down
18 changes: 10 additions & 8 deletions docs/src/tutorials/core_components.md
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Expand Up @@ -532,45 +532,47 @@ Now, that we learned about chains, we can take a look at the secondary structure
s = System()
chain = Chain(Molecule(s))
ss1 = SecondaryStructure(
chain,
Residue(chain, 1),
Residue(chain, 2),
1,
SecondaryStructureElement.Helix;
name="H1"
)

ss2 = SecondaryStructure(
chain,
Residue(chain, 3),
Residue(chain, 4),
2,
SecondaryStructureElement.Coil;
name="C1"
)

ss3 = SecondaryStructure(
chain,
Residue(chain, 5),
Residue(chain, 6),
3,
SecondaryStructureElement.Strand;
name="S1"
)
ss4 = SecondaryStructure(
chain,
Residue(chain, 7),
Residue(chain, 8),
4,
SecondaryStructureElement.Turn;
name="T1"
)

ss3.type = SecondaryStructureElement.Helix
println("Number of secondary structures: ", nsecondary_structures(s))

# get all helices of the chain
helices = (filter(sst -> sst.type == ss1.type, secondary_structures(chain)))
filter(sst -> sst.type == SecondaryStructureElement.Helix, secondary_structures(chain))
```

Number of secondary structures: 4

| **\#** | **idx** | **number** | **type** | **name** |
|-------:|:--------|:-----------|:---------|:---------|
| 1 | 3 | 1 | Helix | H1 |
| 2 | 5 | 3 | Helix | S1 |
| 1 | 5 | 1 | Helix | H1 |

In addition, we can compute the secondary structures for an input file:

Expand Down
4 changes: 2 additions & 2 deletions src/BiochemicalAlgorithms.jl
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Expand Up @@ -53,8 +53,8 @@ include("core/system_internals/_atom_table.jl")
include("core/system_internals/_bond_table.jl")
include("core/system_internals/_molecule_table.jl")
include("core/system_internals/_chain_table.jl")
include("core/system_internals/_secondary_structure_table.jl")
include("core/system_internals/_fragment_table.jl")
include("core/system_internals/_secondary_structure_table.jl")
include("core/system.jl")

# system components
Expand All @@ -63,8 +63,8 @@ include("core/atom.jl")
include("core/bond.jl")
include("core/molecule.jl")
include("core/chain.jl")
include("core/secondary_structure.jl")
include("core/fragment.jl")
include("core/secondary_structure.jl")

# molgraph
include("core/moleculargraph_wrapper.jl")
Expand Down
8 changes: 0 additions & 8 deletions src/core/atom.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -156,14 +156,6 @@ end
chain_by_idx(atom._sys, atom.chain_idx)
end

@inline function parent_secondary_structure(atom::Atom)
pf = parent_fragment(atom)

isnothing(pf) || isnothing(pf.secondary_structure_idx) ?
nothing :
secondary_structure_by_idx(parent(atom), pf.secondary_structure_idx)
end

@inline function parent_fragment(atom::Atom)
isnothing(atom.fragment_idx) ?
nothing :
Expand Down
89 changes: 8 additions & 81 deletions src/core/fragment.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,6 @@ Mutable representation of an individual fragment in a system.
- `flags::Flags`
- `molecule_idx::Int`
- `chain_idx::Int`
- `secondary_structure_idx::Int`

# Constructors
```julia
Expand Down Expand Up @@ -96,14 +95,6 @@ const Fragment{T} = AtomContainer{T, :Fragment}
fragment_by_idx(sys, idx)
end

@inline function Fragment(
ss::SecondaryStructure{T},
number::Int;
kwargs...
) where T
Fragment(parent_chain(ss), number; secondary_structure_idx = ss.idx, kwargs...)
end

"""
FragmentTable{T} <: AbstractSystemComponentTable{T}

Expand Down Expand Up @@ -140,7 +131,6 @@ end

@inline parent_molecule(frag::Fragment) = molecule_by_idx(parent(frag), frag.molecule_idx)
@inline parent_chain(frag::Fragment) = chain_by_idx(parent(frag), frag.chain_idx)
@inline parent_secondary_structure(frag::Fragment) = secondary_structure_by_idx(parent(frag), frag.secondary_structure_idx)

@doc raw"""
parent_fragment(::Atom)
Expand Down Expand Up @@ -178,26 +168,22 @@ Returns a `FragmentTable{T}` containing all fragments of the given atom containe
- `variant::Union{Nothing, FragmentVariantType} = nothing`
- `molecule_idx::MaybeInt = nothing`
- `chain_idx::MaybeInt = nothing`
- `secondary_structure_idx::MaybeInt = nothing`
All keyword arguments limit the results to fragments matching the given IDs or variant type.
Keyword arguments set to `nothing` are ignored.
"""
function fragments(sys::System{T} = default_system();
variant::Union{Nothing, FragmentVariantType} = nothing,
molecule_idx::MaybeInt = nothing,
chain_idx::MaybeInt = nothing,
secondary_structure_idx::MaybeInt = nothing
chain_idx::MaybeInt = nothing
) where T
isnothing(variant) &&
isnothing(molecule_idx) &&
isnothing(chain_idx) &&
isnothing(secondary_structure_idx) &&
return FragmentTable{T}(sys, copy(sys._fragments.idx))
_filter_fragments(frag ->
(isnothing(variant) || frag.variant == something(variant)) &&
(isnothing(molecule_idx) || frag.molecule_idx == something(molecule_idx)) &&
(isnothing(chain_idx) || frag.chain_idx == something(chain_idx)) &&
(isnothing(secondary_structure_idx) || frag.secondary_structure_idx == something(secondary_structure_idx)),
(isnothing(chain_idx) || frag.chain_idx == something(chain_idx)),
sys
)
end
Expand Down Expand Up @@ -283,23 +269,6 @@ end

@inline nfragments(ct::ChainTable; kwargs...) = length(fragments(ct; kwargs...))

#=
SecondaryStructure fragments
=#
@inline fragments(ss::SecondaryStructure; kwargs...) = fragments(parent(ss); secondary_structure_idx = ss.idx, kwargs...)
@inline nfragments(ss::SecondaryStructure; kwargs...) = nfragments(parent(ss); secondary_structure_idx = ss.idx, kwargs...)

@inline function fragments(st::SecondaryStructureTable;
variant::Union{Nothing, FragmentVariantType} = nothing
)
idx = Set(st.idx)
isnothing(variant) ?
_filter_fragments(frag -> frag.secondary_structure_idx in idx, st._sys) :
_filter_fragments(frag -> frag.secondary_structure_idx in idx && frag.variant == something(variant), st._sys)
end

@inline nfragments(st::SecondaryStructureTable; kwargs...) = length(fragments(st; kwargs...))

"""
delete!(::Fragment)
delete!(::FragmentTable)
Expand Down Expand Up @@ -347,23 +316,6 @@ new `idx`.
chain
end

"""
push!(::SecondaryStructure{T}, ::Fragment{T})

Creates a copy of the given fragment in the given SecondaryStructure. The new fragment is automatically assigned a
new `idx`.
"""
@inline function Base.push!(ss::SecondaryStructure{T}, frag::Fragment{T}) where T
Fragment(ss, frag.number;
name = frag.name,
variant = frag.variant,
properties = frag.properties,
flags = frag.flags
)
ss
end


#=
Fragment atoms
=#
Expand Down Expand Up @@ -420,19 +372,6 @@ See [`Fragment`](@ref)
Fragment(chain, number; variant = FragmentVariant.Nucleotide, kwargs...)
end


"""
Nucleotide(ss::SecondaryStructure, number::Int)

`Fragment` constructor defaulting to the [`FragmentVariant.Nucleotide`](@ref FragmentVariant) variant.

# Supported keyword arguments
See [`Fragment`](@ref)
"""
@inline function Nucleotide(ss::SecondaryStructure, number::Int; kwargs...)
Fragment(ss, number; variant = FragmentVariant.Nucleotide, kwargs...)
end

"""
$(TYPEDSIGNATURES)

Expand Down Expand Up @@ -478,7 +417,7 @@ fragments of the given atom container or table.
See [`fragments`](@ref)
"""
@inline function nucleotides(
ac::Union{Chain, ChainTable, SecondaryStructure, SecondaryStructureTable, Molecule, MoleculeTable, System} = default_system();
ac::Union{Chain, ChainTable, Molecule, MoleculeTable, System} = default_system();
kwargs...
)
fragments(ac; variant = FragmentVariant.Nucleotide, kwargs...)
Expand All @@ -497,7 +436,7 @@ atom container.
See [`fragments`](@ref)
"""
@inline function nnucleotides(
ac::Union{Chain, ChainTable, SecondaryStructure, SecondaryStructureTable, Molecule, MoleculeTable, System} = default_system();
ac::Union{Chain, ChainTable, Molecule, MoleculeTable, System} = default_system();
kwargs...
)
nfragments(ac; variant = FragmentVariant.Nucleotide, kwargs...)
Expand All @@ -516,7 +455,7 @@ table.
length(filter(isnucleotide, ft))
end

@inline function nnucleotides(ct::Union{ChainTable, SecondaryStructureTable, MoleculeTable})
@inline function nnucleotides(ct::Union{ChainTable, MoleculeTable})
nfragments(ct; variant = FragmentVariant.Nucleotide)
end

Expand Down Expand Up @@ -546,18 +485,6 @@ See [`Fragment`](@ref)
Fragment(chain, number; variant = FragmentVariant.Residue, kwargs...)
end

"""
Residue(ss::SecondaryStructure, number::Int)

`Fragment` constructor defaulting to the [`FragmentVariant.Residue`](@ref FragmentVariant) variant.

# Supported keyword arguments
See [`Fragment`](@ref)
"""
@inline function Residue(ss::SecondaryStructure, number::Int; kwargs...)
Fragment(ss, number; variant = FragmentVariant.Residue, kwargs...)
end

"""
$(TYPEDSIGNATURES)

Expand Down Expand Up @@ -603,7 +530,7 @@ fragments of the given atom container or table.
See [`fragments`](@ref)
"""
@inline function residues(
ac::Union{Chain, ChainTable, SecondaryStructure, SecondaryStructureTable, Molecule, MoleculeTable, System} = default_system();
ac::Union{Chain, ChainTable, Molecule, MoleculeTable, System} = default_system();
kwargs...
)
fragments(ac; variant = FragmentVariant.Residue, kwargs...)
Expand All @@ -622,7 +549,7 @@ atom container.
See [`fragments`](@ref)
"""
@inline function nresidues(
ac::Union{Chain, ChainTable, SecondaryStructure, SecondaryStructureTable, Molecule, MoleculeTable, System} = default_system();
ac::Union{Chain, ChainTable, Molecule, MoleculeTable, System} = default_system();
kwargs...
)
nfragments(ac; variant = FragmentVariant.Residue, kwargs...)
Expand All @@ -641,7 +568,7 @@ table.
length(filter(isresidue, ft))
end

@inline function nresidues(ct::Union{ChainTable, SecondaryStructureTable, MoleculeTable})
@inline function nresidues(ct::Union{ChainTable, MoleculeTable})
nfragments(ct; variant = FragmentVariant.Residue)
end

Expand Down
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