Misc changes

src/store/io.jl

@@ -100,15 +100,12 @@ function readproperty(group::HDF5.Group, ::Type{ProteinStructure{T}}, ::Val{:cha
 end
 
 function Base.write(group::HDF5.Group, structure::ProteinStructure{T}) where T
-    attributes = HDF5.attributes(group)
-    attributes["T"] = string(T)
-    attributes["n_residues"] = sum(length, structure)
-    attributes["n_chains"] = length(structure)
-
+    HDF5.attributes(group)["T"] = string(T)
+    HDF5.attributes(group)["n_residues"] = sum(length, structure)
+    HDF5.attributes(group)["n_chains"] = length(structure)
     for fieldname in fieldnames(ProteinStructure)
         writeproperty(group, ProteinStructure{T}, Val(fieldname), getproperty(structure, fieldname))
     end
-
     return group
 end
 

src/store/store.jl

@@ -59,7 +59,6 @@ that can be lazily read from the file without loading the structure into memory
 These attributes are only written to the file when the structure is written,
 and are not preserved in memory after the structure has been read.
 
-**Preset attributes:**
 - `T`: type of the coordinates in the structure.
 - `n_residues`: vector of number of residues per model in the structure.
 - `n_chains`: vector of number of chains per model in the structure.

src/store/utils.jl

@@ -1,11 +1,8 @@
-struct InsertionCode
-    index::UInt16
-    code::UInt8
-end
+const InsertionCode = NamedTuple{(:index, :code), Tuple{UInt16, UInt8}}
 
-encode_ins_codes(ins_codes::String) = filter(code -> code.code != 0x20, map(splat(InsertionCode), enumerate(codeunits(ins_codes))))
+encode_ins_codes(ins_codes::String) = filter(code -> code.code != 0x20, map(InsertionCode, enumerate(codeunits(ins_codes))))
 
-function decode_ins_codes(ins_codes, len::Integer)
+function decode_ins_codes(ins_codes::Vector{InsertionCode}, len::Integer)
     data = fill(0x20, len)
     for code in ins_codes
         data[code.index] = code.code

src/structure.jl

@@ -6,12 +6,6 @@
 - `atoms::Vector{Atom{T}}`: free atoms from the structure that were not part of any protein residue.
 - `chains::Vector{ProteinChain{T}}`: a collection of `ProteinChain`s.
 - `properties::NamedProperties`: arbitrary properties.
-
-## Examples
-
-```jldoctest
-julia> structure = pdb"1ASS"
-```
 """
 struct ProteinStructure{T} <: AbstractVector{ProteinChain{T}}
     name::String