From f7bac85876c8517ccff42f5890df83f66b4f1c98 Mon Sep 17 00:00:00 2001
From: AntonOresten <anton.oresten42@gmail.com>
Date: Mon, 18 Nov 2024 19:56:47 +0100
Subject: [PATCH] Support writing dict-like properties with string keys +
 bugfix

---
 Project.toml      | 2 +-
 src/chain.jl      | 2 +-
 src/properties.jl | 1 +
 src/store/io.jl   | 9 +++++++++
 src/structure.jl  | 2 +-
 test/runtests.jl  | 7 ++++---
 6 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/Project.toml b/Project.toml
index dd94e90..dfa74fa 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "ProteinChains"
 uuid = "b8e8f2a5-48d3-44f1-ba0d-c71cb7726ff8"
 authors = ["Anton Oresten <anton.oresten42@gmail.com> and contributors"]
-version = "0.5.0"
+version = "0.5.1"
 
 [deps]
 Backboner = "9ac9c2a2-1cfe-46d3-b3fd-6fa470ea56a7"
diff --git a/src/chain.jl b/src/chain.jl
index 1001dbb..546472c 100644
--- a/src/chain.jl
+++ b/src/chain.jl
@@ -69,7 +69,7 @@ Base.getproperty(chain::ProteinChain, name::Symbol) =
 Base.propertynames(chain::ProteinChain, private::Bool=false) = (setdiff(fieldnames(ProteinChain), private ? () : (:properties,))..., propertynames(chain.properties)...)
 
 function setproperties!(chain::ProteinChain, ps::NamedTuple)
-    chain.properties = setproperties(chain.properties, ps)
+    chain.properties = setproperties(chain.properties, sortnames(ps))
     chain
 end
 
diff --git a/src/properties.jl b/src/properties.jl
index f56afaa..d897c6a 100644
--- a/src/properties.jl
+++ b/src/properties.jl
@@ -24,6 +24,7 @@ function setproperties! end
 function addproperties! end
 function removeproperties! end
 
+# probably shouldnt deepcopy
 setproperties(x, args...) = setproperties!(deepcopy(x), args...)
 addproperties(x, args...; kwargs...) = addproperties!(deepcopy(x), args...; kwargs...)
 removeproperties(x, args...) = removeproperties!(deepcopy(x), args...)
diff --git a/src/store/io.jl b/src/store/io.jl
index 9d125c9..ca93c19 100644
--- a/src/store/io.jl
+++ b/src/store/io.jl
@@ -39,6 +39,15 @@ function deleteproperty(group::HDF5.Group, ::Type, ::Val{:properties}, names::Sy
     return group
 end
 
+function writeproperty(group::HDF5.Group, T::Type, ::Val{name}, dict::AbstractDict{<:AbstractString}) where name
+    haskey(group, string(name)) && HDF5.delete_object(group[string(name)])
+    dict_group = HDF5.create_group(group, string(name))
+    for (key, value) in pairs(dict)
+        writeproperty(dict_group, T, Val(Symbol(key)), value)
+    end
+    return dict_group
+end
+
 ## chain properties
 
 function writeproperty(group::HDF5.Group, ::Type{ProteinChain{T}}, ::Val{:atoms}, atoms::Vector{Vector{Atom{T}}}) where T
diff --git a/src/structure.jl b/src/structure.jl
index 4ef171b..d37e6db 100644
--- a/src/structure.jl
+++ b/src/structure.jl
@@ -80,7 +80,7 @@ Base.getproperty(structure::ProteinStructure, name::Symbol) =
 Base.propertynames(structure::ProteinStructure, private::Bool=false) = (setdiff(fieldnames(ProteinStructure), private ? () : (:properties,))..., propertynames(structure.properties)...)
 
 function setproperties!(structure::ProteinStructure, properties::NamedTuple)
-    structure.properties = setproperties(structure.properties, properties)
+    structure.properties = setproperties(structure.properties, sortnames(properties))
     structure
 end
 
diff --git a/test/runtests.jl b/test/runtests.jl
index e92a734..88b5ca6 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -91,10 +91,10 @@ using Test
             filename = joinpath(dir, "store.h5")
             structures = [pdb"1EYE", pdb"3HFM"]
             for (i, chain) in enumerate(structures[1])
-                structures[1][i] = addproperties(chain, rand3=rand(3))
+                addproperties!(chain, rand3=rand(3))
             end
             for (i, chain) in enumerate(structures[2])
-                structures[2][i] = addproperties(chain, rand3=rand(3), taxid=-1)
+                addproperties!(chain, rand3=rand(3), taxid=-1, dict=Dict("a"=>1, "b"=>2))
             end
             ProteinChains.serialize(filename, structures)
             structures_copy = ProteinChains.deserialize(filename)
@@ -103,7 +103,8 @@ using Test
             store = ProteinStructureStore(filename)
             @test haskey(store, "1EYE.cif")
             @test issubset((:rand3,), propertynames(store["1EYE.cif"][1]))
-            @test all(chain -> issubset((:rand3, :taxid), propertynames(chain)), store["3HFM.cif"])
+            @test all(chain -> issubset((:rand3, :taxid, :dict), propertynames(chain)), store["3HFM.cif"])
+            @test store["3HFM.cif"][1].dict == Dict("a"=>1, "b"=>2)
             delete!(store, "1EYE.cif")
             @test !haskey(store, "1EYE.cif")