Add lazy delete! method

Project.toml

@@ -1,7 +1,7 @@
 name = "ProteinChains"
 uuid = "b8e8f2a5-48d3-44f1-ba0d-c71cb7726ff8"
 authors = ["Anton Oresten <anton.oresten42@gmail.com> and contributors"]
-version = "0.6.3"
+version = "0.6.4"
 
 [deps]
 Backboner = "9ac9c2a2-1cfe-46d3-b3fd-6fa470ea56a7"

examples/examples.jl

@@ -1,6 +1,6 @@
 # # Examples
 
-# ## Basic chain usage
+# ## ProteinStructure and ProteinChain
 
 using ProteinChains
 
@@ -79,9 +79,30 @@ size(frames.rotations)
 #-
 size(frames.translations)
 
+# ## MMCIF utilities
+
+# MMCIF files contain a lot of information that is not present in PDB files.
+# The `mapmmcif` function can be used to map one MMCIF field to another.
+
+mmcifdict = mmcifdict"3HFM";
+#-
+mapmmcif(mmcifdict, "_atom_site.auth_asym_id"   => "_atom_site.label_entity_id")
+#-
+mapmmcif(mmcifdict, "_entity_src_gen.entity_id" => "_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id")
+#-
+chainid_to_taxonomyid = mapmmcif(mmcifdict,
+    "_atom_site.auth_asym_id"   => "_atom_site.label_entity_id",
+    "_entity_src_gen.entity_id" => "_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id")
+#-
+structure = pdb"3HFM"
+for chain in structure
+    chain.taxonomy_id = chainid_to_taxonomyid[chain.id]
+    println("Set taxonomy_id of chain $(chain.id) to $(chain.taxonomy_id)")
+end
+
 # ## ProteinStructureStore
 
-# The `ProteinStructureStore <: AbstractDict{String, ProteinStructure}` type is a lazy wrapper for a disk-based storage of `ProteinStructure`s.
+# The `ProteinStructureStore <: AbstractDict{String, ProteinStructure}` type is a lazy wrapper for a file-based storage of `ProteinStructure`s.
 
 dir = mktempdir();
 store = ProteinStructureStore(joinpath(dir, "structures.pss"));

src/store/io.jl

@@ -26,6 +26,10 @@ function readproperty(lazy::Lazy, ::Val{name}) where name
     return f(value)
 end
 
+function deleteproperty(lazy::Lazy, ::Val{name}) where name
+    haskey(lazy.group, string(name)) && HDF5.delete_object(lazy.group, string(name))
+end
+
 function writeproperty(lazy::Lazy, ::Val{name}, property::AbstractProperty) where name
     HDF5.attributes(lazy.group)[string(name)] = string(typeof(property))
     write(lazy.group, string(name), unwrap(property))

src/store/store.jl

@@ -12,6 +12,9 @@ Base.getproperty(lazy::Lazy, property::Symbol) =
 Base.setproperty!(lazy::Lazy, property::Symbol, value) =
     property == :group ? setfield!(lazy, property, value) : writeproperty(lazy, Val(property), value)
 
+Base.delete!(lazy::Lazy, property::Symbol) =
+    property == :group ? error("group is immutable") : deleteproperty(lazy, Val(property))
+
 include("utils.jl")
 include("io.jl")
 
@@ -174,11 +177,16 @@ Base.getindex(structure::Lazy{ProteinStructure{T}}, index::Integer) where T =
 
 Base.length(chain::Lazy{<:ProteinChain}) = read(HDF5.attributes(chain.group)["n_residues"])
 
+# v0.5 compat
 function Base.getproperty(lazy::Lazy{T}, property::Symbol) where T<:Union{ProteinStructure,ProteinChain}
-    if property == :group || haskey(lazy.group, string(property))
+    property == :group && return getfield(lazy, :group)
+    if haskey(lazy.group, "properties")
+        if property in fieldnames(T)
+            return invoke(getproperty, Tuple{Lazy,Symbol}, lazy, property)
+        else
+            return getproperty(readproperty(lazy, Val(:properties)), property)
+        end
+    else
         return invoke(getproperty, Tuple{Lazy,Symbol}, lazy, property)
-    elseif haskey(lazy.group, "properties")
-        # v0.5 compat
-        return getproperty(readproperty(lazy, Val(:properties)), property)
     end
 end