addproperty -> addproperties

README.md

@@ -29,16 +29,16 @@ julia> propertynames(chain)
 (:id, :atoms, :sequence, :numbering)
 ```
 
-To store additional properties, `addproperty` can be used to attach persistent chain-level properties or indexable residue-level properties:
+To store additional properties, `addproperties` can be used to attach persistent chain-level properties or indexable residue-level properties:
 
 ```julia
 julia> chain = structure["A"]
 256-residue ProteinChain{Float64, @NamedTuple{}} (A)
 
-julia> new_chain = addproperty(chain; taxid=PersistentProperty(83332))
+julia> new_chain = addproperties(chain; taxid=PersistentProperty(83332))
 256-residue ProteinChain{Float64, @NamedTuple{taxid::PersistentProperty{Int64}}} (A)
 
-julia> new_chain = addproperty(new_chain; some_residue_property=IndexableProperty(rand(3,256))) # last dimension gets indexed
+julia> new_chain = addproperties(new_chain; some_residue_property=IndexableProperty(rand(3,256))) # last dimension gets indexed
 256-residue ProteinChain{Float64, @NamedTuple{taxid::PersistentProperty{Int64}, some_residue_property::IndexableProperty{Matrix{Float64}}}} (A)
 
 julia> new_chain[1:100].some_residue_property

src/ProteinChains.jl

@@ -15,7 +15,7 @@ export Atom
 
 include("properties.jl")
 export PersistentProperty, IndexableProperty
-export addproperty
+export addproperties
 @compat public (AbstractProperty, NamedProperties)
 
 include("chain.jl")

src/chain.jl

@@ -2,7 +2,7 @@
     ProteinChain{T<:Real,Ps<:NamedProperties}
 
 Represents a protein chain with a basic set of fields from which some other properties might be derived.
-The [`addproperty`](@ref) function can be used to instantiate new chains with additional properties.
+The [`addproperties`](@ref) function can be used to instantiate new chains with additional properties.
 
 ## Fields
 - `id::String`: Identifier for the protein chain.
@@ -11,7 +11,7 @@ The [`addproperty`](@ref) function can be used to instantiate new chains with ad
 - `numbering::Vector{Int32}`: Residue numbering.
 - `properties::Ps`: Named properties associated with the chain.
 
-See also [`addproperty`](@ref), [`PersistentProperty`](@ref), [`IndexableProperty`](@ref).
+See also [`addproperties`](@ref), [`PersistentProperty`](@ref), [`IndexableProperty`](@ref).
 ```
 """
 struct ProteinChain{T<:Real,Ps<:NamedProperties}
@@ -55,7 +55,7 @@ function Base.getindex(chain::ProteinChain, i::AbstractVector)
 end
 
 """
-    addproperty(chain::ProteinChain; properties...)
+    addproperties(chain::ProteinChain; properties...)
 
 Creates a new `ProteinChain` instance with the added properties.
 Indexing behavior of property values can be specified by wrapping
@@ -65,7 +65,7 @@ Values get wrapped by `PersistentProperty` by default.
 
 See also [`PersistentProperty`](@ref), [`IndexableProperty`](@ref)
 """
-function addproperty(chain::ProteinChain; properties...)
+function addproperties(chain::ProteinChain; properties...)
     properties = map(p -> p isa AbstractProperty ? p : PersistentProperty(p), NamedTuple(properties))
     return ProteinChain(chain.id, chain.atoms, chain.sequence, chain.numbering, merge(chain.properties, properties))
 end
@@ -133,12 +133,12 @@ end
 using AssigningSecondaryStructure: assign_secondary_structure
 
 """
-    addproperty(chain::ProteinChain, names::Symbol...)
-    addproperty(chain::ProteinStructure, names::Symbol...)
+    addproperties(chain::ProteinChain, names::Symbol...)
+    addproperties(chain::ProteinStructure, names::Symbol...)
 
 Add predefined properties to a chain or chains of a structure.
 """
-addproperty(chain::ProteinChain, names::Symbol...) = addproperty(chain; NamedTuple{names}(calculate_property(chain, name) for name in names)...)
+addproperties(chain::ProteinChain, names::Symbol...) = addproperties(chain; NamedTuple{names}(calculate_property(chain, name) for name in names)...)
 
 calculate_property(x, name::Symbol, args...) = calculate_property(x, Val(name), args...)
 

src/properties.jl

@@ -8,7 +8,7 @@ Base.getindex(p::AbstractProperty) = p.value
 A property of arbitrary type that persists after residue indexing of a chain.
 
 ```jldoctest
-julia> chain = addproperty(pdb"1ASS"A; x=PersistentProperty(1));
+julia> chain = addproperties(pdb"1ASS"A; x=PersistentProperty(1));
 
 julia> chain.x == chain[1:10].x
 true
@@ -31,7 +31,7 @@ residue indexing of the chain being propagated to the last dimension of the arra
 ```jldoctest
 julia> chain = pdb"1ASS"A;
 
-julia> chain = addproperty(pdb"1ASS"A; y=IndexableProperty(rand(2,152)));
+julia> chain = addproperties(pdb"1ASS"A; y=IndexableProperty(rand(2,152)));
 
 julia> chain.y == chain[1:10].y
 false
@@ -48,4 +48,4 @@ Base.getindex(p::IndexableProperty, i::AbstractVector) = selectdim(p.value, ndim
 
 const NamedProperties{names} = NamedTuple{names,<:Tuple{Vararg{AbstractProperty}}}
 
-function addproperty end
+function addproperties end

src/structure.jl

@@ -55,5 +55,5 @@ function map_atoms!(f::Function, structure::ProteinStructure, args...)
     return structure
 end
 
-addproperty(structure::ProteinStructure, names::Symbol...) =
-    ProteinStructure(structure.name, structure.atoms, addproperty.(structure.chains, names...))
+addproperties(structure::ProteinStructure, names::Symbol...) =
+    ProteinStructure(structure.name, structure.atoms, addproperties.(structure.chains, names...))

test/runtests.jl

@@ -39,7 +39,7 @@ using Test
     @testset "store" begin
         mktempdir() do dir
             filename = joinpath(dir, "store.h5")
-            structures = [addproperty(pdb"1EYE", :backbone), addproperty(pdb"3HFM", :backbone, :bond_lengths)]
+            structures = [addproperties(pdb"1EYE", :backbone), addproperties(pdb"3HFM", :backbone, :bond_lengths)]
             ProteinChains.serialize(filename, structures)
             structures_copy = ProteinChains.deserialize(filename)
             @test structures == structures_copy