System: allow string-based fields to be passed as AbstractStrings

Signed-off-by: Thomas Kemmer <[email protected]>

src/core/atom.jl

@@ -43,8 +43,8 @@ Atom(
     number::Int,
     element::ElementType;
     # keyword arguments
-    name::String = "",
-    atom_type::String = "",
+    name::AbstractString = "",
+    atom_type::AbstractString = "",
     r::Vector3{T} = Vector3{T}(0, 0, 0),
     v::Vector3{T} = Vector3{T}(0, 0, 0),
     F::Vector3{T} = Vector3{T}(0, 0, 0),
@@ -191,7 +191,7 @@ end
 """
     atom_by_name(
         ac::AbstractAtomContainer{T} = default_system(),
-        name::String
+        name::AbstractString
     ) -> Union{Nothing, Atom{T}}
 
 Returns the first `Atom{T}` associated with the given `name` in `ac`. Returns nothing if no such
@@ -203,14 +203,14 @@ Any value other than `nothing` limits the result to atoms matching this frame ID
 """
 @inline function atom_by_name(
     ac::AbstractAtomContainer{T},
-    name::String;
+    name::AbstractString;
     frame_id::MaybeInt = 1
 ) where T
     idx = filter(atom -> atom.name == name, atoms(ac; frame_id = frame_id)).idx
     isempty(idx) ? nothing : atom_by_idx(parent(ac), first(idx))
 end
 
-@inline function atom_by_name(name::String; kwargs...)
+@inline function atom_by_name(name::AbstractString; kwargs...)
     atom_by_name(default_system(), name; kwargs...)
 end
 

src/core/chain.jl

@@ -25,7 +25,7 @@ Mutable representation of an individual chain in a system.
 Chain(
     mol::Molecule{T};
     # keyword arguments
-    name::String = "",
+    name::AbstractString = "",
     properties::Properties = Properties(),
     flags::Flags = Flags()
 )

src/core/fragment.jl

@@ -51,7 +51,7 @@ Fragment(
     chain::Chain{T},
     number::Int;
     # keyword arguments
-    name::String = "",
+    name::AbstractString = "",
     variant::FragmentVariantType = FragmentVariant.None,
     properties::Properties = Properties(),
     flags::Flags = Flags()
@@ -64,7 +64,7 @@ Fragment(
     secondary_structure::SecondaryStructure{T},
     number::Int;
     # keyword arguments
-    name::String = "",
+    name::AbstractString = "",
     variant::FragmentVariantType = FragmentVariant.None,
     properties::Properties = Properties(),
     flags::Flags = Flags()

src/core/molecule.jl

@@ -31,7 +31,7 @@ Mutable representation of an individual molecule in a system.
 Molecule(
     sys::System{T};
     # keyword arguments
-    name::String = "",
+    name::AbstractString = "",
     variant::MoleculeVariantType = MoleculeVariant.None,
     properties::Properties = Properties(),
     flags::Flags = Flags()
@@ -42,7 +42,7 @@ Creates a new `Molecule{T}` in the given system.
 ```julia
 Molecule(;
     #keyword arguments
-    name::String = "",
+    name::AbstractString = "",
     variant::MoleculeVariantType = MoleculeVariant.None,
     properties::Properties = Properties(),
     flags::Flags = Flags()

src/core/secondary_structure.jl

@@ -30,7 +30,7 @@ SecondaryStructure(
     number::Int,
     type::SecondaryStructureType;
     # keyword arguments
-    name::String = "",
+    name::AbstractString = "",
     properties::Properties = Properties(),
     flags::Flags = Flags()
 )
@@ -43,7 +43,7 @@ const SecondaryStructure{T} = AtomContainer{T, :SecondaryStructure}
     chain::Chain,
     number::Int,
     type::SecondaryStructureType;
-    name::String="",
+    name::AbstractString="",
     kwargs...
 )
     sys = parent(chain)

src/core/system.jl

@@ -98,11 +98,11 @@ Mutable representation of a biomolecular system.
  - `flags::Flags`
 
 # Constructors
-    System(name::String = "", properties::Properties = Properties(), flags::Flags = Flags())
+    System(name::AbstractString = "", properties::Properties = Properties(), flags::Flags = Flags())
 
 Creates a new and empty `System{Float32}`.
 
-    System{T}(name::String = "", properties::Properties = Properties(), flags::Flags = Flags())
+    System{T}(name::AbstractString = "", properties::Properties = Properties(), flags::Flags = Flags())
 
 Creates a new and empty `System{T}`.
 """
@@ -120,7 +120,7 @@ Creates a new and empty `System{T}`.
     _curr_idx::Int
 
     function System{T}(
-        name::String = "",
+        name::AbstractString = "",
         properties::Properties = Properties(),
         flags::Flags = Flags()
     ) where T
@@ -140,7 +140,7 @@ Creates a new and empty `System{T}`.
 end
 
 System(
-    name::String = "",
+    name::AbstractString = "",
     properties::Properties = Properties(),
     flags::Flags = Flags()
 ) = System{Float32}(name, properties, flags)
@@ -336,7 +336,7 @@ end
 end
 
 @inline Base.show(io::IO, ::MIME"text/plain", sc::SystemComponent) = show(io, sc)
-@inline function Base.show(io::IO, sc::SystemComponent; display_name::String=repr(typeof(sc)))
+@inline function Base.show(io::IO, sc::SystemComponent; display_name::AbstractString=repr(typeof(sc)))
     print(io, "$display_name: ")
     show(io, NamedTuple(_row_by_idx(_table(sc), sc._idx)))
 end

src/core/system_internals/_atom_table.jl

@@ -76,8 +76,8 @@ function Base.push!(
     idx::Int,
     number::Int,
     element::ElementType;
-    name::String = "",
-    atom_type::String = "",
+    name::AbstractString = "",
+    atom_type::AbstractString = "",
     r::Vector3{T} = Vector3{T}(0, 0, 0),
     v::Vector3{T} = Vector3{T}(0, 0, 0),
     F::Vector3{T} = Vector3{T}(0, 0, 0),

src/core/system_internals/_chain_table.jl

@@ -52,7 +52,7 @@ function Base.push!(
     ct::_ChainTable,
     idx::Int,
     molecule_idx::Int;
-    name::String = "",
+    name::AbstractString = "",
     properties::Properties = Properties(),
     flags::Flags = Flags()
 )

src/core/system_internals/_fragment_table.jl

@@ -63,7 +63,7 @@ function Base.push!(
     molecule_idx::Int,
     chain_idx::Int;
     secondary_structure_idx::MaybeInt = nothing,
-    name::String = "",
+    name::AbstractString = "",
     variant::FragmentVariantType = FragmentVariant.None,
     properties::Properties = Properties(),
     flags::Flags = Flags()

src/core/system_internals/_molecule_table.jl

@@ -51,7 +51,7 @@ end
 function Base.push!(
     mt::_MoleculeTable,
     idx::Int = 0;
-    name::String = "",
+    name::AbstractString = "",
     variant::MoleculeVariantType = MoleculeVariant.None,
     properties::Properties = Properties(),
     flags::Flags = Flags()

src/core/system_internals/_secondary_structure_table.jl

@@ -61,7 +61,7 @@ function Base.push!(
     type::SecondaryStructureType,
     molecule_idx::Int,
     chain_idx::Int;
-    name::String = "",
+    name::AbstractString = "",
     properties::Properties = Properties(),
     flags::Flags = Flags()
 )