Remove renumber, random fixes

MurrellGroup · Nov 3, 2024 · dfe2947 · dfe2947
1 parent 7d76d43
commit dfe2947
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Showing 7 changed files with 15 additions and 225 deletions.
diff --git a/src/ProteinChains.jl b/src/ProteinChains.jl
@@ -4,19 +4,13 @@ using Backboner
 
 using Compat: @compat
 
-include("ideal.jl")
-export BackboneGeometry
-export IdealResidue, STANDARD_RESIDUE
-export append_residue, prepend_residue
-
 include("atom.jl")
 export Atom
-@compat public (atom_name, atom_number, atom_coords, atom_symbol)
+@compat public (atom_name, atom_number, atom_coords, atom_symbol, atom_mass)
 
 include("properties.jl")
-export StandardProperty, IndexableProperty
+export AbstractProperty, StandardProperty, IndexableProperty
 export setproperties, addproperties, removeproperties
-@compat public AbstractProperty
 
 include("chain.jl")
 export ProteinChain

diff --git a/src/chain.jl b/src/chain.jl
@@ -58,16 +58,16 @@ end
 
 Base.length(chain::ProteinChain) = length(chain.atoms)
 
-Base.getproperty(chain::ProteinChain, name::Symbol) =
-    name in fieldnames(ProteinChain) ? getfield(chain, name) : unpack(getfield(getfield(chain, :properties), name))
-
-Base.propertynames(chain::ProteinChain, private::Bool=false) = (setdiff(fieldnames(ProteinChain), private ? () : (:properties,))..., propertynames(chain.properties)...)
-
 function Base.getindex(chain::ProteinChain, i::Union{AbstractVector,Colon})
     properties = map(p -> p[i], chain.properties)
     ProteinChain(chain.id, chain.atoms[i], chain.sequence[i], chain.numbering[i], properties)
 end
 
+Base.getproperty(chain::ProteinChain, name::Symbol) =
+    name in fieldnames(ProteinChain) ? getfield(chain, name) : unpack(getfield(getfield(chain, :properties), name))
+
+Base.propertynames(chain::ProteinChain, private::Bool=false) = (setdiff(fieldnames(ProteinChain), private ? () : (:properties,))..., propertynames(chain.properties)...)
+
 setproperties(chain::ProteinChain, ps::NamedTuple) =
     ProteinChain(chain.id, chain.atoms, chain.sequence, chain.ins_codes, chain.numbering, setproperties(chain.properties, ps))
 

diff --git a/src/ideal.jl b/src/ideal.jl
diff --git a/src/io/io.jl b/src/io/io.jl
@@ -14,7 +14,6 @@ const pdbextension_to_format = Dict(ext => format for (format, ext) in BioStruct
 
 get_format(path::AbstractString) = get(pdbextension_to_format, lowercase(last(splitext(path))[2:end]), PDBFormat)
 
-include("renumber.jl")
 include("read.jl")
 include("write.jl")
 include("download.jl")

diff --git a/src/io/renumber.jl b/src/io/renumber.jl
diff --git a/src/structure.jl b/src/structure.jl
@@ -63,11 +63,19 @@ function map_atoms!(f::Function, structure::ProteinStructure, args...)
     return structure
 end
 
+Base.getproperty(structure::ProteinStructure, name::Symbol) =
+    name in fieldnames(ProteinStructure) ? getfield(structure, name) : unpack(getfield(getfield(structure, :properties), name))
+
+Base.propertynames(structure::ProteinStructure, private::Bool=false) = (setdiff(fieldnames(ProteinStructure), private ? () : (:properties,))..., propertynames(structure.properties)...)
+
 setproperties(structure::ProteinStructure, properties::NamedTuple) =
     ProteinStructure(structure.name, structure.atoms, structure.chains, setproperties(structure.properties, properties))
 
 addproperties(structure::ProteinStructure, properties::NamedTuple) =
     setproperties(structure, addproperties(structure.properties, properties))
 
+addproperties(structure::ProteinStructure; properties...) =
+    setproperties(structure, addproperties(structure.properties, NamedTuple(properties)))
+
 removeproperties(structure::ProteinStructure, names::Symbol...) =
     setproperties(structure, removeproperties(structure.properties, names...))
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -90,58 +90,6 @@ using Test
             end
         end
 
-        # See https://proteopedia.org/wiki/index.php/Unusual_sequence_numbering
-        @testset "Unusual numbering" begin
-
-            @testset "Arbitrary Numbering" begin
-                structure = ProteinChains.renumber(pdb"1BSZ", mmcifdict"1BSZ")
-                @test !allequal(chain -> chain.numbering, structure)
-                @test allequal(chain -> chain.renumbering, structure)
-            end
-
-            @testset "N-Terminal Residues Missing Coordinates" begin
-                structure = ProteinChains.renumber(pdb"1D66", mmcifdict"1D66")
-                chain = structure["A"]
-                @test chain.numbering[begin] == 8
-                @test chain.renumbering[begin] == 8
-            end
-
-            @testset "Starts With Zero Or Negative Numbers" begin
-                structure = ProteinChains.renumber(pdb"1BXW", mmcifdict"1BXW")
-                chain = structure["A"]
-                @test chain.numbering[begin] == 0
-                @test chain.renumbering[begin] == 1
-
-                structure = ProteinChains.renumber(pdb"1D5T", mmcifdict"1D5T")
-                chain = structure["A"]
-                @test chain.numbering[begin] == -2
-                @test chain.renumbering[begin] == 1
-            end
-
-            @testset "Insertion Codes" begin
-                structure = ProteinChains.renumber(pdb"1IGY", mmcifdict"1IGY")
-                chain = structure["B"]
-                @test count(==(82), chain.numbering) == 4
-                @test allunique(chain.renumbering)
-                @test Set(collect(chain.ins_codes)) == Set([' ', 'A', 'B', 'C'])
-            end
-
-            @testset "Skipping Sequence Numbers" begin
-                structure = ProteinChains.renumber(pdb"2ACE", mmcifdict"2ACE")
-                chain = structure["A"]
-                @test any(!isone, chain.numbering[begin+1:end] - chain.numbering[begin:end-1])
-                @test chain.numbering == chain.renumbering
-            end
-
-            @testset "Not Monotonic" begin
-                structure = ProteinChains.renumber(pdb"1NSA", mmcifdict"1NSA")
-                chain = structure["A"]
-                @test issorted(chain.numbering) # BioStructures sorts automatically with `fixlists!`, so residues are in wrong order
-                @test !issorted(chain.renumbering) # the renumbering is not monotonic. it would be if BioStructures didn't sort.
-            end
-
-        end
-
     end
 
     @testset "store" begin