Add PDBEntry, pdb"" notation

MurrellGroup · Aug 4, 2024 · af4d142 · af4d142 · AntonOresten · Aug 4, 2024
1 parent b19875e
commit af4d142
Show file tree

Hide file tree

Showing 3 changed files with 23 additions and 11 deletions.
diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "Backboner"
 uuid = "9ac9c2a2-1cfe-46d3-b3fd-6fa470ea56a7"
 authors = ["Anton Oresten <anton.oresten42@gmail.com>"]
-version = "0.11.1"
+version = "0.11.2"
 
 [deps]
 BioStructures = "de9282ab-8554-53be-b2d6-f6c222edabfc"

diff --git a/src/protein/oxygen.jl b/src/protein/oxygen.jl
@@ -1,5 +1,3 @@
-export oxygen_coords
-
 ## Warning: wonky code ahead
 
 using LinearAlgebra

diff --git a/src/protein/protein.jl b/src/protein/protein.jl
@@ -2,31 +2,45 @@ module Protein
 
 # TODO: un-export Atom and Residue as they shouldn't really be public (breaking)
 
+using ..Backboner
+
+import BioStructures
+
+include("atom.jl")
 export Atom
 
+include("residue.jl")
 export Residue
 
+include("chain.jl")
 export Chain
 export has_assigned_ss
 
+include("oxygen.jl")
+export oxygen_coords
+
+include("BioStructures-interface.jl")
 export nitrogen_coords, alphacarbon_coords, carbonyl_coords
 export nitrogen_alphacarbon_distances, alphacarbon_carbonyl_distances, carbonyl_nitrogen_distances
 export phi_angles, psi_angles, omega_angles
 
+include("idealization.jl")
 export readchains, writechains
 export readpdb, writepdb
 export readcif, writecif
 export PDBFormat, MMCIFFormat
 
-using ..Backboner
+PDBEntry(pdbid::AbstractString; format=BioStructures.PDBFormat, kwargs...) = mktempdir() do dir
+    path = BioStructures.downloadpdb(pdbid; dir, format, kwargs...)
+    Backboner.Protein.readchains(path, format)
+end
 
-import BioStructures
+macro pdb_str(pdbid)
+    quote
+        PDBEntry($(esc(pdbid)))
+    end
+end
 
-include("atom.jl")
-include("residue.jl")
-include("chain.jl")
-include("oxygen.jl")
-include("BioStructures-interface.jl")
-include("idealization.jl")
+export PDBEntry, @pdb_str
 
 end