Docstrings, tweaks, formatting

src/ProteinChains.jl

@@ -2,8 +2,6 @@ module ProteinChains
 
 using Backboner
 
-using BioStructures: BioStructures, PDBFormat, MMCIFFormat
-
 include("properties.jl")
 
 include("chain.jl")
@@ -19,10 +17,20 @@ export BackboneGeometry
 include("secondary-structure.jl")
 
 include("chain-properties.jl")
+export assign_bond_lengths!
+export assign_bond_angles!
+export assign_torsion_angles!
+export assign_secondary_structure!
+export assign_standard_residue!
+export assign_residue_rotations!
+export assign_residue_rotations_quat!
+export assign_residue_translations!
+export assign_is_knotted!
 
 include("io.jl")
 export readrecord
 export readpdb
 export readcif
+export pdbentry, @pdb_str
 
 end

src/chain-properties.jl

@@ -1,3 +1,5 @@
+# TODO: store non-backbone atoms
+
 function assign_bond_lengths!(chain::ProteinChain)
     chain.bond_lengths = Backboner.get_bond_lengths(Backboner.Backbone(chain.backbone))
 end

src/chain.jl

@@ -1,3 +1,23 @@
+"""
+    ProteinChain
+
+## Examples
+```jldoctest
+julia> structure = pdb"1EYE"
+[ Info: Downloading file from PDB: 1EYE
+1-chain ProteinStructure "1EYE.cif" with 0 properties:
+  256-residue ProteinChain "A" with 0 properties
+
+julia> structure[1]
+256-residue ProteinChain "A" with 0 properties:
+  fields:
+    id::String = "A"
+    aminoacids::String = "PVQVMGVLNVTDDSFSDGGCYLDLDDAVKHGLAMAAAGAGIVDVGGETSRVIPVVKELAAQGITVSIDTMRADVARAALQNGAQMVNDVSGGRADPAM…
+    backbone::Array{Float64, 3} = [45.592 44.171 43.719; -10.864 -10.936 -9.688; 30.192 30.504 31.278;;; 42.568 42.02 40.707; -9.163 …
+    numbers::Vector{Int64} = [5, 6, 7, 8, 9, 10, 11, 12, 13, 14  …  265, 266, 267, 268, 269, 270, 271, 272, 273, 274]
+  properties: (none)
+```
+"""
 mutable struct ProteinChain
     id::String
     aminoacids::String
@@ -30,13 +50,13 @@ end
 Base.summary(chain::ProteinChain) = "$(countresidues(chain))-residue ProteinChain \"$(chain.id)\" with $(length(chain.properties)) properties"
 
 function Base.show(io::IO, ::MIME"text/plain", chain::ProteinChain)
-    print(io, summary(chain), ":")
-    printstyled(io, "\n  fields:", color=:yellow)
     context = IOContext(io, :compact => true, :limit => true)
+    print(context, summary(chain), ":")
+    printstyled(context, "\n  fields:", color=:yellow)
     for fieldname in fieldnames(ProteinChain)[1:end-1]
         printfield(context, chain, fieldname)
     end
-    printstyled(io, "\n  properties:", color=:yellow)
+    printstyled(context, "\n  properties:", color=:yellow)
     isempty(chain.properties) && print(io, " (none)")
     for property in keys(chain.properties)
         printfield(context, chain, property)

src/io.jl

@@ -1,3 +1,5 @@
+using BioStructures: BioStructures, PDBFormat, MMCIFFormat
+
 const ProteinFileFormat = Union{PDBFormat, MMCIFFormat}
 const AMINOACIDS = Set("ACDEFGHIKLMNPQRSTVWY")
 const BACKBONE_ATOM_NAMES = ["N", "CA", "C"]
@@ -34,13 +36,16 @@ get_backbone(chain::BioStructures.Chain, selector) = get_backbone(BioStructures.
 aminoacid_sequence(residues::Vector{BioStructures.AbstractResidue}) = join(oneletter_resname.(residues))
 aminoacid_sequence(chain::BioStructures.Chain, selector) = aminoacid_sequence(BioStructures.collectresidues(chain, selector))
 
-function get_residue_atoms(residues::Vector{BioStructures.AbstractResidue})
-    residue_atoms = Vector{Atom}[]
-    for res in residues
-        push!(residue_atoms, Atom.(BioStructures.collectatoms(res, a -> BioStructures.standardselector(a) && !BioStructures.disorderselector(a))))
+#=function get_residue_atoms(residues::Vector{BioStructures.AbstractResidue})
+    atom_names = Vector{Vector{String}}[]
+    atom_coords = Vector{Vector{Float64}}[]
+    for residue in residues
+        residue_atoms = BioStructures.collectatoms(residue, a -> !backbone_atom_selector(a) && BioStructures.standardselector(a) && !BioStructures.disorderselector(a))
+        push!(atom_names, map(a -> a.name), residue_atoms)
+        push!(atom_coords, map(a -> a.coords), residue_atoms)
     end
-    return residue_atoms
-end
+    return atom_names, atom_coords
+end=#
 
 function ProteinChain(residues::Vector{BioStructures.AbstractResidue})
     id = only(unique(BioStructures.chainid.(residues)))
@@ -89,14 +94,14 @@ Exported formats: `PDBFormat`, `MMCIFFormat`
 
 ## Examples
 
-```jldoctest
-julia> readrecord("example.pdb"); # detects PDB format from extension
+```julia
+readrecord("example.pdb"); # detects PDB format from extension
 
-julia> readrecord("example.cif"); # detects mmCIF format from extension
+readrecord("example.cif"); # detects mmCIF format from extension
 
-julia> readrecord("example.abc", PDBFormat); # force PDB format
+readrecord("example.abc", PDBFormat); # force PDB format
 
-julia> readrecord("example.xyz", MMCIFFormat); # force mmCIF format
+readrecord("example.xyz", MMCIFFormat); # force mmCIF format
 ```
 """
 readrecord(path::AbstractString, format::Type{<:ProteinFileFormat}) = ProteinStructure(read(path, format))
@@ -197,6 +202,4 @@ macro pdb_str(pdbid)
     quote
         pdbentry($(esc(pdbid)))
     end
-end
-
-export @pdb_str
+end

src/properties.jl

@@ -18,15 +18,15 @@ function printfield(io::IO, x, field::Symbol; indent=4)
     printstyled(io, "::"; color=:red)
     printstyled(io, string(typeof(value)); color=:blue)
     printstyled(io, " = "; color=:red)
-    printstyled(io, truncate(repr(value; context=io), 120))
+    printstyled(io, truncate(repr(value; context=io), 100))
 end
 
 function printproperty(io::IO, x, property::Symbol; indent=4)
     value = getproperty(x, property)
     print(io, "\n"*" "^indent)
     printstyled(io, ":", string(property); color=:magenta)
     printstyled(io, " => "; color=:red)
-    printstyled(io, truncate(repr(value; context=io), 120))
+    printstyled(io, truncate(repr(value; context=io), 100))
 end
 
 # TODO: `assign_property!(chain, property)` vs `assign_<property>!(chain)`

src/structure.jl

@@ -1,3 +1,6 @@
+"""
+    ProteinStructure <: AbstractVector{ProteinChain}
+"""
 mutable struct ProteinStructure <: AbstractVector{ProteinChain}
     name::String
     chains::Vector{ProteinChain}
@@ -16,4 +19,16 @@ Base.setproperty!(structure::ProteinStructure, property::Symbol, value) = _setpr
 Base.size(structure::ProteinStructure) = (length(structure.chains),)
 Base.getindex(structure::ProteinStructure, i) = structure.chains[i]
 
-Base.getindex(structure::ProteinStructure, id::AbstractString) = structure[findfirst(c -> c.id == id, structure.chains)]
+Base.getindex(structure::ProteinStructure, id::AbstractString) = structure[findfirst(c -> c.id == id, structure.chains)]
+
+Base.summary(structure::ProteinStructure) = "$(length(structure))-chain ProteinStructure \"$(structure.name)\" with $(length(structure.properties)) properties"
+
+function Base.show(io::IO, ::MIME"text/plain", structure::ProteinStructure)
+    print(io, summary(structure), ":")
+    n, i = 10, 0
+    for chain in structure
+        (i += 1) <= n || break
+        print(io, "\n  ", summary(chain))
+    end
+    i < length(structure) && print("\n  …")
+end