More tests

README.md

@@ -1,6 +1,7 @@
 [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://m3g.github.io/PDBTools.jl/stable)
 [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://m3g.github.io/PDBTools.jl/dev)
 [![Tests](https://img.shields.io/badge/build-passing-green)](https://github.com/m3g/PDBTools.jl/actions)
+[![codecov](https://codecov.io/gh/m3g/PDBTools.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/m3g/PDBTools.jl)
 [![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 
 # PDBTools

src/Atom.jl

@@ -292,12 +292,17 @@ atom_line(atom::Atom) = @sprintf(
     atoms = read_pdb(PDBTools.SMALLPDB, "protein and index 1")
     @test PDBTools.atom_line(atoms[1]) == 
         "       1    N     ALA     A        1        1   -9.229  -14.861   -5.481  0.00  0.00     1    PROT         1"
+    buff = IOBuffer()
+    printatom(buff, atoms[1])
+    @test length(split(String(take!(buff)))) == 28
 end
 
 """
     printatom(atom::Atom)
+    printatom(io::IO, atom::Atom)
 
-Prints an `Atom` structure in a human-readable format, with a title line.
+Prints an `Atom` structure in a human-readable format, with a title line. By default the output is printed to `stdout`,
+and the `io` argument can be used to specify a different output stream.
 
 ### Example
 
@@ -315,10 +320,11 @@ julia> atoms[1] # default show method
 ```
 
 """
-function printatom(atom::Atom)
-    println(atom_title)
-    println(atom_line(atom))
+function printatom(io::IO, atom::Atom)
+    println(io, atom_title)
+    println(io, atom_line(atom))
 end
+printatom(atom::Atom) = printatom(stdout, atom)
 
 #
 # Print a formatted list of atoms
@@ -452,6 +458,8 @@ end
     @test element(Atom(name = "N", pdb_element="A")) == "A" 
     @test element(Atom(name = "A")) === nothing
     @test element(Atom(name = " ")) === nothing
+    atom = Atom(name="", pdb_element="")
+    @test element(atom) === nothing
 end
 
 #
@@ -624,3 +632,19 @@ end
     @test atomic_mass(at) ≈ 14.0067
     @test position(at) ≈ StaticArrays.SVector(0.0, 0.0, 0.0)
 end
+
+@testitem "atom - show" begin
+    using PDBTools: print_short_atom_list
+    at = Atom(;segname="X")
+    buff = IOBuffer()
+    show(buff, at)
+    @test length(split(String(take!(buff)))) == 14
+    print_short_atom_list(buff, [at, at])
+    @test length(split(String(take!(buff)))) == 14*3
+    print_short_atom_list(buff, [at, at])
+    @test length(split(String(take!(buff)))) == 14*3
+    print_short_atom_list(buff, [copy(at) for _ in 1:20])
+    @test length(split(String(take!(buff)))) == 14*7 + 1
+    show(buff, [at])
+    @test String(take!(buff)) == "PDBTools.Atom{Nothing}[       0    X     XXX     X        0        0    0.000    0.000    0.000  0.00  0.00     0       X         0]"
+end

src/distance.jl

@@ -155,6 +155,8 @@ end
     @test all(isapprox.(closest(r1[1], coor(r2[2])),(1, 1, 5.121218702613667); atol=1e-3))
     @test all(isapprox.(closest(coor(r1[1]), r2[2]),(1, 1, 5.121218702613667); atol=1e-3))
     @test all(isapprox.(closest(r1[1], r2[2]),(1, 1, 5.121218702613667); atol=1e-3))
+    @test all(isapprox.(closest(r1[1], r2), (1, 2, 5.121218702613667); atol=1e-3))
+    @test all(isapprox.(closest(r2, r1[1]), (2, 1, 5.121218702613667); atol=1e-3))
 
     @test distance(r1, r2) ≈ 3.6750402718881863 atol=1e-3
     @test distance(coor(r1), r2) ≈ 3.6750402718881863 atol=1e-3
@@ -173,6 +175,10 @@ end
     r = collect(eachresidue(atoms))
     @test all(isapprox.(closest(r[1], [0.0, 0.0, 0.0]), (12, 1, 16.545482827648158); atol=1e-3))
     @test all(isapprox.(closest([0.0, 0.0, 0.0], r[1]), (1, 12, 16.545482827648158); atol=1e-3))
+    @test all(isapprox.(closest(Atom(), r[1]), (1, 12, 16.545482827648158); atol=1e-3))
+    @test all(isapprox.(closest(r[1], Atom()), (12, 1, 16.545482827648158); atol=1e-3))
+    @test all(isapprox.(closest([coor(Atom())], r[1]), (1, 12, 16.545482827648158); atol=1e-3))
+    @test all(isapprox.(closest(r[1], [coor(Atom())]), (12, 1, 16.545482827648158); atol=1e-3))
 
 end
 

src/formula.jl

@@ -4,7 +4,7 @@
 struct Formula
     formula::Vector{Tuple{Atom,Int}}
 end
-Base.getindex(f::Formula, i) = f.formula[i]
+Base.getindex(f::Formula, i) = (String(pdb_element(first(f.formula[i]))), last(f.formula[i]))
 
 const sub_int = (
     "0" => "₀",
@@ -22,7 +22,8 @@ const sub_int = (
 """
     formula(atoms::AbstractVector{<:Atom})
 
-Returns the molecular formula of the current selection. 
+Returns the molecular formula of the current selection. The output is an indexable
+"Formula" structure, where each element is a tuple with the element name and the number of atoms.
 
 ## Example
 
@@ -34,13 +35,17 @@ julia> pdb  = read_pdb(PDBTools.TESTPDB, "residue 1"); # testing PDB file
 julia> resname(pdb[1])
 "ALA"
 
-julia> formula(pdb)
+julia> f = formula(pdb)
 H₇C₃N₁O₁
+
+julia> f[1]
+("H", 7)
+
 ```
 
 """
-function formula(atoms::AbstractVector{<:Atom})
-    f = Formula(Tuple{Atom,Int}[])
+function formula(atoms::AbstractVector{<:AtomType}) where {AtomType<:Atom}
+    f = Formula(Tuple{AtomType,Int}[])
     for at in atoms
         i = findfirst(el -> pdb_element(first(el)) == element(at), f.formula)
         if isnothing(i)
@@ -71,7 +76,7 @@ Returns the stoichiometry of atom selection in a `Formula` structure.
 
 ### Example
 
-```julia-repl
+```jldoctest
 julia> using PDBTools
 
 julia> pdb  = read_pdb(PDBTools.TESTPDB, "water"); # testing PDB file
@@ -89,3 +94,20 @@ function stoichiometry(atoms::AbstractVector{<:Atom})
     end
     f
 end
+
+@testitem "Formula" begin
+    using PDBTools
+    pdb  = read_pdb(PDBTools.TESTPDB, "resname GLY")
+    f = formula(pdb)
+    buff = IOBuffer()
+    show(buff, f)
+    @test String(take!(buff)) == "H₃₆C₂₄N₁₂O₁₂"
+    @test f[1] == ("H", 36)
+    @test f[4] == ("O", 12)
+    s = stoichiometry(pdb)
+    buff = IOBuffer()
+    show(buff, s)
+    @test String(take!(buff)) == "H₃C₂N₁O₁"
+    @test s[1] == ("H", 3)
+    @test s[4] == ("O", 1)
+end

src/getseq.jl

@@ -5,23 +5,25 @@ Returns the sequence of aminoacids from the vector of atoms or file name. Select
 
 ### Example
 
-```julia-repl
-julia> protein = wget("1LBD");
+```jldoctest
+julia> using PDBTools
+
+julia> protein = read_pdb(PDBTools.TESTPDB);
 
 julia> getseq(protein,"residue < 3")
 2-element Vector{String}:
- "S"
  "A"
+ "C"
 
 julia> getseq(protein,"residue < 3", code=2)
 2-element Vector{String}:
- "SER"
  "ALA"
+ "CYS"
 
 julia> getseq(protein,"residue < 3",code=3)
 2-element Vector{String}:
- "Serine"
  "Alanine"
+ "Cysteine"
 
 ```
 
@@ -64,3 +66,26 @@ function getseq(file::String, selection::String; code::Int=1)
 end
 
 getseq(file::String; only=all, code::Int=1) = getseq(read_pdb(file), only=only, code=code)
+
+@testitem "getseq" begin
+    using PDBTools
+    ats = read_pdb(PDBTools.TESTPDB)
+    s = getseq(ats, "residue < 3")
+    @test s == ["A", "C"]
+    s = getseq(ats, "residue < 3"; code=2)
+    @test s == ["ALA", "CYS"]
+    s = getseq(ats, "residue < 3"; code=3)
+    @test s == ["Alanine", "Cysteine"]
+    wat = select(ats, "water")
+    s = getseq(wat, "resnum < 3")
+    @test s == ["T", "T", "T", "T"] 
+    s = getseq(wat, "resnum < 3"; code=2)
+    @test s == ["TIP3", "TIP3", "TIP3", "TIP3"] 
+    s = getseq(wat, "resnum < 3"; code=3)    
+    @test s == ["TIP3", "TIP3", "TIP3", "TIP3"] 
+    s = getseq(PDBTools.TESTPDB, "residue < 3")
+    s = getseq(ats, "residue < 3")
+    @test s == ["A", "C"]
+    s = getseq(PDBTools.TESTPDB; only = at -> resnum(at) == 1)
+    @test s == ["A", "C", "S", "T", "T", "T"]
+end

src/parsers.jl

@@ -19,7 +19,7 @@ function _parse(
     x = _tryparse(T, s)
     !isnothing(x) && return x
     if isnothing(alt)
-        error("Could not read $T from string: \"$s\"")
+        throw(ArgumentError("Could not read $T from string: \"$s\""))
     else
         return alt
     end
@@ -105,16 +105,31 @@ function setfield_recursive!(atom::AtomType, field_values::FIELDS, inds_and_name
     setfield_recursive!(atom, field_values, Base.tail(inds_and_names))
 end
 
-# Alternative implementation using generated functions (same peformance as far as tested)
-# https://discourse.julialang.org/t/unroll-setfield/122545/22?u=lmiq
-@generated function setfield_generated!(atom, field_values::FIELDS, inds_and_names::TUPTUP, ::Val{N}) where {FIELDS,TUPTUP,N}
-    quote
-        @inline
-        Base.@nexprs $N i -> begin
-            ifield, valfield = inds_and_names[i]
-            field = unwrap(valfield)
-            T = typeof(getfield(atom, field))
-            setfield!(atom, field, _parse(T, field_values[ifield]; alt=_alt(T)))
-        end
-    end
+## Alternative implementation using generated functions (same peformance as far as tested)
+## https://discourse.julialang.org/t/unroll-setfield/122545/22?u=lmiq
+#@generated function setfield_generated!(atom, field_values::FIELDS, inds_and_names::TUPTUP, ::Val{N}) where {FIELDS,TUPTUP,N}
+#    quote
+#        @inline
+#        Base.@nexprs $N i -> begin
+#            ifield, valfield = inds_and_names[i]
+#            field = unwrap(valfield)
+#            T = typeof(getfield(atom, field))
+#            setfield!(atom, field, _parse(T, field_values[ifield]; alt=_alt(T)))
+#        end
+#    end
+#end
+
+@testitem "_parse" begin
+    using PDBTools: _parse, _parse_charge
+    @test _parse(Int, "  1  ") == 1
+    @test _parse(Int, "  A  ") == 10
+    @test _parse(Float32, "  1.0  ") == 1.0f0
+    @test_throws ArgumentError _parse(Int, "  ???  ") 
+    @test_throws ArgumentError _parse(Float32, "  A  ") 
+    @test _parse(String, "  A  ") == "A"
+    @test _parse(String, "") === nothing
+    @test _parse_charge("1+") == "1"
+    @test _parse_charge("+1") == "1"
+    @test _parse_charge("1-") == "-1"
+    @test _parse_charge("-1") == "-1"
 end