formatted code

docs/liveserver.jl

@@ -1,10 +1,9 @@
 
 import Pkg
-Pkg.activate("LiveServer"; shared=true)
+Pkg.activate("LiveServer"; shared = true)
 Pkg.add("LiveServer")
 
 import LiveServer
 
 Pkg.activate(@__DIR__)
 LiveServer.servedocs()
-

docs/make.jl

@@ -3,10 +3,10 @@ Pkg.add("Documenter")
 using ComplexMixtures
 using Documenter
 using ComplexMixtures
-push!(LOAD_PATH,"../src/")
+push!(LOAD_PATH, "../src/")
 makedocs(
-    modules=[ComplexMixtures],
-    sitename="ComplexMixtures.jl",
+    modules = [ComplexMixtures],
+    sitename = "ComplexMixtures.jl",
     pages = [
         "Introduction" => "index.md",
         "Installation" => "installation.md",
@@ -24,12 +24,12 @@ makedocs(
         "Tools" => "tools.md",
         "From Python" => "python.md",
         "Help entries" => "help.md",
-        "References" => "references.md"
-    ]
+        "References" => "references.md",
+    ],
 )
 deploydocs(
     repo = "github.com/m3g/ComplexMixtures.jl.git",
     target = "build",
     branch = "gh-pages",
-    versions = ["stable" => "v^", "v#.#" ],
+    versions = ["stable" => "v^", "v#.#"],
 )

src/Selection.jl

@@ -43,7 +43,7 @@ end
 @testitem "Selection Vector{PDBTools.Atom}" begin
     import PDBTools
     pdbfile = ComplexMixtures.Testing.pdbfile
-    atoms = PDBTools.readPDB(pdbfile, "protein and residue 2") 
+    atoms = PDBTools.readPDB(pdbfile, "protein and residue 2")
     s = Selection(atoms, nmols = 1, natomspermol = 11)
     @test s.imol == ones(Int, 11)
     @test s.index == [12 + i for i = 1:11]

src/legacy.jl

@@ -12,12 +12,11 @@ const contrib = contributions
     using ComplexMixtures, PDBTools
     import ComplexMixtures.Testing: test_dir
 
-    pdb = readPDB("$test_dir/data/NAMD/structure.pdb") 
+    pdb = readPDB("$test_dir/data/NAMD/structure.pdb")
     R = load("$test_dir/data/NAMD/protein_tmao.json")
 
     @test R.sum_md_count == R.coordination_number
     @test R.sum_md_count_random == R.coordination_number_random
 
     @test ComplexMixtures.contrib == ComplexMixtures.contributions
 end
-

src/mddf.jl

@@ -14,7 +14,7 @@
 end
 function Buffer(traj::Trajectory, R::Result)
     return Buffer(
-        solute_read = similar(traj.x_solute), 
+        solute_read = similar(traj.x_solute),
         solvent_read = similar(traj.x_solvent),
         ref_solutes = zeros(Int, R.options.n_random_samples),
         list = fill(zero(MinimumDistance), R.solvent.nmols),
@@ -33,7 +33,7 @@ end
     traj = Trajectory("$(Testing.data_dir)/NAMD/trajectory.dcd", protein, tmao)
     R = Result(traj, options)
     b0 = ComplexMixtures.Buffer(
-        solute_read = similar(traj.x_solute), 
+        solute_read = similar(traj.x_solute),
         solvent_read = similar(traj.x_solvent),
         ref_solutes = zeros(Int, R.options.n_random_samples),
         list = fill(zero(ComplexMixtures.MinimumDistance), R.solvent.nmols),
@@ -70,13 +70,13 @@ function randomize_solvent!(
 )
     for isolvent = 1:R.solvent.nmols
         # Choose randomly one molecule from the bulk, if there are bulk molecules
-        if n_solvent_in_bulk > 0 
+        if n_solvent_in_bulk > 0
             jmol = buff.indexes_in_bulk[rand(RNG, 1:n_solvent_in_bulk)]
         else
             jmol = rand(RNG, 1:R.solvent.nmols)
         end
         # Pick coordinates of the molecule to be randomly moved
-        y_new = viewmol(isolvent, system.ypositions, R.solvent) 
+        y_new = viewmol(isolvent, system.ypositions, R.solvent)
         # Copy the coordinates of the random solvent molecule chosen
         y_new .= viewmol(jmol, buff.solvent_read, R.solvent)
         # Randomize rotations and translation for this molecule 
@@ -143,19 +143,20 @@ function mddf(trajectory::Trajectory, options::Options = Options())
     end
 
     # Print some information about this run
-    if !options.silent 
+    if !options.silent
         title(R, trajectory.solute, trajectory.solvent, nchunks)
         progress = Progress(R.nframes_read, 1)
     end
 
     # Loop over the trajectory
     read_lock = ReentrantLock()
-    Threads.@threads for (frame_range, ichunk) in ChunkSplitters.chunks(1:R.nframes_read, nchunks)
+    Threads.@threads for (frame_range, ichunk) in
+                         ChunkSplitters.chunks(1:R.nframes_read, nchunks)
         # Reset the number of frames read by each chunk
         R_chunk[ichunk].nframes_read = 0
         for _ in frame_range
             # Read frame coordinates
-            lock(read_lock) do 
+            lock(read_lock) do
                 # skip frames if stride > 1
                 while (iframe + 1) % options.stride != 0
                     nextframe!(trajectory)
@@ -171,8 +172,9 @@ function mddf(trajectory::Trajectory, options::Options = Options())
                 @. buff[ichunk].solvent_read = trajectory.x_solvent
                 update_unitcell!(system[ichunk], getsides(trajectory, iframe))
                 # Run GC if memory is getting full: this are issues with Chemfiles reading scheme
-                if options.GC && (Sys.free_memory() / Sys.total_memory() < options.GC_threshold)
-                    GC.gc() 
+                if options.GC &&
+                   (Sys.free_memory() / Sys.total_memory() < options.GC_threshold)
+                    GC.gc()
                 end
                 options.silent || next!(progress)
             end # release reading lock
@@ -286,7 +288,8 @@ end
     atoms = readPDB("$(Testing.data_dir)/toy/cross.pdb")
     protein = Selection(select(atoms, "protein and model 1"), nmols = 1)
     water = Selection(select(atoms, "resname WAT and model 1"), natomspermol = 3)
-    traj = Trajectory("$(Testing.data_dir)/toy/cross.pdb", protein, water, format = "PDBTraj")
+    traj =
+        Trajectory("$(Testing.data_dir)/toy/cross.pdb", protein, water, format = "PDBTraj")
 
     for lastframe in [1, 2]
         options = Options(
@@ -309,7 +312,8 @@ end
     # Self correlation
     atoms = readPDB("$(Testing.data_dir)/toy/self_monoatomic.pdb")
     atom = Selection(select(atoms, "resname WAT and model 1"), natomspermol = 1)
-    traj = Trajectory("$(Testing.data_dir)/toy/self_monoatomic.pdb", atom, format="PDBTraj")
+    traj =
+        Trajectory("$(Testing.data_dir)/toy/self_monoatomic.pdb", atom, format = "PDBTraj")
 
     # without atoms in the bulk
     options = Options(
@@ -377,15 +381,15 @@ end
     R = mddf(traj, options)
     # Deterministic
     @test R.volume.total ≈ 603078.4438609097
-    @test sum(R.md_count) ≈ 25.250000000000007 
+    @test sum(R.md_count) ≈ 25.250000000000007
     @test sum(R.rdf_count) ≈ 19.550000000000004
     @test R.density.solute ≈ 1.6581590839128614e-6
     @test R.density.solvent ≈ 0.00030012679418822794
     # Dependent on the random number seed
     @test R.volume.domain ≈ 75368.14585709268 rtol = 0.1
     @test R.volume.bulk ≈ 527710.298003817 rtol = 0.1
     @test R.density.solvent_bulk ≈ 0.000305944380109164 rtol = 0.1
-    @test sum(R.mddf) ≈ 582.8371304452286 rtol = 0.1 
+    @test sum(R.mddf) ≈ 582.8371304452286 rtol = 0.1
     @test sum(R.rdf) ≈ 491.4450029864516 rtol = 0.1
     @test R.kb[end] ≈ -6019.863896959123 rtol = 0.5
     @test R.kb_rdf[end] ≈ -6905.975623304156 rtol = 0.5
@@ -401,10 +405,10 @@ end
     @test R.density.solvent ≈ 0.00030012679418822794
     # Dependent on the random number seed
     @test R.volume.domain ≈ 6801.384672431371 rtol = 0.1
-    @test R.volume.bulk ≈ 596277.0591884783 rtol = 0.1 
+    @test R.volume.bulk ≈ 596277.0591884783 rtol = 0.1
     @test R.density.solvent_bulk ≈ 0.00029875568324470034 rtol = 0.1
     @test sum(R.mddf) ≈ 275.5648734200309 rtol = 0.1
-    @test sum(R.rdf) ≈ 168.77009506954508 rtol = 0.1 
+    @test sum(R.rdf) ≈ 168.77009506954508 rtol = 0.1
     @test R.kb[end] ≈ -386.8513153147712 rtol = 0.5
     @test R.kb_rdf[end] ≈ -326.32083509753284 rtol = 0.5
 end

src/minimum_distances.jl

@@ -92,7 +92,15 @@ Function that updates a list of minimum distances given the indexes of the atoms
 for autocorrelations (such that the identity of `isolute` is needed)
 
 """
-function update_list!(i, j, d2, jref_atom, j_natoms_per_molecule, isolute, list::Vector{MinimumDistance})
+function update_list!(
+    i,
+    j,
+    d2,
+    jref_atom,
+    j_natoms_per_molecule,
+    isolute,
+    list::Vector{MinimumDistance},
+)
     jmol = mol_index(j, j_natoms_per_molecule)
     if jmol != isolute
         d = sqrt(d2)
@@ -150,7 +158,8 @@ function minimum_distances!(
     jnatomspermol = R.solvent.natomspermol
     if R.autocorrelation
         map_pairwise!(
-            (x, y, i, j, d2, list) -> update_list!(i, j, d2, jref_atom, jnatomspermol, isolute, list),
+            (x, y, i, j, d2, list) ->
+                update_list!(i, j, d2, jref_atom, jnatomspermol, isolute, list),
             system;
             update_lists = update_lists,
         )
@@ -183,7 +192,10 @@ function setup_PeriodicSystem(trajectory::Trajectory, options::Options)
     closetraj!(trajectory)
     system = PeriodicSystem(
         xpositions = zeros(SVector{3,Float64}, trajectory.solute.natomspermol),
-        ypositions = zeros(SVector{3,Float64}, trajectory.solvent.nmols * trajectory.solvent.natomspermol),
+        ypositions = zeros(
+            SVector{3,Float64},
+            trajectory.solvent.nmols * trajectory.solvent.natomspermol,
+        ),
         unitcell = unitcell,
         cutoff = options.usecutoff ? options.cutoff : options.dbulk,
         output = fill(zero(MinimumDistance), trajectory.solvent.nmols),

src/precompile.jl

@@ -2,14 +2,17 @@
     # Putting some things in `@setup_workload` instead of `@compile_workload` can reduce the size of the
     # precompile file and potentially make loading faster.
     dir = "$(Testing.data_dir)/NAMD"
-    atoms = readPDB("$dir/structure.pdb","resname TMAO")
+    atoms = readPDB("$dir/structure.pdb", "resname TMAO")
     tmao1 = Selection(select(atoms, "resname TMAO and resnum 1"), natomspermol = 14)
     @compile_workload begin
-        options = Options(lastframe=-1, silent = true)
-        tmao2 = Selection(select(atoms, "resname TMAO and resnum 2 or resname TMAO and resnum 3"), natomspermol = 14)
+        options = Options(lastframe = -1, silent = true)
+        tmao2 = Selection(
+            select(atoms, "resname TMAO and resnum 2 or resname TMAO and resnum 3"),
+            natomspermol = 14,
+        )
         traj = Trajectory("$dir/trajectory.dcd", tmao1, tmao2)
         R = mddf(traj, options)
         traj = Trajectory("$dir/trajectory.dcd", tmao2)
         R = mddf(traj, options)
     end
-end
+end

src/rigid_body.jl

@@ -124,7 +124,9 @@ function random_move!(
 
     # Generate random coordinates for the center of mass
     cmin, cmax = PeriodicSystems.get_computing_box(system)
-    newcm = SVector{3}(scale * (cmin[i] + rand(RNG, Float64) * (cmax[i] - cmin[i])) for i in 1:3)
+    newcm = SVector{3}(
+        scale * (cmin[i] + rand(RNG, Float64) * (cmax[i] - cmin[i])) for i = 1:3
+    )
 
     # Generate random rotation angles 
     beta = 2π * rand(RNG, Float64)
@@ -164,7 +166,12 @@ end
     RNG = ComplexMixtures.init_random(Options())
     # Orthorhombic cell
     x = [-1.0 .+ 2 * rand(SVector{3,Float64}) for _ = 1:5]
-    system = PeriodicSystem(positions=x, cutoff=0.1, unitcell=SVector(10.0, 10.0, 10.0), output=0.0)
+    system = PeriodicSystem(
+        positions = x,
+        cutoff = 0.1,
+        unitcell = SVector(10.0, 10.0, 10.0),
+        output = 0.0,
+    )
     @test check_internal_distances(x, ComplexMixtures.random_move!(copy(x), 1, system, RNG))
     system.xpositions .= [-9.0 .+ 2 * rand(SVector{3,Float64}) for _ = 1:5]
     @test check_internal_distances(x, ComplexMixtures.random_move!(copy(x), 1, system, RNG))
@@ -173,7 +180,12 @@ end
 
     # Triclinic cell
     x = [-1.0 .+ 2 * rand(SVector{3,Float64}) for _ = 1:5]
-    system = PeriodicSystem(positions=x, cutoff=0.1, unitcell=@SMatrix[10.0 5.0 0.0; 0.0 10.0 0.0; 0.0 0.0 10.0], output=0.0)
+    system = PeriodicSystem(
+        positions = x,
+        cutoff = 0.1,
+        unitcell = @SMatrix[10.0 5.0 0.0; 0.0 10.0 0.0; 0.0 0.0 10.0],
+        output = 0.0,
+    )
     @test check_internal_distances(x, ComplexMixtures.random_move!(copy(x), 1, system, RNG))
     system.xpositions .= [-9.0 .+ 2 * rand(SVector{3,Float64}) for _ = 1:5]
     @test check_internal_distances(x, ComplexMixtures.random_move!(copy(x), 1, system, RNG))

src/tools/contributions.jl

@@ -17,10 +17,10 @@ with indexes `[901, 902, 903]`.
 
 """
 function contributions(
-    s::Selection, 
-    atom_contributions::Matrix{Float64}, 
-    indexes::Vector{Int}; 
-    first_atom_is_ref = false
+    s::Selection,
+    atom_contributions::Matrix{Float64},
+    indexes::Vector{Int};
+    first_atom_is_ref = false,
 )
     nbins = size(atom_contributions, 1)
     c = zeros(nbins)
@@ -44,7 +44,9 @@ function contributions(
     else
         for it in indexes
             if it > s.natomspermol
-                error("The index list contains atoms with indexes greater than the number of atoms of one molecule.")
+                error(
+                    "The index list contains atoms with indexes greater than the number of atoms of one molecule.",
+                )
             end
             c += @view(atom_contributions[:, it])
         end
@@ -56,9 +58,9 @@ end
 # If a list of atom names is provided
 #
 function contributions(
-    s::Selection, 
-    atom_contributions::Matrix{Float64}, 
-    names::Vector{String}
+    s::Selection,
+    atom_contributions::Matrix{Float64},
+    names::Vector{String},
 )
     indexes = Vector{Int}(undef, 0)
     for name in names
@@ -119,7 +121,10 @@ end
     atoms = readPDB("$dir/trajectory.pdb", "model 1")
 
     solute = Selection(select(atoms, "resname TMAO and resnum 1"), nmols = 1)
-    solvent = Selection(select(atoms, "resname TMAO and resnum 2 or resname TMAO and resnum 3"), nmols = 2)
+    solvent = Selection(
+        select(atoms, "resname TMAO and resnum 2 or resname TMAO and resnum 3"),
+        nmols = 2,
+    )
 
     traj = Trajectory("$dir/trajectory.pdb", solute, solvent, format = "PDBTraj")
     results = mddf(traj)

src/tools/coordination_number.jl

@@ -57,14 +57,22 @@ residue50_coordination[findlast(<(5), R.d)]
 ```
 
 """
-function coordination_number(s::Selection, atom_contributions::Matrix{Float64}, R::Result, group)
+function coordination_number(
+    s::Selection,
+    atom_contributions::Matrix{Float64},
+    R::Result,
+    group,
+)
     # Extract the group contributions to the MDDF
     group_contributions = contributions(s, atom_contributions, group)
     # Compute the coordination number
     return coordination_number(R, group_contributions)
 end
 function coordination_number(R::Result, group_contributions::Vector{Float64})
-    cn = cumsum(group_contributions[i] * R.md_count_random[i] for i in eachindex(group_contributions)) 
+    cn = cumsum(
+        group_contributions[i] * R.md_count_random[i] for
+        i in eachindex(group_contributions)
+    )
     return cn
 end
 
@@ -73,16 +81,16 @@ end
     using ComplexMixtures, PDBTools
     import ComplexMixtures.Testing: test_dir
 
-    pdb = readPDB("$test_dir/data/NAMD/structure.pdb") 
+    pdb = readPDB("$test_dir/data/NAMD/structure.pdb")
     R = load("$test_dir/data/NAMD/protein_tmao.json")
-    solute = Selection(PDBTools.select(pdb, "protein"), nmols=1)
+    solute = Selection(PDBTools.select(pdb, "protein"), nmols = 1)
     cn = coordination_number(solute, R.solute_atom, R, PDBTools.select(pdb, "residue 50"))
-    @test cn[findlast(<(5), R.d)] ≈ 0.24999999999999997 atol=1e-10
+    @test cn[findlast(<(5), R.d)] ≈ 0.24999999999999997 atol = 1e-10
 
     pdb = readPDB("$test_dir/data/NAMD/Protein_in_Glycerol/system.pdb")
-    R = load("$test_dir/data/NAMD/Protein_in_Glycerol/protein_water.json") 
+    R = load("$test_dir/data/NAMD/Protein_in_Glycerol/protein_water.json")
     group = PDBTools.select(pdb, "protein")
-    solute = Selection(group, nmols=1)
+    solute = Selection(group, nmols = 1)
     cn = coordination_number(solute, R.solute_atom, R, group)
     @test maximum(R.coordination_number .- cn) < 1e-10
-end
+end