small code style change

m3g · May 14, 2024 · 31066aa · 31066aa
1 parent e2fd8a7
commit 31066aa
Show file tree

Hide file tree

Showing 3 changed files with 8 additions and 11 deletions.
diff --git a/src/mddf.jl b/src/mddf.jl
@@ -189,7 +189,7 @@ function mddf(
     Threads.@threads for frame_range in ChunkSplitters.chunks(to_read_frames; n=nchunks)
         # Local data structures for this chunk
         R_chunk = Result(trajectory, options; trajectory_data, frame_weights)
-        system_chunk = setup_ParticleSystem(trajectory, trajectory_data.unitcell, options)
+        system_chunk = ParticleSystem(trajectory, trajectory_data.unitcell, options)
         buff_chunk = Buffer(trajectory, R)
         # Reset the number of frames read by each chunk
         R_chunk.files[1].nframes_read = 0

diff --git a/src/minimum_distances.jl b/src/minimum_distances.jl
@@ -157,20 +157,17 @@ function minimum_distances!(
 end
 
 #=
-    setup_ParticleSystem(trajectory::Trajectory, options::Options)
+    ParticleSystem(trajectory::Trajectory, options::Options)
 
 Setup the periodic system from CellListMap, to compute minimimum distances. The system
 will be setup such that `xpositions` corresponds to one molecule of the solute, and 
 `ypositions` contains all coordinates of all atoms of the solvent. 
 
 =#
-function setup_ParticleSystem(trajectory::Trajectory, unitcell, options::Options)
+function CellListMap.ParticleSystem(trajectory::Trajectory, unitcell, options::Options)
     system = ParticleSystem(
         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),
@@ -182,7 +179,7 @@ function setup_ParticleSystem(trajectory::Trajectory, unitcell, options::Options
     return system
 end
 
-@testitem "setup_ParticleSystem" begin
+@testitem "build ParticleSystem" begin
     using ComplexMixtures
     using PDBTools
     using ComplexMixtures.Testing
@@ -197,7 +194,7 @@ end
     protein = AtomSelection(select(atoms, "protein"), nmols = 1)
     traj = Trajectory("$(Testing.data_dir)/NAMD/trajectory.dcd", protein, tmao)
     tmeta = ComplexMixtures.TrajectoryMetaData(traj, options) 
-    system = ComplexMixtures.setup_ParticleSystem(traj, tmeta.unitcell, options)
+    system = ComplexMixtures.ParticleSystem(traj, tmeta.unitcell, options)
     @test system.cutoff == 10.0
     @test system.list == fill(zero(ComplexMixtures.MinimumDistance), 181)
     @test system.output == fill(zero(ComplexMixtures.MinimumDistance), 181)
@@ -213,7 +210,7 @@ end
     # Auto-correlation
     traj = Trajectory("$(Testing.data_dir)/NAMD/trajectory.dcd", tmao)
     tmeta = ComplexMixtures.TrajectoryMetaData(traj, options)
-    system = ComplexMixtures.setup_ParticleSystem(traj, tmeta.unitcell, options)
+    system = ComplexMixtures.ParticleSystem(traj, tmeta.unitcell, options)
     @test system.cutoff == 10.0
     @test system.list == fill(zero(ComplexMixtures.MinimumDistance), 181) # one molecule less
     @test system.output == fill(zero(ComplexMixtures.MinimumDistance), 181)

diff --git a/test/allocations.jl b/test/allocations.jl
@@ -55,7 +55,7 @@
     @test t_RNG.allocs < 5
 
     tmeta = ComplexMixtures.TrajectoryMetaData(traj, options)
-    system = ComplexMixtures.setup_ParticleSystem(traj, tmeta.unitcell, options)
+    system = ComplexMixtures.ParticleSystem(traj, tmeta.unitcell, options)
     buff = ComplexMixtures.Buffer(traj, R)
     @. buff.solute_read = traj.x_solute
     @. buff.solvent_read = traj.x_solvent