BioStructures update

JuliaMolSim · Jun 21, 2024 · d185519 · d185519
1 parent 63bdd51
commit d185519
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Showing 5 changed files with 5 additions and 4 deletions.
diff --git a/Project.toml b/Project.toml
@@ -51,7 +51,7 @@ MollyPythonCallExt = "PythonCall"
 Atomix = "0.1"
 AtomsBase = "0.3.4"
 AtomsCalculators = "0.1.1"
-BioStructures = "1, 2, 3"
+BioStructures = "4"
 CUDA = "4.2, 5"
 CellListMap = "0.8.11, 0.9"
 ChainRules = "1.44"

diff --git a/src/interactions/harmonic_angle.jl b/src/interactions/harmonic_angle.jl
@@ -6,6 +6,7 @@ export HarmonicAngle
 A harmonic bond angle between three atoms.
 
 `θ0` is in radians.
+The second atom is the middle atom.
 The potential energy is defined as
 ```math
 V(\theta) = \frac{1}{2} k (\theta - \theta_0)^2

diff --git a/test/basic.jl b/test/basic.jl
@@ -330,7 +330,7 @@ end
 
 @testset "Analysis" begin
     pdb_path = joinpath(data_dir, "1ssu.pdb")
-    struc = read(pdb_path, BioStructures.PDB)
+    struc = read(pdb_path, BioStructures.PDBFormat)
     cm_1 = BioStructures.coordarray(struc[1], BioStructures.calphaselector)
     cm_2 = BioStructures.coordarray(struc[2], BioStructures.calphaselector)
     coords_1 = SVector{3, Float64}.(eachcol(cm_1)) / 10 * u"nm"

diff --git a/test/protein.jl b/test/protein.jl
@@ -33,7 +33,7 @@
     s.velocities = [random_velocity(mass(a), temp) .* 0.01 for a in s.atoms]
     @time simulate!(s, simulator, n_steps; n_threads=1)
 
-    traj = read(temp_fp_pdb, BioStructures.PDB)
+    traj = read(temp_fp_pdb, BioStructures.PDBFormat)
     rm(temp_fp_pdb)
     @test BioStructures.countmodels(traj) == 11
     @test BioStructures.countatoms(first(traj)) == 5191

diff --git a/test/simulation.jl b/test/simulation.jl
@@ -151,7 +151,7 @@ end
         @test unit(first(values(s.loggers.potkin_correlation))) == NoUnits
         @test unit(first(values(s.loggers.velocity_autocorrelation; normalize=false))) == u"nm^2 * ps^-2"
 
-        traj = read(temp_fp_pdb, BioStructures.PDB)
+        traj = read(temp_fp_pdb, BioStructures.PDBFormat)
         rm(temp_fp_pdb)
         @test BioStructures.countmodels(traj) == 201
         @test BioStructures.countatoms(first(traj)) == 100