overload PDBTools.center_of_mass to avoid conflict

m3g · Apr 9, 2024 · 178fab9 · 178fab9 · lmiq · Apr 9, 2024
1 parent 94eff54
commit 178fab9
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Showing 4 changed files with 9 additions and 13 deletions.
diff --git a/Project.toml b/Project.toml
@@ -41,7 +41,7 @@ EasyFit = "0.6.6"
 LaTeXStrings = "1.3"
 LinearAlgebra = "1.9"
 OffsetArrays = "1.13"
-PDBTools = "1.2"
+PDBTools = "1.5.1"
 Plots = "1.39"
 ProgressMeter = "1.10"
 Reexport = "1.2.2"

diff --git a/src/MolSimToolkit.jl b/src/MolSimToolkit.jl
@@ -17,6 +17,7 @@ export distances
 export align, align!, rmsd, rmsd_matrix
 export intermittent_correlation
 export bulk_coordination
+export center_of_mass
 
 # Testing module
 include("./Testing.jl")

diff --git a/src/miscelaneous_functions/center_of_mass.jl b/src/miscelaneous_functions/center_of_mass.jl
@@ -1,5 +1,3 @@
-export center_of_mass
-
 """
     center_of_mass(
         indices::AbstractVector{Int};
@@ -36,7 +34,7 @@ julia> cm = center_of_mass(protein_indices, simulation, coor)
 ```
 
 """
-function center_of_mass(
+function PDBTools.center_of_mass(
     indices::AbstractVector{Int},
     simulation::Simulation,
     p::FramePositions;
@@ -66,10 +64,3 @@ end
           [-3.7290442807974906, -1.5339226637687564, 1.960640754560446]
 end
 
-center_of_mass(x::AbstractVector{<:AbstractVector}, ::Nothing) = sum(x) / length(x)
-
-center_of_mass(x::AbstractVector{<:AbstractVector}, mass::AbstractVector) =
-    sum(x[i] * mass[i] for i in eachindex(x, mass)) / sum(mass)
-
-center_of_mass(atoms::AbstractVector{<:PDBTools.Atom}) =
-    sum(PDBTools.coor(atom) * atomic_mass(atom) for atom in atoms) / sum(atomic_mass, atoms)
diff --git a/src/procrustes.jl b/src/procrustes.jl
@@ -1,6 +1,10 @@
 using LinearAlgebra: eigvecs
 using StaticArrays: SVector, MMatrix, SMatrix
 
+_center_of_mass(x::AbstractVector{<:AbstractVector}, ::Nothing) = sum(x) / length(x)
+_center_of_mass(x::AbstractVector{<:AbstractVector}, mass::AbstractVector) =
+    sum(x[i] * mass[i] for i in eachindex(x, mass)) / sum(mass)
+
 """
     align(x, y; mass = nothing)
     align!(x, y; mass = nothing)
@@ -40,8 +44,8 @@ function align!(
     length(x) == length(y) || throw(DimensionMismatch("x and y must have the same length"))
     (length(x[1]) != 3 || length(x[2]) != 3) && throw(DimensionMismatch("x and y must be 3D vectors"))
 
-    cmx = center_of_mass(x, mass)
-    cmy = center_of_mass(y, mass)
+    cmx = _center_of_mass(x, mass)
+    cmy = _center_of_mass(y, mass)
     for i in eachindex(x, y)
         x[i] -= cmx
         y[i] -= cmy