support selection string input

src/miscelaneous_functions/most_representative_structure.jl

@@ -25,25 +25,39 @@ The process is repeated until the structure most similar to the average is the s
 # Arguments
 
 - `simulation::Simulation`: Simulation object.
-- `atoms::Union{Nothing, AbstractVector{<:PDBTools.Atom}, AbstractVector{Int}}`: Atoms to consider in the calculation.
-
-If `atoms` is `nothing`, the function will consider all alpha-carbons in proteins (`"protein and name CA"`).
+- `atoms`: Atoms to consider in the calculation:
+   - `atoms` is `nothing`: the function will consider all alpha-carbons in proteins (`"protein and name CA"`).
+   - `atoms` is an `AbstractVector{<:PDBTools.Atom}`: the function will consider the atoms in the vector.
+   - `atoms` is an `AbstractVector{<:Int}`: the function will consider the atoms with the indices in the vector.
+   - `atoms` is a `String`: the function will consider the atoms selected by the string.
 
 # Returns
 
-- `imin::Int`: Index of the most representative structure.
-- `rmsdmin::Float64`: RMSD of the most representative structure with respect to the average structure.
+- Tuple `(Int, Float64)`, with:
+  - Index of the most representative structure.
+  - RMSD of the most representative structure with respect to the average structure.
 
 # Example
 
 ```julia-repl
-julia> using MolSimToolkit, MolSimToolkit.Testing
+julia> using MolSimToolkit, MolSimToolkit.Testing, PDBTools
 
 julia> simulation = Simulation(Testing.namd_pdb, Testing.namd_traj);
 
+julia> most_representative_structure(simulation) # atoms == nothing (all alpha-carbons in proteins)
+(4, 1.1681526249035976)
+
+julia> most_representative_structure(simulation; atoms = "protein and name CA") # atoms is a String
+(4, 1.1681526249035976)
+
 julia> calphas = select(atoms(simulation), "name CA");
 
-julia> most_representative_structure(simulation; atoms = calphas)
+julia> most_representative_structure(simulation; atoms = calphas) # atoms is an AbstractVector{PDBTools.Atom}
+(4, 1.1681526249035976)
+
+julia> ica = PDBTools.index.(calphas)
+
+julia> most_representative_structure(simulation; atoms = ica) # atoms is an vector of indices
 (4, 1.1681526249035976)
 ```
 
@@ -58,8 +72,12 @@ function most_representative_structure(simulation::Simulation; atoms = nothing)
             indices = PDBTools.index.(atoms)
         elseif atoms isa AbstractVector{Int}
             indices = atoms
+        elseif atoms isa String
+            indices = PDBTools.index.(
+                PDBTools.select(MolSimToolkit.atoms(simulation), atoms)
+            )
         else
-            throw(ArgumentError("atoms must be an AbstractVector{<:PDBTools.Atom} or an AbstractVector{<:Int}, with atom indices."))
+            throw(ArgumentError("atoms must be a selection string, an array of PDBTools.Atom's or vector of integers with atom indices."))
         end
     end
     if length(indices) == 0
@@ -97,12 +115,18 @@ end
     using MolSimToolkit, MolSimToolkit.Testing, PDBTools
     simulation = Simulation(Testing.namd_pdb, Testing.namd_traj)
     calphas = select(atoms(simulation), "name CA")
+    imin, rmsdmin = most_representative_structure(simulation)
+    @test imin == 4
+    @test rmsdmin ≈ 1.1681514813293536
     imin, rmsdmin = most_representative_structure(simulation; atoms = calphas)
     @test imin == 4
     @test rmsdmin ≈ 1.1681514813293536
     imin, rmsdmin = most_representative_structure(simulation; atoms = PDBTools.index.(calphas))
     @test imin == 4
     @test rmsdmin ≈ 1.1681514813293536
+    imin, rmsdmin = most_representative_structure(simulation; atoms = "protein and name CA")
+    @test imin == 4
+    @test rmsdmin ≈ 1.1681514813293536
     @test_throws ArgumentError most_representative_structure(simulation; atoms = 1)
     @test_throws ArgumentError most_representative_structure(simulation; atoms = Int[])
 end