remove unused interface

Author: lmiq

src/MolecularMinimumDistances/AllPairs.jl

@@ -155,9 +155,9 @@ end
     for (iframe, frame) in enumerate(simulation)
         pos = positions(frame)
         local uc = unitcell(current_frame(simulation))
-        sys.xpositions .= @view(pos[popc])
-        sys.ypositions .= @view(pos[protein])
-        sys.unitcell = uc.orthorhombic ? diag(uc.matrix) : uc.matrix
+        sys.system.xpositions .= @view(pos[popc])
+        sys.system.ypositions .= @view(pos[protein])
+        sys.system.unitcell = uc.orthorhombic ? diag(uc.matrix) : uc.matrix
         md = minimum_distances!(sys)
         xmd_min[iframe] = minimum(p -> p.d, md[1])
         ymd_indices[iframe] = minimum(p -> p.i, md[2])

src/MolecularMinimumDistances/CrossPairs.jl

@@ -38,7 +38,7 @@ more general `mol_indices` function, which, for each atomic index, returns the
 corresponding
 molecular index (which is `mol_indices(i) = (i-1)%n + 1` where `n` is the
 number of atoms per molecule if all molecules have the same number of
-atoms and are continously stored in the array of positions). 
+atoms and are continuously stored in the array of positions). 
 
 # Examples
 
@@ -131,9 +131,9 @@ end
     for (iframe, frame) in enumerate(simulation)
         pos = positions(frame)
         local uc = unitcell(frame)
-        sys.xpositions .= @view(pos[popc])
-        sys.ypositions .= @view(pos[protein])
-        sys.unitcell = uc.orthorhombic ? diag(uc.matrix) : uc.matrix
+        sys.system.xpositions .= @view(pos[popc])
+        sys.system.ypositions .= @view(pos[protein])
+        sys.system.unitcell = uc.orthorhombic ? diag(uc.matrix) : uc.matrix
         md = minimum_distances!(sys)
         md_count[iframe] = count(p -> p.within_cutoff, md)
         # Test direct (out-of-place) call
@@ -143,7 +143,7 @@ end
                 ypositions = xsolute,
                 xn_atoms_per_molecule = 134,
                 cutoff = 6.0,
-                unitcell = sys.unitcell
+                unitcell = sys.system.unitcell
             )
             @test all(md_out .≈ md)
         end

src/MolecularMinimumDistances/MolecularMinimumDistances.jl

@@ -203,7 +203,7 @@ julia> init_list(x, i -> (i-1)÷2 + 1)
 
 ```
 
-The above annonymous function `i -> (i-1)÷2 + 1` is equivalent to `i -> mol_indices(i,2)`,
+The above anonymous function `i -> (i-1)÷2 + 1` is equivalent to `i -> mol_indices(i,2)`,
 and can be generalized if the the number of atoms of each molecule is not the same.
 
 =#
@@ -229,7 +229,7 @@ init_list(::Type{T}, n::Integer) where {T} = fill(zero(MinimumDistance{T}), n)
 # Note that we have two types of output variables here: List, and a tuple of List.
 # The List is simply an array of `MinimumDistance{T}`, and we have defined above
 # `copy` and `zero` methods for this type, such that we only need to define 
-# that reseting this variable consists of returing its zero, and set up the reducer.
+# that resetting this variable consists of returning its zero, and set up the reducer.
 # The methods for abstract arrays will take care of the rest.
 #
 # For the Tuple of lists, we need to be more explicit, and define appropriate copy_output,
@@ -261,7 +261,7 @@ end
 Function that computes the minimum distances for an initialized system,
 of `SelfPairs`, `CrossPairs`, or `AllPairs` types. 
 
-The function returs a `Vector{MinimumDistance}` cor `SelfPairs` and `CrossPairs`
+The function returns a `Vector{MinimumDistance}` cor `SelfPairs` and `CrossPairs`
 inputs, and a Tuple of two of such vectors for the `AllPairs` input types.
 
 This function is used as an advanced alternative from preallocated system inputs. Only a few allocations 
@@ -477,24 +477,12 @@ abstract type SystemPairs end
 
 import Base: getproperty, propertynames
 getproperty(sys::SystemPairs, s::Symbol) = getproperty(sys, Val(s))
+getproperty(sys::SystemPairs, ::Val{:minimum_distances}) = sys.system.output
 getproperty(sys::SystemPairs, ::Val{:system}) = getfield(sys, :system)
 getproperty(sys::SystemPairs, ::Val{:mol_indices}) = getfield(sys, :mol_indices)
 getproperty(sys::SystemPairs, ::Val{:xmol_indices}) = getfield(sys, :xmol_indices)
 getproperty(sys::SystemPairs, ::Val{:ymol_indices}) = getfield(sys, :ymol_indices)
-getproperty(sys::SystemPairs, ::Val{:minimum_distances}) = sys.system.output
-getproperty(sys::SystemPairs, ::Val{:xpositions}) = sys.system.xpositions
-getproperty(sys::SystemPairs, ::Val{:ypositions}) = sys.system.ypositions
-getproperty(sys::SystemPairs, ::Val{:cutoff}) = sys.system.cutoff
-getproperty(sys::SystemPairs, ::Val{:unitcell}) = sys.system.unitcell
-getproperty(sys::SystemPairs, ::Val{:parallel}) = sys.system.parallel
-propertynames(sys::SystemPairs, private::Bool) =
-    (:system, :mol_indices, :minimum_distances, :xpositions, :ypositions, :unitcell, :cutoff)
-
-import Base: setproperty!
-setproperty!(sys::SystemPairs, s::Symbol, value) = setproperty!(sys, Val(s), value)
-setproperty!(sys::SystemPairs, ::Val{:cutoff}, cutoff) = update!(sys.system; cutoff=cutoff)
-setproperty!(sys::SystemPairs, ::Val{:unitcell}, unitcell) = update!(sys.system; unitcell=unitcell)
-setproperty!(sys::SystemPairs, ::Val{:parallel}, parallel) = sys.system.parallel = parallel
+propertynames(sys::SystemPairs, private::Bool) = (:system, :minimum_distances)
 
 #
 # Functions for when the lists of minimum-distances is that of a single

src/MolecularMinimumDistances/SelfPairs.jl

@@ -33,7 +33,7 @@ more general `mol_indices` function, which, for each atomic index, returns the
 corresponding
 molecular index (which is `mol_indices(i) = (i-1)%n + 1` where `n` is the
 number of atoms per molecule if all molecules have the same number of
-atoms and are continously stored in the array of positions). 
+atoms and are continuously stored in the array of positions). 
 
 # Examples
 
@@ -84,7 +84,7 @@ function SelfPairs(;
 end
 
 #
-# This file containst the functions for single-sets, that is for those cases where
+# This file contains the functions for single-sets, that is for those cases where
 # the list of minimum-distances is between the molecules of a single component.
 #
 function update_list!(pair, list::List, system::SelfPairs)
@@ -126,8 +126,8 @@ end
     for (iframe, frame) in enumerate(simulation)
         pos = positions(frame)
         local uc = unitcell(frame)
-        sys.xpositions .= @view(pos[popc])
-        sys.unitcell = uc.orthorhombic ? diag(uc.matrix) : uc.matrix
+        sys.system.xpositions .= @view(pos[popc])
+        sys.system.unitcell = uc.orthorhombic ? diag(uc.matrix) : uc.matrix
         md = minimum_distances!(sys)
         md_min[iframe] = minimum(p -> p.d, md)
         # Test direct (out-of-place) call
@@ -136,7 +136,7 @@ end
                 xpositions = xsolvent,
                 xn_atoms_per_molecule = 134,
                 cutoff = 6.0,
-                unitcell = sys.unitcell
+                unitcell = sys.system.unitcell
             )
             @test all(md_out .≈ md)
         end