some example script simplifications

docs/src/assets/scripts/example2/script2.jl

@@ -31,12 +31,12 @@ plot!(
 
 # Plot DMF group contributions to the MDDF. We use a dictionary where
 # the keys are the group names, and the values are the atom names of the group
-groups = Dict( 
+groups = ( 
     "CO" => ["C","O"], # carbonyl
     "N" => ["N"], 
     "Methyl groups" => ["CC","CT","HC1","HC2","HC3","HT1","HT2","HT3"],
 )
-for (group_label, group_atoms) in pairs(groups)
+for (group_label, group_atoms) in groups
     # Retrieve the contributions of the atoms of this group
     group_contrib = contributions(results, SolventGroup(group_atoms))
     # Plot the contributions of this groups, with the appropriate label
@@ -55,11 +55,11 @@ plot!(xlim=(1,5), ylabel="MDDF", subplot=1)
 # Plot ACR group contributions to the MDDF. This is an interesting case,
 # as the groups are repeated along the polymer chain
 #
-groups = Dict(
-    L"\textrm{CH_3}" => ["CF","HF1","HF2","HF3", "CL","HL1","HL2","HL3"], # terminal methyles
+groups = (
+    "CH_3" => ["CF","HF1","HF2","HF3", "CL","HL1","HL2","HL3"], # terminal methyles
     "CO" => ["OE1","CD"], # carbonyl
-    L"\textrm{NH_2}" => ["NE2","HE22","HE21"], # amine
-    L"\textrm{CHCH_2}" => ["C","H2","H1","CA","HA"], # backbone
+    "NH_2" => ["NE2","HE22","HE21"], # amine
+    "CHCH_2" => ["C","H2","H1","CA","HA"], # backbone
 )
 # Plot total mddf 
 plot!(
@@ -69,12 +69,12 @@ plot!(
     subplot=2
 )
 # Plot group contributions
-for (group_name, atom_names) in pairs(groups)
+for (group_name, atom_names) in groups
     group_contrib = contributions(results, SoluteGroup(atom_names))
     plot!(
         results.d,
         movavg(group_contrib,n=10).x, 
-        label=group_name,
+        label=latexstring("\\textrm{$group_name}"),
         subplot=2
     )
 end

docs/src/assets/scripts/example2/script3.jl

@@ -27,7 +27,7 @@ results = load("./mddf.json")
 group_contribs = Vector{Float64}[]
 labels = LaTeXString[]
 for (imer, mer) in enumerate(eachresidue(acr))
-    for (group_label, group_atoms) in pairs(groups)
+    for (group_label, group_atoms) in groups
         # only first residue has a terminal CH3
         if imer != 1 && group_label == "CH_3" 
             continue

docs/src/assets/scripts/example3/script2.jl

@@ -30,14 +30,14 @@ mddf_ethanol_POPC = load("mddf_ethanol_POPC.json")
 #
 # Define the groups using selections. Set a dict, in which the keys are the group names
 # and the values are the selections
-groups = Dict(
+groups = (
     "Hydroxyl" => select(ethanol, "name O1 or name HO1"),
     "Aliphatic chain" => select(ethanol, "not name O1 and not name HO1"),
 )
 # plot the total mddf and the contributions of the groups
 x = mddf_ethanol_POPC.d
 plot(x, movavg(mddf_ethanol_POPC.mddf, n=10).x, label="Total MDDF")
-for (group_name, group_atoms) in pairs(groups)
+for (group_name, group_atoms) in groups
     cont = contributions(mddf_ethanol_POPC, SolventGroup(group_atoms))
     y = movavg(cont, n=10).x
     plot!(x, y, label=group_name)

docs/src/assets/scripts/example3/script3.jl

@@ -29,7 +29,7 @@ mddf_water_POPC = load("mddf_water_POPC.json")
 # Here we define the POPC groups, from the atom names. Each group
 # is a vector of atom names, and the keys are the group names.
 #
-groups = Dict(
+groups = (
     "Choline" => ["N", "C12", "H12A", "H12B", "C13", "H13A", "H13B", "H13C", "C14",
         "H14A", "H14B", "H14C", "C15", "H15A", "H15B", "H15C", "C11", "H11A", "H11B"],
     "Phosphate" => ["P", "O13", "O14", "O12"],
@@ -55,7 +55,7 @@ plot(
     movavg(mddf_water_POPC.mddf, n=10).x,
     label="Total water-POPC MDDF"
 )
-for (group_name, group_atoms) in pairs(groups)
+for (group_name, group_atoms) in groups
     cont = contributions(mddf_water_POPC, SoluteGroup(group_atoms))
     y = movavg(cont, n=10).x
     plot!(x, y, label=group_name)

docs/src/assets/scripts/example3/script4.jl

@@ -29,7 +29,7 @@ mddf_ethanol_POPC = load("mddf_ethanol_POPC.json")
 # Here we define the POPC groups, from the atom names. Each group
 # is a vector of atom names, and the keys are the group names.
 #
-groups = Dict(
+groups = (
     "Choline" => ["N", "C12", "H12A", "H12B", "C13", "H13A", "H13B", "H13C", "C14",
         "H14A", "H14B", "H14C", "C15", "H15A", "H15B", "H15C", "C11", "H11A", "H11B"],
     "Phosphate" => ["P", "O13", "O14", "O12"],
@@ -55,7 +55,7 @@ plot(
     movavg(mddf_ethanol_POPC.mddf, n=10).x,
     label="Total ethanol-POPC MDDF"
 )
-for (group_name, group_atoms) in pairs(groups)
+for (group_name, group_atoms) in groups
     cont = contributions(mddf_ethanol_POPC, SoluteGroup(group_atoms))
     y = movavg(cont, n=10).x
     plot!(x, y, label=group_name)

docs/src/assets/scripts/example3/script5.jl

@@ -28,7 +28,7 @@ mddf_ethanol_POPC = load("mddf_ethanol_POPC.json")
 # Splitting the oleoyl chain into groups along the the chain. 
 # The labels `CH_2` etc stand for `CH₂`, for example, in LaTeX notation, 
 # for a nicer plot axis ticks formatting.
-oleoyl_groups = [
+oleoyl_groups = (
     "CO" => ["O22", "C21"],
     "CH_2" => ["H2R", "H2S", "C22"],
     "CH_2" => ["C23", "H3R", "H3S"],
@@ -47,7 +47,7 @@ oleoyl_groups = [
     "CH_2" => ["C216", "H16R", "H16S"],
     "CH_2" => ["C217", "H17R", "H17S"],
     "CH_3" => ["C218", "H18R", "H18S", "H18T"]
-]
+)
 
 # Format tick labels with LaTeX
 labels_o = [latexstring("\\textrm{$key}") for (key, val) in oleoyl_groups]
@@ -87,7 +87,7 @@ annotate!( 14, 2.7, text("Oleoyl", :left, 12, plot_font), subplot=1)
 #
 # Repeat procedure for the palmitoyl groups
 #
-palmitoyl_groups = [
+palmitoyl_groups = (
     "CO" => ["C31", "O32"],
     "CH_2" => ["C32", "H2X", "H2Y"],
     "CH_2" => ["C33", "H3X", "H3Y"],
@@ -104,7 +104,7 @@ palmitoyl_groups = [
     "CH_2" => ["C314", "H14X", "H14Y"],
     "CH_2" => ["C315", "H15X", "H15Y"],
     "CH_3" => ["C316", "H16X", "H16Y", "H16Z"],
-]
+)
 
 # Format tick labels with LaTeX
 labels_p = [latexstring("\\textrm{$key}") for (key, val) in palmitoyl_groups]

docs/src/assets/scripts/example4/script3.jl

@@ -21,14 +21,14 @@ mddf_glyc_water = load("./mddf_glyc_water.json")
 # 2D maps plot of group contributions
 
 # Glycerol groups
-groups = [
+groups = (
     "OH" => ["O1", "HO1"], # first hydroxyl
     "CH_2" => ["C1", "H11", "H12"], # first CH2
     "OH" => ["O2", "HO2"], # second hydroxyl
     "CH" => ["C2", "H2"], # CH
     "CH_2" => ["C3", "H31", "H32"], # second CH2
     "OH" => ["O3", "HO3"] # third hydroxyl
-]
+)
 labels = latexstring.("\\textrm{$name}" for (name, atoms) in groups)
 
 #