From 4bbdb9dea70ba555709983c0a8557fa28f0a09a0 Mon Sep 17 00:00:00 2001
From: Leandro Martinez <lmartine@unicamp.br>
Date: Tue, 3 Oct 2023 11:36:36 -0300
Subject: [PATCH] change some names

---
 src/Selection.jl |  3 ++-
 src/results.jl   | 26 +++++++++++++-------------
 2 files changed, 15 insertions(+), 14 deletions(-)

diff --git a/src/Selection.jl b/src/Selection.jl
index 83a968a1..2e17e8ba 100644
--- a/src/Selection.jl
+++ b/src/Selection.jl
@@ -13,7 +13,8 @@ struct Selection
     natomspermol::Int # Number of atoms per molecule
     index::Vector{Int} # Index of each atom in the full vector of coordinates
     imol::Vector{Int} # index of the molecule to which each atom belongs
-    names::Vector{String} # Types of the atoms, to be used in the atom-contributions
+    groups::Vector{Vector{Int}}
+    group_names::Vector{String} # Types of the atoms, to be used in the atom-contributions
 end
 
 # Initialize providing the file name, and calling by default PDBTools.select
diff --git a/src/results.jl b/src/results.jl
index 371c010a..eb8173f7 100644
--- a/src/results.jl
+++ b/src/results.jl
@@ -116,8 +116,8 @@ The Result{Vector{Float64}} parametric type is necessary only for reading the JS
     solute::SolSummary
 
     # Atomic contributions to the MDDFs
-    solute_atom::T = zeros(nbins, solute.natomspermol)
-    solvent_atom::T = zeros(nbins, solvent.natomspermol)
+    solute_group_contributions = zeros(nbins, solute.ngroups)
+    solvent_group_contributions = zeros(nbins, solvent.ngroups)
 
     # Data to compute a RDF and the KB integral from this count
     rdf_count::Vector{Float64} = zeros(nbins)
@@ -718,13 +718,13 @@ If the solute and solvent selections are provides, pass on the atom names.
 
 """
 write(R::Result, filename::String, solute::Selection, solvent::Selection) =
-    write(R, filename, solute_names = solute.names, solvent_names = solvent.names)
+    write(R, filename, solute_group_names = solute.names, solvent_group_names = solvent.group_names)
 
 
 """
     write(R::ComplexMixtures.Result, filename::String; 
-          solute_names::Vector{String} = ["nothing"], 
-          solvent_names::Vector{String} = ["nothing"])
+          solute_group_names::Vector{String} = ["nothing"], 
+          solvent_group_names::Vector{String} = ["nothing"])
 
 Optional passing of atom names.
 
@@ -732,8 +732,8 @@ Optional passing of atom names.
 function write(
     R::Result,
     filename::String;
-    solute_names::Vector{String} = ["nothing"],
-    solvent_names::Vector{String} = ["nothing"],
+    solute_group_names::Vector{String} = ["nothing"],
+    solvent_group_names::Vector{String} = ["nothing"],
 )
 
     # Names of output files containing atomic contibutions
@@ -809,20 +809,20 @@ function write(
 
     # Writting gmd per atom contributions for the solvent
 
-    open(atom_contributions_solvent, "w") do output
+    open(group_contributions_solvent, "w") do output
         println(output,
             """
-            # Solvent atomic contributions to total MDDF.
+            # Solvent group contributions to total MDDF.
             #
             # Trajectory files: $(R.files)
             #
             # Atoms: 
             """)
         for i = 1:size(R.solvent_atom, 2)
-            if solvent_names[1] == "nothing"
+            if solvent_group_names[1] == "nothing"
                 println(output, @sprintf("# %9i", i))
             else
-                println(output, @sprintf("# %9i %5s", i, solvent_names[i]))
+                println(output, @sprintf("# %9i %5s", i, solvent_group_names[i]))
             end
         end
         println(output, "#")
@@ -853,10 +853,10 @@ function write(
             # Atoms
             """)
         for i = 1:size(R.solute_atom, 2)
-            if solute_names[1] == "nothing"
+            if solute_group_names[1] == "nothing"
                 println(output, @sprintf("# %9i", i))
             else
-                println(output, @sprintf("# %9i %5s", i, solute_names[i]))
+                println(output, @sprintf("# %9i %5s", i, solute_group_names[i]))
             end
         end
         println(output, "#")