Fixes #2655 Usage of SimulationBuilder in R

src/OSPSuite.R/Domain/Simulation.cs

@@ -1,19 +1,22 @@
 using System;
 using System.Collections.Generic;
 using System.ComponentModel;
+using System.Linq;
 using OSPSuite.CLI.Core.MinimalImplementations;
 using OSPSuite.Core.Chart;
 using OSPSuite.Core.Commands;
 using OSPSuite.Core.Domain;
 using OSPSuite.Core.Domain.Builder;
 using OSPSuite.Core.Domain.Data;
 using OSPSuite.Core.Domain.Services;
+using OSPSuite.Utility.Extensions;
 using OSPSuite.Utility.Visitor;
 
 namespace OSPSuite.R.Domain
 {
    public class Simulation : ISimulation
    {
+      private readonly IReadOnlyList<MoleculeBuilder> _allBuildersInSimulation;
       public IModelCoreSimulation CoreSimulation { get; }
 
       public bool IsLoaded { get; set; } = true;
@@ -50,6 +53,9 @@ public void AddAnalysis(ISimulationAnalysis simulationAnalysis)
       public Simulation(IModelCoreSimulation modelCoreSimulation)
       {
          CoreSimulation = modelCoreSimulation;
+
+         // Initialize the list of molecule builders for which there are initial conditions in the simulation
+         _allBuildersInSimulation = allBuildersFor(allMoleculeNamesInSimulation.ToList()).DistinctBy(x => x.Name).ToList();
       }
 
       public string Name
@@ -127,6 +133,33 @@ public SimulationConfiguration Configuration
 
       public IReadOnlyList<string> CompoundNames => CoreSimulation.CompoundNames;
 
+      public IReadOnlyList<string> AllPresentFloatingMoleculeNames => _allBuildersInSimulation.Where(m => m is { IsFloating: true }).AllNames().ToArray();
+
+      public IReadOnlyList<string> AllPresentXenobioticFloatingMoleculeNames => _allBuildersInSimulation.Where(m => m is { IsFloatingXenobiotic: true }).AllNames().ToArray();
+
+      public IReadOnlyList<string> AllPresentStationaryMoleculeNames => _allBuildersInSimulation.Where(m => m is { IsFloating: false, IsXenobiotic: true }).AllNames().ToArray();
+
+      public IReadOnlyList<string> AllPresentEndogenousStationaryMoleculeNames => _allBuildersInSimulation.Where(m => m is { IsFloating: false, IsXenobiotic: false }).AllNames().ToArray();
+
+      private IEnumerable<string> allMoleculeNamesInSimulation => 
+         CoreSimulation.Configuration.ModuleConfigurations.
+            Where(x => x.SelectedInitialConditions != null).   // Initial conditions are selected
+            SelectMany(x => x.SelectedInitialConditions).      
+            Where(x => x.IsPresent).                           // this initial condition is present
+            Select(ic => ic.MoleculeName).Distinct();
+
+      private IEnumerable<MoleculeBuilder> allMoleculeBuilders => 
+         CoreSimulation.Configuration.ModuleConfigurations.
+            Where(x => x.Module.Molecules != null).            // filter out modules without molecules building blocks
+            SelectMany(x => x.Module.Molecules);
+
+      private IReadOnlyList<MoleculeBuilder> allBuildersFor(IReadOnlyList<string> moleculeNames)
+      {
+         var cache = new CacheByName<MoleculeBuilder>();
+         allMoleculeBuilders.Where(x => moleculeNames.Contains(x.Name)).Each(x => cache.Add(x));
+         return cache.ToList();
+      }
+
       public IEnumerable<T> All<T>() where T : class, IEntity => CoreSimulation.All<T>();
 
       public IParameter BodyWeight => CoreSimulation.BodyWeight;