Merge pull request #104 from topdownproteomics/concrete-chemical-formula

Concrete Chemical Formula

Author: rfellers

src/TopDownProteomics.Benchmarks/Program.cs

@@ -1,5 +1,8 @@
 using System;
+using System.Collections.Generic;
 using System.Diagnostics;
+using System.Linq;
+using TopDownProteomics.Biochemistry;
 using TopDownProteomics.Chemistry;
 using TopDownProteomics.Tools;
 
@@ -11,15 +14,16 @@ internal class Program
 
         private static void Main(string[] args)
         {
-            BenchmarkIsotopicEvelopeGeneration();
+            //BenchmarkIsotopicEnvelopeGeneration();
+            BenchmarkChemicalFormulaAsKey();
         }
 
-        private static void BenchmarkIsotopicEvelopeGeneration()
+        private static void BenchmarkIsotopicEnvelopeGeneration()
         {
             // Generate the formulas
             var random = new Random(1);
 
-            var chemicalFormulas = new IChemicalFormula[MaxRunValue];
+            var chemicalFormulas = new ChemicalFormula[MaxRunValue];
             IElementProvider elementProvider = new MockElementProvider();
 
             for (int i = 2; i < MaxRunValue; i++)
@@ -62,5 +66,30 @@ private static void BenchmarkIsotopicEvelopeGeneration()
 
             Console.WriteLine("Elapsed time for Northwestern Port: " + stopwatch.Elapsed);
         }
+
+        private static void BenchmarkChemicalFormulaAsKey()
+        {
+            IElementProvider elementProvider = new MockElementProvider();
+            IResidueProvider residueProvider = new IupacAminoAcidProvider(elementProvider);
+
+            string sequence = "MLTELEKALNSIIDVYHKYSLIKGNFHAVYRDDLKKLLETECPQYIRKKGADVWFKELDINTDGAVNFQEFLILVIKMGVAAHKKSHEESHKE";
+            var residues = sequence.Select(x => residueProvider.GetResidue(x));
+            ChemicalFormula[] formulas = residues.Select(x => x.GetChemicalFormula()).ToArray();
+
+            Dictionary<ChemicalFormula, bool> dictionary = new();
+            Stopwatch stopwatch = Stopwatch.StartNew();
+
+            for (int i = 0; i < 9_000; i++)
+            {
+                for (int j = 0; j < formulas.Length; j++)
+                {
+                    if (!dictionary.ContainsKey(formulas[j]))
+                        dictionary.Add(formulas[j], true);
+                }
+            }
+
+            stopwatch.Stop();
+            Console.WriteLine(stopwatch.Elapsed);
+        }
     }
 }

src/TopDownProteomics/Biochemistry/GlycanResidue.cs

@@ -32,7 +32,7 @@ public GlycanResidue(string symbol, string name, IReadOnlyCollection<IEntityCard
         /// Gets the chemical formula.
         /// </summary>
         /// <returns></returns>
-        public IChemicalFormula GetChemicalFormula() => new ChemicalFormula(_elements);
+        public ChemicalFormula GetChemicalFormula() => new ChemicalFormula(_elements);
 
         /// <summary>
         /// Gets the elements.

src/TopDownProteomics/Biochemistry/IupacAminoAcidProvider.cs

@@ -227,9 +227,9 @@ public AminoAcid(char symbol, string name, IReadOnlyCollection<IEntityCardinalit
             public string Name { get; }
             public char Symbol { get; }
 
-            public IChemicalFormula GetChemicalFormula() => new ChemicalFormula(_elements);
+            public ChemicalFormula GetChemicalFormula() => new ChemicalFormula(_elements);
 
             public double GetMass(MassType massType) => this.GetChemicalFormula().GetMass(massType);
         }
     }
-}
+}