Readers: Modification Conversion (smith-chem-wisc#853)

* Moved Quantifyable to Readers namespace

* Modification Embedding and Conversion

* Implemented ISpectralMatch on MSPT

* MSPT Mod Tests

* Tested Conversion Code.

* Address shortreed comments.

* Switched over to direct MM Mod Parsing

* Cleanup

* Responded to review comments

* once again

* Fixed file name spelling

* fix namespace issue

---------

Co-authored-by: Alexander-Sol <[email protected]>

Author: nbollis

mzLib/Omics/BioPolymerWithSetModsExtensions.cs

@@ -108,39 +108,6 @@ public static string EssentialSequence(this IBioPolymerWithSetMods withSetMods,
         return essentialSequence;
     }
 
-    /// <summary>
-    /// Determines the full sequence of a BioPolymerWithSetMods from its base sequence and modifications
-    /// </summary>
-    /// <param name="withSetMods"></param>
-    /// <returns></returns>
-    public static string DetermineFullSequence(this IBioPolymerWithSetMods withSetMods)
-    {
-        // start string builder with initial capacity to avoid resizing costs. 
-        var subSequence = new StringBuilder(withSetMods.BaseSequence.Length + withSetMods.AllModsOneIsNterminus.Count * 30);
-
-        // modification on peptide N-terminus
-        if (withSetMods.AllModsOneIsNterminus.TryGetValue(1, out Modification? mod))
-        {
-            subSequence.Append($"[{mod.ModificationType}:{mod.IdWithMotif}]");
-        }
-
-        for (int r = 0; r < withSetMods.Length; r++)
-        {
-            subSequence.Append(withSetMods[r]);
-
-            // modification on this residue
-            if (withSetMods.AllModsOneIsNterminus.TryGetValue(r + 2, out mod))
-            {
-                subSequence.Append($"[{mod.ModificationType}:{mod.IdWithMotif}]");
-            }
-        }
-
-        // modification on peptide C-terminus
-        if (withSetMods.AllModsOneIsNterminus.TryGetValue(withSetMods.Length + 2, out mod))
-        {
-            subSequence.Append($"[{mod.ModificationType}:{mod.IdWithMotif}]");
-        }
-
-        return subSequence.ToString();
-    }
+    public static string DetermineFullSequence(this IBioPolymerWithSetMods withSetMods) => IBioPolymerWithSetMods
+        .DetermineFullSequence(withSetMods.BaseSequence, withSetMods.AllModsOneIsNterminus);
 }

mzLib/Omics/IBioPolymerWithSetMods.cs

@@ -163,5 +163,39 @@ public static Dictionary<int, Modification> GetModificationDictionaryFromFullSeq
         /// <returns></returns>
         public static List<Modification> GetModificationsFromFullSequence(string fullSequence,
             Dictionary<string, Modification> allModsKnown) => [.. GetModificationDictionaryFromFullSequence(fullSequence, allModsKnown).Values];
+
+        /// <summary>
+        /// Determines the full sequence of a BioPolymerWithSetMods from its base sequence and modifications
+        /// </summary>
+        public static string DetermineFullSequence(string baseSequence, IDictionary<int, Modification> allModsOneIsNterminus)
+        {
+            // start string builder with initial capacity to avoid resizing costs. 
+            var subSequence = new StringBuilder(baseSequence.Length + allModsOneIsNterminus.Count * 60);
+
+            // modification on peptide N-terminus
+            if (allModsOneIsNterminus.TryGetValue(1, out Modification? mod))
+            {
+                subSequence.Append($"[{mod.ModificationType}:{mod.IdWithMotif}]");
+            }
+
+            for (int r = 0; r < baseSequence.Length; r++)
+            {
+                subSequence.Append(baseSequence[r]);
+
+                // modification on this residue
+                if (allModsOneIsNterminus.TryGetValue(r + 2, out mod))
+                {
+                    subSequence.Append($"[{mod.ModificationType}:{mod.IdWithMotif}]");
+                }
+            }
+
+            // modification on peptide C-terminus
+            if (allModsOneIsNterminus.TryGetValue(baseSequence.Length + 2, out mod))
+            {
+                subSequence.Append($"[{mod.ModificationType}:{mod.IdWithMotif}]");
+            }
+
+            return subSequence.ToString();
+        }
     }
 }

mzLib/Readers/BaseClasses/ISpectralMatch.cs

@@ -0,0 +1,41 @@
+using Omics.Modifications;
+
+namespace Readers;
+
+public interface ISpectralMatch
+{
+    /// <summary>
+    /// The scan number of the identification
+    /// </summary>
+    public int OneBasedScanNumber { get; }
+
+    /// <summary>
+    /// Primary Sequence
+    /// </summary>
+    public string BaseSequence { get; }
+
+    /// <summary>
+    /// Modified Sequence in MetaMorpheus format
+    /// </summary>
+    public string FullSequence { get; }
+
+    /// <summary>
+    /// The accession (unique identifier) of the identification
+    /// </summary>
+    public string Accession { get; }
+
+    /// <summary>
+    /// If the given Spectral Match is a decoy
+    /// </summary>
+    public bool IsDecoy { get; }
+
+    /// <summary>
+    /// The Mass Spec file name without the extension
+    /// </summary>
+    public string FileNameWithoutExtension { get; }
+
+    /// <summary>
+    /// Modifications on the spectral match
+    /// </summary>
+    public Dictionary<int, Modification> AllModsOneIsNterminus { get; }
+}

mzLib/Readers/BaseClasses/ResultFile.cs

@@ -81,6 +81,12 @@ public bool CanRead(string filePath)
 
         #region Operators
 
+        public TResult this[int index]
+        {
+            get => Results[index];
+            set => Results[index] = value;
+        }
+
         public static ResultFile<TResult> operator +(ResultFile<TResult> thisFile, TResult resultToAdd)
         {
             thisFile.Results.Add(resultToAdd);

mzLib/Readers/ExternalResults/IndividualResultRecords/MsPathFinderTResult.cs

@@ -1,15 +1,12 @@
 using CsvHelper.Configuration.Attributes;
 using CsvHelper.Configuration;
-using System;
-using System.Collections.Generic;
-using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
 using Chemistry;
+using Omics.Modifications;
+using Omics;
 
 namespace Readers
 {
-    public class MsPathFinderTResult
+    public class MsPathFinderTResult : ISpectralMatch
     {
         public static CsvConfiguration CsvConfiguration { get; } = new CsvConfiguration(System.Globalization.CultureInfo.InvariantCulture)
         {
@@ -20,7 +17,6 @@ public class MsPathFinderTResult
             BadDataFound = null,
         };
 
-
         [Name("Scan")]
         public int OneBasedScanNumber { get; set; }
 
@@ -89,13 +85,40 @@ public class MsPathFinderTResult
 
         #region InterpretedFields
 
-        [Ignore] private string _accession = null;
+        [Ignore] private string? _accession = null;
         [Ignore] public string Accession => _accession ??= ProteinName.Split('|')[1].Trim();
 
         [Ignore] private bool? _isDecoy = null;
         [Ignore] public bool IsDecoy => _isDecoy ??= ProteinName.StartsWith("XXX");
         [Optional] public string FileNameWithoutExtension { get; set; }
 
+        [Ignore] private Dictionary<int, Modification>? _allModsOneIsNterminus;
+        [Ignore] public Dictionary<int, Modification> AllModsOneIsNterminus => _allModsOneIsNterminus ??= ParseModifications();
+
+        [Ignore] private string? _fullSequence;
+        [Ignore] public string FullSequence => _fullSequence ??= IBioPolymerWithSetMods.DetermineFullSequence(BaseSequence, AllModsOneIsNterminus);
+
+        private Dictionary<int, Modification> ParseModifications()
+        {
+            var mods = new Dictionary<int, Modification>();
+            if (string.IsNullOrEmpty(Modifications))
+                return mods;
+
+            var modStrings = Modifications.Split(',');
+            foreach (var modString in modStrings)
+            {
+                var modSplits = modString.Split(' ');
+                var name = modSplits[0];
+                var location = int.Parse(modSplits[1]);
+
+                var modifiedResidue = location == 0 ? 'X' : BaseSequence[location - 1];
+                var mmMod = ModificationConverter.GetClosestMod(name, modifiedResidue);
+
+                mods.Add(location+1, mmMod);
+            }
+            return mods;
+        }
+
         #endregion
     }
 }

mzLib/Readers/ExternalResults/ResultFiles/MsPathFinderTResultFile.cs

@@ -1,9 +1,4 @@
 using CsvHelper;
-using System;
-using System.Collections.Generic;
-using System.Linq;
-using System.Text;
-using System.Threading.Tasks;
 using Easy.Common.Extensions;
 
 namespace Readers

mzLib/Readers/ExternalResults/SupportClasses/ExternalResultsConverters.cs

@@ -0,0 +1,69 @@
+using CsvHelper.Configuration;
+using CsvHelper.TypeConversion;
+using CsvHelper;
+using System.Text;
+using MzLibUtil;
+
+namespace Readers;
+
+/// <summary>
+/// Converts the chemical formula from MsPathFinderT to MetaMorpheus
+/// MsPathFinderT: "C(460) H(740) N(136) O(146) S(0)"
+/// MetaMorpheus: "C460H740N136O146S"
+/// </summary>
+internal class MsPathFinderTCompositionToChemicalFormulaConverter : DefaultTypeConverter
+{
+    public override object ConvertFromString(string text, IReaderRow row, MemberMapData memberMapData)
+    {
+        var composition = text.Split(' ').Where(p => p != "").ToArray();
+        var chemicalFormula = new Chemistry.ChemicalFormula();
+        foreach (var element in composition)
+        {
+            var elementSplit = element.Split('(');
+            var elementName = elementSplit[0];
+            var elementCount = int.Parse(elementSplit[1].Replace(")", ""));
+            chemicalFormula.Add(elementName, elementCount);
+        }
+        return chemicalFormula;
+    }
+
+    public override string ConvertToString(object value, IWriterRow row, MemberMapData memberMapData)
+    {
+        var chemicalFormula = value as Chemistry.ChemicalFormula ?? throw new MzLibException("Cannot convert input to ChemicalFormula");
+        var sb = new StringBuilder();
+
+        bool onNumber = false;
+        foreach (var character in chemicalFormula.Formula)
+        {
+            if (!char.IsDigit(character)) // if is a letter
+            {
+                if (onNumber)
+                {
+                    sb.Append(") " + character);
+                    onNumber = false;
+                }
+                else
+                    sb.Append(character);
+            }
+            else
+            {
+                if (!onNumber)
+                {
+                    sb.Append("(" + character);
+                    onNumber = true;
+                }
+                else
+                    sb.Append(character);
+            }
+        }
+
+        var stringForm = sb.ToString();
+        if (char.IsDigit(stringForm.Last()))
+            stringForm += ")";
+        else
+            stringForm += "(1)";
+
+        return stringForm;
+    }
+}
+