Rearranging classes to fit within the Transcriptomics Structure (#743)

* correct Within calculation

* update unit tests

* this is the spot

* add space

* first move

* psmFromTsv unit tests

* moved library spectrum

* empty unit test for library spectrum

* m

* library spectrum unit tests

* lib spec unit tests

* PSMTSV unit tests

* add tests for variants and localized glycans

* capitalization convention

* read internal ions test

* uncomment lines

* moved fragmentation and library spectrum to new project Omics

* Revert "moved fragmentation and library spectrum to new project Omics"

This reverts commit d1bc75c.

* someInterfaces

* good midpont

* omics classes and interfaces seem tobe working

* move LibrarySpectrum class to Omics. Create SpectrumMatchFromTsvHeader interface in Omics

* not working

* Fixed up the PR

* fix broken test

* some unit tests

* dhg

* Expanded test coverage on file classes

* new header and xlink psmtsv reader unit tests

* space update

* update nuspec for omics and added peptide folder to omics fragmentatkion

* Moved around most everything that wil need to be for Transcriptomics implementation

* Made all tests pass

* Moved a few methods out of PeptideWithSetModifications and into IBioPolymerWithSetMods

* Moved methods from ProteolyticPeptide to LysisProduct

* Marked RNase.tsv to copy always

* Cleaned up the code quite a bit

* Updated product class equalit members

* Updated product class equalit members

* This one method keeps fighting me

* Removed AnyCPU

* Added tests to ChemicalFormual operators

* Update mzLib.sln

* Updated Nuspec

* Changed naming convention in Digestion Agent

* Added comment to clarify base loss ions from 5' end
Adjusted Chemical Formula subtraction when null - value

* Added Comments to BioPolymerWithSetModsExtensions
Made LysisProduct and abstract class and its constructor protected

* Renamed LysisProduct to DigestionProduct
Changed IDigestionParams.Enzyme to IDigestionParams.DigestionAgent

* changed name on one method in DigestionProduct

* Renamed get fixed mods method in DigestionProduct

---------

Co-authored-by: MICHAEL SHORTREED <[email protected]>
Co-authored-by: trishorts <[email protected]>

mzLib/Chemistry/ChemicalFormula.cs

@@ -31,7 +31,7 @@ namespace Chemistry
     /// Formula can change!!! If isotopes or elements are changed.
     /// </summary>
     [Serializable]
-    public sealed class ChemicalFormula : IEquatable<ChemicalFormula>
+    public sealed class ChemicalFormula : IEquatable<ChemicalFormula>, IHasChemicalFormula
     {
         // Main data stores, the isotopes and elements
 
@@ -59,12 +59,14 @@ public ChemicalFormula()
             Elements = new Dictionary<Element, int>();
         }
 
-        public ChemicalFormula(ChemicalFormula capFormula)
+        public ChemicalFormula(IHasChemicalFormula capFormula)
         {
-            Isotopes = new Dictionary<Isotope, int>(capFormula.Isotopes);
-            Elements = new Dictionary<Element, int>(capFormula.Elements);
+            Isotopes = new Dictionary<Isotope, int>(capFormula.ThisChemicalFormula.Isotopes);
+            Elements = new Dictionary<Element, int>(capFormula.ThisChemicalFormula.Elements);
         }
 
+        public ChemicalFormula ThisChemicalFormula => this;
+
         /// <summary>
         /// Gets the average mass of this chemical formula
         /// </summary>
@@ -523,5 +525,44 @@ private string GetHillNotation()
             otherParts.Sort();
             return s + string.Join("", otherParts);
         }
+
+        public override string ToString()
+        {
+            return $"{ThisChemicalFormula.Formula} : {MonoisotopicMass}";
+        }
+
+        public static ChemicalFormula operator -(ChemicalFormula left, IHasChemicalFormula right)
+        {
+            if (left == null)
+                if (right == null)
+                    return null;
+                else
+                {
+                    var formula = new ChemicalFormula();
+                    formula.Remove(right);
+                    return formula;
+                }
+            if (right == null)
+                return new ChemicalFormula(left);
+
+
+            ChemicalFormula newFormula = new ChemicalFormula(left);
+            newFormula.Remove(right);
+            return newFormula;
+        }
+
+        public static ChemicalFormula operator +(ChemicalFormula left, IHasChemicalFormula right)
+        {
+            // if left is null, return right. If right is null, return left. If both are null, return null. If both are not null, add them
+            if (left == null)
+                return right == null ? null : new ChemicalFormula(right);
+            if (right == null)
+                return new ChemicalFormula(left);
+
+            ChemicalFormula newFormula = new ChemicalFormula(left);
+            newFormula.Add(right);
+            return newFormula;
+
+        }
     }
 }

mzLib/Omics/BioPolymerWithSetModsExtensions.cs

@@ -0,0 +1,142 @@
+using System.Text;
+using Chemistry;
+using Omics.Modifications;
+
+namespace Omics;
+
+public static class BioPolymerWithSetModsExtensions
+{
+    /// <summary>
+    /// This method returns the full sequence with mass shifts INSTEAD OF PTMs in brackets []
+    /// Some external tools cannot parse PTMs, instead requiring a numerical input indicating the mass of a PTM in brackets
+    /// after the position of that modification
+    /// N-terminal mas shifts are in brackets prior to the first amino acid and apparently missing the + sign
+    /// </summary>
+    /// <returns></returns>
+    public static string FullSequenceWithMassShift(this IBioPolymerWithSetMods withSetMods)
+    {
+        var subsequence = new StringBuilder();
+
+        // modification on peptide N-terminus
+        if (withSetMods.AllModsOneIsNterminus.TryGetValue(1, out Modification mod))
+        {
+            subsequence.Append('[' + mod.MonoisotopicMass.RoundedDouble(6).ToString() + ']');
+        }
+
+        for (int r = 0; r < withSetMods.Length; r++)
+        {
+            subsequence.Append(withSetMods[r]);
+
+            // modification on this residue
+            if (withSetMods.AllModsOneIsNterminus.TryGetValue(r + 2, out mod))
+            {
+                if (mod.MonoisotopicMass > 0)
+                {
+                    subsequence.Append("[+" + mod.MonoisotopicMass.RoundedDouble(6).ToString() + ']');
+                }
+                else
+                {
+                    subsequence.Append("[" + mod.MonoisotopicMass.RoundedDouble(6).ToString() + ']');
+                }
+            }
+        }
+
+        // modification on peptide C-terminus
+        if (withSetMods.AllModsOneIsNterminus.TryGetValue(withSetMods.Length + 2, out mod))
+        {
+            if (mod.MonoisotopicMass > 0)
+            {
+                subsequence.Append("[+" + mod.MonoisotopicMass.RoundedDouble(6).ToString() + ']');
+            }
+            else
+            {
+                subsequence.Append("[" + mod.MonoisotopicMass.RoundedDouble(6).ToString() + ']');
+            }
+        }
+        return subsequence.ToString();
+    }
+
+    /// <summary>
+    /// This method returns the full sequence only with the specified modifications in the modstoWritePruned dictionary
+    /// </summary>
+    /// <param name="withSetMods"></param>
+    /// <param name="modstoWritePruned"></param>
+    /// <returns></returns>
+    public static string EssentialSequence(this IBioPolymerWithSetMods withSetMods,
+        IReadOnlyDictionary<string, int> modstoWritePruned)
+    {
+        string essentialSequence = withSetMods.BaseSequence;
+        if (modstoWritePruned != null)
+        {
+            var sbsequence = new StringBuilder();
+
+            // variable modification on peptide N-terminus
+            if (withSetMods.AllModsOneIsNterminus.TryGetValue(1, out Modification pep_n_term_variable_mod))
+            {
+                if (modstoWritePruned.ContainsKey(pep_n_term_variable_mod.ModificationType))
+                {
+                    sbsequence.Append('[' + pep_n_term_variable_mod.ModificationType + ":" + pep_n_term_variable_mod.IdWithMotif + ']');
+                }
+            }
+            for (int r = 0; r < withSetMods.Length; r++)
+            {
+                sbsequence.Append(withSetMods[r]);
+                // variable modification on this residue
+                if (withSetMods.AllModsOneIsNterminus.TryGetValue(r + 2, out Modification residue_variable_mod))
+                {
+                    if (modstoWritePruned.ContainsKey(residue_variable_mod.ModificationType))
+                    {
+                        sbsequence.Append('[' + residue_variable_mod.ModificationType + ":" + residue_variable_mod.IdWithMotif + ']');
+                    }
+                }
+            }
+
+            // variable modification on peptide C-terminus
+            if (withSetMods.AllModsOneIsNterminus.TryGetValue(withSetMods.Length + 2, out Modification pep_c_term_variable_mod))
+            {
+                if (modstoWritePruned.ContainsKey(pep_c_term_variable_mod.ModificationType))
+                {
+                    sbsequence.Append('[' + pep_c_term_variable_mod.ModificationType + ":" + pep_c_term_variable_mod.IdWithMotif + ']');
+                }
+            }
+
+            essentialSequence = sbsequence.ToString();
+        }
+        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)
+    {
+        var subSequence = new StringBuilder();
+
+        // 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();
+    }
+}

mzLib/Proteomics/ProteolyticDigestion/CleavageSpecificity.cs → mzLib/Omics/Digestion/CleavageSpecificity.cs

@@ -1,4 +1,4 @@
-namespace Proteomics.ProteolyticDigestion
+namespace Omics.Digestion
 {
     public enum CleavageSpecificity
     {

mzLib/Omics/Digestion/DigestionAgent.cs

@@ -0,0 +1,107 @@
+using Omics.Modifications;
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+
+namespace Omics.Digestion
+{
+    public abstract class DigestionAgent
+    {
+        protected DigestionAgent(string name, CleavageSpecificity cleavageSpecificity, List<DigestionMotif> motifList, Modification cleavageMod)
+        {
+            Name = name;
+            CleavageSpecificity = cleavageSpecificity;
+            DigestionMotifs = motifList ?? new List<DigestionMotif>();
+            CleavageMod = cleavageMod;
+        }
+
+        public string Name { get; init; }
+        public CleavageSpecificity CleavageSpecificity { get; init; }
+        public List<DigestionMotif> DigestionMotifs { get; init; }
+        public Modification CleavageMod { get; set; }
+
+        public override string ToString()
+        {
+            return Name;
+        }
+
+        /// <summary>
+        /// Is length of given peptide okay, given minimum and maximum?
+        /// </summary>
+        /// <param name="length"></param>
+        /// <param name="minLength"></param>
+        /// <param name="maxLength"></param>
+        /// <returns></returns>
+        protected static bool ValidLength(int length, int minLength, int maxLength)
+        {
+            return ValidMinLength(length, minLength) && ValidMaxLength(length, maxLength);
+        }
+
+        /// <summary>
+        /// Is length of given peptide okay, given minimum?
+        /// </summary>
+        /// <param name="length"></param>
+        /// <param name="minLength"></param>
+        /// <returns></returns>
+        protected static bool ValidMinLength(int length, int minLength)
+        {
+            return length >= minLength;
+        }
+
+        /// <summary>
+        /// Is length of given peptide okay, given maximum?
+        /// </summary>
+        /// <param name="length"></param>
+        /// <param name="maxLength"></param>
+        /// <returns></returns>
+        protected static bool ValidMaxLength(int? length, int maxLength)
+        {
+            return !length.HasValue || length <= maxLength;
+        }
+
+        /// <summary>
+        /// Gets the indices after which this protease will cleave a given protein sequence
+        /// </summary>
+        /// <param name="sequence"></param>
+        /// <returns></returns>
+        public List<int> GetDigestionSiteIndices(string sequence)
+        {
+            var indices = new List<int>();
+
+            for (int r = 0; r < sequence.Length; r++)
+            {
+                var cutSiteIndex = -1;
+                bool cleavagePrevented = false;
+
+                foreach (DigestionMotif motif in DigestionMotifs)
+                {
+                    var motifResults = motif.Fits(sequence, r);
+                    bool motifFits = motifResults.Item1;
+                    bool motifPreventsCleavage = motifResults.Item2;
+
+                    if (motifFits && r + motif.CutIndex < sequence.Length)
+                    {
+                        cutSiteIndex = Math.Max(r + motif.CutIndex, cutSiteIndex);
+                    }
+
+                    if (motifPreventsCleavage) // if any motif prevents cleave
+                    {
+                        cleavagePrevented = true;
+                    }
+                }
+
+                // if no motif prevents cleave
+                if (!cleavagePrevented && cutSiteIndex != -1)
+                {
+                    indices.Add(cutSiteIndex);
+                }
+            }
+
+            indices.Add(0); // The start of the protein is treated as a cleavage site to retain the n-terminal peptide
+            indices.Add(sequence.Length); // The end of the protein is treated as a cleavage site to retain the c-terminal peptide
+            return indices.Distinct().OrderBy(i => i).ToList();
+        }
+    }
+}

mzLib/Proteomics/ProteolyticDigestion/DigestionMotif.cs → mzLib/Omics/Digestion/DigestionMotif.cs

@@ -1,9 +1,7 @@
-using MzLibUtil;
-using System.Collections.Generic;
-using System.Linq;
-using System.Text.RegularExpressions;
+using System.Text.RegularExpressions;
+using MzLibUtil;
 
-namespace Proteomics.ProteolyticDigestion
+namespace Omics.Digestion
 {
     public class DigestionMotif
     {