Make use of isotope label information in InChi values in transition lists and .msp files

pwiz_tools/Skyline/Model/CustomMolecule.cs

@@ -102,6 +102,16 @@ public static Dictionary<string, string> FormatAccessionNumbers(string keysTSV,
             return keys;
         }
 
+        public static MoleculeAccessionNumbers Create(Dictionary<string, string> accessions)
+        {
+            if (accessions==null || accessions.Count == 0)
+            {
+                return EMPTY;
+            }
+
+            return new MoleculeAccessionNumbers(accessions);
+        }
+
         public MoleculeAccessionNumbers(string keysTSV, string inChiKey = null)
         {
             var keys = FormatAccessionNumbers(keysTSV, inChiKey);
@@ -115,6 +125,57 @@ public MoleculeAccessionNumbers(string keysTSV, string inChiKey = null)
             AccessionNumbers = ImmutableSortedList<string, string>.FromValues(keys, ACCESSION_TYPE_SORTER); 
         }
 
+        private static readonly Regex REGEX_INCHI_ISOTOPES = new Regex(@"\d+([A-Za-z]+\d+)", // Position, isotope, weight (or isotope and count, for D and T)
+            RegexOptions.CultureInvariant | RegexOptions.Compiled); // N.B. we ignore position, as we don't carry that much structure detail
+
+        // Look for labels buried in descriptions, e.g. InChi's /i section
+        public Dictionary<string, int> FindLabels()
+        {
+            Dictionary<string, int> result = null;
+            var inchi = GetInChI();
+            if (!string.IsNullOrEmpty(inchi))
+            {
+                // e.g. InChI=1S/C8H8O/c1-7(9)8-5-3-2-4-6-8/h2-6H,1H3/i1D4 (replace 4 H with H')
+                // e.g. InChI=1S/C8H8O/c1-7(9)8-5-3-2-4-6-8/h2-6H,1H3/i1C13,2C13,3C13,4C13 (replace C with C' at positions 1,2,3, and 4)
+                var parts = inchi.Split('/');
+                if (parts.Length > 4)
+                {
+                    var matches = REGEX_INCHI_ISOTOPES.Matches(parts[4]);
+
+                    foreach (Match match in matches)
+                    {
+                        var isotope = match.Groups[1].Value;
+                        var count = 1;
+                        if (isotope.StartsWith(BioMassCalc.D) || isotope.StartsWith(BioMassCalc.T)) // e.g. "D4" in ".../i1D4" (replace 4 H with H') 
+                        {
+                            if (!int.TryParse(isotope.Substring(1), out count)) // Get the count, if any e.g. 3 in "/i1T3"
+                            {
+                                count = 1;
+                            }
+                            isotope = isotope.Substring(0, 1);
+                        }
+                        if (Adduct.DICT_ADDUCT_ISOTOPE_NICKNAMES.TryGetValue(isotope, out var skylineIsotope)) // e.g. "C13" => "C'"
+                        {
+                            if (result == null)
+                            {
+                                result = new Dictionary<string, int>() { { skylineIsotope, count } };
+                            }
+                            else if (!result.TryGetValue(skylineIsotope, out var existing))
+                            {
+                                result.Add(skylineIsotope, count);
+                            }
+                            else
+                            {
+                                result[skylineIsotope] = existing + count;
+                            }
+                        }
+                    }
+                }
+            }
+
+            return result;
+        }
+
         public bool IsEmpty {
             get
             {

pwiz_tools/Skyline/Model/Lib/LibResources.resx

@@ -344,4 +344,7 @@
   <data name="NistLibraryBase_GetMod_Unknown_modification__0__at_line__1_" xml:space="preserve">
       <value>Unknown modification {0} at line {1}</value>
   </data>
+  <data name="NistLibraryBase_CreateCache_Missing_details_for__0__at_line__1___ignored" xml:space="preserve">
+      <value>Missing details for {0} at line {1}, ignored</value>
+  </data>
 </root>

pwiz_tools/Skyline/Model/Lib/Library.cs

@@ -2142,6 +2142,14 @@ public static SmallMoleculeLibraryAttributes Create(string moleculeName, string
             return Create(moleculeName, chemicalFormulaOrMassesString, inChiKey, otherKeys == null ? string.Empty : string.Join(@"\t", otherKeys.Select(kvp => kvp.Key + @":" + kvp.Value)));
         }
 
+        public static SmallMoleculeLibraryAttributes Create(string moleculeName, string chemicalFormulaOrMassesString,
+            IDictionary<string, string> accessions)
+        {
+            accessions.TryGetValue(MoleculeAccessionNumbers.TagInChiKey, out var inChiKey);
+            return Create(moleculeName, chemicalFormulaOrMassesString, inChiKey, 
+                string.Join(@"\t", accessions.Where(kvp => kvp.Key != MoleculeAccessionNumbers.TagInChiKey).Select(kvp => kvp.Key + @":" + kvp.Value)));
+        }
+
         public static SmallMoleculeLibraryAttributes Create(string moleculeName, string chemicalFormulaOrMassesString,
             string inChiKey, string otherKeys)
         {