From f8f46bb7222cb736db59fe462727068d6fd1a578 Mon Sep 17 00:00:00 2001 From: nbollis Date: Tue, 2 Sep 2025 18:08:37 -0500 Subject: [PATCH 1/9] Basic Loading --- .../Transcriptomics/ModomicsLoaderTests.cs | 46 + mzLib/Transcriptomics/Nucleotide.cs | 2 +- .../Transcriptomics/ModomicsDto.cs | 23 + .../Transcriptomics/ModomicsLoader.cs | 140 + .../Transcriptomics/modomics.json | 6816 +++++++++++++++++ .../UsefulProteomicsDatabases.csproj | 10 + 6 files changed, 7036 insertions(+), 1 deletion(-) create mode 100644 mzLib/Test/Transcriptomics/ModomicsLoaderTests.cs create mode 100644 mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsDto.cs create mode 100644 mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs create mode 100644 mzLib/UsefulProteomicsDatabases/Transcriptomics/modomics.json diff --git a/mzLib/Test/Transcriptomics/ModomicsLoaderTests.cs b/mzLib/Test/Transcriptomics/ModomicsLoaderTests.cs new file mode 100644 index 000000000..e68bf2a4f --- /dev/null +++ b/mzLib/Test/Transcriptomics/ModomicsLoaderTests.cs @@ -0,0 +1,46 @@ +using System; +using System.IO; +using System.Linq; +using System.Reflection; +using NUnit.Framework; +using UsefulProteomicsDatabases.Transcriptomics; +using Omics.Modifications; + +namespace Test.Transcriptomics +{ + [TestFixture] + public class ModomicsLoaderTests + { + [Test] + public void LoadModomics_ParsesEntriesCorrectly() + { + // Adjust resource name to match your project/namespace + var resourceName = "UsefulProteomicsDatabases.Transcriptomics.modomics.json"; + + var mods = ModomicsLoader.LoadModomics(); + + Assert.That(mods, Is.Not.Empty); + Assert.That(mods.All(m => m is Modification), Is.True); + Assert.That(mods.All(m => !string.IsNullOrWhiteSpace(m.IdWithMotif)), Is.True); + + // Check a known modification + var m5Cm = mods.FirstOrDefault(m => m.IdWithMotif == "m5Cm"); + Assert.That(m5Cm, Is.Not.Null); + Assert.That(m5Cm.ModificationType, Is.EqualTo("RNA")); + Assert.That(m5Cm.FeatureType, Is.EqualTo("MODOMICS")); + Assert.That(m5Cm.ChemicalFormula, Is.Not.Null); + Assert.That(m5Cm.MonoisotopicMass, Is.GreaterThan(0)); + } + + [Test] + public void LoadModomics_SkipsUnknownBases() + { + var resourceName = "UsefulProteomicsDatabases.Transcriptomics.modomics.json"; + + var mods = ModomicsLoader.LoadModomics(); + + // Should skip modifications with unknown bases (e.g. "X") + Assert.That(mods.Any(m => m.IdWithMotif == "Xm" || m.IdWithMotif == "xX"), Is.False); + } + } +} diff --git a/mzLib/Transcriptomics/Nucleotide.cs b/mzLib/Transcriptomics/Nucleotide.cs index 389686c78..4942ae5e9 100644 --- a/mzLib/Transcriptomics/Nucleotide.cs +++ b/mzLib/Transcriptomics/Nucleotide.cs @@ -34,7 +34,7 @@ public class Nucleotide : INucleotide, IEquatable /// /// A dictionary of all known residues, can be searched via one letter, three letter, or the name of the residue /// - internal static readonly Dictionary AllKnownResidues; + public static readonly Dictionary AllKnownResidues; internal static readonly Nucleotide[] ResiduesByLetter; diff --git a/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsDto.cs b/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsDto.cs new file mode 100644 index 000000000..0ca6935c3 --- /dev/null +++ b/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsDto.cs @@ -0,0 +1,23 @@ +using System.Collections.Generic; + +namespace UsefulProteomicsDatabases.Transcriptomics; + +/// +/// Intermediate Data Transfer Object (DTO) for Modomics entries. +/// +public class ModomicsDto +{ + public int Id { get; set; } + public string Abbrev { get; set; } + public string Formula { get; set; } + public string LcElutionComment { get; set; } + public string LcElutionTime { get; set; } + public double MassAvg { get; set; } + public double MassMonoiso { get; set; } + public double? MassProt { get; set; } + public string Name { get; set; } + public string ProductIons { get; set; } + public List ReferenceMoiety { get; set; } + public string ShortName { get; set; } + public string Smile { get; set; } +} \ No newline at end of file diff --git a/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs b/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs new file mode 100644 index 000000000..63006573e --- /dev/null +++ b/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs @@ -0,0 +1,140 @@ +#nullable enable +using Omics.Modifications; +using System.Collections.Generic; +using System.IO; +using System.Linq; +using System.Text.Json; +using Chemistry; +using Transcriptomics; +using System.Reflection; + +namespace UsefulProteomicsDatabases.Transcriptomics; + +public static class ModomicsLoader +{ + private static string _modomicsResourceName = "UsefulProteomicsDatabases.Transcriptomics.modomics.json"; + public static List? ModomicsModifications { get; private set; } + + public static List LoadModomics() + { + // Cache results + if (ModomicsModifications != null) + return ModomicsModifications; + ModomicsModifications = new(); + + // Load embedded resource + var info = Assembly.GetExecutingAssembly().GetName().Name; + var modomicsStream = Assembly.GetExecutingAssembly().GetManifestResourceStream($"{info}.Transcriptomics.modomics.json"); + + if (modomicsStream is null) + throw new FileNotFoundException("Could not find embedded resource", _modomicsResourceName); + var modsDict = JsonSerializer.Deserialize>(modomicsStream)!; + + // Parse each entry into a DTO + var dtos = new List(); + foreach (var kvp in modsDict) + { + var modEntry = kvp.Value; + + // Declare each property, find the value, and then build the dto + string abbrev = modEntry.GetProperty("abbrev").GetString()!; + string formula = modEntry.GetProperty("formula").GetString()!.Replace("+", string.Empty); + string name = modEntry.GetProperty("name").GetString()!; + string? lcElutionComment = modEntry.TryGetProperty("lc_elution_comment", out var elutionComment) ? elutionComment.GetString() : null; + string? lcElutionTime = modEntry.TryGetProperty("lc_elution_time", out var elutionTime) ? elutionTime.GetString() : null; + double massAvg = modEntry.TryGetProperty("mass_avg", out var massAvgElem) && massAvgElem.ValueKind == JsonValueKind.Number + ? massAvgElem.TryGetDouble(out var parsedMass) ? parsedMass : 0 + : 0; + double massMonoiso = modEntry.TryGetProperty("mass_monoiso", out var massMonoElem) && massMonoElem.ValueKind == JsonValueKind.Number + ? massMonoElem.TryGetDouble(out var parsedMass2) ? parsedMass2 : 0 + : 0; + double massProt = modEntry.TryGetProperty("mass_prot", out var massProtElem) && massProtElem.ValueKind == JsonValueKind.Number + ? massProtElem.TryGetDouble(out var parsedMass3) ? parsedMass3 : 0 + : 0; + string? productIons = modEntry.TryGetProperty("product_ions", out var productIonsElem) ? productIonsElem.GetString()! : null; + List referenceMoiety = modEntry.GetProperty("reference_moiety").EnumerateArray().Select(x => x.GetString()).Where(x => x != null).ToList(); + string shortName = modEntry.GetProperty("short_name").GetString()!; + string? smile = modEntry.TryGetProperty("smile", out var smileElem) ? smileElem.GetString() : null; + + var dto = new ModomicsDto + { + Id = kvp.Key, + Abbrev = abbrev, + Formula = formula, + LcElutionComment = lcElutionComment, + LcElutionTime = lcElutionTime, + MassAvg = massAvg, + MassMonoiso = massMonoiso, + MassProt = massProt, + Name = name, + ProductIons = productIons, + ReferenceMoiety = referenceMoiety, + ShortName = shortName, + Smile = smile + }; + + dtos.Add(dto); + } + + var dtosToParse = dtos + .Where(p => !p.Name.Contains("unknown", System.StringComparison.InvariantCultureIgnoreCase)); + + ModomicsModifications = dtosToParse + .Select(dto => dto.ToModification()) + .Where(p => p is not null) + .Cast() + .ToList(); + return ModomicsModifications; + } + + + public static Modification? ToModification(this ModomicsDto dto) + { + // Stand in mods for unknown residues, ignore them + if (dto.Name.Contains("unknown", System.StringComparison.InvariantCultureIgnoreCase)) + return null!; + + // Caps and other weird mods. TODO: handle those that are appropriate to do so + if (dto.ReferenceMoiety.Count > 1) + return null!; + + + + // Defensive: Only use first reference moiety + var refMoiety = dto.ReferenceMoiety?.FirstOrDefault(); + Nucleotide baseNuc = null; + if (!string.IsNullOrEmpty(refMoiety) && Nucleotide.AllKnownResidues.TryGetValue(refMoiety, out var nuc)) + baseNuc = nuc; + + // Subtract nucleoside formula/mass if possible + ChemicalFormula modFormula = null; + double? modMonoMass = null; + if (!string.IsNullOrWhiteSpace(dto.Formula) && baseNuc != null) + { + var fullFormula = ChemicalFormula.ParseFormula(dto.Formula); + modFormula = new ChemicalFormula(fullFormula); + modFormula.Remove(baseNuc.NucleosideChemicalFormula); + } + if (dto.MassMonoiso > 0 && baseNuc != null) + { + var baseMonoMass = baseNuc.NucleosideChemicalFormula.MonoisotopicMass; + modMonoMass = dto.MassMonoiso - baseMonoMass; + } + + ModificationMotif motif = null; + if (!string.IsNullOrEmpty(refMoiety) && ModificationMotif.TryGetMotif(refMoiety, out var m)) + motif = m; + + return new Modification( + _originalId: dto.ShortName, + _modificationType: "RNA", + _featureType: "MODOMICS", + _target: motif, + _locationRestriction: "Anywhere.", + _chemicalFormula: modFormula, + _monoisotopicMass: modMonoMass, + _databaseReference: new Dictionary> { { "MODOMICS", new List { dto.ShortName } } }, + _keywords: new List { dto.Abbrev, dto.Name } + ); + } +} \ No newline at end of file diff --git a/mzLib/UsefulProteomicsDatabases/Transcriptomics/modomics.json b/mzLib/UsefulProteomicsDatabases/Transcriptomics/modomics.json new file mode 100644 index 000000000..d6fe87c49 --- /dev/null +++ b/mzLib/UsefulProteomicsDatabases/Transcriptomics/modomics.json @@ -0,0 +1,6816 @@ +{ + "2": { + "abbrev": "\u03c4", + "formula": "C11H17N3O5", + "lc_elution_comment": "", + "lc_elution_time": "", + "mass_avg": 271.27, + "mass_monoiso": 271.1168, + "mass_prot": 272.1246, + "name": "5,2'-O-dimethylcytidine", + "product_ions": "126", + "reference_moiety": [ + "C" + ], + "short_name": "m5Cm", + "smile": "CO[C@H]1[C@H]([n]2c(=O)nc(N)c(C)c2)O[C@H](CO)[C@H]1O" + }, + "3": { + "abbrev": "F", + "formula": "C10H14N2O5S", + "lc_elution_comment": "between G and A (Kellner 2014)", + "lc_elution_time": "1,36 (Kellner 2014)", + "mass_avg": 274.294, + "mass_monoiso": 274.0623, + "mass_prot": 275.0701, + "name": "5-methyl-2-thiouridine", + "product_ions": "143", + "reference_moiety": [ + "U" + ], + "short_name": "m5s2U", + "smile": "Cc1c[n]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=S)[nH]c1=O" + }, + "4": { + "abbrev": "\u2228", + "formula": "C12H17N5O5+", + "lc_elution_comment": "", + "lc_elution_time": "", + "mass_avg": 311.294, + "mass_monoiso": 313.1386, + "mass_prot": 312.1308, + "name": "N2,7-dimethylguanosine", + "product_ions": "180", + "reference_moiety": [ + "G" + ], + "short_name": "m2,7G", + "smile": "CNc1nc(=O)c2c([n]([C@H]3[C@H](O)[C@H](O)[C@@H](CO)O3)c[n+]2C)n1" + }, + "5": { + "abbrev": 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"CNc1nc(=O)[n]([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)cc1" + }, + "10": { + "abbrev": "`", + "formula": "C15H21N5O5", + "lc_elution_comment": "after m6A (Kellner 2014)", + "lc_elution_time": "2,59 (Kellner 2014)", + "mass_avg": 351.358, + "mass_monoiso": 351.1543, + "mass_prot": 352.1621, + "name": "N6-(cis-hydroxyisopentenyl)adenosine", + "product_ions": "220", + "reference_moiety": [ + "A" + ], + "short_name": "io6A", + "smile": "CC(CO)=CCNc1ncnc2c1nc[n]2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O" + }, + "11": { + "abbrev": "\u2118", + "formula": "C11H14N2O7S", + "lc_elution_comment": "", + "lc_elution_time": "", + "mass_avg": 318.303, + "mass_monoiso": 318.0522, + "mass_prot": 319.06, + "name": "5-carboxymethyl-2-thiouridine", + "product_ions": "187/169/141", + "reference_moiety": [ + "U" + ], + "short_name": "cm5s2U", + "smile": "OC(Cc1c[n]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=S)[nH]c1=O)=O" + }, + "12": { + "abbrev": "T", + "formula": "C10H14N2O6", + "lc_elution_comment": "co-eluting with G 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"mass_monoiso": null, + "mass_prot": null, + "name": "undermodified hydroxywybutosine-5'-monophospate", + "product_ions": "", + "reference_moiety": [ + "G" + ], + "short_name": "pOHyWx", + "smile": "Cc1nc2[n](C)c3c(c(=O)[n]2c1CC(O)C(N)C(=O)O)nc[n]3[C@@H]1O[C@H](COP(=O)([O-])[O-])[C@@H](O)[C@H]1O" + }, + "425": { + "abbrev": "", + "formula": "C12H15N2O12P", + "lc_elution_comment": "", + "lc_elution_time": "", + "mass_avg": 410.227, + "mass_monoiso": null, + "mass_prot": null, + "name": "uridine 5-oxyacetic acid methyl ester-5'-monophospate", + "product_ions": "", + "reference_moiety": [ + "U" + ], + "short_name": "pmcmo5U", + "smile": "COC(=O)COc1c[n](C2O[C@H](COP(=O)([O-])[O-])[C@@H](O)[C@H]2O)c(=O)[nH]c1=O" + }, + "426": { + "abbrev": "", + "formula": "C14H16N5O8P", + "lc_elution_comment": "", + "lc_elution_time": "", + "mass_avg": 413.279, + "mass_monoiso": null, + "mass_prot": null, + "name": "wyosine-5'-monophospate", + "product_ions": "", + "reference_moiety": [ + "G" + ], + 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"product_ions": "", + "reference_moiety": [ + "A" + ], + "short_name": "pm6,6Am", + "smile": "CO[C@@H]1[C@H](O)[C@@H](COP(=O)([O-])[O-])O[C@H]1[n]1cnc2c(N(C)C)ncnc12" + }, + "432": { + "abbrev": "`", + "formula": "C15H20N5O8P", + "lc_elution_comment": "", + "lc_elution_time": "", + "mass_avg": 429.322, + "mass_monoiso": null, + "mass_prot": null, + "name": "N6-(cis-hydroxyisopentenyl)adenosine-5'-monophospate", + "product_ions": "", + "reference_moiety": [ + "A" + ], + "short_name": "pio6A", + "smile": "CC(=CCNc1ncnc2c1nc[n]2[C@@H]1O[C@H](COP(=O)([O-])[O-])[C@@H](O)[C@H]1O)CO" + }, + "433": { + "abbrev": "", + "formula": "C12H14N5O8P", + "lc_elution_comment": "", + "lc_elution_time": "", + "mass_avg": 387.242, + "mass_monoiso": null, + "mass_prot": null, + "name": "N6-acetyladenosine-5'-monophospate", + "product_ions": "", + "reference_moiety": [ + "A" + ], + "short_name": "pac6A", + "smile": "CC(=O)Nc1ncnc2c1nc[n]2[C@@H]1O[C@H](COP(=O)([O-])[O-])[C@@H](O)[C@H]1O" + }, + "434": { + 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"", + "lc_elution_time": "", + "mass_avg": 345.205, + "mass_monoiso": null, + "mass_prot": null, + "name": "adenosine-5'-monophosphate", + "product_ions": "", + "reference_moiety": [ + "A" + ], + "short_name": "pA", + "smile": "Nc1c2c([n]([C@H]3[C@H](O)[C@H](O)[C@@H](COP(=O)([O-])[O-])O3)cn2)ncn1" + } +} \ No newline at end of file diff --git a/mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj b/mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj index 9e99d073a..b2fe10135 100644 --- a/mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj +++ b/mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj @@ -10,6 +10,10 @@ true + + + + @@ -34,4 +38,10 @@ + + + PreserveNewest + + + From 28cab2a3070023dbe246410ed5bfa39a882ec80a Mon Sep 17 00:00:00 2001 From: nbollis Date: Tue, 2 Sep 2025 18:50:39 -0500 Subject: [PATCH 2/9] Parsed in internal Mods --- .../Transcriptomics/ModomicsLoaderTests.cs | 66 +++++++++++++++---- .../Transcriptomics/ModomicsLoader.cs | 55 ++++++---------- 2 files changed, 73 insertions(+), 48 deletions(-) diff --git a/mzLib/Test/Transcriptomics/ModomicsLoaderTests.cs b/mzLib/Test/Transcriptomics/ModomicsLoaderTests.cs index e68bf2a4f..afb189465 100644 --- a/mzLib/Test/Transcriptomics/ModomicsLoaderTests.cs +++ b/mzLib/Test/Transcriptomics/ModomicsLoaderTests.cs @@ -2,9 +2,10 @@ using System.IO; using System.Linq; using System.Reflection; +using Chemistry; using NUnit.Framework; +using NUnit.Framework.Legacy; using UsefulProteomicsDatabases.Transcriptomics; -using Omics.Modifications; namespace Test.Transcriptomics { @@ -20,27 +21,66 @@ public void LoadModomics_ParsesEntriesCorrectly() var mods = ModomicsLoader.LoadModomics(); Assert.That(mods, Is.Not.Empty); - Assert.That(mods.All(m => m is Modification), Is.True); Assert.That(mods.All(m => !string.IsNullOrWhiteSpace(m.IdWithMotif)), Is.True); - - // Check a known modification - var m5Cm = mods.FirstOrDefault(m => m.IdWithMotif == "m5Cm"); - Assert.That(m5Cm, Is.Not.Null); - Assert.That(m5Cm.ModificationType, Is.EqualTo("RNA")); - Assert.That(m5Cm.FeatureType, Is.EqualTo("MODOMICS")); - Assert.That(m5Cm.ChemicalFormula, Is.Not.Null); - Assert.That(m5Cm.MonoisotopicMass, Is.GreaterThan(0)); + Assert.That(mods.All(m => m.IdWithMotif.Contains(" on ")), Is.True); } [Test] public void LoadModomics_SkipsUnknownBases() { - var resourceName = "UsefulProteomicsDatabases.Transcriptomics.modomics.json"; - var mods = ModomicsLoader.LoadModomics(); // Should skip modifications with unknown bases (e.g. "X") - Assert.That(mods.Any(m => m.IdWithMotif == "Xm" || m.IdWithMotif == "xX"), Is.False); + Assert.That(mods.Any(m => m.IdWithMotif.Contains("on X")), Is.False); + } + + [Test] + public void LoadModomics_CachesResults() + { + var firstLoad = ModomicsLoader.LoadModomics(); + var secondLoad = ModomicsLoader.LoadModomics(); + Assert.That(ReferenceEquals(firstLoad, secondLoad), Is.True); + } + + [Test] + public static void MethylsHaveCorrectFormula() + { + var mods = ModomicsLoader.LoadModomics(); + var singleMethylMods = mods.Where(m => + System.Text.RegularExpressions.Regex.IsMatch( + m.IdWithMotif, + @"^m\d+[ACGU] on [ACGU]$")) + .ToList(); + + // Exception to normal CH2 formula rule + var m3C = singleMethylMods.FirstOrDefault(m => m.IdWithMotif.StartsWith("m3C on C")); + Assert.That(m3C, Is.Not.Null, "Expected to find m3C modification"); + Assert.That(m3C.ChemicalFormula.Equals(ChemicalFormula.ParseFormula("C1H3")), Is.True, "m3C should have formula C1H3"); + singleMethylMods.Remove(m3C); + + var expectedFormula = ChemicalFormula.ParseFormula("C1H2"); + CollectionAssert.AreEqual( + Enumerable.Repeat(expectedFormula, singleMethylMods.Count), + singleMethylMods.Select(p => p.ChemicalFormula) + ); + + var diMethylMods = mods.Where(m => + m.DatabaseReference["Modomics"].Any(p => p.Contains("dimethyl") && !p.Contains("inosine")) && !m.IdWithMotif.Contains("AA")) + .ToList(); + + var phosphoDiMethyl = diMethylMods.Where(p => p.IdWithMotif.StartsWith("pm")).ToList(); + expectedFormula = ChemicalFormula.ParseFormula("C2H3O3P"); + CollectionAssert.AreEqual( + Enumerable.Repeat(expectedFormula, phosphoDiMethyl.Count), + phosphoDiMethyl.Select(p => p.ChemicalFormula)); + foreach (var pdm in phosphoDiMethyl) + diMethylMods.Remove(pdm); + + expectedFormula = ChemicalFormula.ParseFormula("C2H4"); + CollectionAssert.AreEqual( + Enumerable.Repeat(expectedFormula, diMethylMods.Count).ToList(), + diMethylMods.Select(p => p.ChemicalFormula).ToList() + ); } } } diff --git a/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs b/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs index 63006573e..2f5448651 100644 --- a/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs +++ b/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs @@ -13,7 +13,7 @@ namespace UsefulProteomicsDatabases.Transcriptomics; public static class ModomicsLoader { private static string _modomicsResourceName = "UsefulProteomicsDatabases.Transcriptomics.modomics.json"; - public static List? ModomicsModifications { get; private set; } + internal static List? ModomicsModifications { get; private set; } public static List LoadModomics() { @@ -84,56 +84,41 @@ public static List LoadModomics() .Where(p => p is not null) .Cast() .ToList(); + return ModomicsModifications; } - - public static Modification? ToModification(this ModomicsDto dto) + internal static Modification? ToModification(this ModomicsDto dto) { // Stand in mods for unknown residues, ignore them if (dto.Name.Contains("unknown", System.StringComparison.InvariantCultureIgnoreCase)) - return null!; - - // Caps and other weird mods. TODO: handle those that are appropriate to do so - if (dto.ReferenceMoiety.Count > 1) - return null!; - + return null; + // Caps and other weird mods. TODO: Handle those that are appropriate to do so + if (dto.ReferenceMoiety.Count != 1) + return null; + string refMoiety = dto.ReferenceMoiety.First(); - // Defensive: Only use first reference moiety - var refMoiety = dto.ReferenceMoiety?.FirstOrDefault(); - Nucleotide baseNuc = null; - if (!string.IsNullOrEmpty(refMoiety) && Nucleotide.AllKnownResidues.TryGetValue(refMoiety, out var nuc)) - baseNuc = nuc; + // Filters out X as a moiety which occurs when mods are aimed at purine or pyrimidines TODO: Handle these appropriately + if (!Nucleotide.AllKnownResidues.TryGetValue(refMoiety, out var baseNuc)) + return null; - // Subtract nucleoside formula/mass if possible - ChemicalFormula modFormula = null; - double? modMonoMass = null; - if (!string.IsNullOrWhiteSpace(dto.Formula) && baseNuc != null) - { - var fullFormula = ChemicalFormula.ParseFormula(dto.Formula); - modFormula = new ChemicalFormula(fullFormula); - modFormula.Remove(baseNuc.NucleosideChemicalFormula); - } - if (dto.MassMonoiso > 0 && baseNuc != null) - { - var baseMonoMass = baseNuc.NucleosideChemicalFormula.MonoisotopicMass; - modMonoMass = dto.MassMonoiso - baseMonoMass; - } + // Subtract nucleoside formula/mass + var fullFormula = ChemicalFormula.ParseFormula(dto.Formula); + ChemicalFormula modFormula = new ChemicalFormula(fullFormula); + modFormula.Remove(baseNuc.NucleosideChemicalFormula); - ModificationMotif motif = null; - if (!string.IsNullOrEmpty(refMoiety) && ModificationMotif.TryGetMotif(refMoiety, out var m)) - motif = m; + if (!ModificationMotif.TryGetMotif(refMoiety, out var motif)) + return null; return new Modification( _originalId: dto.ShortName, - _modificationType: "RNA", - _featureType: "MODOMICS", + _modificationType: "Modomics", _target: motif, _locationRestriction: "Anywhere.", _chemicalFormula: modFormula, - _monoisotopicMass: modMonoMass, - _databaseReference: new Dictionary> { { "MODOMICS", new List { dto.ShortName } } }, + _monoisotopicMass: modFormula.MonoisotopicMass, + _databaseReference: new Dictionary> { { "Modomics", new List { dto.ShortName, dto.Name } } }, _keywords: new List { dto.Abbrev, dto.Name } ); } From cacb9461049afd29085890c35f9e225d92a00e32 Mon Sep 17 00:00:00 2001 From: nbollis Date: Tue, 2 Sep 2025 18:56:04 -0500 Subject: [PATCH 3/9] converted to yield return --- .../Transcriptomics/ModomicsLoader.cs | 62 ++++++++++--------- 1 file changed, 32 insertions(+), 30 deletions(-) diff --git a/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs b/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs index 2f5448651..022e643bc 100644 --- a/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs +++ b/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs @@ -80,46 +80,48 @@ public static List LoadModomics() .Where(p => !p.Name.Contains("unknown", System.StringComparison.InvariantCultureIgnoreCase)); ModomicsModifications = dtosToParse - .Select(dto => dto.ToModification()) - .Where(p => p is not null) - .Cast() + .SelectMany(dto => dto.ToModification()) .ToList(); return ModomicsModifications; } - internal static Modification? ToModification(this ModomicsDto dto) + internal static IEnumerable ToModification(this ModomicsDto dto) { + string localizationRestriction = "Anywhere."; + // Stand in mods for unknown residues, ignore them if (dto.Name.Contains("unknown", System.StringComparison.InvariantCultureIgnoreCase)) - return null; + yield break; // Caps and other weird mods. TODO: Handle those that are appropriate to do so if (dto.ReferenceMoiety.Count != 1) - return null; - string refMoiety = dto.ReferenceMoiety.First(); - - // Filters out X as a moiety which occurs when mods are aimed at purine or pyrimidines TODO: Handle these appropriately - if (!Nucleotide.AllKnownResidues.TryGetValue(refMoiety, out var baseNuc)) - return null; - - // Subtract nucleoside formula/mass - var fullFormula = ChemicalFormula.ParseFormula(dto.Formula); - ChemicalFormula modFormula = new ChemicalFormula(fullFormula); - modFormula.Remove(baseNuc.NucleosideChemicalFormula); - - if (!ModificationMotif.TryGetMotif(refMoiety, out var motif)) - return null; - - return new Modification( - _originalId: dto.ShortName, - _modificationType: "Modomics", - _target: motif, - _locationRestriction: "Anywhere.", - _chemicalFormula: modFormula, - _monoisotopicMass: modFormula.MonoisotopicMass, - _databaseReference: new Dictionary> { { "Modomics", new List { dto.ShortName, dto.Name } } }, - _keywords: new List { dto.Abbrev, dto.Name } - ); + yield break; + + foreach (var refMoiety in dto.ReferenceMoiety) + { + // Filters out X as a moiety which occurs when mods are aimed at purine or pyrimidines TODO: Handle these appropriately + if (!Nucleotide.AllKnownResidues.TryGetValue(refMoiety, out var baseNuc)) + continue; + + // Subtract nucleoside formula/mass + var fullFormula = ChemicalFormula.ParseFormula(dto.Formula); + ChemicalFormula modFormula = new ChemicalFormula(fullFormula); + modFormula.Remove(baseNuc.NucleosideChemicalFormula); + + if (!ModificationMotif.TryGetMotif(refMoiety, out var motif)) + continue; + + yield return new Modification( + _originalId: dto.ShortName, + _modificationType: "Modomics", + _target: motif, + _locationRestriction: localizationRestriction, + _chemicalFormula: modFormula, + _monoisotopicMass: modFormula.MonoisotopicMass, + _databaseReference: new Dictionary> { { "Modomics", new List { dto.ShortName, dto.Name } } }, + _keywords: new List { dto.Abbrev, dto.Name } + ); + } } } \ No newline at end of file From 28177da71c14bbac3d9a578a06964cb07e76bc43 Mon Sep 17 00:00:00 2001 From: nbollis Date: Tue, 2 Sep 2025 16:04:34 -0500 Subject: [PATCH 4/9] Multipy operator on chemical formula --- mzLib/Chemistry/ChemicalFormula.cs | 17 +++++++++++++++++ mzLib/Test/TestChemicalFormula.cs | 19 +++++++++++++++++++ 2 files changed, 36 insertions(+) diff --git a/mzLib/Chemistry/ChemicalFormula.cs b/mzLib/Chemistry/ChemicalFormula.cs index d9a24649f..a652f954f 100644 --- a/mzLib/Chemistry/ChemicalFormula.cs +++ b/mzLib/Chemistry/ChemicalFormula.cs @@ -564,7 +564,24 @@ public override string ToString() ChemicalFormula newFormula = new ChemicalFormula(left); newFormula.Add(right); return newFormula; + } + public static ChemicalFormula operator *(ChemicalFormula formula, int multiplier) + { + if (formula == null) + return null; + ChemicalFormula newFormula = new ChemicalFormula(formula); + newFormula.Multiply(multiplier); + return newFormula; + } + + public static ChemicalFormula operator *(int multiplier, ChemicalFormula formula) + { + if (formula == null) + return null; + ChemicalFormula newFormula = new ChemicalFormula(formula); + newFormula.Multiply(multiplier); + return newFormula; } } } \ No newline at end of file diff --git a/mzLib/Test/TestChemicalFormula.cs b/mzLib/Test/TestChemicalFormula.cs index 483974a1f..843115782 100644 --- a/mzLib/Test/TestChemicalFormula.cs +++ b/mzLib/Test/TestChemicalFormula.cs @@ -1029,6 +1029,25 @@ public static void TestAddChemicalFormulaOperator() Assert.AreEqual(null, bothNull); } + [Test] + public static void TestMultiplyChemicalFormulaOperator() + { + ChemicalFormula formula = ChemicalFormula.ParseFormula("C3"); + + var multipliedFormula = formula * 3; + Assert.AreEqual("C9", multipliedFormula.Formula); + + multipliedFormula = 3 * formula; + Assert.AreEqual("C9", multipliedFormula.Formula); + + ChemicalFormula nullFormula = null; + var leftNull = nullFormula * 3; + Assert.AreEqual(null, leftNull); + + var rightNull = 3 * nullFormula; + Assert.AreEqual(null, rightNull); + } + [Test] [TestCase("C", "N", "CN-1")] [TestCase(null, "N", "N-1")] From 57139dd615772040285232a9a7eea8e1fb7c2f49 Mon Sep 17 00:00:00 2001 From: nbollis Date: Wed, 3 Sep 2025 11:59:47 -0500 Subject: [PATCH 5/9] Water chemical formula --- mzLib/Chemistry/Constants.cs | 2 ++ mzLib/Proteomics/AminoAcidPolymer/AminoAcidPolymer.cs | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/mzLib/Chemistry/Constants.cs b/mzLib/Chemistry/Constants.cs index 2b36439a6..79d462622 100644 --- a/mzLib/Chemistry/Constants.cs +++ b/mzLib/Chemistry/Constants.cs @@ -57,5 +57,7 @@ public static class Constants internal const int CarbonAtomicNumber = 6; internal const int HydrogenAtomicNumber = 1; + + public static readonly ChemicalFormula WaterChemicalFormula = ChemicalFormula.ParseFormula("H2O"); } } \ No newline at end of file diff --git a/mzLib/Proteomics/AminoAcidPolymer/AminoAcidPolymer.cs b/mzLib/Proteomics/AminoAcidPolymer/AminoAcidPolymer.cs index 1abb40e99..f29d2f4ba 100644 --- a/mzLib/Proteomics/AminoAcidPolymer/AminoAcidPolymer.cs +++ b/mzLib/Proteomics/AminoAcidPolymer/AminoAcidPolymer.cs @@ -453,7 +453,7 @@ public int ElementCountWithIsotopes(string element) if (_modifications != null) count += _modifications.Where(mod => mod is IHasChemicalFormula).Cast().Sum(mod => mod.ThisChemicalFormula.CountWithIsotopes(element)); - count += ChemicalFormula.ParseFormula("H2O").CountWithIsotopes(element); + count += Constants.WaterChemicalFormula.CountWithIsotopes(element); return count; } From 5acb1b4d7ad524f41166ffc49efde9668155c1d9 Mon Sep 17 00:00:00 2001 From: nbollis Date: Wed, 3 Sep 2025 12:15:54 -0500 Subject: [PATCH 6/9] Moved Mods --- .../Resources/modomicsmods.csv | 450 ++++++++++++++++++ .../modomicsmods.json} | 0 .../UsefulProteomicsDatabases.csproj | 6 +- 3 files changed, 455 insertions(+), 1 deletion(-) create mode 100644 mzLib/UsefulProteomicsDatabases/Resources/modomicsmods.csv rename mzLib/UsefulProteomicsDatabases/{Transcriptomics/modomics.json => Resources/modomicsmods.json} (100%) diff --git a/mzLib/UsefulProteomicsDatabases/Resources/modomicsmods.csv b/mzLib/UsefulProteomicsDatabases/Resources/modomicsmods.csv new file mode 100644 index 000000000..22f9bf01e --- /dev/null +++ b/mzLib/UsefulProteomicsDatabases/Resources/modomicsmods.csv @@ -0,0 +1,450 @@ +"Name","Short Name","RNAMods code (2023)","MODOMICS code new (2023)","Moiety type","SMILES","Reference NucleoBase","MODOMICS code old","Old RNAMods code (old)","MODOMICS Database ID" +"((2R,3S,4R,5S)-5-(2,6-diamino-9H-purin-9-YL)-3,4-dihydroxy-tetrahydrofuran-2-YL)methyl dihydrogen phosphate","N6G","㐏","","nucleotide","[O-]P(OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)[n]1c[n]c2c1[n]c(N)[n]c2N)(=O)[O-]","X","2000000052X","㐏","293" +"((2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3-(2- ((((2R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)- 3,4-dihydroxytetrahydrofuran-2-yl)methyl)amino)-2-oxoethyl)-4- hydroxytetrahydrofuran-2-yl)methyl phosphate","URU","㐿","","nucleotide","[O-]P(OC[C@H]1O[C@H]([C@H](O)[C@@H]1CC(NC[C@H]1O[C@@H](N2C(=O)NC(=O)C=C2)[C@H](O)[C@@H]1O)=O)N1C(NC(=O)C=C1)=O)(=O)[O-]","U","3000000075U","㐿","264" +"(1S)-1,4-anhydro-1-(1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-xylitol","M1Y","㑀","","nucleotide","[O-]P(OC[C@H]1O[C@H]([C@H](O)[C@H]1O)C1C(NC(=O)N(C=1)C)=O)(=O)[O-]","X","3000000048X","㑀","309" +"(1S)-1,4-anhydro-1-(2,4-difluoro-5-methylphenyl)-5-O-phosphono-D-ribitol","NF2","㑁","","nucleotide","[O-]P(OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)c1c(F)cc(F)c(c1)C)(=O)[O-]","X","2000000053X","㑁","246" +"(1S)-1,4-anhydro-1-(3-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-ribitol","3TD","㑂","","nucleotide","[O-]P(OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC(=O)N(C1=O)C)(=O)[O-]","X","2000000008X","㑂","225" +"(2R,4S)-1-[(4R)-3,4-dihydroxytetrahydrofuran-2-YL]-5-[(methylamino)methyl]-1,2,3,4-tetrahydropyrimidine-2,4-diol-5'-monophosphate","pmnm5U","{","2000511551U","nucleotide","CNCc1c(=O)[nH]c(=O)[n]([C@H]2[C@H](O)[C@H](O)[C@@H](COP(=O)([O-])[O-])O2)c1","U","511551U","{","297" +"(2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid","B8N","㑃","","nucleotide","[O-]P(OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1C(N(CC[C@@H](N)C(O)=O)C(=O)N(C=1)C)=O)(=O)[O-]","U","333000012Y","㑃","286" +"(5S)-5-{3-[(3S)-3-amino-3-carboxypropyl]-1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl}-2,5-anhydro-1-O-phosphono-L-arabinitol","C4J","㑄","","nucleotide","[O-]P(OC[C@@H]1O[C@H]([C@H](O)[C@@H]1O)C1C(N(CC[C@H](N)C(O)=O)C(=O)N(C=1)C)=O)(=O)[O-]","X","3000000028X","㑄","260" +"(5S,6R)-5-fluoro-6-hydroxy-pseudouridine-5'-monophosphate","FHU","㑅","","nucleotide","[O-]P(OC[C@H]1O[C@@H]([C@@]2(F)C(=O)NC(=O)N[C@@H]2O)[C@H](O)[C@@H]1O)(=O)[O-]","X","3000000035X","㑅","308" +"(D)-2'-methylselenyl-2'-deoxycytidine-5'-phosphate","CSL","㐃","","nucleotide","Nc1cc[n]([C@@H]2O[C@H](COP([O-])([O-])=O)[C@@H](O)[C@H]2[Se]C)c(=O)n1","C","3000000084C","㐃","245" +"(E)-N-{[4-oxo-1-(5-O-phosphono-beta-D-arabinofuranosyl)-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl]methylidene}glycin","1RN","㑆","","nucleotide","[O-]P(OC[C@H]1O[C@H]([C@@H](O)[C@@H]1O)N1C=C(/C=N/CC(O)=O)C(NC1=S)=O)(=O)[O-]","X","3000000003X","㑆","307" +"1,2'-O-dimethyladenosine","m1Am","œ","2000000901A","nucleoside","CO[C@H]1[C@H]([n]2c3nc[n](c(=N)c3nc2)C)O[C@H](CO)[C@H]1O","A","01A","œ","32" +"1,2'-O-dimethyladenosine-5'-monophosphate","pm1Am","œ","2000901551A","nucleotide","CO[C@@H]1[C@H](O)[C@@H](COP(=O)([O-])[O-])O[C@H]1[n]1cnc2c(=N)[n](C)cnc12","A","01551A","","340" +"1,2'-O-dimethylguanosine","m1Gm","ε","2000000901G","nucleoside","CO[C@H]1[C@H]([n]2c3nc([n](c(=O)c3nc2)C)N)O[C@H](CO)[C@H]1O","G","01G","ε","63" +"1,2'-O-dimethylguanosine-5'-monophosphate","pm1Gm","ε","2000901551G","nucleotide","CO[C@@H]1[C@H](O)[C@@H](COP(=O)([O-])[O-])O[C@H]1[n]1cnc2c(=O)[n](C)c(N)nc12","G","01551G","ε","341" +"1,2'-O-dimethylinosine","m1Im","ξ","2000009019A","nucleoside","CO[C@H]1[C@H]([n]2c3nc[n](c(=O)c3nc2)C)O[C@H](CO)[C@H]1O","A","019A","ξ","33" +"1,2'-O-dimethylinosine-5'-monophosphate","pm1Im","ξ","2009019551A","nucleotide","CO[C@@H]1[C@H](O)[C@@H](COP(=O)([O-])[O-])O[C@H]1[n]1cnc2c(=O)[n](C)cnc12","A","019551A","ξ","342" +"1-(2,6-dideoxy-2-fluoro-5-O-phosphono-alpha-L-talofuranosyl)pyrimidine-2,4(1H,3H)-dione","U5M","㑇","","nucleotide","[O-]P(O[C@@H](C)[C@H]1O[C@@H](N2C(=O)NC(=O)C=C2)[C@H](F)[C@@H]1O)(=O)[O-]","U","3000000067U","㑇","272" 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arabinose-5'-phosphate","UAR","㑔","","nucleotide","[O-]P(OC[C@H]1O[C@H]([C@@H](O)[C@@H]1O)N1C(NC(=O)C=C1)=O)(=O)[O-]","U","3000000069U","㑔","314" +"uridine","U","U","U","nucleoside","OC[C@H]1O[C@@H]([n]2ccc(=O)[nH]c2=O)[C@H](O)[C@@H]1O","U","U","U","60" +"uridine 5'-monothiophosphate","U37","㑕","","nucleotide","O[C@@H]1[C@@H](COP(=O)([S-])[O-])O[C@@H](N2C(=O)NC(=O)C=C2)[C@@H]1O","U","5000000065U","㑕","224" +"uridine 5-oxyacetic acid","cmo5U","V","2000000502U","nucleoside","OC[C@@H]1[C@@H](O)[C@@H](O)[C@H]([n]2c(=O)[nH]c(=O)c(OCC(=O)O)c2)O1","U","502U","V","47" +"uridine 5-oxyacetic acid methyl ester","mcmo5U","υ","2000000503U","nucleoside","COC(COc1c[n](C2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)[nH]c1=O)=O","U","503U","υ","58" +"uridine 5-oxyacetic acid methyl ester-5'-monophospate","pmcmo5U","υ","2000503551U","nucleotide","COC(=O)COc1c[n](C2O[C@H](COP(=O)([O-])[O-])[C@@H](O)[C@H]2O)c(=O)[nH]c1=O","U","503551U","","425" +"uridine-5'-monophosphate","pU","U","U","nucleotide","O=c1cc[n]([C@@H]2O[C@H](COP(=O)([O-])[O-])[C@@H](O)[C@H]2O)c(=O)[nH]1","U","551U","U","255" +"uridine-5'-monophosphate-2',3'-cyclic phosphate","pU2'3'cp","Ҋ","2003377551U","nucleotide","[O-]P1(O[C@H]2[C@@H](O[C@H](COP(=O)([O-])[O-])[C@H]2O1)N1C(NC(=O)C=C1)=O)=O","U","3377551U","","268" +"wybutosine","yW","Y","2000003483G","nucleoside","COC(NC(C(OC)=O)CCc1[n]2c([n](c3c(c2=O)nc[n]3[C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)C)nc1C)=O","G","3483G","Y","30" +"wybutosine-5'-monophosphate","pyW","Y","2003483551G","nucleotide","COC(N[C@@H](C(OC)=O)CCc1[n]2c([n](c3c(c2=O)nc[n]3[C@H]2[C@H](O)[C@H](O)[C@@H](COP(=O)([O-])[O-])O2)C)nc1C)=O","G","3483551G","Y","213" +"wybutosine[C15(S)]-5'-monophosphate","pyyW","ϓ","2034831551G","nucleotide","COC(N[C@H](C(OC)=O)CCc1[n]2c([n](c3c(c2=O)nc[n]3[C@H]2[C@H](O)[C@H](O)[C@@H](COP(=O)([O-])[O-])O2)C)nc1C)=O","G","34831551G","","244" +"wyosine","imG","€","2000000034G","nucleoside","C[n]1c2c(nc[n]2[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)[n]2cc(C)nc12","G","34G","€","139" +"wyosine-5'-monophospate","pimG","€","2000034551G","nucleotide","Cc1c[n]2c(=O)c3nc[n]([C@@H]4O[C@H](COP(=O)([O-])[O-])[C@@H](O)[C@H]4O)c3[n](C)c2n1","G","34551G","","426" \ No newline at end of file diff --git a/mzLib/UsefulProteomicsDatabases/Transcriptomics/modomics.json b/mzLib/UsefulProteomicsDatabases/Resources/modomicsmods.json similarity index 100% rename from mzLib/UsefulProteomicsDatabases/Transcriptomics/modomics.json rename to mzLib/UsefulProteomicsDatabases/Resources/modomicsmods.json diff --git a/mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj b/mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj index b2fe10135..00b756357 100644 --- a/mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj +++ b/mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj @@ -11,6 +11,7 @@ + @@ -39,7 +40,10 @@ - + + PreserveNewest + + PreserveNewest From 6969aa2c188e231d96051d0e0a3025360a56a5f4 Mon Sep 17 00:00:00 2001 From: nbollis Date: Wed, 3 Sep 2025 12:16:14 -0500 Subject: [PATCH 7/9] Added interface to modification --- mzLib/Omics/Modifications/Modification.cs | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) diff --git a/mzLib/Omics/Modifications/Modification.cs b/mzLib/Omics/Modifications/Modification.cs index 756b7fcce..60899d8b1 100644 --- a/mzLib/Omics/Modifications/Modification.cs +++ b/mzLib/Omics/Modifications/Modification.cs @@ -8,7 +8,7 @@ namespace Omics.Modifications /// Represents a modification /// Mods.txt format was taken from https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs/ptmlist.txt /// - public class Modification : IComparable + public class Modification : IComparable, IHasChemicalFormula { public string IdWithMotif { get; protected set; } public string OriginalId { get; protected set; } @@ -18,18 +18,12 @@ public class Modification : IComparable public ModificationMotif Target { get; protected set; } public string LocationRestriction { get; protected set; } public ChemicalFormula ChemicalFormula { get; protected set; } - private double? monoisotopicMass = null; + private readonly double? _monoisotopicMass = null; public double? MonoisotopicMass { - get - { - return ClassExtensions.RoundedDouble(monoisotopicMass); - } - private set - { - monoisotopicMass = value; - } + get => _monoisotopicMass.RoundedDouble(); + private init => _monoisotopicMass = value; } public Dictionary> DatabaseReference { get; protected set; } @@ -313,5 +307,9 @@ public int CompareTo(Modification? other) return Nullable.Compare(this.MonoisotopicMass, other.MonoisotopicMass); } + + // IHasChemicalFormula Implementations. + double IHasMass.MonoisotopicMass => MonoisotopicMass.Value; + public ChemicalFormula ThisChemicalFormula => this.ChemicalFormula; } } \ No newline at end of file From 9831b0826d4fed41081eec86e289645a0e949341 Mon Sep 17 00:00:00 2001 From: nbollis Date: Wed, 3 Sep 2025 12:54:13 -0500 Subject: [PATCH 8/9] nucleotide and side parsing --- .../Transcriptomics/ModomicsDto.cs | 1 + .../Transcriptomics/ModomicsLoader.cs | 86 +++++++++++++++---- 2 files changed, 71 insertions(+), 16 deletions(-) diff --git a/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsDto.cs b/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsDto.cs index 0ca6935c3..d57470a2a 100644 --- a/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsDto.cs +++ b/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsDto.cs @@ -20,4 +20,5 @@ public class ModomicsDto public List ReferenceMoiety { get; set; } public string ShortName { get; set; } public string Smile { get; set; } + public string MoietyType { get; set; } } \ No newline at end of file diff --git a/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs b/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs index 022e643bc..cf15348dc 100644 --- a/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs +++ b/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs @@ -7,12 +7,19 @@ using Chemistry; using Transcriptomics; using System.Reflection; +using System.Diagnostics; +using CsvHelper; +using System.Globalization; namespace UsefulProteomicsDatabases.Transcriptomics; public static class ModomicsLoader { - private static string _modomicsResourceName = "UsefulProteomicsDatabases.Transcriptomics.modomics.json"; + // Json gives us most of the information + private static string _modomicsJsonPath = "UsefulProteomicsDatabases.Resources.modomics.json"; + + // Csv tells us if the chemical formula is for a nucleotide or nucleoside. + private static string _modomicsCsvPath = "UsefulProteomicsDatabases.Resources.modomics.csv"; internal static List? ModomicsModifications { get; private set; } public static List LoadModomics() @@ -24,15 +31,35 @@ public static List LoadModomics() // Load embedded resource var info = Assembly.GetExecutingAssembly().GetName().Name; - var modomicsStream = Assembly.GetExecutingAssembly().GetManifestResourceStream($"{info}.Transcriptomics.modomics.json"); + var modomicsJsonStream = Assembly.GetExecutingAssembly().GetManifestResourceStream($"{info}.Resources.modomicsmods.json"); + + if (modomicsJsonStream is null) + throw new FileNotFoundException("Could not find embedded resource", _modomicsJsonPath); + var jsonDict = JsonSerializer.Deserialize>(modomicsJsonStream)!; - if (modomicsStream is null) - throw new FileNotFoundException("Could not find embedded resource", _modomicsResourceName); - var modsDict = JsonSerializer.Deserialize>(modomicsStream)!; + var modomicsCsvStream = Assembly.GetExecutingAssembly().GetManifestResourceStream($"{info}.Resources.modomicsmods.csv"); + if (modomicsCsvStream is null) + throw new FileNotFoundException("Could not find embedded resource", _modomicsCsvPath); - // Parse each entry into a DTO + // Parse CSV to get MoietyType (nucleotide vs nucleoside) mapping + var moietyTypeByShortName = new Dictionary(); + using (var reader = new StreamReader(modomicsCsvStream)) + using (var csv = new CsvReader(reader, CultureInfo.InvariantCulture)) + { + csv.Read(); + csv.ReadHeader(); + while (csv.Read()) + { + var shortName = csv.GetField("Short Name"); + var moietyType = csv.GetField("Moiety type"); + if (!string.IsNullOrWhiteSpace(shortName) && !string.IsNullOrWhiteSpace(moietyType)) + moietyTypeByShortName[shortName] = moietyType; + } + } + + // Parse each entry into a DTO from the json var dtos = new List(); - foreach (var kvp in modsDict) + foreach (var kvp in jsonDict) { var modEntry = kvp.Value; @@ -70,16 +97,14 @@ public static List LoadModomics() ProductIons = productIons, ReferenceMoiety = referenceMoiety, ShortName = shortName, - Smile = smile + Smile = smile, + MoietyType = moietyTypeByShortName.GetValueOrDefault(shortName) }; dtos.Add(dto); } - var dtosToParse = dtos - .Where(p => !p.Name.Contains("unknown", System.StringComparison.InvariantCultureIgnoreCase)); - - ModomicsModifications = dtosToParse + ModomicsModifications = dtos .SelectMany(dto => dto.ToModification()) .ToList(); @@ -89,6 +114,7 @@ public static List LoadModomics() internal static IEnumerable ToModification(this ModomicsDto dto) { string localizationRestriction = "Anywhere."; + string modificationType = "Modomics"; // Stand in mods for unknown residues, ignore them if (dto.Name.Contains("unknown", System.StringComparison.InvariantCultureIgnoreCase)) @@ -96,7 +122,7 @@ internal static IEnumerable ToModification(this ModomicsDto dto) // Caps and other weird mods. TODO: Handle those that are appropriate to do so if (dto.ReferenceMoiety.Count != 1) - yield break; + Debugger.Break(); foreach (var refMoiety in dto.ReferenceMoiety) { @@ -107,20 +133,48 @@ internal static IEnumerable ToModification(this ModomicsDto dto) // Subtract nucleoside formula/mass var fullFormula = ChemicalFormula.ParseFormula(dto.Formula); ChemicalFormula modFormula = new ChemicalFormula(fullFormula); - modFormula.Remove(baseNuc.NucleosideChemicalFormula); + + if (dto.MoietyType == "nucleoside") + { + modFormula.Remove(baseNuc.NucleosideChemicalFormula); + } + else if (dto.MoietyType == "nucleotide") + { + var sugarToRemove = baseNuc.NucleosideChemicalFormula - baseNuc.BaseChemicalFormula - Constants.WaterChemicalFormula; + modFormula.Remove(sugarToRemove); + } + else if (dto.MoietyType == "base") + { + // These are unique bases due to modifications, will need to create a new nucleotide or create an x->This mod for each nucleotide. + yield break; + } + else + { + // fallback or throw + modFormula.Remove(baseNuc.NucleosideChemicalFormula); + } + //if (dto.Name.Contains("cap")) // Caps are in the database as mod + sugar + //{ + // var sugarToRemove = baseNuc.NucleosideChemicalFormula - baseNuc.BaseChemicalFormula - Constants.WaterChemicalFormula; + // modFormula.Remove(sugarToRemove); + //} + //else // The rest are in the database as full nucleotides. + //{ + // modFormula.Remove(baseNuc.NucleosideChemicalFormula); + //} if (!ModificationMotif.TryGetMotif(refMoiety, out var motif)) continue; yield return new Modification( _originalId: dto.ShortName, - _modificationType: "Modomics", + _modificationType: modificationType, _target: motif, _locationRestriction: localizationRestriction, _chemicalFormula: modFormula, _monoisotopicMass: modFormula.MonoisotopicMass, _databaseReference: new Dictionary> { { "Modomics", new List { dto.ShortName, dto.Name } } }, - _keywords: new List { dto.Abbrev, dto.Name } + _keywords: new List { dto.Abbrev, dto.ShortName, dto.Name } ); } } From 96a43384d4f175a8108efb6f78748bba299476af Mon Sep 17 00:00:00 2001 From: nbollis Date: Wed, 3 Sep 2025 13:38:49 -0500 Subject: [PATCH 9/9] fixed up tests --- .../Transcriptomics/ModomicsLoaderTests.cs | 19 ++++++++---------- .../Transcriptomics/ModomicsLoader.cs | 20 +++++++------------ 2 files changed, 15 insertions(+), 24 deletions(-) diff --git a/mzLib/Test/Transcriptomics/ModomicsLoaderTests.cs b/mzLib/Test/Transcriptomics/ModomicsLoaderTests.cs index afb189465..0ad6b62ac 100644 --- a/mzLib/Test/Transcriptomics/ModomicsLoaderTests.cs +++ b/mzLib/Test/Transcriptomics/ModomicsLoaderTests.cs @@ -45,7 +45,10 @@ public void LoadModomics_CachesResults() [Test] public static void MethylsHaveCorrectFormula() { - var mods = ModomicsLoader.LoadModomics(); + var mods = ModomicsLoader.LoadModomics() + .Where(p => !p.ModificationType.Contains("Cap")) + .ToList(); + var singleMethylMods = mods.Where(m => System.Text.RegularExpressions.Regex.IsMatch( m.IdWithMotif, @@ -65,16 +68,10 @@ public static void MethylsHaveCorrectFormula() ); var diMethylMods = mods.Where(m => - m.DatabaseReference["Modomics"].Any(p => p.Contains("dimethyl") && !p.Contains("inosine")) && !m.IdWithMotif.Contains("AA")) - .ToList(); - - var phosphoDiMethyl = diMethylMods.Where(p => p.IdWithMotif.StartsWith("pm")).ToList(); - expectedFormula = ChemicalFormula.ParseFormula("C2H3O3P"); - CollectionAssert.AreEqual( - Enumerable.Repeat(expectedFormula, phosphoDiMethyl.Count), - phosphoDiMethyl.Select(p => p.ChemicalFormula)); - foreach (var pdm in phosphoDiMethyl) - diMethylMods.Remove(pdm); + System.Text.RegularExpressions.Regex.IsMatch( + m.IdWithMotif, + @"^m\d+[ACGU]m on [ACGU]$")) + .ToList(); expectedFormula = ChemicalFormula.ParseFormula("C2H4"); CollectionAssert.AreEqual( diff --git a/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs b/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs index cf15348dc..4a429c628 100644 --- a/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs +++ b/mzLib/UsefulProteomicsDatabases/Transcriptomics/ModomicsLoader.cs @@ -105,6 +105,7 @@ public static List LoadModomics() } ModomicsModifications = dtos + .Where(p => p.Formula != string.Empty) .SelectMany(dto => dto.ToModification()) .ToList(); @@ -120,9 +121,11 @@ internal static IEnumerable ToModification(this ModomicsDto dto) if (dto.Name.Contains("unknown", System.StringComparison.InvariantCultureIgnoreCase)) yield break; - // Caps and other weird mods. TODO: Handle those that are appropriate to do so - if (dto.ReferenceMoiety.Count != 1) - Debugger.Break(); + if (dto.Name.Contains(" cap")) + { + modificationType = "5' Terminal Cap"; + localizationRestriction = "5'-terminal."; + } foreach (var refMoiety in dto.ReferenceMoiety) { @@ -151,17 +154,8 @@ internal static IEnumerable ToModification(this ModomicsDto dto) else { // fallback or throw - modFormula.Remove(baseNuc.NucleosideChemicalFormula); + yield break; } - //if (dto.Name.Contains("cap")) // Caps are in the database as mod + sugar - //{ - // var sugarToRemove = baseNuc.NucleosideChemicalFormula - baseNuc.BaseChemicalFormula - Constants.WaterChemicalFormula; - // modFormula.Remove(sugarToRemove); - //} - //else // The rest are in the database as full nucleotides. - //{ - // modFormula.Remove(baseNuc.NucleosideChemicalFormula); - //} if (!ModificationMotif.TryGetMotif(refMoiety, out var motif)) continue;