Markup-driven lipid CID spectrum generator (experimental)

.gitignore

@@ -238,4 +238,4 @@ Assemblies/*.dll
 /src/MSFINDER/MsfinderCommonStandard/Resources/InchikeyClassyfireDB-VS*.icd
 /src/MSFINDER/MsfinderCommonStandard/Resources/MINEs-StructureDB-vs*.msd
 /src/MSFINDER/MsfinderCommonStandard/Resources/MsfinderStructureDB-VS*.esd
-/src/MSFINDER/MsfinderCommonStandard/Resources/MSMS-DBs-vs*.etm
+/src/MSFINDER/MsfinderCommonStandard/Resources/MSMS-DBs-vs*.etm

MsdialWorkbench.sln

@@ -190,6 +190,10 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "docs", "docs", "{DC2AD876-6
 		THIRD-PARTY-LICENSE-README.md = THIRD-PARTY-LICENSE-README.md
 	EndProjectSection
 EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "CompMs.Common.Lipidomics.SourceGenerator", "src\Common\CompMs.Common.Lipidomics.SourceGenerator\CompMs.Common.Lipidomics.SourceGenerator.csproj", "{DF6C0B4E-9148-423A-A8A0-F17B034FEEFA}"
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "CompMs.Common.Lipidomics.SourceGeneratorTests", "tests\Common\CompMs.Common.Lipidomics.SourceGeneratorTests\CompMs.Common.Lipidomics.SourceGeneratorTests.csproj", "{ACFCA3C6-FE86-4AE0-A890-D3C01E206A46}"
+EndProject
 Global
 	GlobalSection(SolutionConfigurationPlatforms) = preSolution
 		Debug vendor unsupported|Any CPU = Debug vendor unsupported|Any CPU
@@ -1864,6 +1868,46 @@ Global
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+		{DF6C0B4E-9148-423A-A8A0-F17B034FEEFA}.Debug vendor unsupported|Any CPU.ActiveCfg = Debug|Any CPU
+		{DF6C0B4E-9148-423A-A8A0-F17B034FEEFA}.Debug vendor unsupported|Any CPU.Build.0 = Debug|Any CPU
+		{DF6C0B4E-9148-423A-A8A0-F17B034FEEFA}.Debug vendor unsupported|x64.ActiveCfg = Debug|Any CPU
+		{DF6C0B4E-9148-423A-A8A0-F17B034FEEFA}.Debug vendor unsupported|x64.Build.0 = Debug|Any CPU
+		{DF6C0B4E-9148-423A-A8A0-F17B034FEEFA}.Debug with args|Any CPU.ActiveCfg = Debug|Any CPU
+		{DF6C0B4E-9148-423A-A8A0-F17B034FEEFA}.Debug with args|Any CPU.Build.0 = Debug|Any CPU
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+		{ACFCA3C6-FE86-4AE0-A890-D3C01E206A46}.Debug vendor unsupported|Any CPU.Build.0 = Debug|Any CPU
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+		{ACFCA3C6-FE86-4AE0-A890-D3C01E206A46}.Debug vendor unsupported|x64.Build.0 = Debug|Any CPU
+		{ACFCA3C6-FE86-4AE0-A890-D3C01E206A46}.Debug with args|Any CPU.ActiveCfg = Debug|Any CPU
+		{ACFCA3C6-FE86-4AE0-A890-D3C01E206A46}.Debug with args|Any CPU.Build.0 = Debug|Any CPU
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+		{ACFCA3C6-FE86-4AE0-A890-D3C01E206A46}.Debug with args|x64.Build.0 = Debug|Any CPU
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+		{ACFCA3C6-FE86-4AE0-A890-D3C01E206A46}.Debug|x64.Build.0 = Debug|Any CPU
+		{ACFCA3C6-FE86-4AE0-A890-D3C01E206A46}.Release vendor unsupported|Any CPU.ActiveCfg = Release|Any CPU
+		{ACFCA3C6-FE86-4AE0-A890-D3C01E206A46}.Release vendor unsupported|Any CPU.Build.0 = Release|Any CPU
+		{ACFCA3C6-FE86-4AE0-A890-D3C01E206A46}.Release vendor unsupported|x64.ActiveCfg = Release|Any CPU
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 	EndGlobalSection
 	GlobalSection(SolutionProperties) = preSolution
 		HideSolutionNode = FALSE
@@ -1888,6 +1932,7 @@ Global
 		{D8B8B716-2710-41F3-9C0F-A6709420C96F} = {B1471530-7779-4A57-9664-1E3A06F1A449}
 		{AF6A5BEF-8D19-4846-BC82-03782B53C092} = {765ED28C-F085-4C96-8E81-683BBAE67B01}
 		{B1A4AFD3-ACF3-48B7-A55C-E37E082FEEBD} = {26C4466E-49D5-404B-8777-8A92DDBBC35D}
+		{ACFCA3C6-FE86-4AE0-A890-D3C01E206A46} = {765ED28C-F085-4C96-8E81-683BBAE67B01}
 	EndGlobalSection
 	GlobalSection(ExtensibilityGlobals) = postSolution
 		SolutionGuid = {A1654BE4-26EA-48AA-841E-6C2E3DEBDCCF}

src/Common/CommonStandard/Lipidomics/ADGGALipidParser.cs

@@ -0,0 +1,56 @@
+using CompMs.Common.Enum;
+using CompMs.Common.FormulaGenerator.DataObj;
+using System.Linq;
+using System.Text.RegularExpressions;
+
+namespace CompMs.Common.Lipidomics
+{
+    public class ADGGALipidParser : ILipidParser
+    {
+        public string Target { get; } = "ADGGA";
+
+        private static readonly TotalChainParser chainsParser = TotalChainParser.BuildParser(3);
+        public static readonly string Pattern = $"^ADGGA\\s*(\\(O-)?(?<sn>{chainsParser.Pattern})$";
+        private static readonly Regex pattern = new Regex(Pattern, RegexOptions.Compiled);
+        private static readonly string AcylChainsPattern = $"(?<Chain>{AcylChainParser.Pattern})";
+
+        private static readonly TotalChainParser chainsParserSub = TotalChainParser.BuildParser(2);
+        public static readonly string PatternSub = $"^ADGGA\\s*\\(O-(?<OAcyl>{AcylChainsPattern})\\)?(?<sn1sn2>{chainsParserSub.Pattern})*?$";
+        private static readonly Regex patternSub = new Regex(PatternSub, RegexOptions.Compiled);
+
+
+        private static readonly double Skelton = new[]
+        {
+            MassDiffDictionary.CarbonMass * 9,
+            MassDiffDictionary.HydrogenMass * 13,
+            MassDiffDictionary.OxygenMass * 9,
+        }.Sum();
+
+
+        public ILipid Parse(string lipidStr)
+        {
+            var match = pattern.Match(lipidStr); //need consider
+            if (match.Success)
+            {
+                var group = match.Groups;
+                var chains = chainsParser.Parse(group["sn"].Value);
+                return new Lipid(LbmClass.ADGGA, Skelton + chains.Mass, chains);
+            }
+            else
+            {
+                var matchSub = patternSub.Match(lipidStr);
+                if (matchSub.Success)
+                {
+                    matchSub = patternSub.Match(lipidStr.Replace("_","/"));
+                    var groupSub = matchSub.Groups;
+                    if (groupSub["sn1sn2"].Value != "")
+                    {
+                        var chains = chainsParser.Parse(groupSub["OAcyl"].Value + "/" + groupSub["sn1sn2"].Value);
+                        return new Lipid(LbmClass.ADGGA, Skelton + chains.Mass, chains);
+                    }
+                }
+            }
+            return null;
+        }
+    }
+}

src/Common/CommonStandard/Lipidomics/AHexCerLipidParser.cs

@@ -0,0 +1,115 @@
+using CompMs.Common.Enum;
+using CompMs.Common.FormulaGenerator.DataObj;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text.RegularExpressions;
+
+namespace CompMs.Common.Lipidomics
+{
+    public class AHexCerLipidParser : ILipidParser
+    {
+        public string Target { get; } = "AHexCer";
+
+        private static readonly AHexCerChainParser chainsParser = new AHexCerChainParser();
+        public static readonly string AHexCerPattern = $"^AHexCer\\s*(?<sn>{chainsParser.Pattern})$";
+        private static readonly Regex AHexCerpattern = new Regex(AHexCerPattern, RegexOptions.Compiled);
+
+        private static readonly double Skelton = new[]
+        {
+            MassDiffDictionary.CarbonMass * 6,
+            MassDiffDictionary.HydrogenMass * 9,
+            MassDiffDictionary.OxygenMass * 5,
+        }.Sum();
+
+
+        public ILipid Parse(string lipidStr)
+        {
+            var match = AHexCerpattern.Match(lipidStr);
+            if (match.Success)
+            {
+                var group = match.Groups;
+                var chains = chainsParser.Parse(group["sn"].Value);
+                if (group["MolecularSpeciesLevel"].Success)
+                {
+                    return new Lipid(LbmClass.AHexCer, Skelton + MassDiffDictionary.OxygenMass - MassDiffDictionary.HydrogenMass + chains.Mass, chains);
+                }
+                return new Lipid(LbmClass.AHexCer, Skelton + chains.Mass, chains);
+            }
+            return null;
+        }
+    }
+    public class AHexCerChainParser : TotalChainParser
+    {
+        private static readonly string CarbonPattern = @"(?<carbon>\d+)";
+        private static readonly string DoubleBondPattern = @"(?<db>\d+)";
+        private static readonly string OxidizedPattern = @";(?<ox>O(?<oxnum>\d+)?)";
+        private static readonly string AcylChainsPattern = $"(?<CerAcyl>{AcylChainParser.Pattern})?";
+        private static readonly string OAcylPattern = $"\\(O-(?<OChain>{CarbonPattern}:{DoubleBondPattern})\\)";
+
+        private static readonly AcylChainParser AcylParser = new AcylChainParser();
+        private static readonly SphingoChainParser SphingoParser = new SphingoChainParser();
+
+        public int ChainCount { get; }
+        public int Capacity { get; }
+        public string Pattern { get; }
+        public bool HasSphingosine { get; }
+        private readonly Regex Expression;
+
+        private static readonly int chainCount = 3;
+        private static readonly int capacity = 3;
+        private readonly bool hasSphingosine;
+
+        public AHexCerChainParser()
+            : base(chainCount: chainCount, capacity: capacity, hasSphingosine: true, hasEther: false, atLeastSpeciesLevel: false)
+        {
+            ChainCount = chainCount;
+            Capacity = capacity;
+            var submolecularLevelPattern = $"(?<TotalChain>{CarbonPattern}:{DoubleBondPattern}({OxidizedPattern})?)";
+            var molecularSpeciesLevelPattern =
+                $"(?<MolecularSpeciesLevel>{OAcylPattern}(?<Sph>{CarbonPattern}:{DoubleBondPattern}({OxidizedPattern})?)?)";
+            var positionLevelPattern =
+                $"(?<PositionLevel>{OAcylPattern}(?<Sph>{SphingoChainParser.Pattern})/({AcylChainsPattern}))";
+
+            var totalPattern = new[] { positionLevelPattern, molecularSpeciesLevelPattern, submolecularLevelPattern };
+            Pattern = string.Join("|", totalPattern);
+            Expression = new Regex(Pattern, RegexOptions.Compiled);
+            HasSphingosine = hasSphingosine;
+        }
+
+        public new ITotalChain Parse(string lipidStr)
+        {
+            var match = Expression.Match(lipidStr);
+            if (match.Success)
+            {
+                var groups = match.Groups;
+                if (groups["TotalChain"].Success)
+                {
+                    return ParseTotalChains(groups, ChainCount);
+                }
+                else
+                {
+                    var chains = ParsePositionLevelChains(groups);
+                    return chains;
+                }
+            }
+            return null;
+        }
+        private new PositionLevelChains ParsePositionLevelChains(GroupCollection groups)
+        {
+            var OAcyl = groups["OChain"].Captures.Cast<Capture>();
+            var Sph = SphingoParser.Parse(groups["Sph"].Value);
+            var CerAcyl = AcylParser.Parse(groups["CerAcyl"].Value);
+            var chains = OAcyl
+                    .Select(c => AcylParser.Parse(c.Value))
+                    .ToList();
+            chains.Add(Sph);
+            if (CerAcyl != null)
+            {
+                chains.Add(CerAcyl);
+            }
+            return new PositionLevelChains(chains.ToArray());
+        }
+
+    }
+}
+

src/Common/CommonStandard/Lipidomics/ASHexCerLipidParser.cs

@@ -0,0 +1,116 @@
+using CompMs.Common.Enum;
+using CompMs.Common.FormulaGenerator.DataObj;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text.RegularExpressions;
+
+namespace CompMs.Common.Lipidomics
+{
+    public class ASHexCerLipidParser : ILipidParser
+    {
+        public string Target { get; } = "ASHexCer";
+
+        private static readonly ASHexCerChainParser chainsParser = new ASHexCerChainParser();
+        public static readonly string ASHexCerPattern = $"^ASHexCer\\s*(?<sn>{chainsParser.Pattern})$";
+        private static readonly Regex ASHexCerpattern = new Regex(ASHexCerPattern, RegexOptions.Compiled);
+
+        private static readonly double Skelton = new[]
+        {
+            MassDiffDictionary.CarbonMass * 6,
+            MassDiffDictionary.HydrogenMass * 9,
+            MassDiffDictionary.OxygenMass * 8,
+            MassDiffDictionary.SulfurMass * 1,
+        }.Sum();
+
+
+        public ILipid Parse(string lipidStr)
+        {
+            var match = ASHexCerpattern.Match(lipidStr);
+            if (match.Success)
+            {
+                var group = match.Groups;
+                var chains = chainsParser.Parse(group["sn"].Value);
+                if (group["MolecularSpeciesLevel"].Success)
+                {
+                    return new Lipid(LbmClass.ASHexCer, Skelton + MassDiffDictionary.OxygenMass - MassDiffDictionary.HydrogenMass + chains.Mass, chains);
+                }
+                return new Lipid(LbmClass.ASHexCer, Skelton + chains.Mass, chains);
+            }
+            return null;
+        }
+    }
+    public class ASHexCerChainParser : TotalChainParser
+    {
+        private static readonly string CarbonPattern = @"(?<carbon>\d+)";
+        private static readonly string DoubleBondPattern = @"(?<db>\d+)";
+        private static readonly string OxidizedPattern = @";(?<ox>O(?<oxnum>\d+)?)";
+        private static readonly string AcylChainsPattern = $"(?<CerAcyl>{AcylChainParser.Pattern})?";
+        private static readonly string OAcylPattern = $"\\(O-(?<OChain>{AcylChainParser.Pattern})\\)";
+
+        private static readonly AcylChainParser AcylParser = new AcylChainParser();
+        private static readonly SphingoChainParser SphingoParser = new SphingoChainParser();
+
+        public int ChainCount { get; }
+        public int Capacity { get; }
+        public string Pattern { get; }
+        public bool HasSphingosine { get; }
+        private readonly Regex Expression;
+
+        private static readonly int chainCount = 3;
+        private static readonly int capacity = 3;
+        private readonly bool hasSphingosine;
+
+        public ASHexCerChainParser()
+            : base(chainCount: chainCount, capacity: capacity, hasSphingosine: true, hasEther: false, atLeastSpeciesLevel: false)
+        {
+            ChainCount = chainCount;
+            Capacity = capacity;
+            var submolecularLevelPattern = $"(?<TotalChain>{CarbonPattern}:{DoubleBondPattern}({OxidizedPattern})?)";
+            var molecularSpeciesLevelPattern =
+                $"(?<MolecularSpeciesLevel>{OAcylPattern}(?<Sph>{CarbonPattern}:{DoubleBondPattern}({OxidizedPattern})?)?)";
+            var positionLevelPattern =
+                $"(?<PositionLevel>{OAcylPattern}(?<Sph>{SphingoChainParser.Pattern})/({AcylChainsPattern}))";
+
+            var totalPattern = new[] { positionLevelPattern, molecularSpeciesLevelPattern, submolecularLevelPattern };
+            Pattern = string.Join("|", totalPattern);
+            Expression = new Regex(Pattern, RegexOptions.Compiled);
+            HasSphingosine = hasSphingosine;
+        }
+
+        public new ITotalChain Parse(string lipidStr)
+        {
+            var match = Expression.Match(lipidStr);
+            if (match.Success)
+            {
+                var groups = match.Groups;
+                if (groups["TotalChain"].Success)
+                {
+                    return ParseTotalChains(groups, ChainCount);
+                }
+                else
+                {
+                    var chains = ParsePositionLevelChains(groups);
+                    return chains;
+                }
+            }
+            return null;
+        }
+        private new PositionLevelChains ParsePositionLevelChains(GroupCollection groups)
+        {
+            var OAcyl = groups["OChain"].Captures.Cast<Capture>();
+            var Sph = SphingoParser.Parse(groups["Sph"].Value);
+            var CerAcyl = AcylParser.Parse(groups["CerAcyl"].Value);
+            var chains = OAcyl
+                    .Select(c => AcylParser.Parse(c.Value))
+                    .ToList();
+            chains.Add(Sph);
+            if (CerAcyl != null)
+            {
+                chains.Add(CerAcyl);
+            }
+            return new PositionLevelChains(chains.ToArray());
+        }
+
+    }
+}
+