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Merged
htsugawa merged 4 commits into from
Feb 18, 2026
Merged

Add sdf format exporter #709

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0d60619
Add sdf format exporter
Feb 13, 2026
e043a19
fix tag line("_" change to " ")
Feb 13, 2026
8cff4a1
minor
Feb 17, 2026
b098b31
change to use stringBuilder
Feb 17, 2026
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2 changes: 1 addition & 1 deletion src/Common/CommonStandard/Enum/CommonEnums.cs
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Expand Up @@ -39,7 +39,7 @@ public enum RiCompoundType { Alkanes, Fames }
public enum AlignmentIndexType { RT, RI }
public enum TargetOmics { Metabolomics, Lipidomics, Proteomics }
public enum Ionization { ESI, EI }
public enum ExportSpectraFileFormat { mgf, msp, txt, mat, ms }
public enum ExportSpectraFileFormat { mgf, msp, txt, mat, ms, sdf }
public enum ExportspectraType { profile, centroid, deconvoluted }
public enum IonAbundanceUnit {
Intensity, Height, Area, pmol, fmol, ng, pg,
Expand Down
28 changes: 28 additions & 0 deletions src/MSDIAL5/MsdialCore/Export/AlignmentSdfExporter.cs
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@@ -0,0 +1,28 @@
using CompMs.MsdialCore.DataObj;
using CompMs.MsdialCore.MSDec;
using System.IO;

namespace CompMs.MsdialCore.Export;

public sealed class AlignmentSdfExporter : IAlignmentSpectraExporter
{
private readonly bool _exportNoMs2Molecule;
private readonly bool _set2dCoordinates;
public AlignmentSdfExporter(bool exportNoMs2Molecule, bool set2dCoordinates)
{
_exportNoMs2Molecule = exportNoMs2Molecule;
_set2dCoordinates = set2dCoordinates;
}
public AlignmentSdfExporter() : this(exportNoMs2Molecule: true, set2dCoordinates: true) { }

void IAlignmentSpectraExporter.Export(Stream stream, AlignmentSpotProperty spot, MSDecResult msdecResult)
{
SpectraExport.SaveSpectraTableAsSdfFormat(
stream,
spot,
msdecResult.Spectrum,
_exportNoMs2Molecule,
_set2dCoordinates
);
}
}
31 changes: 31 additions & 0 deletions src/MSDIAL5/MsdialCore/Export/AnalysisSdfExporter.cs
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@@ -0,0 +1,31 @@
using CompMs.MsdialCore.DataObj;
using CompMs.MsdialCore.Parser;
using System;
using System.IO;

namespace CompMs.MsdialCore.Export
{
public sealed class AnalysisSdfExporter : IAnalysisExporter<ChromatogramPeakFeatureCollection>
{
private readonly Func<AnalysisFileBean, IMsScanPropertyLoader<ChromatogramPeakFeature>> _loaderFactory;

public AnalysisSdfExporter(Func<AnalysisFileBean, IMsScanPropertyLoader<ChromatogramPeakFeature>> loaderFuctory) {
_loaderFactory = loaderFuctory ?? throw new ArgumentNullException(nameof(loaderFuctory));
}
private readonly bool _exportNoMs2Molecule = true;
private readonly bool _set2dCoordinates = true;

void IAnalysisExporter<ChromatogramPeakFeatureCollection>.Export(Stream stream, AnalysisFileBean analysisFile, ChromatogramPeakFeatureCollection peakFeatureCollection, ExportStyle exportStyle) {
var loader = _loaderFactory(analysisFile);
foreach (var peak in peakFeatureCollection.Items) {
SpectraExport.SaveSpectraTableAsSdfFormat(
stream,
peak,
loader.Load(peak).Spectrum,
_exportNoMs2Molecule,
_set2dCoordinates
);
}
}
}
}
160 changes: 159 additions & 1 deletion src/MSDIAL5/MsdialCore/Export/SpectraExport.cs
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Expand Up @@ -9,8 +9,13 @@
using CompMs.MsdialCore.DataObj;
using CompMs.MsdialCore.Parameter;
using CompMs.MsdialCore.Utility;
using NCDK;
using NCDK.IO;
using NCDK.Layout;
using NCDK.Smiles;
using System;
using System.Collections.Generic;
using System.Globalization;
using System.IO;
using System.Linq;
using System.Text;
Expand All @@ -34,6 +39,9 @@ public static void SaveSpectraTable(
case ExportSpectraFileFormat.mgf:
SaveSpectraTableAsMgfFormat(exportStream, chromPeakFeature, scan.Spectrum);
break;
case ExportSpectraFileFormat.sdf:
SaveSpectraTableAsSdfFormat(exportStream, chromPeakFeature, scan.Spectrum, true, true);
break;
case ExportSpectraFileFormat.mat:
SaveSpectraTableAsMatFormat(exportStream, chromPeakFeature, scan.Spectrum, spectrumList, mapper, parameter);
break;
Expand All @@ -53,14 +61,18 @@ public static void SaveSpectraTable(
IMSScanProperty scan,
DataBaseMapper mapper,
ParameterBase parameter,
AlignmentSpotProperty isotopeTrackedLastSpot = null) {
AlignmentSpotProperty isotopeTrackedLastSpot = null)
{
switch (spectraFormat) {
case ExportSpectraFileFormat.msp:
SaveSpectraTableAsNistFormat(exportStream, spotProperty, scan.Spectrum, mapper, parameter);
break;
case ExportSpectraFileFormat.mgf:
SaveSpectraTableAsMgfFormat(exportStream, spotProperty, scan.Spectrum);
break;
case ExportSpectraFileFormat.sdf:
SaveSpectraTableAsSdfFormat(exportStream, spotProperty, scan.Spectrum, true, true);
break;
case ExportSpectraFileFormat.mat:
SaveSpectraTableAsMatFormat(exportStream, spotProperty, scan.Spectrum, mapper, parameter, isotopeTrackedLastSpot);
break;
Expand Down Expand Up @@ -308,6 +320,152 @@ private static void WriteChromXFieldAsMGF(
}
#endregion

#region sdf
public static void SaveSpectraTableAsSdfFormat(
Stream stream,
AlignmentSpotProperty spotProperty,
IEnumerable<ISpectrumPeak> spectrum,
bool exportNoMs2Molecule,
bool Set2dCoordinates
)
{
if (!exportNoMs2Molecule && !spotProperty.IsMsmsAssigned)
{
return;
}
var sb = new StringBuilder(8 * 1024);
if(spotProperty.IsMsmsAssigned)
{
MolBlockFromSmiles(sb, spotProperty.SMILES, Set2dCoordinates);
}
else
{
EmptyMolBlock(sb);
}
WriteChromPeakFeatureInfoAsSdf(sb, spotProperty, spectrum);
sb.AppendLine("$$$$");
sb.AppendLine();
var bytes = Encoding.ASCII.GetBytes(sb.ToString());
stream.Write(bytes, 0, bytes.Length);
}
public static void SaveSpectraTableAsSdfFormat(
Stream stream,
ChromatogramPeakFeature chromPeakFeature,
IEnumerable<ISpectrumPeak> spectrum,
bool exportNoMs2Molecule,
bool Set2dCoordinates
)
{
if (!exportNoMs2Molecule && !chromPeakFeature.IsMsmsContained)
{
return;
}
var sb = new StringBuilder(8 * 1024);
if (chromPeakFeature.IsMsmsContained)
{
MolBlockFromSmiles(sb, chromPeakFeature.SMILES, Set2dCoordinates);
}
else
{
EmptyMolBlock(sb);
}
WriteChromPeakFeatureInfoAsSdf(sb, chromPeakFeature, spectrum);
sb.AppendLine("$$$$");
sb.AppendLine();
var bytes = Encoding.ASCII.GetBytes(sb.ToString());
stream.Write(bytes, 0, bytes.Length);
}
private static void WriteSdfDataItem(StringBuilder sb, string fieldName, string value)
{
sb.AppendLine("> <" + fieldName + ">");
sb.AppendLine(value ?? string.Empty);
}
private static void EmptyMolBlock(StringBuilder sb)
{
sb.AppendLine("");
sb.AppendLine(" MS-DIAL");
sb.AppendLine();
sb.AppendLine(" 0 0 0 0 0 0 999 V2000");
sb.AppendLine("M END");

}
private static void MolBlockFromSmiles(StringBuilder sb, string smiles, bool Set2dCoordinates)
{
var sp = new SmilesParser();
IAtomContainer mol = sp.ParseSmiles(smiles);
var sdg = new StructureDiagramGenerator
{
Molecule = mol
};
if(Set2dCoordinates)
{
sdg.GenerateCoordinates();
}
mol = sdg.Molecule;
using var tw = new StringWriter(sb, CultureInfo.InvariantCulture);
using (var w = new MDLV2000Writer(tw))
{
w.Write(mol);
};
}
private static void WriteChromPeakFeatureInfoAsSdf(
StringBuilder sb,
AlignmentSpotProperty spotProperty,
IEnumerable<ISpectrumPeak> spectrum)
{
WriteSdfDataItem(sb, "NAME", string.IsNullOrWhiteSpace(spotProperty.Name)? "Unknown": spotProperty.Name);
WriteSdfDataItem(sb, "SCANS", spotProperty.MasterAlignmentID.ToString());
WriteSdfDataItem(sb, "PRECURSOR MZ", Math.Round(spotProperty.MassCenter,5).ToString());
WriteSdfDataItem(sb, "ION MODE", spotProperty.IonMode.ToString());

if (spotProperty.IsMsmsAssigned)
{
if (spotProperty.AdductType != null) WriteSdfDataItem(sb, "PRECURSOR TYPE", spotProperty.AdductType.AdductIonName);
if (!string.IsNullOrWhiteSpace(spotProperty.Formula.FormulaString)) WriteSdfDataItem(sb, "FORMULA", spotProperty.Formula.FormulaString);
if (!string.IsNullOrWhiteSpace(spotProperty.InChIKey)) WriteSdfDataItem(sb, "FORMULA", spotProperty.InChIKey);
if (!string.IsNullOrWhiteSpace(spotProperty.SMILES)) WriteSdfDataItem(sb, "FORMULA", spotProperty.SMILES);
WriteSdfDataItem(sb, "MS LEVEL", "MS2");
var peaks = spectrum.Where(spec => spec.Intensity > 0).ToList();
WriteSdfDataItem(sb, "NUM PEAKS", peaks.Count.ToString());
var peaksText = string.Join(
"\n",
spectrum.Select(p =>
$"{Math.Round(p.Mass, 5)} {Math.Round(p.Intensity,0)}"
)
);
WriteSdfDataItem(sb, "MASS SPECTRAL PEAKS", peaksText);
}
}
private static void WriteChromPeakFeatureInfoAsSdf(
StringBuilder sb,
ChromatogramPeakFeature spotProperty,
IEnumerable<ISpectrumPeak> spectrum)
{
WriteSdfDataItem(sb, "NAME", string.IsNullOrWhiteSpace(spotProperty.Name) ? "Unknown" : spotProperty.Name);
WriteSdfDataItem(sb, "SCANS", spotProperty.PeakID.ToString());
WriteSdfDataItem(sb, "PRECURSOR MZ", Math.Round(spotProperty.PrecursorMz, 5).ToString());
WriteSdfDataItem(sb, "ION MODE", spotProperty.IonMode.ToString());

if (spotProperty.IsMsmsContained)
{
if (spotProperty.AdductType != null) WriteSdfDataItem(sb, "PRECURSOR TYPE", spotProperty.AdductType.AdductIonName);
if (!string.IsNullOrWhiteSpace(spotProperty.Formula.FormulaString)) WriteSdfDataItem(sb, "FORMULA", spotProperty.Formula.FormulaString);
if (!string.IsNullOrWhiteSpace(spotProperty.InChIKey)) WriteSdfDataItem(sb, "FORMULA", spotProperty.InChIKey);
if (!string.IsNullOrWhiteSpace(spotProperty.SMILES)) WriteSdfDataItem(sb, "FORMULA", spotProperty.SMILES);
WriteSdfDataItem(sb, "MS LEVEL", "MS2");
var peaks = spectrum.Where(spec => spec.Intensity > 0).ToList();
WriteSdfDataItem(sb, "NUM PEAKS", peaks.Count.ToString());
var peaksText = string.Join(
"\n",
spectrum.Select(p =>
$"{Math.Round(p.Mass, 5)} {Math.Round(p.Intensity, 0)}"
)
);
WriteSdfDataItem(sb, "MASS SPECTRAL PEAKS", peaksText);
}
}
#endregion

#region mat
private static void SaveSpectraTableAsMatFormat(
Stream stream,
Expand Down
1 change: 1 addition & 0 deletions src/MSDIAL5/MsdialGuiApp/Model/Dims/DimsMethodModel.cs
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Expand Up @@ -99,6 +99,7 @@ public DimsMethodModel(
peakSpotSupplyer,
new AlignmentSpectraExportFormat("Msp", "msp", new AlignmentMspExporter(storage.DataBaseMapper, storage.Parameter)),
new AlignmentSpectraExportFormat("Mgf", "mgf", new AlignmentMgfExporter()),
new AlignmentSpectraExportFormat("Sdf", "sdf", new AlignmentSdfExporter()),
new AlignmentSpectraExportFormat("Mat", "mat", new AlignmentMatExporter(storage.DataBaseMapper, storage.Parameter)));
var gnps = new AlignmentGnpsExportModel("GNPS", quantTypes, new GnpsMetadataAccessor(storage.DataBaseMapper, storage.Parameter), peakMeta.GetAccessor(), fileMeta.GetAccessor(), analysisFileBeanModelCollection);
var spectraAndReference = new AlignmentMatchedSpectraExportModel(peakSpotSupplyer, storage.DataBaseMapper, analysisFileBeanModelCollection.IncludedAnalysisFiles, CompoundSearcherCollection.BuildSearchers(storage.DataBases, storage.DataBaseMapper));
Expand Down
1 change: 1 addition & 0 deletions src/MSDIAL5/MsdialGuiApp/Model/Gcms/GcmsMethodModel.cs
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Expand Up @@ -112,6 +112,7 @@ public GcmsMethodModel(AnalysisFileBeanModelCollection analysisFileBeanModelColl
peakSpotSupplyer,
new AlignmentSpectraExportFormat("Msp", "msp", new AlignmentMspExporter(storage.DataBaseMapper, storage.Parameter)),
new AlignmentSpectraExportFormat("Mgf", "mgf", new AlignmentMgfExporter()),
new AlignmentSpectraExportFormat("Sdf", "sdf", new AlignmentSdfExporter()),
new AlignmentSpectraExportFormat("Mat", "mat", new AlignmentMatExporter(storage.DataBaseMapper, storage.Parameter)));
var gnps = new AlignmentGnpsExportModel("GNPS", quantTypes, new GnpsMetadataAccessor(storage.DataBaseMapper, storage.Parameter), peakMeta.GetAccessor(), fileMeta.GetAccessor(), analysisFileBeanModelCollection);
var exportGroups = new List<IAlignmentResultExportModel> { peakGroup, spectraGroup, gnps, };
Expand Down
10 changes: 10 additions & 0 deletions src/MSDIAL5/MsdialGuiApp/Model/ImagingImms/ImagingImmsMethodModel.cs
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Expand Up @@ -15,6 +15,7 @@
using System;
using System.Collections.Generic;
using System.Collections.ObjectModel;
using System.ComponentModel;
using System.Diagnostics;
using System.Linq;
using System.Threading;
Expand Down Expand Up @@ -150,6 +151,15 @@ public AnalysisResultExportModel CreateExportAnalysisModel() {
FileSuffix = "mgf",
Label = "MASCOT format (*.mgf)"
},
new SpectraTypeSelectableMsdialAnalysisExportModel(new Dictionary<ExportspectraType, IAnalysisExporter<ChromatogramPeakFeatureCollection>> {
[ExportspectraType.deconvoluted] = new AnalysisSdfExporter(file => new MSDecLoader(file.DeconvolutionFilePath, file.DeconvolutionFilePathList)),
[ExportspectraType.centroid] = new AnalysisSdfExporter(file => new CentroidMsScanPropertyLoader(_storage.Parameter.ProviderFactoryParameter.Create().Create(file.LoadRawMeasurement(true, true, 5, 5000)), _storage.Parameter.MS2DataType)),
})
{
FilePrefix = "Sdf",
FileSuffix = "sdf",
Label = "MDL SDfile (*.sdf)"
},
new MsdialAnalysisMassBankRecordExportModel(_storage.Parameter.ProjectParam, StudyContext),
};

Expand Down
10 changes: 10 additions & 0 deletions src/MSDIAL5/MsdialGuiApp/Model/Imms/ImmsMethodModel.cs
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Expand Up @@ -104,6 +104,7 @@ public ImmsMethodModel(AnalysisFileBeanModelCollection analysisFileBeanModelColl
peakSpotSupplyer,
new AlignmentSpectraExportFormat("Msp", "msp", new AlignmentMspExporter(storage.DataBaseMapper, storage.Parameter)),
new AlignmentSpectraExportFormat("Mgf", "mgf", new AlignmentMgfExporter()),
new AlignmentSpectraExportFormat("Sdf", "sdf", new AlignmentSdfExporter()),
new AlignmentSpectraExportFormat("Mat", "mat", new AlignmentMatExporter(storage.DataBaseMapper, storage.Parameter)));
var gnps = new AlignmentGnpsExportModel("GNPS", quantTypes, new GnpsMetadataAccessor(storage.DataBaseMapper, storage.Parameter), peakMeta.GetAccessor(), fileMeta.GetAccessor(), analysisFileBeanModelCollection);
var spectraAndReference = new AlignmentMatchedSpectraExportModel(peakSpotSupplyer, storage.DataBaseMapper, analysisFileBeanModelCollection.IncludedAnalysisFiles, CompoundSearcherCollection.BuildSearchers(storage.DataBases, storage.DataBaseMapper));
Expand Down Expand Up @@ -317,6 +318,15 @@ public AnalysisResultExportModel CreateExportAnalysisResult() {
FileSuffix = "mgf",
Label = "MASCOT format (*.mgf)"
},
new SpectraTypeSelectableMsdialAnalysisExportModel(new Dictionary<ExportspectraType, IAnalysisExporter<ChromatogramPeakFeatureCollection>> {
[ExportspectraType.deconvoluted] = new AnalysisSdfExporter(file => new MSDecLoader(file.DeconvolutionFilePath, file.DeconvolutionFilePathList)),
[ExportspectraType.centroid] = new AnalysisSdfExporter(file => new CentroidMsScanPropertyLoader(ProviderFactory.Create(file), _storage.Parameter.MS2DataType)),
})
{
FilePrefix = "Sdf",
FileSuffix = "sdf",
Label = "MDL SDfile (*.sdf)"
},
new MsdialAnalysisMassBankRecordExportModel(_storage.Parameter.ProjectParam, StudyContext),
};
return new AnalysisResultExportModel(AnalysisFileModelCollection, _storage.Parameter.ProjectParam.ProjectFolderPath, _broker, models);
Expand Down
11 changes: 11 additions & 0 deletions src/MSDIAL5/MsdialGuiApp/Model/Lcimms/LcimmsMethodModel.cs
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Expand Up @@ -26,6 +26,7 @@
using Reactive.Bindings.Notifiers;
using System;
using System.Collections.Generic;
using System.ComponentModel;
using System.Diagnostics;
using System.Linq;
using System.Reactive.Linq;
Expand Down Expand Up @@ -100,6 +101,7 @@ public LcimmsMethodModel(AnalysisFileBeanModelCollection analysisFileBeanModelCo
peakSpotSupplyer,
new AlignmentSpectraExportFormat("Msp", "msp", new AlignmentMspExporter(storage.DataBaseMapper, storage.Parameter)),
new AlignmentSpectraExportFormat("Mgf", "mgf", new AlignmentMgfExporter()),
new AlignmentSpectraExportFormat("Sdf", "sdf", new AlignmentSdfExporter()),
new AlignmentSpectraExportFormat("Mat", "mat", new AlignmentMatExporter(storage.DataBaseMapper, storage.Parameter)));
var gnps = new AlignmentGnpsExportModel("GNPS", quantTypes, new GnpsMetadataAccessor(storage.DataBaseMapper, storage.Parameter), peakMeta.GetAccessor(), fileMeta.GetAccessor(), analysisFileBeanModelCollection);
var spectraAndReference = new AlignmentMatchedSpectraExportModel(peakSpotSupplyer, storage.DataBaseMapper, analysisFileBeanModelCollection.IncludedAnalysisFiles, CompoundSearcherCollection.BuildSearchers(storage.DataBases, storage.DataBaseMapper));
Expand Down Expand Up @@ -319,6 +321,15 @@ static RawMeasurement map(AnalysisFileBean file) {
FileSuffix = "mgf",
Label = "MASCOT format (*.mgf)"
},
new SpectraTypeSelectableMsdialAnalysisExportModel(new Dictionary<ExportspectraType, IAnalysisExporter<ChromatogramPeakFeatureCollection>> {
[ExportspectraType.deconvoluted] = new AnalysisSdfExporter(file => new MSDecLoader(file.DeconvolutionFilePath, file.DeconvolutionFilePathList)),
[ExportspectraType.centroid] = new AnalysisSdfExporter(file => new CentroidMsScanPropertyLoader(factory.Create(file), Storage.Parameter.MS2DataType)),
})
{
FilePrefix = "Sdf",
FileSuffix = "sdf",
Label = "MDL SDfile (*.sdf)"
},
new MsdialAnalysisMassBankRecordExportModel(Storage.Parameter.ProjectParam, _studyContext),
};
return new AnalysisResultExportModel(AnalysisFileModelCollection, Storage.Parameter.ProjectParam.ProjectFolderPath, _broker, models);
Expand Down
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