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Add sdf format exporter #713

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Merged
YukiMatsuzawa merged 9 commits into from
Mar 10, 2026
+14 −7
Merged

Add sdf format exporter #713

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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
925fbd2
Fix Sdf export item
Mar 2, 2026
882c540
change decimal
Mar 2, 2026
7f49b3a
Merge branch 'master' into add_sdf_format_exporter
Mar 10, 2026
7b28f8e
Update src/MSDIAL5/MsdialCore/Export/SpectraExport.cs
mikikot113 Mar 10, 2026
2e466b9
Update src/MSDIAL5/MsdialCore/Export/SpectraExport.cs
mikikot113 Mar 10, 2026
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21 changes: 14 additions & 7 deletions src/MSDIAL5/MsdialCore/Export/SpectraExport.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -415,22 +415,26 @@ private static void WriteChromPeakFeatureInfoAsSdf(
{
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, "PRECURSOR M/Z", 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);
if (spotProperty.Formula.Mass > 0d) WriteSdfDataItem(sb, "EXACT MASS", Math.Round(spotProperty.Formula.Mass, 5).ToString());
if (!string.IsNullOrWhiteSpace(spotProperty.InChIKey)) WriteSdfDataItem(sb, "INCHIKEY", spotProperty.InChIKey);
if (!string.IsNullOrWhiteSpace(spotProperty.SMILES)) WriteSdfDataItem(sb, "SMILES", spotProperty.SMILES);
if (spotProperty.TimesCenter != null && spotProperty.TimesCenter.RT != null && spotProperty.TimesCenter.RT.Value >= 0)
WriteSdfDataItem(sb, "RETENTION TIME", Math.Round(spotProperty.TimesCenter.RT.Value, 3).ToString());
if (!string.IsNullOrWhiteSpace(spotProperty.Ontology)) WriteSdfDataItem(sb, "ONTOLOGY", spotProperty.Ontology);
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)}"
$"{Math.Round(p.Mass, 4)} {Math.Round(p.Intensity,0)}"
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)
);
WriteSdfDataItem(sb, "MASS SPECTRAL PEAKS", peaksText);
Expand All @@ -443,15 +447,18 @@ private static void WriteChromPeakFeatureInfoAsSdf(
{
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, "PRECURSOR M/Z", 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);
if (!string.IsNullOrWhiteSpace(spotProperty.Formula.Mass.ToString())) WriteSdfDataItem(sb, "EXACT MASS", Math.Round(spotProperty.Formula.Mass, 5).ToString());
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if (!string.IsNullOrWhiteSpace(spotProperty.InChIKey)) WriteSdfDataItem(sb, "INCHIKEY", spotProperty.InChIKey);
if (!string.IsNullOrWhiteSpace(spotProperty.SMILES)) WriteSdfDataItem(sb, "SMILES", spotProperty.SMILES);
if (!string.IsNullOrWhiteSpace(spotProperty.ChromXs.RT.Value.ToString())) WriteSdfDataItem(sb, "RETENTION TIME", spotProperty.ChromXs.RT.Value.ToString());
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if (!string.IsNullOrWhiteSpace(spotProperty.Ontology)) WriteSdfDataItem(sb, "ONTOLOGY", spotProperty.Ontology);
WriteSdfDataItem(sb, "MS LEVEL", "MS2");
var peaks = spectrum.Where(spec => spec.Intensity > 0).ToList();
WriteSdfDataItem(sb, "NUM PEAKS", peaks.Count.ToString());
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