public void TestGetIonFormula()
{
SequenceMassCalc sequenceMassCalc = new SequenceMassCalc(MassType.Monoisotopic);
Assert.AreEqual(147.11, sequenceMassCalc.GetPrecursorMass("K"), .1);
Assert.AreEqual("C6H14N2O2", sequenceMassCalc.GetMolecularFormula("K"));
var label13C6K = new StaticMod("label13C6K", "K", null, LabelAtoms.C13);
sequenceMassCalc.AddStaticModifications(new [] { label13C6K });
Assert.AreEqual(153.11, sequenceMassCalc.GetPrecursorMass("K"), .1);
Assert.AreEqual("C'6H14N2O2", sequenceMassCalc.GetMolecularFormula("K"));
var label15N2K = new StaticMod("label15N2K", "K", null, LabelAtoms.N15);
sequenceMassCalc.AddStaticModifications(new[] { label15N2K });
Assert.AreEqual(155.11, sequenceMassCalc.GetPrecursorMass("K"), .1);
Assert.AreEqual("C'6H14N'2O2", sequenceMassCalc.GetMolecularFormula("K"));
var labelLaK = new StaticMod("labelLaK", "K", null, "La");
sequenceMassCalc.AddStaticModifications(new[] { labelLaK });
Assert.AreEqual(294.033, sequenceMassCalc.GetPrecursorMass("K"), .1);
Assert.AreEqual("C'6H14LaN'2O2", sequenceMassCalc.GetMolecularFormula("K"));
// Check our ability to handle strangely constructed chemical formulas
Assert.AreEqual(Molecule.Parse("C12H9S2P0").ToString(), Molecule.Parse("C12H9S2").ToString()); // P0 is weird
Assert.AreEqual(Molecule.Parse("C12H9S2P1").ToString(), Molecule.Parse("C12H9S2P").ToString()); // P1 is weird
Assert.AreEqual(Molecule.Parse("C12H9S0P").ToString(), Molecule.Parse("C12H9P").ToString()); // S0 is weird, and not at end
}
public void TestSingleAminoAcidLinkedPeptide()
{
var srmSettings = SrmSettingsList.GetDefault();
var mainPeptide = new Peptide("A");
var staticMod = new StaticMod("crosslinker", null, null, "-C2");
var linkedPeptide = new LinkedPeptide(new Peptide("D"), 0, null);
var mainTransitionGroup = new TransitionGroup(mainPeptide, Adduct.SINGLY_PROTONATED, IsotopeLabelType.light);
var mainTransitionGroupDocNode = new TransitionGroupDocNode(mainTransitionGroup,
Annotations.EMPTY, srmSettings, null, null,
ExplicitTransitionGroupValues.EMPTY, null, new TransitionDocNode[0], false);
var modsWithoutLinkedPeptide = new ExplicitMods(mainPeptide, new[] { new ExplicitMod(0, staticMod), }, new TypedExplicitModifications[0]);
Assert.AreEqual("C3H7NO2", AminoAcidFormulas.Default.GetFormula("A").ToString());
Assert.AreEqual("C3H7NO2", mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, null).Molecule.ToString());
Assert.AreEqual("CH7NO2", mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, modsWithoutLinkedPeptide).Molecule.ToString());
Assert.AreEqual("C4H7NO4", AminoAcidFormulas.Default.GetFormula("D").ToString());
var modsWithLinkedPeptide = new ExplicitMods(mainPeptide,
new[] { new ExplicitMod(0, staticMod).ChangeLinkedPeptide(linkedPeptide) },
new TypedExplicitModifications[0]);
Assert.AreEqual("C5H14N2O6", mainTransitionGroupDocNode.GetNeutralFormula(srmSettings, modsWithLinkedPeptide).Molecule.ToString());
var mainComplexFragmentIon = new ComplexFragmentIon(new Transition(mainTransitionGroup, IonType.precursor, mainPeptide.Length - 1, 0, Adduct.SINGLY_PROTONATED), null, modsWithLinkedPeptide.Crosslinks);
var linkedComplexFragmentIon = new ComplexFragmentIon(
new Transition(linkedPeptide.GetTransitionGroup(IsotopeLabelType.light, Adduct.SINGLY_PROTONATED),
IonType.precursor, linkedPeptide.Peptide.Length - 1, 0, Adduct.SINGLY_PROTONATED), null, LinkedPeptide.EMPTY_CROSSLINK_STRUCTURE);
var complexFragmentIon =
mainComplexFragmentIon.AddChild(new ModificationSite(0, staticMod.Name), linkedComplexFragmentIon);
var transition = complexFragmentIon.MakeTransitionDocNode(srmSettings, modsWithLinkedPeptide, null);
var sequenceMassCalc = new SequenceMassCalc(MassType.Monoisotopic);
var expectedMz = sequenceMassCalc.GetPrecursorMass("A") + sequenceMassCalc.GetPrecursorMass("D") - 24 - BioMassCalc.MassProton;
Assert.AreEqual(expectedMz, transition.Mz, .00001);
}
public static double CalculateFeature(EspFeatureDb.FeatureDef feature, Target target)
{
var seq = target.Sequence ?? string.Empty;
switch (feature)
{
case EspFeatureDb.FeatureDef.length:
return(seq.Length);
case EspFeatureDb.FeatureDef.mass:
return(MASS_CALC.GetPrecursorMass(seq));
case EspFeatureDb.FeatureDef.pI:
return(PiCalc.Calculate(seq));
case EspFeatureDb.FeatureDef.AVG_Gas_phase_basicity:
return(GasPhaseBasicityCalc.Calculate(seq).Average());
case EspFeatureDb.FeatureDef.nAcidic:
return(AminoAcid.Count(seq, 'D', 'E')); // Amino acid
case EspFeatureDb.FeatureDef.nBasic:
return(AminoAcid.Count(seq, 'R', 'H', 'K')); // Amino acid
default:
return(EspFeatureDb.CalculateFeature(feature, seq));
}
}
/// <summary>
/// Test only method for creating a <see cref="BiblioSpecLibrary"/> file
/// from another loaded <see cref="Library"/>. Should this move into test project?
/// </summary>
/// <param name="streamManager">Provides access to the file system</param>
/// <param name="path">Path to write to</param>
/// <param name="library">The loaded library to use as a data source</param>
public static void Write(IStreamManager streamManager, string path, Library library)
{
using (FileSaver fs = new FileSaver(path, streamManager))
using (Stream outStream = streamManager.CreateStream(fs.SafeName, FileMode.Create, true))
{
outStream.Write(BitConverter.GetBytes(library.SpectrumCount), 0, sizeof(int)); // num_spectra
outStream.Write(BitConverter.GetBytes(0), 0, sizeof(int)); // filtered
outStream.Write(BitConverter.GetBytes(1), 0, sizeof(int)); // version1
outStream.Write(BitConverter.GetBytes(1), 0, sizeof(int)); // version2
outStream.Write(BitConverter.GetBytes(0), 0, sizeof(int)); // next_id
SequenceMassCalc calc = new SequenceMassCalc(MassType.Monoisotopic);
byte[] seqBuffer = new byte[1024];
int scanNum = 1;
foreach (var key in library.Keys)
{
SpectrumPeaksInfo peaksInfo;
if (!library.TryLoadSpectrum(key, out peaksInfo))
{
continue;
}
string sequence = key.Sequence;
// Only works for unmodified sequence
Debug.Assert(!key.IsModified);
double precursorMH = calc.GetPrecursorMass(sequence);
int charge = key.Charge;
float precursorMz = (float)SequenceMassCalc.GetMZ(precursorMH, charge);
outStream.Write(BitConverter.GetBytes(scanNum), 0, sizeof(int)); // scan_num
outStream.Write(BitConverter.GetBytes(2), 0, sizeof(int)); // scan_type
outStream.Write(BitConverter.GetBytes(precursorMz), 0, sizeof(float)); // pre_mz
outStream.Write(BitConverter.GetBytes(charge), 0, sizeof(int)); // scan_type
outStream.Write(BitConverter.GetBytes(0f), 0, sizeof(int)); // r_time
outStream.Write(BitConverter.GetBytes(peaksInfo.Peaks.Length), 0, sizeof(int)); // num_peaks
outStream.Write(BitConverter.GetBytes(0), 0, sizeof(int)); // 32-bit peak_ptr
outStream.Write(BitConverter.GetBytes(sequence.Length), 0, sizeof(int)); // seq_len
outStream.Write(BitConverter.GetBytes(0), 0, sizeof(int)); // annot
outStream.Write(BitConverter.GetBytes(scanNum), 0, sizeof(int)); // copies (bogus value for ranking)
outStream.Write(BitConverter.GetBytes(0), 0, sizeof(int)); // lib_id
scanNum++;
// Sequence
int len = sequence.Length;
seqBuffer[len] = 0;
Encoding.UTF8.GetBytes(sequence, 0, len, seqBuffer, 0);
outStream.Write(seqBuffer, 0, len + 1);
// Modifications
const string zeros = "000000000000000000000000000000000000000000000000000"; // Not L10N
Encoding.UTF8.GetBytes(zeros.Substring(0, len), 0, len, seqBuffer, 0);
outStream.Write(seqBuffer, 0, len + 1);
// Peaks
foreach (var mi in peaksInfo.Peaks)
{
outStream.Write(BitConverter.GetBytes((float)mi.Mz), 0, sizeof(float));
outStream.Write(BitConverter.GetBytes(mi.Intensity), 0, sizeof(float));
}
}
streamManager.Finish(outStream);
fs.Commit();
}
}
/// <summary>
/// Test only method for creating a <see cref="XHunterLibrary"/> file
/// from another loaded <see cref="Library"/>. Should this move into test project?
/// </summary>
/// <param name="streamManager">Provides access to the file system</param>
/// <param name="path">Path to write to</param>
/// <param name="library">The loaded library to use as a data source</param>
/// <param name="lowIntensity">True to use 20 lowest intensity peaks for bad spectrum</param>
public static void Write(IStreamManager streamManager, string path, Library library, bool lowIntensity)
{
using (FileSaver fs = new FileSaver(path, streamManager))
using (Stream outStream = streamManager.CreateStream(fs.SafeName, FileMode.Create, true))
{
outStream.Write(BitConverter.GetBytes(0), 0, sizeof(int));
outStream.Write(BitConverter.GetBytes(library.SpectrumCount), 0, sizeof(int));
byte[] header = new byte[256 - 8];
const string headerText = @"HLF v=2 s=test.hlf d=2009.02.04";
Encoding.UTF8.GetBytes(headerText, 0, headerText.Length, header, 0);
outStream.Write(header, 0, header.Length);
SequenceMassCalc calc = new SequenceMassCalc(MassType.Monoisotopic);
byte[] seqBuffer = new byte[1024];
foreach (var key in library.Keys)
{
SpectrumPeaksInfo peaksInfo;
if (!library.TryLoadSpectrum(key, out peaksInfo))
{
continue;
}
// Fake X! Hunter filtering by choosing just the to 20 peaks
SpectrumPeaksInfo.MI[] peaks = peaksInfo.Peaks.ToArray();
// Sort by intensity
if (lowIntensity)
{
Array.Sort(peaks, (p1, p2) => Comparer.Default.Compare(p1.Intensity, p2.Intensity)); // ascending
}
else
{
Array.Sort(peaks, (p1, p2) => Comparer.Default.Compare(p2.Intensity, p1.Intensity)); // descending
}
float maxI = peaks.Length == 0 ? 0 : peaks[0].Intensity;
// Take 20 most intense peaks
SpectrumPeaksInfo.MI[] peaksFiltered = new SpectrumPeaksInfo.MI[Math.Min(20, peaks.Length)];
Array.Copy(peaks, peaksFiltered, peaksFiltered.Length);
// Resort by m/z (ineffient, but this is test code)
Array.Sort(peaksFiltered, (p1, p2) => Comparer.Default.Compare(p1.Mz, p2.Mz));
double totalI = 0;
byte[] peakBytes = new byte[(sizeof(byte) + sizeof(float)) * peaksFiltered.Length];
for (int i = 0; i < peaksFiltered.Length; i++)
{
var mi = peaksFiltered[i];
// Calculate the X! Hunter processed intensity value
float intensity = 100f * mi.Intensity / maxI;
totalI += intensity;
// Fill the peaks buffer
peakBytes[i] = (byte)(int)intensity;
Array.Copy(BitConverter.GetBytes((float)mi.Mz), 0, peakBytes, peaksFiltered.Length + i * 4, sizeof(float));
}
var sequence = key.Target.ToString();
// Only works for unmodified sequence
Debug.Assert(!key.IsModified);
double precursorMH = calc.GetPrecursorMass(sequence);
outStream.Write(BitConverter.GetBytes(precursorMH), 0, sizeof(double));
outStream.Write(BitConverter.GetBytes(key.Charge), 0, sizeof(int));
// Value rounded for consistent serialization round-tripping
float i2 = (float)Math.Round(Math.Sqrt(totalI), 4);
outStream.Write(BitConverter.GetBytes(i2), 0, sizeof(float));
outStream.Write(BitConverter.GetBytes(0.0001f), 0, sizeof(float));
outStream.Write(BitConverter.GetBytes(sequence.Length), 0, sizeof(int));
// Sequence
Encoding.UTF8.GetBytes(sequence, 0, sequence.Length, seqBuffer, 0);
outStream.Write(seqBuffer, 0, sequence.Length);
// Peaks
outStream.Write(BitConverter.GetBytes(peaksFiltered.Length), 0, sizeof(int));
outStream.Write(peakBytes, 0, peakBytes.Length);
// Modifications
outStream.Write(BitConverter.GetBytes(0), 0, sizeof(int));
// Homologs
outStream.Write(BitConverter.GetBytes(0), 0, sizeof(int));
}
streamManager.Finish(outStream);
fs.Commit();
}
}
public void CalcMass(SequenceMassCalc massCalc)
{
MassH = massCalc.GetPrecursorMass(Sequence);
}
public void CalcMass(SequenceMassCalc massCalc)
{
MassH = massCalc.GetPrecursorMass(Sequence);
}
/// <summary>
/// Test only method for creating a <see cref="BiblioSpecLibrary"/> file
/// from another loaded <see cref="Library"/>. Should this move into test project?
/// </summary>
/// <param name="streamManager">Provides access to the file system</param>
/// <param name="path">Path to write to</param>
/// <param name="library">The loaded library to use as a data source</param>
public static void Write(IStreamManager streamManager, string path, Library library)
{
using (FileSaver fs = new FileSaver(path, streamManager))
using (Stream outStream = streamManager.CreateStream(fs.SafeName, FileMode.Create, true))
{
outStream.Write(BitConverter.GetBytes(library.SpectrumCount), 0, sizeof(int)); // num_spectra
outStream.Write(BitConverter.GetBytes(0), 0, sizeof(int)); // filtered
outStream.Write(BitConverter.GetBytes(1), 0, sizeof(int)); // version1
outStream.Write(BitConverter.GetBytes(1), 0, sizeof(int)); // version2
outStream.Write(BitConverter.GetBytes(0), 0, sizeof(int)); // next_id
SequenceMassCalc calc = new SequenceMassCalc(MassType.Monoisotopic);
byte[] seqBuffer = new byte[1024];
int scanNum = 1;
foreach (var key in library.Keys)
{
SpectrumPeaksInfo peaksInfo;
if (!library.TryLoadSpectrum(key, out peaksInfo))
continue;
string sequence = key.Sequence;
// Only works for unmodified sequence
Debug.Assert(!key.IsModified);
double precursorMH = calc.GetPrecursorMass(sequence);
int charge = key.Charge;
float precursorMz = (float) SequenceMassCalc.GetMZ(precursorMH, charge);
outStream.Write(BitConverter.GetBytes(scanNum), 0, sizeof(int)); // scan_num
outStream.Write(BitConverter.GetBytes(2), 0, sizeof(int)); // scan_type
outStream.Write(BitConverter.GetBytes(precursorMz), 0, sizeof(float)); // pre_mz
outStream.Write(BitConverter.GetBytes(charge), 0, sizeof(int)); // scan_type
outStream.Write(BitConverter.GetBytes(0f), 0, sizeof(int)); // r_time
outStream.Write(BitConverter.GetBytes(peaksInfo.Peaks.Length), 0, sizeof(int)); // num_peaks
outStream.Write(BitConverter.GetBytes(0), 0, sizeof(int)); // 32-bit peak_ptr
outStream.Write(BitConverter.GetBytes(sequence.Length), 0, sizeof(int)); // seq_len
outStream.Write(BitConverter.GetBytes(0), 0, sizeof(int)); // annot
outStream.Write(BitConverter.GetBytes(scanNum), 0, sizeof(int)); // copies (bogus value for ranking)
outStream.Write(BitConverter.GetBytes(0), 0, sizeof(int)); // lib_id
scanNum++;
// Sequence
int len = sequence.Length;
seqBuffer[len] = 0;
Encoding.UTF8.GetBytes(sequence, 0, len, seqBuffer, 0);
outStream.Write(seqBuffer, 0, len + 1);
// Modifications
const string zeros = "000000000000000000000000000000000000000000000000000"; // Not L10N
Encoding.UTF8.GetBytes(zeros.Substring(0, len), 0, len, seqBuffer, 0);
outStream.Write(seqBuffer, 0, len + 1);
// Peaks
foreach (var mi in peaksInfo.Peaks)
{
outStream.Write(BitConverter.GetBytes((float)mi.Mz), 0, sizeof(float));
outStream.Write(BitConverter.GetBytes(mi.Intensity), 0, sizeof(float));
}
}
streamManager.Finish(outStream);
fs.Commit();
}
}