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removed fixed mods changes
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@nbollis
nbollis committed Jan 16, 2025
1 parent 0b59b0b commit 9096c21
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Showing 2 changed files with 4 additions and 35 deletions.
4 changes: 2 additions & 2 deletions mzLib/Omics/Modifications/ModificationLocalization.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -32,9 +32,9 @@ public static bool ModFits(Modification attemptToLocalize, string sequence, int
switch (attemptToLocalize.LocationRestriction)
{
case "N-terminal." when bioPolymerOneBasedIndex > 2:
case "Peptide N-terminal." when digestionProductOneBasedIndex > 1 || bioPolymerOneBasedIndex == 1:
case "Peptide N-terminal." when digestionProductOneBasedIndex > 1:
case "C-terminal." when bioPolymerOneBasedIndex < sequence.Length:
case "Peptide C-terminal." when digestionProductOneBasedIndex < digestionProductLength || bioPolymerOneBasedIndex == sequence.Length:
case "Peptide C-terminal." when digestionProductOneBasedIndex < digestionProductLength:
case "5'-terminal." when bioPolymerOneBasedIndex > 2:
// first residue in oligo but not first in nucleic acid
case "Oligo 5'-terminal." when digestionProductOneBasedIndex > 1
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35 changes: 2 additions & 33 deletions mzLib/Test/TestProteinDigestion.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -220,7 +220,7 @@ public static void TestPeptideWithSetModifications()
variableModifications.Add(new Modification(_originalId: "ProtCmod", _target: motif, _locationRestriction: "C-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));

var ye = prot.Digest(digestionParams, new List<Modification>(), variableModifications).ToList();
Assert.AreEqual(2 * 2 * 2, ye.Count);
Assert.AreEqual(3 * 2 * 3, ye.Count);
Assert.AreEqual("[H]M[H][H]", ye.Last().SequenceWithChemicalFormulas);

double m1 = 5 * GetElement("H").PrincipalIsotope.AtomicMass + Residue.ResidueMonoisotopicMass['M'] + GetElement("O").PrincipalIsotope.AtomicMass;
Expand Down Expand Up @@ -251,43 +251,12 @@ public static void TestPeptideWithFixedModifications()

Assert.AreEqual(1, ok.Count);

Assert.AreEqual("[:ProtNmod on M]M[:resMod on M][:ProtCmod on M]", ok.First().FullSequence);
Assert.AreEqual("[:pepNmod on M]M[:resMod on M][:ProtCmod on M]", ok.First().FullSequence);

Assert.AreEqual("[H]M[H][H]", ok.First().SequenceWithChemicalFormulas);
Assert.AreEqual(5 * GetElement("H").PrincipalIsotope.AtomicMass + Residue.ResidueMonoisotopicMass['M'] + GetElement("O").PrincipalIsotope.AtomicMass, ok.Last().MonoisotopicMass, 1e-9);
}

[Test]
public static void TestPeptideWithFixedModifications_TwoProducts()
{
var prot = new Protein("MKM", null);
DigestionParams digestionParams = new DigestionParams(maxMissedCleavages: 0, minPeptideLength: 1, maxModsForPeptides: 3, initiatorMethionineBehavior: InitiatorMethionineBehavior.Retain);
List<Modification> fixedMods = new List<Modification>();
ModificationMotif.TryGetMotif("M", out ModificationMotif mMotif);
ModificationMotif.TryGetMotif("K", out ModificationMotif kMotif);

fixedMods.Add(new Modification(_originalId: "ProtNmod", _target: mMotif, _locationRestriction: "N-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
fixedMods.Add(new Modification(_originalId: "ProtNmod", _target: kMotif, _locationRestriction: "N-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
fixedMods.Add(new Modification(_originalId: "pepNmod", _target: mMotif, _locationRestriction: "Peptide N-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
fixedMods.Add(new Modification(_originalId: "pepNmod", _target: kMotif, _locationRestriction: "Peptide N-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
fixedMods.Add(new Modification(_originalId: "resMod", _target: mMotif, _locationRestriction: "Anywhere.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
fixedMods.Add(new Modification(_originalId: "PepCmod", _target: mMotif, _locationRestriction: "Peptide C-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
fixedMods.Add(new Modification(_originalId: "PepCmod", _target: kMotif, _locationRestriction: "Peptide C-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
fixedMods.Add(new Modification(_originalId: "ProtCmod", _target: mMotif, _locationRestriction: "C-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));
fixedMods.Add(new Modification(_originalId: "ProtCmod", _target: kMotif, _locationRestriction: "C-terminal.", _chemicalFormula: ChemicalFormula.ParseFormula("H"), _monoisotopicMass: GetElement(1).PrincipalIsotope.AtomicMass));

var ok = prot.Digest(digestionParams, fixedMods, new List<Modification>()).ToList();

Assert.AreEqual(2, ok.Count);

Assert.AreEqual("[:ProtNmod on M]M[:resMod on M]K[:PepCmod on K]", ok.First().FullSequence);
Assert.AreEqual("[:pepNmod on M]M[:resMod on M][:ProtCmod on M]", ok.Skip(1).First().FullSequence);

Assert.AreEqual("[H]M[H]K[H]", ok.First().SequenceWithChemicalFormulas);
Assert.AreEqual("[H]M[H][H]", ok.Skip(1).First().SequenceWithChemicalFormulas);
Assert.AreEqual(5 * GetElement("H").PrincipalIsotope.AtomicMass + Residue.ResidueMonoisotopicMass['M'] + GetElement("O").PrincipalIsotope.AtomicMass, ok.Last().MonoisotopicMass, 1e-9);
}

[Test]
public static void TestDigestIndices()
{
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