From 9096c217838459e713c40bc6b0e2a34820366f9f Mon Sep 17 00:00:00 2001 From: nbollis Date: Wed, 15 Jan 2025 18:13:38 -0600 Subject: [PATCH] removed fixed mods changes --- .../Modifications/ModificationLocalization.cs | 4 +-- mzLib/Test/TestProteinDigestion.cs | 35 ++----------------- 2 files changed, 4 insertions(+), 35 deletions(-) diff --git a/mzLib/Omics/Modifications/ModificationLocalization.cs b/mzLib/Omics/Modifications/ModificationLocalization.cs index 8928d8c9a..e2c57fa2d 100644 --- a/mzLib/Omics/Modifications/ModificationLocalization.cs +++ b/mzLib/Omics/Modifications/ModificationLocalization.cs @@ -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 diff --git a/mzLib/Test/TestProteinDigestion.cs b/mzLib/Test/TestProteinDigestion.cs index 821288dae..02cc3aed5 100644 --- a/mzLib/Test/TestProteinDigestion.cs +++ b/mzLib/Test/TestProteinDigestion.cs @@ -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(), 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; @@ -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 fixedMods = new List(); - 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()).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() {