Merge pull request #469 from lschaffer2/master

ptm loss bug fix
smith-chem-wisc · Dec 15, 2017 · bd5545f · bd5545f
2 parents d2fc670 + 4988525
commit bd5545f
Show file tree

Hide file tree

Showing 2 changed files with 39 additions and 2 deletions.
diff --git a/ProteoformSuiteInternal/Proteoform.cs b/ProteoformSuiteInternal/Proteoform.cs
@@ -105,7 +105,7 @@ public List<ExperimentalProteoform> identify_connected_experimentals(List<PtmSet
  bool within_loss_tolerance = deltaM >= -set.mass - mass_tolerance && deltaM <= -set.mass + mass_tolerance;
  List<ModificationWithMass> these_mods = this.ptm_set.ptm_combination.Select(ptm => ptm.modification).ToList();
  List<ModificationWithMass> those_mods = set.ptm_combination.Select(ptm => ptm.modification).ToList(); // all must be in the current set to remove them
- bool can_be_removed = those_mods.All(m => these_mods.Contains(m));
+ bool can_be_removed = those_mods.All(m1 => these_mods.Count(m2 => m2.id == m1.id) >= those_mods.Count(m2 => m2.id == m1.id)); //# of each mod in current set must be greater than or equal to # in set to remove.
  bool better_than_current_best_loss = best_loss == null || Math.Abs(deltaM - (-set.mass)) < Math.Abs(deltaM - (-best_loss.mass));
  if (can_be_removed && within_loss_tolerance && better_than_current_best_loss)
  {

diff --git a/Test/TestProteoformIdentification.cs b/Test/TestProteoformIdentification.cs
@@ -50,20 +50,57 @@ public void loss_of_ptm_set()
  {
  new Ptm(0, new ModificationWithMass("acetyl", new Tuple<string, string>("", ""), motif, TerminusLocalization.Any, 42.01, new Dictionary<string, IList<string>>(), new List<double>(), new List<double>(), "Mod")),
  });
+ PtmSet set4 = new PtmSet(new List<Ptm>
+ {
+ new Ptm(0, new ModificationWithMass("acetyl", new Tuple<string, string>("", ""), motif, TerminusLocalization.Any, 42.01, new Dictionary<string, IList<string>>(), new List<double>(), new List<double>(), "Mod")),
+ new Ptm(0, new ModificationWithMass("acetyl", new Tuple<string, string>("", ""), motif, TerminusLocalization.Any, 42.01, new Dictionary<string, IList<string>>(), new List<double>(), new List<double>(), "Mod")),
+ new Ptm(0, new ModificationWithMass("acetyl", new Tuple<string, string>("", ""), motif, TerminusLocalization.Any, 42.01, new Dictionary<string, IList<string>>(), new List<double>(), new List<double>(), "Mod")),
+ new Ptm(0, new ModificationWithMass("acetyl", new Tuple<string, string>("", ""), motif, TerminusLocalization.Any, 42.01, new Dictionary<string, IList<string>>(), new List<double>(), new List<double>(), "Mod")),
+ });
+
  e.ptm_set = set;
  Sweet.lollipop.theoretical_database.possible_ptmset_dictionary = new Dictionary<double, List<PtmSet>>
  {
  { Math.Round(set.mass, 1), new List<PtmSet> { set } },
  { Math.Round(set2.mass, 1), new List<PtmSet> { set2 } },
  { Math.Round(set3.mass, 1), new List<PtmSet> { set3 } },
+ { Math.Round(set4.mass, 1), new List<PtmSet> { set4 } },
  };
+
  ExperimentalProteoform e2 = ConstructorsForTesting.ExperimentalProteoform("", 10042.01, 0, true);
+ ConstructorsForTesting.make_relation(e, e2, ProteoformComparison.ExperimentalExperimental, 126.03);
+ e.relationships.First().Accepted = true;
+ e.relationships.First().peak = new DeltaMassPeak(e.relationships.First(), new HashSet<ProteoformRelation> { e.relationships.First() });
+ e.identify_connected_experimentals(new List<PtmSet> { set }, new List<ModificationWithMass> { set.ptm_combination.First().modification });
+ Assert.IsNotNull(e2.linked_proteoform_references);
+ Assert.AreEqual(0, e2.ptm_set.mass);
+
+ e.relationships.Clear();
+ e2 = ConstructorsForTesting.ExperimentalProteoform("", 10042.01, 0, true);
  ConstructorsForTesting.make_relation(e, e2, ProteoformComparison.ExperimentalExperimental, 84.02);
  e.relationships.First().Accepted = true;
  e.relationships.First().peak = new DeltaMassPeak(e.relationships.First(), new HashSet<ProteoformRelation> { e.relationships.First() });
- e.identify_connected_experimentals(new List<PtmSet> { set, set2, set3 }, new List<ModificationWithMass> { set.ptm_combination.First().modification });
+ e.identify_connected_experimentals(new List<PtmSet> { set2 }, new List<ModificationWithMass> { set2.ptm_combination.First().modification });
  Assert.IsNotNull(e2.linked_proteoform_references);
  Assert.AreEqual(42.01, e2.ptm_set.mass);
+
+ e.relationships.Clear();
+ e2 = ConstructorsForTesting.ExperimentalProteoform("", 10042.01, 0, true);
+ ConstructorsForTesting.make_relation(e, e2, ProteoformComparison.ExperimentalExperimental, 42.01);
+ e.relationships.First().Accepted = true;
+ e.relationships.First().peak = new DeltaMassPeak(e.relationships.First(), new HashSet<ProteoformRelation> { e.relationships.First() });
+ e.identify_connected_experimentals(new List<PtmSet> { set3 }, new List<ModificationWithMass> { set3.ptm_combination.First().modification });
+ Assert.IsNotNull(e2.linked_proteoform_references);
+ Assert.AreEqual(84.02, e2.ptm_set.mass);
+
+ //can't remove more acetylations than in e's ptmset
+ e.relationships.Clear();
+ e2 = ConstructorsForTesting.ExperimentalProteoform("", 10042.01, 0, true);
+ ConstructorsForTesting.make_relation(e, e2, ProteoformComparison.ExperimentalExperimental, 168.04);
+ e.relationships.First().Accepted = true;
+ e.relationships.First().peak = new DeltaMassPeak(e.relationships.First(), new HashSet<ProteoformRelation> { e.relationships.First() });
+ e.identify_connected_experimentals(new List<PtmSet> { set4 }, new List<ModificationWithMass> { set4.ptm_combination.First().modification });
+ Assert.IsNull(e2.linked_proteoform_references);
  }
 
  [Test]