public void TestCustomMoleculeToTSV()
{
var moleculeAccessionNumbers = new MoleculeAccessionNumbers(new Dictionary <string, string>
{
{ MoleculeAccessionNumbers.TagCAS, "MyCAS" },
{ MoleculeAccessionNumbers.TagHMDB, "MyHMDB" },
{ MoleculeAccessionNumbers.TagInChI, "MyInChI" },
{ MoleculeAccessionNumbers.TagSMILES, "MySmiles" },
{ MoleculeAccessionNumbers.TagKEGG, "MyKegg" }
});
var smallMoleculeLibraryAttributes =
SmallMoleculeLibraryAttributes.Create("MyMolecule", "H2O", "MyInChiKey", moleculeAccessionNumbers.GetNonInChiKeys());
for (var loop = 0; loop < 2; loop++)
{
var customMolecule = CustomMolecule.FromSmallMoleculeLibraryAttributes(smallMoleculeLibraryAttributes);
var target = new Target(customMolecule);
var serializableString = target.ToSerializableString();
var roundTrip = Target.FromSerializableString(serializableString);
Assert.AreEqual(target, roundTrip);
Assert.AreEqual(customMolecule, roundTrip.Molecule);
Assert.AreEqual(customMolecule.AccessionNumbers, roundTrip.Molecule.AccessionNumbers);
smallMoleculeLibraryAttributes = // Masses instead of formula
SmallMoleculeLibraryAttributes.Create("MyMolecule", null, new TypedMass(123.4, MassType.Monoisotopic), new TypedMass(123.45, MassType.Average), "MyInChiKey", moleculeAccessionNumbers.GetNonInChiKeys());
}
}
public void TestLibIonMobilityInfo()
{
const string caffeineFormula = "C8H10N4O2";
const string caffeineInChiKey = "RYYVLZVUVIJVGH-UHFFFAOYSA-N";
const string caffeineHMDB = "HMDB01847";
const double HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC = -.01;
var dbIon1 = new DbIonMobilityPeptide(new Target("JKLMN"), Adduct.SINGLY_PROTONATED, 1.2, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
{
Id = 12345
};
for (var loop = 0; loop < 2; loop++)
{
var dbIon2 = new DbIonMobilityPeptide(dbIon1);
DbIonMobilityPeptide dbIon3 = null;
Assert.AreEqual(dbIon1.GetHashCode(), dbIon2.GetHashCode());
Assert.IsFalse(dbIon1.Equals(null));
Assert.IsTrue(dbIon1.Equals(dbIon2 as object));
// ReSharper disable once ExpressionIsAlwaysNull
Assert.IsFalse(dbIon1.Equals(dbIon3 as object));
Assert.IsTrue(dbIon1.Equals(dbIon1));
Assert.IsTrue(dbIon1.Equals(dbIon1 as object));
Assert.IsTrue(dbIon1.Equals(dbIon2));
dbIon1.CollisionalCrossSection = 1.3;
Assert.AreNotEqual(dbIon1.CollisionalCrossSection, dbIon2.CollisionalCrossSection);
if (loop == 1)
{
dbIon1.ModifiedTarget = new Target("foo");
Assert.AreNotEqual(dbIon1.Target, dbIon2.Target);
Assert.AreNotEqual(dbIon1.ModifiedTarget, dbIon2.ModifiedTarget);
}
else
{
Assert.AreEqual(dbIon1.ModifiedTarget, dbIon2.ModifiedTarget);
Assert.AreEqual(dbIon1.ModifiedTarget.Molecule, dbIon2.ModifiedTarget.Molecule);
}
dbIon1 = new DbIonMobilityPeptide(
SmallMoleculeLibraryAttributes.Create("caffeine", caffeineFormula, caffeineInChiKey, caffeineHMDB),
Adduct.FromStringAssumeProtonated("M+Na"),
1.2, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
{
Id = 12345
};
}
var dictCCS1 = new Dictionary <LibKey, IonMobilityAndCCS[]>();
var ccs1 = new List <IonMobilityAndCCS> {
IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.EMPTY, 1, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC), IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.EMPTY, 2, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
}; // Collisional cross sections
var ccs2 = new List <IonMobilityAndCCS> {
IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.EMPTY, 3, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC), IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.EMPTY, 4, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
}; // Collisional cross sections
const string seq1 = "JKLM";
const string seq2 = "KLMN";
dictCCS1.Add(new LibKey(seq1, 1), ccs1.ToArray());
dictCCS1.Add(new LibKey(seq2, 1), ccs2.ToArray());
var lib = new List <LibraryIonMobilityInfo> {
new LibraryIonMobilityInfo("test", dictCCS1)
};
var peptideTimes = CollisionalCrossSectionGridViewDriver.ConvertDriftTimesToCollisionalCrossSections(null,
lib, 1, null);
var validatingIonMobilityPeptides = peptideTimes as ValidatingIonMobilityPeptide[] ?? peptideTimes.ToArray();
Assert.AreEqual(2, validatingIonMobilityPeptides.Length);
Assert.AreEqual(1.5, validatingIonMobilityPeptides[0].CollisionalCrossSection);
Assert.AreEqual(3.5, validatingIonMobilityPeptides[1].CollisionalCrossSection);
Assert.AreEqual(HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC, validatingIonMobilityPeptides[1].HighEnergyDriftTimeOffsetMsec);
// Test serialization of molecule with '$' in it, which we use as a tab replacement against XML parser variability
var molser = CustomMolecule.FromSmallMoleculeLibraryAttributes(SmallMoleculeLibraryAttributes.Create("caffeine$", caffeineFormula, caffeineInChiKey, caffeineHMDB));
var text = molser.ToSerializableString();
Assert.AreEqual(molser, CustomMolecule.FromSerializableString(text));
// Test handling of SmallMoleculeLibraryAttributes for mass-only descriptions
var molserB = CustomMolecule.FromSmallMoleculeLibraryAttributes(SmallMoleculeLibraryAttributes.Create("caffeine$", null, new TypedMass(123.4, MassType.Monoisotopic), new TypedMass(123.45, MassType.Average), caffeineInChiKey, caffeineHMDB));
var textB = molserB.ToSerializableString();
Assert.AreEqual(molserB, CustomMolecule.FromSerializableString(textB));
var dictCCS2 = new Dictionary <LibKey, IonMobilityAndCCS[]>();
var ccs3 = new List <IonMobilityAndCCS> {
IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(4, eIonMobilityUnits.drift_time_msec), null, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC), IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(5, eIonMobilityUnits.drift_time_msec), null, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
}; // Drift times
const string seq3 = "KLMNJ";
dictCCS2.Add(new LibKey(seq3, Adduct.SINGLY_PROTONATED), ccs3.ToArray());
lib.Add(new LibraryIonMobilityInfo("test2", dictCCS2));
List <LibraryIonMobilityInfo> lib1 = lib;
AssertEx.ThrowsException <Exception>(() => CollisionalCrossSectionGridViewDriver.ConvertDriftTimesToCollisionalCrossSections(null,
lib1, 2, null),
String.Format(
Resources.CollisionalCrossSectionGridViewDriver_ProcessIonMobilityValues_Cannot_import_measured_ion_mobility_for_sequence__0___no_collisional_cross_section_conversion_parameters_were_provided_for_charge_state__1__,
seq3, 1));
var regressions = new Dictionary <int, RegressionLine> {
{ 1, new RegressionLine(2, 1) }
};
lib = new List <LibraryIonMobilityInfo> {
new LibraryIonMobilityInfo("test", dictCCS2)
};
peptideTimes = CollisionalCrossSectionGridViewDriver.ConvertDriftTimesToCollisionalCrossSections(null,
lib, 1, regressions);
validatingIonMobilityPeptides = peptideTimes as ValidatingIonMobilityPeptide[] ?? peptideTimes.ToArray();
Assert.AreEqual(1, validatingIonMobilityPeptides.Length);
Assert.AreEqual(1.75, validatingIonMobilityPeptides[0].CollisionalCrossSection);
}
public void TestLibIonMobilityInfo()
{
const string caffeineFormula = "C8H10N4O2";
const string caffeineInChiKey = "RYYVLZVUVIJVGH-UHFFFAOYSA-N";
const string caffeineHMDB = "HMDB01847";
const double HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC = -.01;
var dbMolecule = new DbMolecule(new Target("JKLMN"))
{
Id = 123456
};
var dbPrecursorIon = new DbPrecursorIon(dbMolecule, Adduct.SINGLY_PROTONATED)
{
Id = 1234567
};
var dbIonMobilityValue = new DbPrecursorAndIonMobility(dbPrecursorIon,
1.2, 2.3, eIonMobilityUnits.drift_time_msec, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
{
Id = 12345
};
DbPrecursorAndIonMobility dbPrecursorAndIonMobilityValue2 = new DbPrecursorAndIonMobility(dbIonMobilityValue);
for (var loop = 0; loop < 2; loop++)
{
Assert.AreEqual(dbIonMobilityValue.GetHashCode(), dbPrecursorAndIonMobilityValue2.GetHashCode());
Assert.IsFalse(dbIonMobilityValue.Equals(null));
Assert.IsTrue(dbIonMobilityValue.Equals(dbPrecursorAndIonMobilityValue2 as object));
Assert.IsTrue(dbIonMobilityValue.Equals(dbIonMobilityValue));
Assert.IsTrue(dbIonMobilityValue.Equals(dbIonMobilityValue as object));
Assert.IsTrue(dbPrecursorAndIonMobilityValue2.Equals(dbIonMobilityValue));
dbIonMobilityValue.CollisionalCrossSectionSqA = 1.3;
Assert.AreNotEqual(dbIonMobilityValue.CollisionalCrossSectionSqA, dbPrecursorAndIonMobilityValue2.CollisionalCrossSectionSqA);
if (loop == 1)
{
dbIonMobilityValue.DbPrecursorIon = new DbPrecursorIon(new Target("foo"), Adduct.SINGLY_PROTONATED)
{
Id = 1234567
};
Assert.AreNotEqual(dbIonMobilityValue.DbPrecursorIon.GetTarget(), dbMolecule);
}
else
{
Assert.AreEqual(dbIonMobilityValue.DbPrecursorIon.DbMolecule, dbMolecule);
}
dbIonMobilityValue = new DbPrecursorAndIonMobility(
new DbPrecursorIon(
SmallMoleculeLibraryAttributes.Create("caffeine", caffeineFormula, caffeineInChiKey, caffeineHMDB),
Adduct.FromStringAssumeProtonated("M+Na"))
{
Id = 23456
},
1.2, 2.3, eIonMobilityUnits.drift_time_msec, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
{
Id = 12345
};
dbPrecursorAndIonMobilityValue2 = new DbPrecursorAndIonMobility(dbIonMobilityValue);
}
var dictCCS1 = new Dictionary <LibKey, IonMobilityAndCCS[]>();
var im = IonMobilityValue.GetIonMobilityValue(12, eIonMobilityUnits.drift_time_msec);
var ccs1 = new List <IonMobilityAndCCS> {
IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.EMPTY, 1, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC), IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.EMPTY, 2, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
}; // Collisional cross sections
var ccs2 = new List <IonMobilityAndCCS> {
IonMobilityAndCCS.GetIonMobilityAndCCS(im, 3, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC), IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.EMPTY, 4, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
}; // Collisional cross sections
const string seq1 = "JKLM";
const string seq2 = "KLMN";
dictCCS1.Add(new LibKey(seq1, 1), ccs1.ToArray());
dictCCS1.Add(new LibKey(seq2, 1), ccs2.ToArray());
var lib = new List <LibraryIonMobilityInfo> {
new LibraryIonMobilityInfo("test", false, dictCCS1)
};
var peptideTimes = CollisionalCrossSectionGridViewDriver.CollectIonMobilitiesAndCollisionalCrossSections(null,
lib, 1);
var validatingIonMobilityPeptides = peptideTimes as ValidatingIonMobilityPrecursor[] ?? peptideTimes.ToArray();
Assert.AreEqual(2, validatingIonMobilityPeptides.Length);
Assert.AreEqual(1.5, validatingIonMobilityPeptides[0].CollisionalCrossSectionSqA);
Assert.AreEqual(3.5, validatingIonMobilityPeptides[1].CollisionalCrossSectionSqA);
Assert.AreEqual(HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC, validatingIonMobilityPeptides[1].HighEnergyIonMobilityOffset);
// This time with multiple CCS conformers supported
lib = new List <LibraryIonMobilityInfo> {
new LibraryIonMobilityInfo("test", true, dictCCS1)
};
peptideTimes = CollisionalCrossSectionGridViewDriver.CollectIonMobilitiesAndCollisionalCrossSections(null,
lib, 1);
validatingIonMobilityPeptides = peptideTimes as ValidatingIonMobilityPrecursor[] ?? peptideTimes.ToArray();
Assert.AreEqual(4, validatingIonMobilityPeptides.Length);
Assert.AreEqual(1, validatingIonMobilityPeptides[0].CollisionalCrossSectionSqA);
Assert.AreEqual(2, validatingIonMobilityPeptides[1].CollisionalCrossSectionSqA);
Assert.AreEqual(3, validatingIonMobilityPeptides[2].CollisionalCrossSectionSqA);
Assert.AreEqual(4, validatingIonMobilityPeptides[3].CollisionalCrossSectionSqA);
Assert.AreEqual(HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC, validatingIonMobilityPeptides[1].HighEnergyIonMobilityOffset);
// Test serialization of molecule with '$' in it, which we use as a tab replacement against XML parser variability
var molser = CustomMolecule.FromSmallMoleculeLibraryAttributes(SmallMoleculeLibraryAttributes.Create("caffeine$", caffeineFormula, caffeineInChiKey, caffeineHMDB));
var text = molser.ToSerializableString();
Assert.AreEqual(molser, CustomMolecule.FromSerializableString(text));
// Test handling of SmallMoleculeLibraryAttributes for mass-only descriptions
var molserB = CustomMolecule.FromSmallMoleculeLibraryAttributes(SmallMoleculeLibraryAttributes.Create("caffeine$", null, new TypedMass(123.4, MassType.Monoisotopic), new TypedMass(123.45, MassType.Average), caffeineInChiKey, caffeineHMDB));
var textB = molserB.ToSerializableString();
Assert.AreEqual(molserB, CustomMolecule.FromSerializableString(textB));
var dictCCS2 = new Dictionary <LibKey, IonMobilityAndCCS[]>();
var ccs3 = new List <IonMobilityAndCCS> {
IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(4, eIonMobilityUnits.drift_time_msec), 1.75, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC), IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(5, eIonMobilityUnits.drift_time_msec), null, HIGH_ENERGY_DRIFT_TIME_OFFSET_MSEC)
}; // Drift times
const string seq3 = "KLMNJ";
dictCCS2.Add(new LibKey(seq3, Adduct.SINGLY_PROTONATED), ccs3.ToArray());
lib = new List <LibraryIonMobilityInfo> {
new LibraryIonMobilityInfo("test", false, dictCCS2)
};
peptideTimes = CollisionalCrossSectionGridViewDriver.CollectIonMobilitiesAndCollisionalCrossSections(null,
lib, 1);
validatingIonMobilityPeptides = peptideTimes as ValidatingIonMobilityPrecursor[] ?? peptideTimes.ToArray();
Assert.AreEqual(1, validatingIonMobilityPeptides.Length);
Assert.AreEqual(1.75, validatingIonMobilityPeptides[0].CollisionalCrossSectionSqA);
}