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());
}
}
private static SmallMoleculeLibraryAttributes Normalize(
ValueCache valueCache,
SmallMoleculeLibraryAttributes smallMoleculeLibraryAttributes)
{
if (smallMoleculeLibraryAttributes == null)
{
return(SmallMoleculeLibraryAttributes.EMPTY);
}
if (null == smallMoleculeLibraryAttributes.MoleculeName ||
null == smallMoleculeLibraryAttributes.ChemicalFormula ||
null == smallMoleculeLibraryAttributes.InChiKey ||
null == smallMoleculeLibraryAttributes.OtherKeys)
{
smallMoleculeLibraryAttributes = SmallMoleculeLibraryAttributes.Create(
smallMoleculeLibraryAttributes.MoleculeName ?? string.Empty,
smallMoleculeLibraryAttributes.ChemicalFormula ?? string.Empty,
smallMoleculeLibraryAttributes.InChiKey ?? string.Empty,
smallMoleculeLibraryAttributes.OtherKeys ?? string.Empty);
}
if (valueCache != null)
{
if (!valueCache.TryGetCachedValue(ref smallMoleculeLibraryAttributes))
{
smallMoleculeLibraryAttributes = valueCache.CacheValue(SmallMoleculeLibraryAttributes.Create(
valueCache.CacheValue(smallMoleculeLibraryAttributes.MoleculeName),
valueCache.CacheValue(smallMoleculeLibraryAttributes.ChemicalFormula),
valueCache.CacheValue(smallMoleculeLibraryAttributes.InChiKey),
valueCache.CacheValue(smallMoleculeLibraryAttributes.OtherKeys)
));
}
}
return(smallMoleculeLibraryAttributes);
}
public static SpectrumPeakAnnotation Create(SmallMoleculeLibraryAttributes mol, Adduct adduct, string comment, double?mzTheoretical)
{
double?massTheoretical = mzTheoretical.HasValue ? adduct.MassFromMz(mzTheoretical.Value, MassType.Monoisotopic).Value : (double?)null;
var ion = new CustomIon(mol, adduct, massTheoretical);
if ((mzTheoretical ?? 0.0) > 0)
{
if (Equals(ion.MonoisotopicMassMz, 0.0))
{
// We didn't have enough info to calculate mz, use the provided theoretical value
var massMono = adduct.MassFromMz(mzTheoretical.Value, MassType.Monoisotopic);
var massAverage = adduct.MassFromMz(mzTheoretical.Value, MassType.Average);
ion = new CustomIon(ion.GetSmallMoleculeLibraryAttributes(), ion.Adduct, massMono, massAverage);
}
else
{
// Check our calculated value against provided theoretical value, allowing quite a lot of wiggle (not everybody is using the same precision out there)
var delta = .5; // Generous error for sanity check
if (Math.Abs(ion.MonoisotopicMassMz - mzTheoretical.Value) > delta)
{
Assume.Fail(string.Format(@"SpectrumPeakAnnotation: mzTheoretical {0} and mzActual {1} disagree by more than {2} in {3} {4}",
mzTheoretical, ion.MonoisotopicMassMz, delta, ion, comment ?? string.Empty));
}
}
}
return(ion.IsEmpty && string.IsNullOrEmpty(comment) ?
EMPTY :
new SpectrumPeakAnnotation(ion, comment));
}
public DbIonMobilityPeptide(SmallMoleculeLibraryAttributes smallMoleculeLibraryAttributes,
Adduct precursorAdduct,
double collisionalCrossSection,
double highEnergyDriftTimeOffsetMsec)
: this(new Target(smallMoleculeLibraryAttributes), collisionalCrossSection, highEnergyDriftTimeOffsetMsec,
precursorAdduct)
{
}
public MoleculeLibraryKey(ValueCache valueCache, SmallMoleculeLibraryAttributes smallMoleculeLibraryAttributes,
Adduct adduct)
{
SmallMoleculeLibraryAttributes = Normalize(valueCache, smallMoleculeLibraryAttributes);
PreferredKey = SmallMoleculeLibraryAttributes.GetPreferredKey() ??
SmallMoleculeLibraryAttributes.MoleculeName ?? String.Empty;
_adduct = adduct;
}
public ValidatingIonMobilityPeptide(SmallMoleculeLibraryAttributes smallMoleculeLibraryAttributes,
Adduct precursorAdduct,
double collisionalCrossSection,
double highEnergyDriftTimeOffsetMsec)
: base(smallMoleculeLibraryAttributes, precursorAdduct,
collisionalCrossSection, highEnergyDriftTimeOffsetMsec)
{
}
internal MoleculeLibraryKey(ValueCache valueCache, LibraryKeyProto libraryKeyProto) : this(
valueCache,
SmallMoleculeLibraryAttributes.Create(
valueCache.CacheValue(libraryKeyProto.MoleculeName),
valueCache.CacheValue(libraryKeyProto.ChemicalFormula),
libraryKeyProto.InChiKey, libraryKeyProto.OtherKeys),
Adduct.FromString(libraryKeyProto.Adduct, Adduct.ADDUCT_TYPE.non_proteomic, null))
{
}
public ValidatingIonMobilityPrecursor(SmallMoleculeLibraryAttributes smallMoleculeLibraryAttributes,
Adduct precursorAdduct,
double collisionalCrossSection,
double ionMobility,
double highEnergyIonMobilityOffset,
eIonMobilityUnits units)
: base(new DbPrecursorIon(new Target(smallMoleculeLibraryAttributes), precursorAdduct),
collisionalCrossSection, ionMobility, units, highEnergyIonMobilityOffset)
{
}
// Single conformer ctor
public PrecursorIonMobilities(SmallMoleculeLibraryAttributes smallMoleculeLibraryAttributes,
Adduct precursorAdduct,
double collisionalCrossSection,
double ionMobility,
double highEnergyIonMobilityOffset,
eIonMobilityUnits units)
: this(new LibKey(new Target(smallMoleculeLibraryAttributes), precursorAdduct),
IonMobilityAndCCS.GetIonMobilityAndCCS(ionMobility, units, collisionalCrossSection, highEnergyIonMobilityOffset))
{
}
public void TestCustomMoleculeToTSV()
{
var moleculeAccessionNumbers = new MoleculeAccessionNumbers(new Dictionary <string, string>
{
{ MoleculeAccessionNumbers.TagCAS, "MyCAS" },
{ MoleculeAccessionNumbers.TagHMDB, "MyHMDB" },
{ MoleculeAccessionNumbers.TagInChI, "MyInChI" },
{ MoleculeAccessionNumbers.TagSMILES, "MySmiles" }
});
var smallMoleculeLibraryAttributes =
SmallMoleculeLibraryAttributes.Create("MyMolecule", "H2O", "MyInChiKey", moleculeAccessionNumbers.GetNonInChiKeys());
var customMolecule = new CustomMolecule(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);
}
protected const string massFormatRegex = @"(?:[a-z][a-z]+)\s+\[([+-]?\d*\.\d+)(?![-+0-9\.])\/([+-]?\d*\.\d+)(?![-+0-9\.])\]"; // Not L10N
public SmallMoleculeLibraryAttributes GetSmallMoleculeLibraryAttributes()
{
return(SmallMoleculeLibraryAttributes.Create(Name, Formula,
AccessionNumbers.GetInChiKey(), AccessionNumbers.GetNonInChiKeys()));
}
public CustomIon(SmallMoleculeLibraryAttributes mol, Adduct adduct, double?monoisotopicMass = null, double?averageMass = null)
: this(mol.ChemicalFormula, adduct, monoisotopicMass, averageMass, mol.MoleculeName)
{
}
public CustomMolecule(SmallMoleculeLibraryAttributes libraryAttributes)
: this(libraryAttributes.ChemicalFormula, libraryAttributes.MoleculeName, libraryAttributes.CreateMoleculeID())
{
Assume.IsFalse(libraryAttributes.IsEmpty);
}
public DbPrecursorIon(SmallMoleculeLibraryAttributes smallMoleculeLibraryAttributes,
Adduct precursorAdduct)
: this(new Target(smallMoleculeLibraryAttributes),
precursorAdduct)
{
}
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 '$' in it, which we use as a tab replacement against XML parser variability
var molser = new CustomMolecule(SmallMoleculeLibraryAttributes.Create("caffeine$", caffeineFormula, caffeineInChiKey, caffeineHMDB));
var text = molser.ToSerializableString();
Assert.AreEqual(molser, CustomMolecule.FromSerializableString(text));
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 Target(SmallMoleculeLibraryAttributes molecule)
{
Molecule = new CustomMolecule(molecule);
}
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);
}
public override string ToString()
{
return(SmallMoleculeLibraryAttributes.ToString() + Adduct);
}
public Target(SmallMoleculeLibraryAttributes molecule)
{
Molecule = CustomMolecule.FromSmallMoleculeLibraryAttributes(molecule);
}
public MoleculeLibraryKey(SmallMoleculeLibraryAttributes smallMoleculeLibraryAttributes, Adduct adduct) : this(null, smallMoleculeLibraryAttributes, adduct)
{
}
public override int GetHashCode()
{
unchecked
{
return(((_adduct != null ? _adduct.GetHashCode() : 0) * 397) ^ (SmallMoleculeLibraryAttributes != null ? SmallMoleculeLibraryAttributes.GetHashCode() : 0));
}
}
public static CustomMolecule FromSmallMoleculeLibraryAttributes(SmallMoleculeLibraryAttributes libraryAttributes)
{
Assume.IsFalse(libraryAttributes.IsEmpty);
SmallMoleculeLibraryAttributes.ParseMolecularFormulaOrMassesString(libraryAttributes.ChemicalFormulaOrMassesString, out var formula, out var monoMass, out var averageMass);
return(new CustomMolecule(formula, monoMass, averageMass, libraryAttributes.MoleculeName, libraryAttributes.CreateMoleculeID()));
}
public DbMolecule(SmallMoleculeLibraryAttributes smallMoleculeLibraryAttributes)
: this(new Target(smallMoleculeLibraryAttributes))
{
}
private void MainTest()
{
// Clean-up before running the test
RunUI(() => SkylineWindow.ModifyDocument("Set default settings",
doc => doc.ChangeSettings(SrmSettingsList.GetDefault())));
// Check using libkey with small molecules
var adduct = Adduct.FromStringAssumeProtonated("M+3Na");
var z = adduct.AdductCharge;
const string caffeineFormula = "C8H10N4O2";
const string caffeineInChiKey = "RYYVLZVUVIJVGH-UHFFFAOYSA-N";
const string caffeineHMDB = "HMDB01847";
const string caffeineInChi = "InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3";
const string caffeineCAS = "58-08-2";
const string caffeineSMILES = "Cn1cnc2n(C)c(=O)n(C)c(=O)c12";
const string caffeineKEGG = "C07481";
var mId = new MoleculeAccessionNumbers(string.Join("\t", MoleculeAccessionNumbers.TagHMDB + ":" + caffeineHMDB,
MoleculeAccessionNumbers.TagInChI + ":" + caffeineInChi, MoleculeAccessionNumbers.TagCAS + ":" + caffeineCAS, MoleculeAccessionNumbers.TagInChiKey + ":" + caffeineInChiKey,
MoleculeAccessionNumbers.TagSMILES + ":" + caffeineSMILES, MoleculeAccessionNumbers.TagKEGG + ":" + caffeineKEGG));
Assert.AreEqual(caffeineInChiKey, mId.GetInChiKey());
Assert.AreEqual(caffeineCAS, mId.GetCAS());
Assert.AreEqual(caffeineSMILES, mId.GetSMILES());
Assert.AreEqual(caffeineKEGG, mId.GetKEGG());
var moleculeName = "caffeine";
var smallMolAttributes = SmallMoleculeLibraryAttributes.Create(moleculeName, caffeineFormula, caffeineInChiKey,
string.Join("\t", MoleculeAccessionNumbers.TagHMDB + ":" + caffeineHMDB,
MoleculeAccessionNumbers.TagInChI + ":" + caffeineInChi, MoleculeAccessionNumbers.TagCAS + ":" + caffeineCAS,
MoleculeAccessionNumbers.TagSMILES + ":" + caffeineSMILES, MoleculeAccessionNumbers.TagKEGG + ":" + caffeineKEGG));
LibKey key;
for (var loop = 0; loop++ < 2;)
{
key = new LibKey(smallMolAttributes, adduct);
Assert.IsFalse(key.IsPrecursorKey);
Assert.IsFalse(key.IsProteomicKey);
Assert.IsTrue(key.IsSmallMoleculeKey);
Assert.IsFalse(key.IsModified);
Assert.AreEqual(0, key.ModificationCount);
Assert.AreEqual(z, key.Charge);
Assert.AreEqual(adduct, key.Adduct);
Assert.AreEqual(caffeineInChiKey, key.Target.ToString());
var viewLibPepInfo = new ViewLibraryPepInfo(key);
Assert.AreEqual(key, viewLibPepInfo.Key);
var smallMolInfo = viewLibPepInfo.GetSmallMoleculeLibraryAttributes();
Assert.AreEqual(moleculeName, smallMolInfo.MoleculeName);
Assert.AreEqual(caffeineInChiKey, smallMolInfo.InChiKey);
Assert.AreEqual(caffeineFormula, smallMolInfo.ChemicalFormula);
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineCAS));
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineInChi));
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineHMDB));
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineSMILES));
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineKEGG));
adduct = Adduct.FromString("M+3Si", Adduct.ADDUCT_TYPE.non_proteomic, z = -17); // Not realistic, but let's see if it's handled consistently
}
// Check general libkey operation
var seq = "YTQSNSVC[+57.0]YAK";
key = new LibKey(seq, Adduct.DOUBLY_PROTONATED);
Assert.IsFalse(key.IsPrecursorKey);
Assert.IsTrue(key.IsProteomicKey);
Assert.IsFalse(key.IsSmallMoleculeKey);
Assert.IsTrue(key.IsModified);
Assert.AreEqual(2, key.Charge);
Assert.AreEqual(1, key.ModificationCount);
Assert.AreEqual(Adduct.DOUBLY_PROTONATED, key.Adduct);
Assert.AreEqual(seq, key.Target.ToString());
// Test error conditions
BuildLibraryError("missing_charge.pep.XML", TestFilesDir.FullPath);
BuildLibraryError("non_int_charge.pep.XML", null);
BuildLibraryError("zero_charge.pep.XML", null);
BuildLibraryError("truncated.pep.XML", null);
BuildLibraryError("no_such_file.pep.XML", null, "Failed to open");
BuildLibraryError("missing_mzxml.pep.XML", null, "Could not find spectrum file");
// Check for proper handling of labeled addducts in small molecule files
// (formerly this would throw on a null object, fixed with the use of ExplicitMods.EMPTY)
BuildLibraryValid("heavy_adduct.ssl", true, false, false, 1);
// Make sure explorer handles this adduct type
var viewLibUI = ShowDialog <ViewLibraryDlg>(SkylineWindow.ViewSpectralLibraries);
RunUI(() => AssertEx.IsTrue(viewLibUI.GraphItem.IonLabels.Any()));
RunUI(viewLibUI.CancelDialog);
// Barbara added code to ProteoWizard to rebuild a missing or invalid mzXML index
// BuildLibraryError("bad_mzxml.pep.XML", "<index> not found");
BuildLibraryValid(TestFilesDir.GetTestPath("library_errors"), new[] { "bad_mzxml.pep.XML" }, false, false, false, 1);
string libraryBaseName = _libraryName;
// Test mascot parser
_libraryName = libraryBaseName + "mascot";
string libraryMascot = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("mascot"), new[] { "F027319.dat" },
true, false, false, 121, 4);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryMascot)));
// Test successful builds
_libraryName = libraryBaseName + "a";
string libraryA = _libraryName + BiblioSpecLiteSpec.EXT;
string libraryARedundant = _libraryName + BiblioSpecLiteSpec.EXT_REDUNDANT;
BuildLibraryValid("CPTAC_Set4_725_091509.pep.XML", true, false, false, 1);
BuildLibraryValid("CPTAC_Set4_610_080509.pep.XML", true, false, true, 2);
_libraryName = libraryBaseName + "b";
string libraryB = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid("CPTAC_Set4_624_072409.pep.XML", false, false, false, 6);
_libraryName = libraryBaseName + "c";
string libraryC = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.FullPath, new[] { libraryA, libraryB },
false, false, false, 8);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryA)));
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryARedundant)));
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryB)));
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryC)));
// Test peptide filter
const string filterList = "ACARPIISVYSEK\n" +
// TODO: Having the modified sequence as the first line causes an error with European number formats
"ADRDESSPYAAM[+{0:F01}]IAAQDVAQR\n" +
"ADAIQAGASQFETSAAK";
PastePeptideList(string.Format(filterList, 16.0), true, 0, 3, true);
_libraryName = libraryBaseName + "filter";
string libraryFilter = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("maxquant"), new[] { "test.msms.txt" },
false, true, false, 2);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryFilter)));
RunUI(SkylineWindow.Undo);
RunUI(SkylineWindow.Undo);
// Test AddPathsDlg (file not found)
EnsurePeptideSettings();
var buildLibraryDlg = ShowDialog <BuildLibraryDlg>(PeptideSettingsUI.ShowBuildLibraryDlg);
string[] invalidPaths =
{
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "test.msms.xml"),
Path.Combine(TestFilesDir.GetTestPath("library_valid"), "CPTAC_Set4_624_072409.pep.XML")
};
TestAddPaths(buildLibraryDlg, invalidPaths, true);
// Test AddPathsDlg (file invalid type)
string[] invalidTypes =
{
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "test.msms.txt"),
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "mqpar.xml")
};
TestAddPaths(buildLibraryDlg, invalidTypes, true);
// Test AddPathsDlg (valid files)
string[] goodPaths =
{
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "test.msms.txt"),
Path.Combine(TestFilesDir.GetTestPath("library_valid"), "CPTAC_Set4_624_072409.pep.XML")
};
TestAddPaths(buildLibraryDlg, goodPaths, false);
OkDialog(buildLibraryDlg, buildLibraryDlg.CancelDialog);
const string heavyRPeptide = "TPAQFDADELR";
const string oxidizedMPeptide = "LVGNMHGDETVSR";
const string peptideList = heavyRPeptide + "\n" +
oxidizedMPeptide + "\n" +
"ALSIGFETCR\n" +
"GNMHGDETVSR\n" +
"VGNMHGDETVSR";
PastePeptideList(peptideList, true, 0, 1);
// Set modifications on peptides to verify they connect with library spectra.
const LabelAtoms labelAtoms = LabelAtoms.C13 | LabelAtoms.N15;
const string heavyR = "Heavy R";
Settings.Default.HeavyModList.Add(new StaticMod(heavyR, "R", ModTerminus.C, null, labelAtoms, null, null));
const string oMeth = "Oxidized Methionine";
Settings.Default.StaticModList.Add(new StaticMod(oMeth, "M", null, "O"));
var sequenceTree = SkylineWindow.SequenceTree;
var docCurrent = SkylineWindow.Document;
// Select the heavyR peptide
PeptideTreeNode nodePepTree = null;
IdentityPath pathPep = docCurrent.GetPathTo((int)SrmDocument.Level.Molecules, 0);
RunUI(() =>
{
sequenceTree.SelectedPath = pathPep;
nodePepTree = sequenceTree.SelectedNode as PeptideTreeNode;
});
Assert.IsNotNull(nodePepTree);
Assert.AreEqual(heavyRPeptide, nodePepTree.DocNode.Peptide.Sequence);
// Set the Heavy R modification explicitly
var editPepModsDlg = ShowDialog <EditPepModsDlg>(SkylineWindow.ModifyPeptide);
RunUI(() =>
{
editPepModsDlg.SetModification(heavyRPeptide.Length - 1, IsotopeLabelType.heavy, heavyR);
editPepModsDlg.OkDialog();
});
WaitForCondition(() => (SkylineWindow.Document.Molecules.First().TransitionGroupCount == 2));
// The peptide should now match the spectrum in the library, and have
// both heavy and light precursors, with ranked transitions
PeptideDocNode nodePep = null;
RunUI(() => nodePep = nodePepTree.DocNode);
Assert.IsNotNull(nodePep);
Debug.Assert(nodePep != null);
Assert.AreEqual(2, nodePep.Children.Count, "Missing precursor for heavy R peptide.");
docCurrent = SkylineWindow.Document;
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
AssertLibInfo(docCurrent, nodeGroup);
}
// Which means all transition groups should now have spectrum info
foreach (var nodeGroup in docCurrent.PeptideTransitionGroups)
{
AssertLibInfo(docCurrent, nodeGroup);
}
// New document
var docNew = new SrmDocument(SrmSettingsList.GetDefault());
var docNewCopy = docNew;
RunUI(() => SkylineWindow.SwitchDocument(docNewCopy, null));
const string idpList3 = "FHYKTDQGIK\n" +
"WCAIGHQER\n" +
"WCTISTHEANK";
int idpCount3 = idpList3.Split('\n').Length;
const string idpList = "ADVTLGGGAK\n" +
"AGFAGDDAPR\n" +
"ALEFAKK\n" +
"CCTESLVNR\n" +
"DSYVGDEAQSK\n" +
"YICDNQDTISSK\n" +
// charge 3 peptides all have 2 also
idpList3;
int idpCount = idpList.Split('\n').Length;
_libraryName = libraryBaseName + "_idp";
string libraryIdp = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("idp_xml"), new[] { "orbi-small-eg.idpXML" },
false, false, false, idpCount + idpCount3);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryIdp)));
// Add peptides expected to have charge 2 spectra in the library
PastePeptideList(idpList, true, 0, 0);
// Undo the paste
RunUI(SkylineWindow.Undo);
// Try filtering for only charge 3 spectra
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(
SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.PrecursorCharges = "3";
transitionSettingsUI.OkDialog();
});
PastePeptideList(idpList, false, idpCount - idpCount3 + 1 /* missing cleavage*/, 0);
// New document
var docNewCopy2 = docNew;
RunUI(() => SkylineWindow.SwitchDocument(docNewCopy2, null));
_libraryName = libraryBaseName + "_cpas1";
string libraryCpas1 = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("cpas"), null,
false, false, false, 3);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryCpas1)));
// These are very poor searches, so repeat with no filter
Settings.Default.LibraryResultCutOff = 0;
_libraryName = libraryBaseName + "_cpas2";
BuildLibraryValid(TestFilesDir.GetTestPath("cpas"), null,
false, false, false, 100, 100);
// And, since the spectra are really poor, allow lots of
// possibilities for fragment ions.
var transitionSettingsCpas = ShowDialog <TransitionSettingsUI>(
SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsCpas.PrecursorCharges =
transitionSettingsCpas.ProductCharges = "1,2,3";
transitionSettingsCpas.FragmentTypes = "y,b";
transitionSettingsCpas.InstrumentMaxMz = 2000;
transitionSettingsCpas.OkDialog();
});
EnsurePeptideSettings();
RunUI(() =>
{
// Turn off carbamidomethyl cys, since not in these searches
PeptideSettingsUI.PickedStaticMods = new string[0];
PeptideSettingsUI.OkDialog();
});
// Get the set of peptides to paste from the library, since there
// are a lot.
var setPeptides = new HashSet <Target>();
var library = SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries[0];
foreach (var libKey in library.Keys)
{
if (!libKey.IsModified)
{
setPeptides.Add(libKey.Target);
}
}
string cpasPeptides = string.Join("\n", setPeptides.Select(p => p.ToString()).ToArray());
var pasteFilteredPeptideDlg = ShowDialog <PasteFilteredPeptidesDlg>(
() => SkylineWindow.Paste(cpasPeptides));
RunUI(pasteFilteredPeptideDlg.NoDialog);
Assert.IsTrue(WaitForCondition(() => SkylineWindow.Document.PeptideCount == setPeptides.Count),
string.Format("Expecting {0} peptides, found {1}.", setPeptides.Count, SkylineWindow.Document.PeptideCount));
Assert.AreEqual(setPeptides.Count, SkylineWindow.Document.PeptideTransitionGroupCount,
"Expecting precursors for peptides matched to library spectrum.");
// New document
docNew = new SrmDocument(SrmSettingsList.GetDefault());
RunUI(() => SkylineWindow.SwitchDocument(docNew, null));
// Tests for adding iRTs to spectral library after building
// 1. ask to recalibrate iRTs
// 2. ask to add iRTs
// 3. if added iRTs, ask to add RT predictor
// no recalibrate, add iRTs, no add predictor
_libraryName = libraryBaseName + "_irt1"; // library_test_irt1
BuildLibraryIrt(true, false, false);
RunUI(() => Assert.IsTrue(PeptideSettingsUI.Prediction.RetentionTime == null));
// no recalibrate, add iRTs, add predictor
_libraryName = libraryBaseName + "_irt2"; // library_test_irt2
BuildLibraryIrt(true, false, true);
RunUI(() => Assert.IsTrue(PeptideSettingsUI.Prediction.RetentionTime.Name.Equals(_libraryName)));
var editIrtDlg2 = ShowDialog <EditIrtCalcDlg>(PeptideSettingsUI.EditCalculator);
RunUI(() => Assert.IsTrue(ReferenceEquals(editIrtDlg2.IrtStandards, IrtStandard.BIOGNOSYS_10)));
OkDialog(editIrtDlg2, editIrtDlg2.CancelDialog);
// recalibrate, add iRTs, no add predictor
_libraryName = libraryBaseName + "_irt3"; // library_test_irt3
BuildLibraryIrt(true, true, false);
RunUI(() => Assert.IsTrue(PeptideSettingsUI.Prediction.RetentionTime.Name.Equals(libraryBaseName + "_irt2")));
// recalibrate, add iRTs, add predictor
_libraryName = libraryBaseName + "_irt4"; // library_test_irt4
BuildLibraryIrt(true, true, true);
RunUI(() => Assert.IsTrue(PeptideSettingsUI.Prediction.RetentionTime.Name.Equals(_libraryName)));
var editIrtDlg4 = ShowDialog <EditIrtCalcDlg>(PeptideSettingsUI.EditCalculator);
RunUI(() => Assert.IsTrue(ReferenceEquals(editIrtDlg4.IrtStandards, IrtStandard.EMPTY)));
OkDialog(editIrtDlg4, editIrtDlg4.CancelDialog);
OkDialog(PeptideSettingsUI, PeptideSettingsUI.CancelDialog);
}
private void PerformTestMeasuredDriftValues(bool asSmallMolecules)
{
if (asSmallMolecules)
{
if (!RunSmallMoleculeTestVersions)
{
Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
}
var testFilesDir = new TestFilesDir(TestContext, @"TestData\Results\BlibDriftTimeTest.zip"); // Re-used from BlibDriftTimeTest
// Open document with some peptides but no results
var docPath = testFilesDir.GetTestPath("BlibDriftTimeTest.sky");
// This was a malformed document, which caused problems after a fix to not recalculate
// document library settings on open. To avoid rewriting this test for the document
// which now contains 2 precursors, the first precursor is removed immediately.
SrmDocument docOriginal = ResultsUtil.DeserializeDocument(docPath);
var pathFirstPeptide = docOriginal.GetPathTo((int)SrmDocument.Level.Molecules, 0);
var nodeFirstPeptide = (DocNodeParent)docOriginal.FindNode(pathFirstPeptide);
docOriginal = (SrmDocument)docOriginal.RemoveChild(pathFirstPeptide, nodeFirstPeptide.Children[0]);
if (asSmallMolecules)
{
var refine = new RefinementSettings();
docOriginal = refine.ConvertToSmallMolecules(docOriginal, testFilesDir.FullPath);
}
using (var docContainer = new ResultsTestDocumentContainer(docOriginal, docPath))
{
var doc = docContainer.Document;
// Import an mz5 file that contains drift info
const string replicateName = "ID12692_01_UCA168_3727_040714";
var chromSets = new[]
{
new ChromatogramSet(replicateName, new[]
{ new MsDataFilePath(testFilesDir.GetTestPath("ID12692_01_UCA168_3727_040714" + ExtensionTestContext.ExtMz5)), }),
};
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(chromSets));
Assert.IsTrue(docContainer.SetDocument(docResults, docOriginal, true));
docContainer.AssertComplete();
var document = docContainer.Document;
// Clear out any current settings
document = document.ChangeSettings(document.Settings.ChangeTransitionIonMobilityFiltering(s => TransitionIonMobilityFiltering.EMPTY));
// Verify ability to extract predictions from raw data
var libraryName0 = "test0";
var dbPath0 = testFilesDir.GetTestPath(libraryName0 + IonMobilityDb.EXT);
var newIMFiltering = document.Settings.TransitionSettings.IonMobilityFiltering.ChangeLibrary(
IonMobilityLibrary.CreateFromResults(
document, docContainer.DocumentFilePath, true,
libraryName0, dbPath0));
var result = newIMFiltering.IonMobilityLibrary.GetIonMobilityLibKeyMap().AsDictionary();
Assert.AreEqual(1, result.Count);
var expectedDT = 4.0019;
var expectedOffset = .4829;
Assert.AreEqual(expectedDT, result.Values.First().First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(expectedOffset, result.Values.First().First().HighEnergyIonMobilityValueOffset ?? 0, .001);
// Check ability to update, and to preserve unchanged
var revised = new List <PrecursorIonMobilities>();
var libKey = result.Keys.First();
revised.Add(new PrecursorIonMobilities(libKey, IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(expectedDT = 4, eIonMobilityUnits.drift_time_msec), null, expectedOffset = 0.234))); // N.B. CCS handling would require actual raw data in this test, it's covered in a perf test
var pepSequence = "DEADEELS";
var libKey2 = asSmallMolecules ?
new LibKey(SmallMoleculeLibraryAttributes.Create(pepSequence, "C12H5", null, null, null, null), Adduct.M_PLUS_2H) :
new LibKey(pepSequence, Adduct.DOUBLY_PROTONATED);
revised.Add(new PrecursorIonMobilities(libKey2, IonMobilityAndCCS.GetIonMobilityAndCCS(IonMobilityValue.GetIonMobilityValue(5, eIonMobilityUnits.drift_time_msec), null, 0.123)));
var libraryName = "test";
var dbPath = testFilesDir.GetTestPath(libraryName + IonMobilityDb.EXT);
var imsdb = IonMobilityDb.CreateIonMobilityDb(dbPath, libraryName, false, revised);
var newLibIM = new IonMobilityLibrary(libraryName, dbPath, imsdb);
var ionMobilityWindowWidthCalculator = new IonMobilityWindowWidthCalculator(
IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.resolving_power, 40, 0, 0, 0);
var calculator = ionMobilityWindowWidthCalculator;
document = document.ChangeSettings(
document.Settings.ChangeTransitionIonMobilityFiltering(
imf => imf.ChangeFilterWindowWidthCalculator(calculator).
ChangeLibrary(newLibIM)));
result = document.Settings.TransitionSettings.IonMobilityFiltering.IonMobilityLibrary.GetIonMobilityLibKeyMap().AsDictionary();
Assert.AreEqual(2, result.Count);
Assert.AreEqual(expectedDT, result[libKey].First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(expectedOffset, result[libKey].First().HighEnergyIonMobilityValueOffset ?? 0, .001);
Assert.AreEqual(5, result[libKey2].First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(0.123, result[libKey2].First().HighEnergyIonMobilityValueOffset ?? 0, .001);
ionMobilityWindowWidthCalculator = new IonMobilityWindowWidthCalculator(
IonMobilityWindowWidthCalculator.IonMobilityWindowWidthType.fixed_width, 40, 0, 0, 100);
document = document.ChangeSettings(
document.Settings.ChangeTransitionIonMobilityFiltering(
imf => imf.ChangeFilterWindowWidthCalculator(ionMobilityWindowWidthCalculator).
ChangeLibrary(newLibIM)));
result = document.Settings.TransitionSettings.IonMobilityFiltering.IonMobilityLibrary.GetIonMobilityLibKeyMap().AsDictionary();
Assert.AreEqual(2, result.Count);
Assert.AreEqual(expectedDT, result[libKey].First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(expectedOffset, result[libKey].First().HighEnergyIonMobilityValueOffset ?? 0, .001);
Assert.AreEqual(5, result[libKey2].First().IonMobility.Mobility.Value, .001);
Assert.AreEqual(0.123, result[libKey2].First().HighEnergyIonMobilityValueOffset ?? 0, .001);
}
}
public SmallMoleculeLibraryAttributes GetSmallMoleculeLibraryAttributes()
{
return(SmallMoleculeLibraryAttributes.Create(Name, Formula,
MonoisotopicMass, AverageMass, // In case forumla is empty
AccessionNumbers.GetInChiKey(), AccessionNumbers.GetNonInChiKeys()));
}
