protected virtual void ReadAttributes(XmlReader reader, out Adduct embeddedAdduct) { var formula = reader.GetAttribute(ATTR.formula); if (!string.IsNullOrEmpty(formula)) { formula = BioMassCalc.AddH(formula); // Update this old style formula to current by adding the hydrogen we formerly left out due to assuming protonation } else { var text = reader.GetAttribute(ATTR.ion_formula) ?? reader.GetAttribute(ATTR.neutral_formula); if (text != null) { text = text.Trim(); // We've seen some trailing spaces in the wild } formula = text; } string neutralFormula; Molecule mol; // We commonly see the adduct inline with the neutral formula ("C12H5[M+Na]"), so be ready to preserve that if (IonInfo.IsFormulaWithAdduct(formula, out mol, out embeddedAdduct, out neutralFormula)) { formula = neutralFormula; } else { embeddedAdduct = Adduct.EMPTY; } if (string.IsNullOrEmpty(formula)) { AverageMass = ReadAverageMass(reader); MonoisotopicMass = ReadMonoisotopicMass(reader); } Formula = formula; Name = reader.GetAttribute(ATTR.custom_ion_name); if (string.IsNullOrEmpty(Name)) { Name = reader.GetAttribute(ATTR.name) ?? string.Empty; } AccessionNumbers = MoleculeAccessionNumbers.FromSerializableString(reader.GetAttribute(ATTR.id)); Validate(); }
public static CustomMolecule FromSerializableString(string val) { var tsv = MoleculeAccessionNumbers.UnescapeTabsForXML(val); return(FromTSV(tsv)); }
public CustomMolecule(string formula, TypedMass monoisotopicMass, TypedMass averageMass, string name, MoleculeAccessionNumbers moleculeAccessionNumbers) { Formula = formula; MonoisotopicMass = monoisotopicMass; AverageMass = averageMass; Name = name ?? string.Empty; AccessionNumbers = moleculeAccessionNumbers ?? MoleculeAccessionNumbers.EMPTY; Validate(); }
public CustomMolecule(TypedMass monoisotopicMass, TypedMass averageMass, string name = null, MoleculeAccessionNumbers moleculeAccessionNumbers = null) : this(null, monoisotopicMass, averageMass, name, moleculeAccessionNumbers) { }
public CustomMolecule(string formula, string name = null, MoleculeAccessionNumbers moleculeAccessionNumbers = null) : this(formula, null, null, name, moleculeAccessionNumbers) { }
/// <summary> /// A simple object used to represent any molecule /// </summary> /// <param name="formula">The molecular formula of the molecule, possibly including an adduct description if subclassed as a CustomIon</param> /// <param name="monoisotopicMass">The monoisotopic mass of the molecule(can be calculated from formula)</param> /// <param name="averageMass">The average mass of the molecule (can be calculated by the formula)</param> /// <param name="name">The arbitrary name given to this molecule</param> /// <param name="moleculeAccessionNumbers">Provides InChiKey, CAS number etc</param> protected CustomMolecule(string formula, double?monoisotopicMass, double?averageMass, string name, MoleculeAccessionNumbers moleculeAccessionNumbers = null) : this(formula, new TypedMass(monoisotopicMass ?? averageMass ?? 0, MassType.Monoisotopic), new TypedMass(averageMass ?? monoisotopicMass ?? 0, MassType.Average), name, moleculeAccessionNumbers) { }
public static TransitionDocNode FromTransitionProto(AnnotationScrubber scrubber, SrmSettings settings, TransitionGroup group, ExplicitMods mods, IsotopeDistInfo isotopeDist, ExplicitTransitionValues pre422ExplicitTransitionValues, SkylineDocumentProto.Types.Transition transitionProto) { var stringPool = scrubber.StringPool; IonType ionType = DataValues.FromIonType(transitionProto.FragmentType); MeasuredIon measuredIon = null; if (transitionProto.MeasuredIonName != null) { measuredIon = settings.TransitionSettings.Filter.MeasuredIons.SingleOrDefault( i => i.Name.Equals(transitionProto.MeasuredIonName.Value)); if (measuredIon == null) { throw new InvalidDataException(string.Format(Resources.TransitionInfo_ReadXmlAttributes_The_reporter_ion__0__was_not_found_in_the_transition_filter_settings_, transitionProto.MeasuredIonName)); } ionType = IonType.custom; } bool isCustom = Transition.IsCustom(ionType, group); bool isPrecursor = Transition.IsPrecursor(ionType); CustomMolecule customIon = null; if (isCustom) { if (measuredIon != null) { customIon = measuredIon.SettingsCustomIon; } else if (isPrecursor) { customIon = group.CustomMolecule; } else { var formula = DataValues.FromOptional(transitionProto.Formula); var moleculeID = MoleculeAccessionNumbers.FromString(DataValues.FromOptional(transitionProto.MoleculeId)); // Tab separated list of InChiKey, CAS etc var monoMassH = DataValues.FromOptional(transitionProto.MonoMassH); var averageMassH = DataValues.FromOptional(transitionProto.AverageMassH); var monoMass = DataValues.FromOptional(transitionProto.MonoMass) ?? monoMassH; var averageMass = DataValues.FromOptional(transitionProto.AverageMass) ?? averageMassH; customIon = new CustomMolecule(formula, new TypedMass(monoMass.Value, monoMassH.HasValue ? MassType.MonoisotopicMassH : MassType.Monoisotopic), new TypedMass(averageMass.Value, averageMassH.HasValue ? MassType.AverageMassH : MassType.Average), DataValues.FromOptional(transitionProto.CustomIonName), moleculeID); } } Transition transition; var adductString = DataValues.FromOptional(transitionProto.Adduct); var adduct = string.IsNullOrEmpty(adductString) ? Adduct.FromChargeProtonated(transitionProto.Charge) : Adduct.FromStringAssumeChargeOnly(adductString); if (isCustom) { transition = new Transition(group, isPrecursor ? group.PrecursorAdduct :adduct, transitionProto.MassIndex, customIon, ionType); } else if (isPrecursor) { transition = new Transition(group, ionType, group.Peptide.Length - 1, transitionProto.MassIndex, group.PrecursorAdduct, DataValues.FromOptional(transitionProto.DecoyMassShift)); } else { int offset = Transition.OrdinalToOffset(ionType, transitionProto.FragmentOrdinal, group.Peptide.Length); transition = new Transition(group, ionType, offset, transitionProto.MassIndex, adduct, DataValues.FromOptional(transitionProto.DecoyMassShift)); } var losses = TransitionLosses.FromLossProtos(settings, transitionProto.Losses); var mass = settings.GetFragmentMass(group, mods, transition, isotopeDist); var isotopeDistInfo = GetIsotopeDistInfo(transition, losses, isotopeDist); if (group.DecoyMassShift.HasValue && transitionProto.DecoyMassShift == null) { throw new InvalidDataException(Resources.SrmDocument_ReadTransitionXml_All_transitions_of_decoy_precursors_must_have_a_decoy_mass_shift); } TransitionLibInfo libInfo = null; if (transitionProto.LibInfo != null) { libInfo = new TransitionLibInfo(transitionProto.LibInfo.Rank, transitionProto.LibInfo.Intensity); } var annotations = scrubber.ScrubAnnotations(Annotations.FromProtoAnnotations(transitionProto.Annotations), AnnotationDef.AnnotationTarget.transition); var results = TransitionChromInfo.FromProtoTransitionResults(scrubber, settings, transitionProto.Results); var explicitTransitionValues = pre422ExplicitTransitionValues ?? ExplicitTransitionValues.Create( DataValues.FromOptional(transitionProto.ExplicitCollisionEnergy), DataValues.FromOptional(transitionProto.ExplicitIonMobilityHighEnergyOffset), DataValues.FromOptional(transitionProto.ExplicitSLens), DataValues.FromOptional(transitionProto.ExplicitConeVoltage), DataValues.FromOptional(transitionProto.ExplicitDeclusteringPotential)); return(new TransitionDocNode(transition, annotations, losses, mass, new TransitionQuantInfo(isotopeDistInfo, libInfo, !transitionProto.NotQuantitative), explicitTransitionValues, results)); }