Rearranging classes to fit within the Transcriptomics Structure #743
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| @@ -235,32 +219,51 @@ public string GetEnsemblFastaHeader() | |||
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| /// <summary> | |||
| /// Gets peptides for digestion of a protein | |||
| /// Legacy | |||
| /// </summary> | |||
| public IEnumerable<PeptideWithSetModifications> Digest(DigestionParams digestionParams, | |||
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I do not think so. If one wanted to digest but only cared about proteins (such as in the XL or Glyco search task) this method would be called.
trishorts
reviewed
Dec 7, 2023
| int MaxLength { get; set; } | ||
| int MaxModificationIsoforms { get; set; } | ||
| int MaxMods { get; set; } | ||
| DigestionAgent Enzyme { get; } |
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might not be an Enzyme. For example cyanogen bromide
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Renamed Enzyme to DigestionAgent
trishorts
reviewed
Dec 7, 2023
trishorts
reviewed
Dec 7, 2023
| } | ||
| } | ||
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| protected Dictionary<int, Modification> GetFixedModsOneIsNterminusOrFivePrime(int peptideLength, |
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GetFixedModsOneIsNorFivePrimeTerminus?
trishorts
reviewed
Dec 7, 2023
| { | ||
| switch (mod.LocationRestriction) | ||
| { | ||
| case "5'-terminal.": |
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This maintains naming convention from terminal mods from proteomics
trishorts
reviewed
Dec 7, 2023
| { | ||
| case "5'-terminal.": | ||
| case "Oligo 5'-terminal.": | ||
| case "N-terminal.": |
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need comments here and below that clearly distinguish peptide and protein terminus mods (with something also that distinguishes cleaved oligo termini with the parent oligo termini
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There is zero distinction between how modifications are handled on 5'-terminal vs N-terminal when applying fixed modificaitons to a DigestionProduct
trishorts
reviewed
Dec 7, 2023
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| private static IEnumerable<int[]> GetVariableModificationPatterns(List<KeyValuePair<int, List<Modification>>> possibleVariableModifications, | ||
| int unmodifiedResiduesDesired, int[] variableModificationPattern, int index) |
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i'm not familiar with unmodifiedResiduesDesired. is there an explainer comment
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This was copied and pasted from ProteolyticPeptide, I have no idea what unmodifiedResiduesDesired does, but it worked for peptides and has simply been moved
trishorts
reviewed
Dec 7, 2023
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| using System;using System.Collections.Generic;using System.Linq;using System.Text;using System.Threading.Tasks;using Chemistry;using MassSpectrometry;namespace Omics.Fragmentation.Oligo{ /// <summary> /// Methods dealing with specific product type for RNA molecules /// </summary> public static class DissociationTypeCollection { /// <summary> /// Product Ion types by dissociation method /// </summary> private static readonly Dictionary<DissociationType, List<ProductType>> ProductsFromDissociationType = new Dictionary<DissociationType, List<ProductType>>() { { DissociationType.Unknown, new List<ProductType>() }, { DissociationType.CID, new List<ProductType> { ProductType.aBaseLoss, ProductType.c, ProductType.dWaterLoss, ProductType.w, ProductType.y, ProductType.yWaterLoss, ProductType.M } }, { DissociationType.LowCID, new List<ProductType>() { } }, { DissociationType.IRMPD, new List<ProductType>() { } }, { DissociationType.ECD, new List<ProductType> { } }, { DissociationType.PQD, new List<ProductType> { ProductType.a, ProductType.aBaseLoss, ProductType.b, ProductType.c, ProductType.d, ProductType.dWaterLoss, ProductType.w, ProductType.x, ProductType.y, ProductType.yWaterLoss, ProductType.d, ProductType.M } }, { DissociationType.ETD, new List<ProductType> { } }, { DissociationType.HCD, new List<ProductType> { ProductType.w, ProductType.y, ProductType.aBaseLoss, ProductType.dWaterLoss, ProductType.M } }, { DissociationType.AnyActivationType, new List<ProductType> { } }, { DissociationType.EThcD, new List<ProductType> { } }, { DissociationType.Custom, new List<ProductType> { } }, { DissociationType.ISCID, new List<ProductType> { } } }; /// <summary> /// Returns list of products types based upon the dissociation type /// </summary> /// <param name="dissociationType"></param> /// <returns></returns> public static List<ProductType> GetRnaProductTypesFromDissociationType(this DissociationType dissociationType) => ProductsFromDissociationType[dissociationType]; /// <summary> /// Mass to be added or subtracted /// </summary> private static readonly Dictionary<ProductType, ChemicalFormula> FragmentIonCaps = new Dictionary<ProductType, ChemicalFormula> { { ProductType.a, ChemicalFormula.ParseFormula("H") }, { ProductType.aWaterLoss, ChemicalFormula.ParseFormula("H-1O-1") }, { ProductType.b, ChemicalFormula.ParseFormula("OH") }, { ProductType.bWaterLoss, ChemicalFormula.ParseFormula("H-1") }, { ProductType.c, ChemicalFormula.ParseFormula("O3H2P") }, { ProductType.cWaterLoss, ChemicalFormula.ParseFormula("O2P") }, { ProductType.d, ChemicalFormula.ParseFormula("O4H2P") }, { ProductType.dWaterLoss, ChemicalFormula.ParseFormula("O3P") }, { ProductType.w, ChemicalFormula.ParseFormula("H") }, { ProductType.wWaterLoss, ChemicalFormula.ParseFormula("H-1O-1") }, { ProductType.x, ChemicalFormula.ParseFormula("O-1H") }, { ProductType.xWaterLoss, ChemicalFormula.ParseFormula("O-2H-1") }, { ProductType.y, ChemicalFormula.ParseFormula("O-3P-1") }, { ProductType.yWaterLoss, ChemicalFormula.ParseFormula("O-4H-2P-1") }, { ProductType.z, ChemicalFormula.ParseFormula("O-4P-1") }, { ProductType.zWaterLoss, ChemicalFormula.ParseFormula("O-5H-2P-1") }, //fragment - Base chemical formula is the corresponding fragment chemical formula subtracing 1 H as H is lost when base is removed { ProductType.aBaseLoss, ChemicalFormula.ParseFormula("H-2") }, // "H-1" -H { ProductType.bBaseLoss, ChemicalFormula.ParseFormula("O1H-2") }, //"OH1" -H { ProductType.cBaseLoss, ChemicalFormula.ParseFormula("O3H-1P") }, //"O3P" -H { ProductType.dBaseLoss, ChemicalFormula.ParseFormula("O4H-1P") }, //"O4H2P" -H { ProductType.wBaseLoss, ChemicalFormula.ParseFormula("H-2") }, //"H"-H { ProductType.xBaseLoss, ChemicalFormula.ParseFormula("O-1H-2") }, //"O-1H" -H { ProductType.yBaseLoss, ChemicalFormula.ParseFormula("O-3H-2P-1") }, //"O-3P-1" -H { ProductType.zBaseLoss, ChemicalFormula.ParseFormula("O-4H-3P-1") }, //"O-4H-1P-1" -1 { ProductType.M, new ChemicalFormula() } }; /// <summary> /// Returns mass shift by product type /// </summary> /// <param name="type"></param> /// <returns></returns> public static double GetRnaMassShiftFromProductType(this ProductType type) => FragmentIonCaps[type].MonoisotopicMass; public static FragmentationTerminus GetRnaTerminusType(this ProductType fragmentType) { switch (fragmentType) { case ProductType.a: case ProductType.aWaterLoss: case ProductType.aBaseLoss: case ProductType.b: case ProductType.bWaterLoss: case ProductType.bBaseLoss: case ProductType.c: case ProductType.cWaterLoss: case ProductType.cBaseLoss: case ProductType.d: case ProductType.dWaterLoss: case ProductType.dBaseLoss: return FragmentationTerminus.FivePrime; case ProductType.w: case ProductType.wWaterLoss: case ProductType.wBaseLoss: case ProductType.x: case ProductType.xWaterLoss: case ProductType.xBaseLoss: case ProductType.y: case ProductType.yWaterLoss: case ProductType.yBaseLoss: case ProductType.z: case ProductType.zWaterLoss: case ProductType.zBaseLoss: return FragmentationTerminus.ThreePrime; case ProductType.M: return FragmentationTerminus.None; case ProductType.aStar: case ProductType.aDegree: case ProductType.bAmmoniaLoss: case ProductType.yAmmoniaLoss: case ProductType.zPlusOne: case ProductType.D: case ProductType.Ycore: case ProductType.Y: default: throw new ArgumentOutOfRangeException(nameof(fragmentType), fragmentType, null); } } /// <summary> /// Product ion types by Fragmentation Terminus /// </summary> private static readonly Dictionary<FragmentationTerminus, List<ProductType>> ProductIonTypesFromSpecifiedTerminus = new Dictionary<FragmentationTerminus, List<ProductType>> { { FragmentationTerminus.FivePrime, new List<ProductType> { ProductType.a, ProductType.aWaterLoss, ProductType.aBaseLoss, ProductType.b, ProductType.bWaterLoss, ProductType.bBaseLoss, ProductType.c, ProductType.cWaterLoss, ProductType.cBaseLoss, ProductType.d, ProductType.dWaterLoss, ProductType.dBaseLoss, } }, { FragmentationTerminus.ThreePrime, new List<ProductType> { ProductType.w, ProductType.wWaterLoss, ProductType.wBaseLoss, ProductType.x, ProductType.xWaterLoss, ProductType.xBaseLoss, ProductType.y, ProductType.yWaterLoss, ProductType.yBaseLoss, ProductType.z, ProductType.zWaterLoss, ProductType.zBaseLoss, } }, { FragmentationTerminus.Both, new List<ProductType> { ProductType.a, ProductType.aWaterLoss, ProductType.aBaseLoss, ProductType.b, ProductType.bWaterLoss, ProductType.bBaseLoss, ProductType.c, ProductType.cWaterLoss, ProductType.cBaseLoss, ProductType.d, ProductType.dWaterLoss, ProductType.dBaseLoss, ProductType.w, ProductType.wWaterLoss, ProductType.wBaseLoss, ProductType.x, ProductType.xWaterLoss, ProductType.xBaseLoss, ProductType.y, ProductType.yWaterLoss, ProductType.yBaseLoss, ProductType.z, ProductType.zWaterLoss, ProductType.zBaseLoss, ProductType.M } } }; public static List<ProductType> GetRnaTerminusSpecificProductTypes( this FragmentationTerminus fragmentationTerminus) { return ProductIonTypesFromSpecifiedTerminus[fragmentationTerminus]; } /// <summary> /// Returns all product ion types based upon specified terminus /// </summary> /// <param name="dissociationType"></param> /// <param name="fragmentationTerminus"></param> /// <returns></returns> public static List<ProductType> GetRnaTerminusSpecificProductTypesFromDissociation( this DissociationType dissociationType, FragmentationTerminus fragmentationTerminus) { var terminusSpecific = fragmentationTerminus.GetRnaTerminusSpecificProductTypes(); var dissociationSpecific = dissociationType.GetRnaProductTypesFromDissociationType(); return terminusSpecific.Intersect(dissociationSpecific).ToList(); } }} | |||
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somehting weird showing up.
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For some reason, github thinks there is zero whitespace in this class
trishorts
reviewed
Dec 7, 2023
trishorts
reviewed
Dec 7, 2023
Adjusted Chemical Formula subtraction when null - value
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reviewed
Dec 7, 2023
trishorts
reviewed
Dec 7, 2023
trishorts
reviewed
Dec 7, 2023
trishorts
reviewed
Dec 7, 2023
Made LysisProduct and abstract class and its constructor protected
trishorts
reviewed
Dec 7, 2023
Changed IDigestionParams.Enzyme to IDigestionParams.DigestionAgent
elaboy
approved these changes
Dec 7, 2023
Alexander-Sol
approved these changes
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trishorts
approved these changes
Dec 8, 2023
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Review after PsmFromTsv is in MzLib
Moved several classes into the omics project and created parent classes and interfaces to work with both Proteins and RNA
Omics - novel and moved code
Digestion
Fragmentation
Modifications
Interfaces
Adjustments made to existing code
Transcriptomics