diff --git a/mzLib/Proteomics/Protein/CircularProtein.cs b/mzLib/Proteomics/Protein/CircularProtein.cs new file mode 100644 index 000000000..af3fb2211 --- /dev/null +++ b/mzLib/Proteomics/Protein/CircularProtein.cs @@ -0,0 +1,598 @@ +using System; +using System.Collections.Generic; +using System.Linq; +using Omics; +using Omics.BioPolymer; +using Omics.Digestion; +using Omics.Modifications; +using Proteomics.AminoAcidPolymer; +using Proteomics.ProteolyticDigestion; + +namespace Proteomics +{ + /// + /// Represents a head-to-tail cyclic protein or peptide. + /// + /// CANONICAL FORM AND NUMBERING + /// ---------------------------- + /// The sequence is always stored as the lexicographically smallest rotation + /// (canonical form), regardless of the input rotation. This is the shared + /// numbering system for both the protein and all peptides derived from it: + /// + /// - Residue 1 is the first character of . + /// - Residues are numbered 1..N continuously around the ring. + /// - For fragments that wrap past residue N, numbering continues into a + /// conceptual second copy of the ring: residue N+1 = residue 1, N+2 = 2, + /// etc. A wrap-around fragment starting at residue s of length L is + /// annotated [s, s+L-1] where s+L-1 may exceed N. + /// + /// Example: ring G-K-A-E-C, canonical form A-E-C-G-K. + /// Residue 1=A, 2=E, 3=C, 4=G, 5=K. + /// A fragment covering K,A,E (wrapping) starts at residue 5 with length 3: + /// annotation [5, 7]. + /// + /// Because both and + /// are always canonicalized, + /// two circular molecules represent the same ring if and only if their + /// strings are equal. + /// + /// DIGESTION + /// --------- + /// Digestion is performed on a doubled (2N−1) proxy sequence + /// ( + [..^1]), then filtered + /// to peptides of length ≤ N and deduplicated by full sequence. Wrapping peptides + /// have OneBasedEndResidueInProtein > N, consistent with the annotation + /// convention above. + /// + /// DISPATCH NOTE + /// ------------- + /// is a virtual override of . + /// Callers may hold any reference type (, + /// , etc.) and the circular digestion logic will be + /// dispatched correctly at runtime via standard polymorphic dispatch. + /// + public class CircularProtein : Protein + { + /// + /// The canonical circular sequence (lexicographically smallest rotation of the input). + /// Identical to ; exposed under this name for clarity. + /// + public string CircularSequence => BaseSequence; + + /// + /// Monoisotopic mass of the cyclic molecule: sum of residue masses with no H₂O addition, + /// since there are no free N- or C-termini in a head-to-tail cyclized molecule. + /// + public double CyclicMonoisotopicMass { get; } + + // ── Constructors ────────────────────────────────────────────────────── + + /// + /// Constructs a . The sequence is canonicalized + /// to the lexicographically smallest rotation before being stored. + /// + public CircularProtein( + string sequence, + string accession, + string organism = null, + List> geneNames = null, + IDictionary> oneBasedModifications = null, + string name = null, + string fullName = null, + bool isDecoy = false, + bool isContaminant = false, + List databaseReferences = null, + string databaseFilePath = null) + : this( + GetCanonicalRotationWithOffset(sequence), + sequence?.Length ?? 0, + accession, + organism, + geneNames, + oneBasedModifications, + name, + fullName, + isDecoy, + isContaminant, + databaseReferences, + databaseFilePath) + { + } + + /// + /// Private constructor that receives the pre-computed canonical rotation and offset, + /// avoiding a redundant second call to . + /// + private CircularProtein( + (string Canonical, int Offset) rotation, + int originalLength, + string accession, + string organism, + List> geneNames, + IDictionary> oneBasedModifications, + string name, + string fullName, + bool isDecoy, + bool isContaminant, + List databaseReferences, + string databaseFilePath) + : base( + sequence: rotation.Canonical, + accession: accession, + organism: organism, + geneNames: geneNames, + oneBasedModifications: RemapModifications(oneBasedModifications, originalLength, rotation.Offset), + name: name, + fullName: fullName, + isDecoy: isDecoy, + isContaminant: isContaminant, + databaseReferences: databaseReferences, + databaseFilePath: databaseFilePath) + { + CyclicMonoisotopicMass = BaseSequence.Sum(aa => Residue.ResidueMonoisotopicMass[aa]); + } + + /// + /// Creates a from an existing , + /// canonicalizing its sequence and remapping any one-based modifications to their + /// correct positions in the canonical rotation. + /// Use after loading entries from a FASTA or XML database. + /// + public static CircularProtein FromProtein(Protein source) => + new(source.BaseSequence, + source.Accession, + source.Organism, + source.GeneNames, + source.OneBasedPossibleLocalizedModifications + .ToDictionary(kv => kv.Key, kv => kv.Value), + source.Name, + source.FullName, + source.IsDecoy, + source.IsContaminant, + source.DatabaseReferences, + source.DatabaseFilePath); + + // ── Digestion ───────────────────────────────────────────────────────── + + /// + /// Digests the circular sequence by running linear digestion on a doubled + /// proxy sequence of length 2N-1, then filtering and deduplicating results. + /// Wrapping peptides have OneBasedEndResidueInProtein > N. + /// This is a virtual override of and will be + /// dispatched correctly regardless of the compile-time reference type. + /// + public override IEnumerable Digest( + IDigestionParams digestionParams, + List allKnownFixedModifications, + List variableModifications, + List silacLabels = null, + (SilacLabel startLabel, SilacLabel endLabel)? turnoverLabels = null, + bool topDownTruncationSearch = false) + { + int n = Length; + + // ── Step 1: Identify cleavage sites in the ring ─────────────────── + // + // Find all 1-based positions in the canonical ring at which the + // protease cuts after that residue. + var cleavagePositions = GetCleavagePositionsInRing(digestionParams); + int numCleavageSites = cleavagePositions.Count; + int maxMissedCleavages = ((DigestionParams)digestionParams).MaxMissedCleavages; + + // ── Step 2: Emit the CircularPeptideWithSetModifications (1:1) ──── + // + // The CircularPeptideWithSetModifications is ALWAYS a direct 1:1 + // conversion of the CircularProtein — the whole ring, intact. + // It is NEVER produced by cutting: not even a single cut. + // It is emitted here, independently of the proxy digestion below. + // + // It is only possible when the missed-cleavage budget is large enough + // to absorb every cleavage site in the ring, meaning the entire ring + // is one un-cut cyclic segment with no free N- or C-termini. + // + // A CircularPeptideWithSetModifications is ALWAYS length N. + // It is NEVER shorter than N and NEVER starts at any position other + // than position 1 (the canonical origin). + if (maxMissedCleavages >= numCleavageSites) + { + // ── Apply fixed modifications to the ring ───────────────────── + // Circular peptides have no termini, so only "Anywhere." + // fixed modifications are applicable. Key convention: + // residue at 1-based position pos → key = pos + 1. + var fixedModsDict = new Dictionary(); + if (allKnownFixedModifications != null) + { + foreach (var mod in allKnownFixedModifications) + { + if (mod.LocationRestriction != "Anywhere.") continue; + + for (int pos = 1; pos <= n; pos++) + { + int key = pos + 1; + if (fixedModsDict.ContainsKey(key)) continue; + + if (ModificationLocalization.ModFits( + mod, + BaseSequence, + digestionProductOneBasedIndex: pos, + digestionProductLength: n, + bioPolymerOneBasedIndex: pos)) + { + fixedModsDict[key] = mod; + } + } + } + } + + int numFixed = fixedModsDict.Count; + + // Full-ring product with fixed mods only — always emitted when the budget allows. + yield return new CircularPeptideWithSetModifications( + protein: this, + digestionParams: digestionParams, + oneBasedStartResidueInProtein: 1, + oneBasedEndResidueInProtein: n, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: null, + missedCleavages: numCleavageSites, + allModsOneIsNterminus: new Dictionary(fixedModsDict), + numFixedMods: numFixed, + baseSequence: BaseSequence); + + // Variable-modified full-ring products. + // Circular peptides have no N- or C-termini, so only + // "Anywhere." modifications are applicable. + // + // We enumerate all combinations of up to MaxMods modifications + // across all matching (key, mod) pairs, mirroring the combinatorial + // enumeration that linear peptide digestion performs. + // MaxMods == 0 means no modified forms are produced. + { + // Build the list of all (key, mod) pairs that fit this ring, from BOTH + // the caller-supplied variable modifications AND the protein's + // database/XML-annotated localized modifications. The linear digestion + // path applies OneBasedPossibleLocalizedModifications as variable mods, + // so the intact-ring forms must include them too — otherwise the ring + // loses annotated PTM isoforms that the ring-opening linear products carry. + // + // Key convention: side-chain at 1-based position pos → key = pos + 1. + // Circular peptides have no termini, so only "Anywhere." mods apply. + var applicableSites = new List<(int Key, Modification Mod)>(); + var seenSites = new HashSet<(int Pos, string Id)>(); + + void AddSiteIfApplicable(int pos, Modification mod) + { + if (mod.LocationRestriction != "Anywhere.") return; + if (pos < 1 || pos > n) return; + if (!ModificationLocalization.ModFits( + mod, + BaseSequence, + digestionProductOneBasedIndex: pos, + digestionProductLength: n, + bioPolymerOneBasedIndex: pos)) + return; + if (seenSites.Add((pos, mod.IdWithMotif))) + applicableSites.Add((pos + 1, mod)); + } + + if (variableModifications != null) + foreach (var mod in variableModifications) + for (int pos = 1; pos <= n; pos++) + AddSiteIfApplicable(pos, mod); + + foreach (var kv in OneBasedPossibleLocalizedModifications) + foreach (var mod in kv.Value) + AddSiteIfApplicable(kv.Key, mod); + + // Enumerate subsets of applicableSites of size 1..MaxMods (one mod per + // residue), bounded by MaxModificationIsoforms to match the linear + // pathway's cap and avoid a combinatorial explosion of ring forms. + int maxMods = ((DigestionParams)digestionParams).MaxMods; + int maxIsoforms = ((DigestionParams)digestionParams).MaxModificationIsoforms; + int isoformCount = 0; + foreach (var subset in GetModSubsets(applicableSites, maxMods)) + { + if (isoformCount >= maxIsoforms) + break; + + // Merge fixed mods into the variable-mod subset so that every + // variable-modified form also carries fixed modifications. + // Variable mods at the same key override the fixed mod there. + var merged = new Dictionary(fixedModsDict); + foreach (var kvp in subset) + merged[kvp.Key] = kvp.Value; + + // Recompute the fixed-mod count from what survives the merge: a + // variable mod overriding a fixed mod at the same key removes one + // fixed mod, so the precomputed count would overstate it. + int actualFixedMods = 0; + foreach (var fk in fixedModsDict.Keys) + if (!subset.ContainsKey(fk)) + actualFixedMods++; + + isoformCount++; + yield return new CircularPeptideWithSetModifications( + protein: this, + digestionParams: digestionParams, + oneBasedStartResidueInProtein: 1, + oneBasedEndResidueInProtein: n, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: null, + missedCleavages: numCleavageSites, + allModsOneIsNterminus: merged, + numFixedMods: actualFixedMods, + baseSequence: BaseSequence); + } + } + } + + // ── Step 3: Emit linear PeptideWithSetModifications products ────── + // + // All linear products come from the proxy digestion of a doubled + // sequence (BaseSequence + BaseSequence[..^1], length 2N-1), which + // allows the linear digestion engine to discover wrap-around fragments. + // + // CRITICAL: Every product from the proxy digestion is ALWAYS a + // PeptideWithSetModifications — linear, with free termini. + // The CircularPeptideWithSetModifications was emitted above and must + // NEVER be produced from the proxy. + // + // There are two sub-cases, both yielding PeptideWithSetModifications: + // + // Single cut (Length == N): + // The ring was opened at exactly one cleavage site. The product + // spans the full canonical sequence and has the same length N as + // the circular product, but it is a completely different object: + // it has free N- and C-termini and carries the standard +H2O mass. + // Do NOT conflate length equality with type equality. + // + // Two or more cuts (Length < N): + // The ring was opened and sub-divided. Always linear, always < N. + if (numCleavageSites == 0) + yield break; // No cuts possible; only the circular product exists. + + // Valid start positions: one position after each cleavage site in + // 1-based canonical ring coordinates. + var validStartPositions = new HashSet( + cleavagePositions.Select(p => p == n ? 1 : p + 1)); + + // Replicate database/XML-localized modifications onto the second copy of the + // doubled proxy. The Protein(Protein, string) clone keeps localized-mod keys + // only in 1..N, but wrap-around fragments span proxy positions N+1..2N-1 + // (ring positions 1..N-1); without the replicated keys those wrapped residues + // would silently lose their annotated modifications, producing wrong masses + // and fragment ions for exactly the peptides that distinguish circular topology. + var proxyMods = new Dictionary>(); + foreach (var kv in OneBasedPossibleLocalizedModifications) + { + proxyMods[kv.Key] = kv.Value; // first copy: positions 1..N + if (kv.Key <= n - 1) + proxyMods[kv.Key + n] = kv.Value; // second copy: positions N+1..2N-1 + } + + var proxyProtein = new Protein( + sequence: BaseSequence + BaseSequence[..^1], + accession: Accession, + oneBasedModifications: proxyMods, + name: Name, + fullName: FullName, + organism: Organism, + isDecoy: IsDecoy, + isContaminant: IsContaminant, + databaseFilePath: DatabaseFilePath); + var proxyPeptides = proxyProtein.Digest(digestionParams, + allKnownFixedModifications, variableModifications, + silacLabels, turnoverLabels, topDownTruncationSearch); + + var seen = new HashSet(); + + foreach (var peptide in proxyPeptides) + { + if (peptide is not PeptideWithSetModifications pwsm) + continue; // Non-linear proxy products are not expected; skip. + + // Discard fragments longer than N, or starting in the second copy + // of the proxy (those duplicate first-copy fragments). + if (pwsm.Length > n || pwsm.OneBasedStartResidueInProtein > n) + continue; + + // Discard proxy artifacts not starting at a genuine cut boundary. + if (!validStartPositions.Contains(pwsm.OneBasedStartResidueInProtein)) + continue; + + // Deduplicate by full sequence AND start position. + // Two peptides with the same sequence at different ring positions + // are distinct cleavage products and must both be retained. + if (!seen.Add($"{pwsm.OneBasedStartResidueInProtein}:{pwsm.FullSequence}")) + continue; + + // Every proxy product is linear — length N (single-cut) or < N (multi-cut). + // Neither case is ever a CircularPeptideWithSetModifications. + yield return new PeptideWithSetModifications( + protein: this, + digestionParams: pwsm.DigestionParams, + oneBasedStartResidueInProtein: pwsm.OneBasedStartResidueInProtein, + oneBasedEndResidueInProtein: pwsm.OneBasedEndResidueInProtein, + cleavageSpecificity: pwsm.CleavageSpecificityForFdrCategory, + peptideDescription: pwsm.PeptideDescription, + missedCleavages: pwsm.MissedCleavages, + allModsOneIsNterminus: pwsm.AllModsOneIsNterminus, + numFixedMods: pwsm.NumFixedMods, + baseSequence: pwsm.BaseSequence); + } + } + + /// + /// Yields all non-empty subsets of of size at most + /// , where every key in the subset is distinct + /// (one modification per residue). Each subset is returned as a + /// ready for use as + /// AllModsOneIsNterminus. + /// + private static IEnumerable> GetModSubsets( + List<(int Key, Modification Mod)> sites, + int maxMods) + { + if (maxMods <= 0 || sites.Count == 0) + yield break; + + // Enumerate subsets via recursive backtracking. + var current = new Dictionary(); + + foreach (var subset in Backtrack(sites, 0, current, maxMods)) + yield return subset; + } + + private static IEnumerable> Backtrack( + List<(int Key, Modification Mod)> sites, + int startIndex, + Dictionary current, + int maxMods) + { + // Yield a copy of the current non-empty subset. + if (current.Count > 0) + yield return new Dictionary(current); + + if (current.Count == maxMods) + yield break; + + for (int i = startIndex; i < sites.Count; i++) + { + var (key, mod) = sites[i]; + + // Skip if this residue already has a mod in the current subset. + if (current.ContainsKey(key)) + continue; + + current[key] = mod; + + foreach (var subset in Backtrack(sites, i + 1, current, maxMods)) + yield return subset; + + current.Remove(key); + } + } + + internal HashSet GetCleavagePositionsInRing(IDigestionParams digestionParams) + { + // Use the protease's cleavage-site detection directly on the doubled + // proxy sequence (length 2N-1) to discover all cut positions in the ring. + // The doubled sequence ensures that cleavage motifs spanning the + // wrap-around boundary (position N -> position 1) are evaluated correctly. + // + // GetDigestionSiteIndices returns 0-based cut-after indices and always + // includes the virtual boundaries 0 and proxySequence.Length. We keep + // only indices in [1, N], which correspond to 1-based positions in the + // canonical ring where the protease cuts after that residue. + var protease = ((DigestionParams)digestionParams).Protease; + var positions = new HashSet(); + // Top-down search mode does not perform any cuts, so skip the protease call + if (protease.Name != "top-down") + { + string proxySequence = BaseSequence + BaseSequence[..^1]; + var allIndices = protease.GetDigestionSiteIndices(proxySequence); + int n = Length; + + foreach (var index in allIndices) + { + if (index >= 1 && index <= n) + positions.Add(index); + } + } + + return positions; + } + + // ── Shared numbering system ─────────────────────────────────────────── + + + /// + /// Returns the lexicographically smallest rotation of . + /// This is the single shared implementation used by both + /// and . + /// + /// The algorithm reads all N rotations, comparing character by character, and + /// selects the one that sorts earliest under ordinal (byte-value) comparison — + /// i.e., 'A' < 'C' < ... < 'Y', with subsequent characters as tiebreakers. + /// + public static string GetCanonicalRotation(string sequence) + { + return GetCanonicalRotationWithOffset(sequence).Canonical; + } + + /// + /// Returns the lexicographically smallest rotation of + /// along with the 0-based offset into the original string at which the canonical + /// rotation begins. An offset of 0 means the input was already in canonical form. + /// + /// The circular amino acid sequence. + /// + /// A tuple of (Canonical, Offset) where Canonical is the + /// smallest rotation and Offset is the starting index in the original string. + /// + public static (string Canonical, int Offset) GetCanonicalRotationWithOffset(string sequence) + { + if (string.IsNullOrEmpty(sequence)) + return (sequence, 0); + + int n = sequence.Length; + string best = sequence; + int bestOffset = 0; + + for (int i = 1; i < n; i++) + { + for (int k = 0; k < n; k++) + { + char ci = sequence[(i + k) % n]; + char cb = best[k]; + + if (ci < cb) + { + best = (sequence + sequence).Substring(i, n); + bestOffset = i; + break; + } + if (ci > cb) break; + } + } + + return (best, bestOffset); + } + + /// + /// Remaps 1-based modification positions to account for the rotational offset + /// introduced by canonicalization. Returns null when no modifications + /// are present, and returns the dictionary unchanged when the offset is zero. + /// + private static IDictionary> RemapModifications( + IDictionary> oneBasedModifications, + int sequenceLength, + int offset) + { + if (oneBasedModifications == null || oneBasedModifications.Count == 0) + return oneBasedModifications; + + if (offset == 0) + return oneBasedModifications; + + int n = sequenceLength; + var remapped = new Dictionary>(); + foreach (var kvp in oneBasedModifications) + { + int oldPos = kvp.Key; + // Only remap valid 1-based ring positions; pass through any + // out-of-range keys (e.g. 0 for N-term) unchanged. + if (oldPos >= 1 && oldPos <= n) + { + int newPos = (oldPos - 1 - offset + n) % n + 1; + remapped[newPos] = kvp.Value; + } + else + { + remapped[oldPos] = kvp.Value; + } + } + return remapped; + } + } +} \ No newline at end of file diff --git a/mzLib/Proteomics/Protein/Protein.cs b/mzLib/Proteomics/Protein/Protein.cs index 691add534..d88717762 100644 --- a/mzLib/Proteomics/Protein/Protein.cs +++ b/mzLib/Proteomics/Protein/Protein.cs @@ -328,10 +328,12 @@ public IEnumerable Digest(DigestionParams digestion .Cast(); /// - /// Gets peptides for digestion of a protein - /// Implemented with interfaces to allow for use of both Proteomics and Omics classes + /// Gets peptides for digestion of a protein. + /// Implemented with interfaces to allow for use of both Proteomics and Omics classes. + /// Virtual to allow derived classes (e.g., ) to override + /// with specialized digestion behavior while preserving polymorphic dispatch. /// - public IEnumerable Digest(IDigestionParams digestionParams, List allKnownFixedModifications, + public virtual IEnumerable Digest(IDigestionParams digestionParams, List allKnownFixedModifications, List variableModifications, List silacLabels = null, (SilacLabel startLabel, SilacLabel endLabel)? turnoverLabels = null, bool topDownTruncationSearch = false) { diff --git a/mzLib/Proteomics/ProteolyticDigestion/CircularPeptideWithSetModifications.cs b/mzLib/Proteomics/ProteolyticDigestion/CircularPeptideWithSetModifications.cs new file mode 100644 index 000000000..e7b997f52 --- /dev/null +++ b/mzLib/Proteomics/ProteolyticDigestion/CircularPeptideWithSetModifications.cs @@ -0,0 +1,368 @@ +using Chemistry; +using MassSpectrometry; +using Omics.Digestion; +using Omics.Fragmentation; +using Omics.Fragmentation.Peptide; +using Omics.Modifications; +using Proteomics.AminoAcidPolymer; +using System; +using System.Collections.Generic; + +namespace Proteomics.ProteolyticDigestion +{ + /// + /// Represents a circular (head-to-tail cyclized) peptide with set modifications, + /// always bound to a parent. + /// + /// NUMBERING + /// --------- + /// All residue numbering is inherited from the parent . + /// Residue 1 is the first character of + /// (the canonical origin — the lexicographically smallest rotation of the ring). + /// Fragment annotations [s, e] use this numbering, with e > N for wrap-around fragments. + /// + /// MASS + /// ---- + /// A circular peptide has no free termini. Its monoisotopic mass equals the sum of + /// residue masses plus modification masses, with no added H₂O: + /// MonoisotopicMass = base.MonoisotopicMass − H₂O + /// + /// FRAGMENTATION + /// ------------- + /// Only is supported. A single backbone cleavage + /// opens the ring and produces a linear ion mass-equivalent to the precursor — no + /// additional sequence information is gained and these ions are not scored. + /// + /// enumerates all contiguous sub-sequences of length + /// [minLength, peptideLength−1] within this peptide's span in the parent ring, + /// including wrap-around fragments for full-ring peptides. Residue masses are looked + /// up from the parent ring via a doubled prefix-sum for O(1) sub-sequence mass + /// calculation. + /// + [Serializable] + public class CircularPeptideWithSetModifications : PeptideWithSetModifications + { + // ── Mass constant ───────────────────────────────────────────────────── + private static readonly double WaterMonoisotopicMass = + PeriodicTable.GetElement("H").PrincipalIsotope.AtomicMass * 2 + + PeriodicTable.GetElement("O").PrincipalIsotope.AtomicMass; + + // ── Cached mass arrays (lazy-initialized, immutable after first use) ── + private double[] _cachedRingMasses; + private double[] _cachedDoubledPrefix; + + // ── Parent protein (typed) ──────────────────────────────────────────── + + /// + /// The parent . Always non-null; the constructor + /// enforces this. Use this reference to access the canonical numbering system + /// and ring-level properties (e.g., ). + /// + public CircularProtein CircularParent { get; } + + // ── Constructor ─────────────────────────────────────────────────────── + + /// + /// Constructs a from a + /// parent. + /// + /// No canonicalization is performed here: the parent + /// guarantees its and all sub-sequences derived + /// from are already in canonical form. + /// + /// The intended way to obtain instances is via . + /// + /// + /// Thrown if is null. + /// + /// + /// Thrown if is not a . + /// + public CircularPeptideWithSetModifications( + Protein protein, + IDigestionParams digestionParams, + int oneBasedStartResidueInProtein, + int oneBasedEndResidueInProtein, + CleavageSpecificity cleavageSpecificity, + string peptideDescription, + int missedCleavages, + Dictionary allModsOneIsNterminus, + int numFixedMods, + string baseSequence = null) + : base(ValidateProtein(protein), digestionParams, + oneBasedStartResidueInProtein, oneBasedEndResidueInProtein, + cleavageSpecificity, peptideDescription, missedCleavages, + allModsOneIsNterminus, numFixedMods, baseSequence) + { + // ValidateProtein already guarantees protein is a non-null CircularProtein. + CircularParent = (CircularProtein)protein; + + // Terminal modifications are chemically invalid on a circular peptide + // (no free N- or C-terminus). Reject them early so that mass accounting + // in MonoisotopicMass and FragmentInternally stays consistent. + if (allModsOneIsNterminus != null) + { + int peptideLen = oneBasedEndResidueInProtein - oneBasedStartResidueInProtein + 1; + if (allModsOneIsNterminus.ContainsKey(1)) + throw new ArgumentException( + "N-terminal modifications are not valid for circular peptides (no free N-terminus).", + nameof(allModsOneIsNterminus)); + if (allModsOneIsNterminus.ContainsKey(peptideLen + 2)) + throw new ArgumentException( + "C-terminal modifications are not valid for circular peptides (no free C-terminus).", + nameof(allModsOneIsNterminus)); + } + } + + /// + /// Validates that is a non-null + /// before the base constructor executes. Called inline in the constructor initializer + /// so that callers receive descriptive exceptions instead of opaque crashes from the + /// base class. + /// + private static Protein ValidateProtein(Protein protein) + { + if (protein is null) + throw new ArgumentNullException(nameof(protein), + $"{nameof(CircularPeptideWithSetModifications)} requires a non-null protein."); + + if (protein is not CircularProtein) + throw new ArgumentException( + $"{nameof(CircularPeptideWithSetModifications)} requires a " + + $"{nameof(CircularProtein)} parent, but received {protein.GetType().Name}.", + nameof(protein)); + + return protein; + } + + // ── Mass override ───────────────────────────────────────────────────── + + /// + /// Monoisotopic mass of the circular peptide: sum of residue and modification + /// masses with no added water (no free termini). + /// Equals the parent protein's + /// when unmodified. + /// + /// + /// Monoisotopic mass of the circular peptide: sum of residue and modification + /// masses with no added water (no free termini). + /// Overrides the base implementation to subtract H2O, reflecting the absence of + /// free termini in a head-to-tail cyclized peptide. + /// + public override double MonoisotopicMass => + (double)ClassExtensions.RoundedDouble( + base.MonoisotopicMass - WaterMonoisotopicMass); + + // ── Fragmentation ───────────────────────────────────────────────────── + + /// + /// Generates internal fragment ions for this circular peptide. + /// + /// NUMBERING + /// --------- + /// Fragment positions are expressed in the parent 's + /// canonical 1-based numbering. For a fragment of length L starting at canonical + /// residue s: + /// FragmentNumber = s (1-based canonical start) + /// SecondaryFragmentNumber = s + L − 1 (end; exceeds N for wrap-around) + /// ResiduePosition = L (fragment length) + /// + /// MASS + /// ---- + /// neutralMass = sum(residueMasses in parent ring over [s, s+L-1]) + /// + nTermCap + cTermCap − H₂O + /// + /// SPAN RESTRICTION + /// ---------------- + /// Only fragments within this peptide's span in the ring are generated — both + /// cleavage sites must fall within the peptide. For a full-ring peptide + /// (Length == N) this covers all ring positions including wrap-around. For a + /// sub-peptide (Length < N) wrap-around internal fragments are excluded because + /// they would require a cleavage outside the peptide's span. + /// + public override void FragmentInternally( + DissociationType dissociationType, + int minLengthOfFragments, + List products, + IFragmentationParams? fragmentationParams = null) + { + if (minLengthOfFragments < 1) + throw new ArgumentOutOfRangeException(nameof(minLengthOfFragments), + minLengthOfFragments, + $"{nameof(minLengthOfFragments)} must be at least 1."); + + products.Clear(); + + int peptideLength = BaseSequence.Length; + int ringLength = CircularParent.Length; + + // Internal fragments require at least 2 residues: one cleavage on each side + // of the fragment within the peptide span. + if (minLengthOfFragments < 2 || minLengthOfFragments >= peptideLength) + return; + + // ── Build doubled prefix sum over the parent ring ───────────────── + // Masses come from the parent ring (not just the peptide subsequence) + // so that mod positions and residue masses are correct for the full ring. + // Arrays are cached because this peptide's state is immutable after + // construction, so the values never change between calls. + double[] ringMasses = GetOrBuildRingMasses(); + int peptideStartInRing = OneBasedStartResidueInProtein - 1; // 0-based + + double[] doubledPrefix = GetOrBuildDoubledPrefix(ringMasses, peptideStartInRing, peptideLength, ringLength); + + // ── Ion type caps ───────────────────────────────────────────────── + var massCaps = DissociationTypeCollection + .GetNAndCTerminalMassShiftsForDissociationType(dissociationType); + + List nTermProductTypes = + DissociationTypeCollection.GetTerminusSpecificProductTypesFromDissociation( + dissociationType, FragmentationTerminus.N); + + List cTermProductTypes = + DissociationTypeCollection.GetTerminusSpecificProductTypesFromDissociation( + dissociationType, FragmentationTerminus.C); + + // ── Enumerate internal fragments ────────────────────────────────── + // localStart: 0-based offset from this peptide's first residue. + // + // Sub-peptide (peptideLength < ringLength): + // Both cleavage sites must fall within [0, peptideLength), so + // maxLength = peptideLength - localStart - 1, preventing wrap-around. + // + // Full-ring peptide (peptideLength == ringLength): + // Every pair of backbone cleavage sites on the ring is valid. A fragment + // may wrap around the origin, so maxLength = peptideLength - 1 for all + // starting positions (the doubled prefix-sum handles the wrap). + + bool isFullRing = peptideLength == ringLength; + + for (int localStart = 0; localStart < peptideLength; localStart++) + { + int oneBasedStart = OneBasedStartResidueInProtein + localStart; + int maxLength = isFullRing + ? peptideLength - 1 + : peptideLength - localStart - 1; + + for (int length = minLengthOfFragments; length <= maxLength; length++) + { + double fragmentResidueMass = + doubledPrefix[localStart + length] - doubledPrefix[localStart]; + + int oneBasedEnd = oneBasedStart + length - 1; + + for (int i = 0; i < nTermProductTypes.Count; i++) + { + double nTermCap = massCaps.Item1[i]; + for (int j = 0; j < cTermProductTypes.Count; j++) + { + double cTermCap = massCaps.Item2[j]; + + products.Add(new Product( + productType: cTermProductTypes[j], + terminus: FragmentationTerminus.None, + neutralMass: fragmentResidueMass + nTermCap + cTermCap - WaterMonoisotopicMass, + fragmentNumber: oneBasedStart, + residuePosition: length, + neutralLoss: 0, + secondaryProductType: nTermProductTypes[i], + secondaryFragmentNumber: oneBasedEnd)); + } + } + } + } + } + + // ── Private helper ──────────────────────────────────────────────────── + + /// + /// Builds a residue mass array of length N (the parent ring length) from + /// the parent ring's canonical sequence, with this peptide's modifications + /// mapped back to their correct ring positions. + /// + /// This is the single mass array used by . + /// Using the full ring (not just the peptide subsequence) ensures that: + /// (a) residue masses are always read from the correct ring position, and + /// (b) the doubled prefix-sum correctly handles wrap-around for full-ring + /// peptides without re-entering the peptide's own residues out of order. + /// + /// Modifications in + /// use keys relative to the peptide's local sequence. We convert each to a + /// 0-based ring index: + /// ringIndex = (OneBasedStartResidueInProtein − 1 + localIndex) % ringLength + /// + /// + /// Returns the cached ring mass array, building it on first access. + /// + private double[] GetOrBuildRingMasses() + { + return _cachedRingMasses ??= BuildParentRingMassArray(); + } + + /// + /// Returns the cached doubled prefix-sum array, building it on first access. + /// + private double[] GetOrBuildDoubledPrefix(double[] ringMasses, int peptideStartInRing, int peptideLength, int ringLength) + { + if (_cachedDoubledPrefix != null) + return _cachedDoubledPrefix; + + var doubledPrefix = new double[2 * peptideLength + 1]; + for (int i = 0; i < 2 * peptideLength; i++) + { + int ringIndex = (peptideStartInRing + i) % ringLength; + doubledPrefix[i + 1] = doubledPrefix[i] + ringMasses[ringIndex]; + } + + _cachedDoubledPrefix = doubledPrefix; + return _cachedDoubledPrefix; + } + + private double[] BuildParentRingMassArray() + { + int ringLength = CircularParent.Length; + string ringSeq = CircularParent.BaseSequence; + double[] masses = new double[ringLength]; + + for (int i = 0; i < ringLength; i++) + { + if (!Residue.TryGetResidue(ringSeq[i], out Residue res)) + throw new InvalidOperationException( + $"Unrecognized amino acid '{ringSeq[i]}' at position {i + 1} " + + $"in the ring sequence of protein '{CircularParent.Accession}'. " + + $"Cannot compute fragment masses."); + + masses[i] = res.MonoisotopicMass; + } + + // Map each mod from its peptide-local key to its ring position. + // Keys: 1 → local index 0 (N-term mod) + // i+2 → local index i (side-chain, 0-based) + // n+2 → local index n-1 (C-term mod, n = peptide length) + int n = BaseSequence.Length; + int startInRing = OneBasedStartResidueInProtein - 1; + + foreach (var kvp in AllModsOneIsNterminus) + { + // Only side-chain mods (keys 2..n+1) are valid; terminal mods + // are rejected by the constructor. + int localIndex = kvp.Key - 2; + + if (localIndex < 0 || localIndex >= n) + throw new InvalidOperationException( + $"Unexpected modification key {kvp.Key} for circular peptide of length {n}. " + + "Only side-chain modifications (keys 2 to n+1) are supported."); + + int ringIndex = (startInRing + localIndex) % ringLength; + masses[ringIndex] += kvp.Value.MonoisotopicMass.Value; + } + + return masses; + } + + // ── ToString ────────────────────────────────────────────────────────── + + public override string ToString() => + $"[Circular] {FullSequence} [{OneBasedStartResidueInProtein}-{OneBasedEndResidueInProtein}]"; + } +} \ No newline at end of file diff --git a/mzLib/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs b/mzLib/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs index 570356470..b9927025c 100644 --- a/mzLib/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs +++ b/mzLib/Proteomics/ProteolyticDigestion/PeptideWithSetModifications.cs @@ -96,7 +96,12 @@ public PeptideWithSetModifications(string sequence, Dictionary NumMods - NumFixedMods; - public double MonoisotopicMass + /// + /// The monoisotopic mass of this peptide, including residue masses, modification masses, + /// and water (for free termini). Virtual to allow derived types (e.g., circular peptides) + /// to adjust the mass calculation. + /// + public virtual double MonoisotopicMass { get { @@ -557,13 +562,15 @@ public void Fragment(DissociationType dissociationType, FragmentationTerminus fr } /// - /// Generates theoretical internal fragments for given dissociation type for this peptide. + /// Generates theoretical internal fragments for given dissociation type for this peptide. /// The "products" parameter is filled with these fragments. - /// The "minLengthOfFragments" parameter is the minimum number of amino acids for an internal fragment to be included + /// The "minLengthOfFragments" parameter is the minimum number of amino acids for an internal fragment to be included. + /// Virtual to allow derived types (e.g., circular peptides) to provide + /// topology-specific fragmentation. /// TODO: Implement neutral losses (e.g. phospho) /// TODO: Implement Star/Degree ions from CID /// - public void FragmentInternally(DissociationType dissociationType, int minLengthOfFragments, List products, IFragmentationParams? fragmentationParams = null) + public virtual void FragmentInternally(DissociationType dissociationType, int minLengthOfFragments, List products, IFragmentationParams? fragmentationParams = null) { products.Clear(); diff --git a/mzLib/Test/CircularProteinsAndPeptide/CircularProteinDigestionTests.cs b/mzLib/Test/CircularProteinsAndPeptide/CircularProteinDigestionTests.cs new file mode 100644 index 000000000..687f806f6 --- /dev/null +++ b/mzLib/Test/CircularProteinsAndPeptide/CircularProteinDigestionTests.cs @@ -0,0 +1,225 @@ +using NUnit.Framework; +using Omics.Modifications; +using Proteomics; +using Proteomics.ProteolyticDigestion; +using System.Collections.Generic; +using System.Linq; + +namespace Test.CircularSearch +{ + [TestFixture] + public static class CircularSearchEngineTests + { + /// + /// Verifies the exact digestion products of CircularProtein "PEPTIDEKAAK" + /// using trypsin, 2 missed cleavages, min peptide length 1. + /// + /// The circular protein canonicalises to "AAKPEPTIDEK" (alphabetically + /// earliest rotation). Trypsin then produces: + /// Linear: AAK (pos 1-3) + /// Linear: PEPTIDEK (pos 4-11) + /// Linear: AAKPEPTIDEK (pos 1-11, 1 missed cleavage) + /// Linear: PEPTIDEKAAK (pos 4-14, 1 missed cleavage, wraps) + /// Circular: AAKPEPTIDEK (two-cut cyclic product) + /// + [Test] + public static void Digest_PEPTIDEKAAK_ProducesExactExpectedProducts() + { + var circularProtein = CircularProtein.FromProtein( + new Protein("PEPTIDEKAAK", accession: "TEST01")); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 2, + minPeptideLength: 1); + + var allProducts = circularProtein + .Digest(digestionParams, + new List(), + new List()) + .ToList(); + + // ── Linear products ─────────────────────────────────────────────── + + var linearProducts = allProducts + .OfType() + .Where(p => p is not CircularPeptideWithSetModifications) + .ToList(); + + Assert.That(linearProducts.Count, Is.EqualTo(4), + "Expected exactly 4 linear (PeptideWithSetModifications) products."); + + var aak = linearProducts.SingleOrDefault(p => p.BaseSequence == "AAK"); + Assert.That(aak, Is.Not.Null, "Expected linear product AAK."); + Assert.That(aak.OneBasedStartResidue, Is.EqualTo(1)); + Assert.That(aak.OneBasedEndResidue, Is.EqualTo(3)); + + var peptidek = linearProducts.SingleOrDefault(p => p.BaseSequence == "PEPTIDEK"); + Assert.That(peptidek, Is.Not.Null, "Expected linear product PEPTIDEK."); + Assert.That(peptidek.OneBasedStartResidue, Is.EqualTo(4)); + Assert.That(peptidek.OneBasedEndResidue, Is.EqualTo(11)); + + var aakpeptidek = linearProducts.SingleOrDefault(p => p.BaseSequence == "AAKPEPTIDEK"); + Assert.That(aakpeptidek, Is.Not.Null, "Expected linear product AAKPEPTIDEK."); + Assert.That(aakpeptidek.OneBasedStartResidue, Is.EqualTo(1)); + Assert.That(aakpeptidek.OneBasedEndResidue, Is.EqualTo(11)); + + var peptidekaak = linearProducts.SingleOrDefault(p => p.BaseSequence == "PEPTIDEKAAK"); + Assert.That(peptidekaak, Is.Not.Null, "Expected linear product PEPTIDEKAAK."); + Assert.That(peptidekaak.OneBasedStartResidue, Is.EqualTo(4)); + Assert.That(peptidekaak.OneBasedEndResidue, Is.EqualTo(14)); + + // ── Circular product ────────────────────────────────────────────── + + var circularProducts = allProducts + .OfType() + .ToList(); + + Assert.That(circularProducts.Count, Is.EqualTo(1), + "Expected exactly 1 CircularPeptideWithSetModifications."); + + var circPeptide = circularProducts.Single(); + Assert.That(circPeptide.BaseSequence, Is.EqualTo("AAKPEPTIDEK")); + + Assert.That(allProducts.Count, Is.EqualTo(5), + "Expected exactly 5 digestion products in total."); + } + + /// + /// Same CircularProtein and DigestionParams as above, but with variable + /// phosphorylation on T. + /// + /// Canonical sequence: A-A-K-P-E-P-T-I-D-E-K (N=11) + /// 1-2-3-4-5-6-7-8-9-10-11 + /// T is at canonical position 7. + /// + /// Key convention: AllModsOneIsNterminus key = localIndex + 2, + /// where localIndex = (canonical position of T) - (OneBasedStartResidue), 0-based. + /// + /// Products and phosphorylation keys: + /// + /// AAK [1-3] no T → 1 form, no phospho + /// PEPTIDEK [4-11] T at canonical 7: localIndex=7-4=3, key=5 → 2 forms + /// AAKPEPTIDEK [1-11] T at canonical 7: localIndex=7-1=6, key=8 → 2 forms + /// PEPTIDEKAAK [4-14] T at canonical 7: localIndex=7-4=3, key=5 → 2 forms + /// Circular AAKPEPTIDEK [1-11] T at canonical 7: localIndex=7-1=6, key=8 → 2 forms + /// + /// Total: 1 + 2 + 2 + 2 + 2 = 9 products. + /// + [Test] + public static void Digest_PEPTIDEKAAK_WithPhosphoT_ProducesCorrectProducts() + { + ModificationMotif.TryGetMotif("T", out ModificationMotif tMotif); + var phospho = new Modification( + _originalId: "Phosphorylation on T", + _modificationType: "Common Variable", + _target: tMotif, + _locationRestriction: "Anywhere.", + _monoisotopicMass: 79.966331); + + var circularProtein = CircularProtein.FromProtein( + new Protein("PEPTIDEKAAK", accession: "TEST01")); + + Assert.That(circularProtein.BaseSequence, Is.EqualTo("AAKPEPTIDEK")); + Assert.That(circularProtein.BaseSequence[6], Is.EqualTo('T'), + "T is at 1-based canonical position 7 (0-based index 6)."); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 2, + minPeptideLength: 1); + + var allProducts = circularProtein + .Digest(digestionParams, + new List(), + new List { phospho }) + .ToList(); + + Assert.That(allProducts.Count, Is.EqualTo(9), + "Expected 9 total products: 5 unmodified + 4 phosphorylated (one per T-containing product)."); + + // ── Linear products ─────────────────────────────────────────────── + + var linearProducts = allProducts + .OfType() + .Where(p => p is not CircularPeptideWithSetModifications) + .ToList(); + + Assert.That(linearProducts.Count, Is.EqualTo(7), + "Expected 7 linear products: AAK(1) + PEPTIDEK(2) + AAKPEPTIDEK(2) + PEPTIDEKAAK(2)."); + + // AAK [1-3] — no T → exactly 1 form, no phosphorylation + var aakForms = linearProducts.Where(p => p.BaseSequence == "AAK").ToList(); + Assert.That(aakForms.Count, Is.EqualTo(1), "AAK has no T: 1 form only."); + Assert.That(aakForms[0].AllModsOneIsNterminus, Is.Empty, + "AAK: no modification expected."); + + // PEPTIDEK [4-11] — T at canonical pos 7, localIndex=3, key=5 + var peptidekForms = linearProducts.Where(p => p.BaseSequence == "PEPTIDEK").ToList(); + Assert.That(peptidekForms.Count, Is.EqualTo(2), "PEPTIDEK: 2 forms (±phospho)."); + var peptidekUnmod = peptidekForms.Single(p => p.AllModsOneIsNterminus.Count == 0); + var peptidekPhospho = peptidekForms.Single(p => p.AllModsOneIsNterminus.Count == 1); + Assert.That(peptidekPhospho.AllModsOneIsNterminus.ContainsKey(5), Is.True, + "PEPTIDEK phospho key: T at canonical 7, start 4 → localIndex=3, key=5."); + Assert.That(peptidekPhospho.AllModsOneIsNterminus[5].OriginalId, + Does.Contain("Phosphorylation")); + Assert.That( + peptidekPhospho.MonoisotopicMass - peptidekUnmod.MonoisotopicMass, + Is.EqualTo(79.966331).Within(1e-5), + "PEPTIDEK: phospho mass shift = +79.966331 Da."); + + // AAKPEPTIDEK [1-11] — T at canonical pos 7, localIndex=6, key=8 + var aakpeptidekForms = linearProducts.Where(p => p.BaseSequence == "AAKPEPTIDEK").ToList(); + Assert.That(aakpeptidekForms.Count, Is.EqualTo(2), "AAKPEPTIDEK: 2 forms (±phospho)."); + var aakpeptidekUnmod = aakpeptidekForms.Single(p => p.AllModsOneIsNterminus.Count == 0); + var aakpeptidekPhospho = aakpeptidekForms.Single(p => p.AllModsOneIsNterminus.Count == 1); + Assert.That(aakpeptidekPhospho.AllModsOneIsNterminus.ContainsKey(8), Is.True, + "AAKPEPTIDEK phospho key: T at canonical 7, start 1 → localIndex=6, key=8."); + Assert.That(aakpeptidekPhospho.AllModsOneIsNterminus[8].OriginalId, + Does.Contain("Phosphorylation")); + Assert.That( + aakpeptidekPhospho.MonoisotopicMass - aakpeptidekUnmod.MonoisotopicMass, + Is.EqualTo(79.966331).Within(1e-5), + "AAKPEPTIDEK: phospho mass shift = +79.966331 Da."); + + // PEPTIDEKAAK [4-14] — T at canonical pos 7, localIndex=3, key=5 + var peptidekaakForms = linearProducts.Where(p => p.BaseSequence == "PEPTIDEKAAK").ToList(); + Assert.That(peptidekaakForms.Count, Is.EqualTo(2), "PEPTIDEKAAK: 2 forms (±phospho)."); + var peptidekaakUnmod = peptidekaakForms.Single(p => p.AllModsOneIsNterminus.Count == 0); + var peptidekaakPhospho = peptidekaakForms.Single(p => p.AllModsOneIsNterminus.Count == 1); + Assert.That(peptidekaakPhospho.AllModsOneIsNterminus.ContainsKey(5), Is.True, + "PEPTIDEKAAK phospho key: T at canonical 7, start 4 → localIndex=3, key=5."); + Assert.That(peptidekaakPhospho.AllModsOneIsNterminus[5].OriginalId, + Does.Contain("Phosphorylation")); + Assert.That( + peptidekaakPhospho.MonoisotopicMass - peptidekaakUnmod.MonoisotopicMass, + Is.EqualTo(79.966331).Within(1e-5), + "PEPTIDEKAAK: phospho mass shift = +79.966331 Da."); + + // ── Circular products ───────────────────────────────────────────── + // AAKPEPTIDEK [1-11] — T at canonical pos 7, localIndex=6, key=8 + + var circularProducts = allProducts + .OfType() + .ToList(); + + Assert.That(circularProducts.Count, Is.EqualTo(2), + "Expected 2 circular products: unmodified and phosphorylated AAKPEPTIDEK."); + + var circUnmod = circularProducts.Single(p => p.AllModsOneIsNterminus.Count == 0); + var circPhospho = circularProducts.Single(p => p.AllModsOneIsNterminus.Count == 1); + + Assert.That(circUnmod.BaseSequence, Is.EqualTo("AAKPEPTIDEK")); + Assert.That(circPhospho.BaseSequence, Is.EqualTo("AAKPEPTIDEK")); + + Assert.That(circPhospho.AllModsOneIsNterminus.ContainsKey(8), Is.True, + "Circular AAKPEPTIDEK phospho key: T at canonical 7, start 1 → localIndex=6, key=8."); + Assert.That(circPhospho.AllModsOneIsNterminus[8].OriginalId, + Does.Contain("Phosphorylation")); + Assert.That( + circPhospho.MonoisotopicMass - circUnmod.MonoisotopicMass, + Is.EqualTo(79.966331).Within(1e-5), + "Circular AAKPEPTIDEK: phospho mass shift = +79.966331 Da."); + } + } +} \ No newline at end of file diff --git a/mzLib/Test/CircularProteinsAndPeptide/TestCircularProteinLocalizedModRegression.cs b/mzLib/Test/CircularProteinsAndPeptide/TestCircularProteinLocalizedModRegression.cs new file mode 100644 index 000000000..b0f077bb1 --- /dev/null +++ b/mzLib/Test/CircularProteinsAndPeptide/TestCircularProteinLocalizedModRegression.cs @@ -0,0 +1,202 @@ +using NUnit.Framework; +using Omics; +using Omics.Modifications; +using Proteomics; +using Proteomics.ProteolyticDigestion; +using System; +using System.Collections.Generic; +using System.Linq; +using UsefulProteomicsDatabases; + +namespace Test.CircularSearch +{ + /// + /// Regression tests for localized-modification handling in + /// . Each test is constructed to FAIL on the + /// pre-fix code and pass after the corresponding fix: + /// + /// • Wrap-around fragments must carry XML/database-localized mods on the wrapped + /// (second-copy) residues — the proxy now replicates localized-mod keys onto + /// positions N+1..2N-1. + /// • Intact-ring forms must include annotated localized mods even when they are + /// not supplied via variableModifications, matching the linear path. + /// • The full-ring variable-mod enumeration must be bounded by + /// . + /// • NumFixedMods must not count a fixed mod that a variable mod overrides + /// at the same residue. + /// + [TestFixture] + public static class TestCircularProteinLocalizedModRegression + { + private const double PhosphoMass = 79.966331; + private const double FixedSerineMass = 100.0; + private const double Tol = 1e-3; + + [OneTimeSetUp] + public static void OneTimeSetup() + { + Loaders.LoadElements(); + } + + // ── Helpers ───────────────────────────────────────────────────────────── + + private static Modification BuildPhospho() + { + ModificationMotif.TryGetMotif("S", out ModificationMotif motifS); + return new Modification( + _originalId: "Phospho", + _modificationType: "Test", + _target: motifS, + _locationRestriction: "Anywhere.", + _monoisotopicMass: PhosphoMass); + } + + private static Modification BuildFixedSerineMod() + { + ModificationMotif.TryGetMotif("S", out ModificationMotif motifS); + return new Modification( + _originalId: "FixedSerineMod", + _modificationType: "Test", + _target: motifS, + _locationRestriction: "Anywhere.", + _monoisotopicMass: FixedSerineMass); + } + + /// + /// Builds a from an already-canonical sequence + /// (so positions are preserved through ) + /// carrying a single localized modification at . + /// + private static CircularProtein BuildCircularWithLocalizedMod( + string canonicalSequence, int oneBasedPos, Modification mod) + { + var mods = new Dictionary> + { + { oneBasedPos, new List { mod } } + }; + var source = new Protein(canonicalSequence, "TESTACC", oneBasedModifications: mods); + return CircularProtein.FromProtein(source); + } + + private static bool CarriesPhospho(IBioPolymerWithSetMods peptide) => + peptide.AllModsOneIsNterminus.Values.Any(m => + m.MonoisotopicMass.HasValue && + Math.Abs(m.MonoisotopicMass.Value - PhosphoMass) < Tol); + + // ── Fix A (Critical / Codex #1): wrap-around localized mods ─────────────── + + /// + /// Ring "ASDKEFGHR" (N=9): trypsin cuts after K(4) and R(9). With one missed + /// cleavage the proxy yields the wrap-around product "EFGHRASDK" (ring 5..9 + 1..4), + /// whose only serine is the wrapped residue at ring position 2 (proxy position 11). + /// The phospho is annotated as a LOCALIZED mod (not passed as a variable mod), so it + /// is applied by position; the wrapped S can only receive it if the proxy carries the + /// localized-mod key at N+2 = 11. Pre-fix, that key was absent and the mod was dropped. + /// + [Test] + public static void WrapAroundFragment_CarriesLocalizedModOnWrappedResidue() + { + var phospho = BuildPhospho(); + var circular = BuildCircularWithLocalizedMod("ASDKEFGHR", oneBasedPos: 2, phospho); + + var dp = new DigestionParams(protease: "trypsin", maxMissedCleavages: 2, minPeptideLength: 1); + + var wrapPeptides = circular + .Digest(dp, new List(), new List()) + .OfType() + .Where(p => p.BaseSequence == "EFGHRASDK") + .ToList(); + + Assert.That(wrapPeptides, Is.Not.Empty, + "Expected the wrap-around product \"EFGHRASDK\" to be produced."); + Assert.That(wrapPeptides.Any(CarriesPhospho), Is.True, + "The wrap-around peptide must carry the annotated phosphoserine on its wrapped S residue " + + "(proxy position 11). Pre-fix the localized mod was silently dropped on the wrapped portion."); + } + + // ── Fix B (Codex #2): full-ring includes annotated localized mods ───────── + + /// + /// Ring "ALLLLALPGS" (N=10) has no K/R, so trypsin yields only the intact-ring + /// product. The phospho is annotated on the S (position 10) but NOT passed as a + /// variable mod. The linear path applies OneBasedPossibleLocalizedModifications as + /// variable mods; the full-ring branch must too, or it drops the modified isoform. + /// + [Test] + public static void FullRing_IncludesAnnotatedLocalizedMod_WithoutVariableModsArg() + { + var phospho = BuildPhospho(); + var circular = BuildCircularWithLocalizedMod("ALLLLALPGS", oneBasedPos: 10, phospho); + + var dp = new DigestionParams(protease: "trypsin", maxMissedCleavages: 2, minPeptideLength: 1); + + var rings = circular + .Digest(dp, new List(), new List()) + .OfType() + .ToList(); + + Assert.That(rings, Is.Not.Empty, "Expected the intact-ring product."); + Assert.That(rings.Any(CarriesPhospho), Is.True, + "The intact-ring form must include the annotated localized phospho isoform " + + "even though it was not supplied via variableModifications."); + } + + // ── Fix C (Major): full-ring variable-mod isoform cap ───────────────────── + + /// + /// Ring "ASASASLLPG" (N=10) has three serines (positions 2,4,6) and no K/R. With + /// phospho as a variable mod and MaxMods=2 there are six distinct modified ring + /// forms; MaxModificationIsoforms=2 must bound how many are emitted. + /// + [Test] + public static void FullRing_VariableModForms_BoundedByMaxModificationIsoforms() + { + var phospho = BuildPhospho(); + var circular = CircularProtein.FromProtein(new Protein("ASASASLLPG", "TESTACC")); + + var dp = new DigestionParams(protease: "trypsin", maxMissedCleavages: 2, + minPeptideLength: 1, maxModificationIsoforms: 2, maxModsForPeptides: 2); + + var phosphoRingForms = circular + .Digest(dp, new List(), new List { phospho }) + .OfType() + .Count(CarriesPhospho); + + Assert.That(phosphoRingForms, Is.GreaterThan(0), + "At least one modified ring form should be produced."); + Assert.That(phosphoRingForms, Is.LessThanOrEqualTo(2), + "Modified ring forms must be capped at MaxModificationIsoforms (2); " + + "pre-fix the enumeration was uncapped and produced six."); + } + + // ── Fix D (Major): NumFixedMods not overcounted on override ─────────────── + + /// + /// Ring "ASLLLLLLPG" (N=10) has a single serine (position 2) and no K/R. A fixed + /// mod and a variable phospho both target that S. In the ring form where the variable + /// phospho occupies the S, the fixed mod is overridden, so NumFixedMods must be 0. + /// + [Test] + public static void FullRing_NumFixedMods_NotOvercounted_WhenVariableOverridesFixed() + { + var phospho = BuildPhospho(); + var fixedSerine = BuildFixedSerineMod(); + var circular = CircularProtein.FromProtein(new Protein("ASLLLLLLPG", "TESTACC")); + + var dp = new DigestionParams(protease: "trypsin", maxMissedCleavages: 2, minPeptideLength: 1); + + var rings = circular + .Digest(dp, new List { fixedSerine }, new List { phospho }) + .OfType() + .ToList(); + + var phosphoForm = rings.FirstOrDefault(CarriesPhospho); + + Assert.That(phosphoForm, Is.Not.Null, + "Expected a ring form where the serine carries the variable phospho."); + Assert.That(phosphoForm.NumFixedMods, Is.EqualTo(0), + "When the variable phospho overrides the fixed mod at the same serine, " + + "NumFixedMods must not count the overridden fixed mod (pre-fix it reported 1)."); + } + } +} diff --git a/mzLib/Test/CircularProteinsAndPeptide/TestCircularProteinXmlLoading.cs b/mzLib/Test/CircularProteinsAndPeptide/TestCircularProteinXmlLoading.cs new file mode 100644 index 000000000..c3247ffdb --- /dev/null +++ b/mzLib/Test/CircularProteinsAndPeptide/TestCircularProteinXmlLoading.cs @@ -0,0 +1,153 @@ +using NUnit.Framework; +using Omics.Modifications; +using Proteomics; +using Proteomics.ProteolyticDigestion; +using System.Collections.Generic; +using System.IO; +using System.Linq; +using UsefulProteomicsDatabases; + +namespace Test.CircularSearch +{ + [TestFixture] + public static class TestCircularProteinXmlLoading + { + [OneTimeSetUp] + public static void OneTimeSetup() + { + Loaders.LoadElements(); + } + + /// + /// Verifies that a UniProt-format protein XML database can be read via + /// and that each resulting + /// entry can be successfully converted into a + /// via . + /// + /// The test database (simpleCircularProtein.xml) contains one entry: + /// Accession : P05067 + /// Sequence : LPGLALLLLA (length 10) + /// Full name : Amyloid-beta precursor protein + /// Organism : Homo sapiens + /// Gene : APP + /// + /// The expected canonical rotation of "LPGLALLLLA" is "ALLLLALPGL" + /// (lexicographically smallest rotation, offset 4). + /// + [Test] + public static void LoadProteinXml_SingleEntry_ConvertsToCircularProtein() + { + string xmlPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", "simpleCircularProtein.xml"); + + // ── Load proteins from XML ──────────────────────────────────────── + List proteins = ProteinDbLoader.LoadProteinXML( + xmlPath, + generateTargets: true, + decoyType: DecoyType.None, + allKnownModifications: new List(), + isContaminant: false, + modTypesToExclude: new List(), + unknownModifications: out _); + + Assert.That(proteins, Is.Not.Null); + Assert.That(proteins, Is.Not.Empty, + "Expected at least one protein to be loaded from the XML database."); + + // ── Convert each Protein to CircularProtein ─────────────────────── + List circularProteins = proteins + .Select(p => CircularProtein.FromProtein(p)) + .ToList(); + + Assert.That(circularProteins, Has.Count.EqualTo(proteins.Count), + "Every loaded Protein should convert to a CircularProtein without loss."); + + Assert.That(circularProteins.All(cp => cp is CircularProtein), Is.True, + "FromProtein must return CircularProtein instances."); + + // ── Validate the single entry ───────────────────────────────────── + CircularProtein entry = circularProteins.Single(cp => cp.Accession == "P05067"); + + Assert.Multiple(() => + { + // Sequence must be the canonical (lexicographically smallest) rotation + // of the original "LPGLALLLLA". + // Rotations and their canonical: offset 4 → "ALLLLALPGL" + Assert.That(entry.BaseSequence, Is.EqualTo("ALLLLALPGL"), + "BaseSequence must be the canonical rotation of the original XML sequence."); + + Assert.That(entry.CircularSequence, Is.EqualTo(entry.BaseSequence), + "CircularSequence must equal BaseSequence for a CircularProtein."); + + Assert.That(entry.Length, Is.EqualTo(10), + "Circular protein length must equal the original sequence length."); + + Assert.That(entry.FullName, Is.EqualTo("Amyloid-beta precursor protein"), + "FullName must be read from the XML element."); + + Assert.That(entry.Organism, Is.EqualTo("Homo sapiens"), + "Organism must be read from the XML element."); + + Assert.That(entry.GeneNames.Any(g => g.Item2 == "APP"), Is.True, + "Gene name 'APP' must be read from the XML element."); + + Assert.That(entry.DatabaseFilePath, Does.EndWith("simpleCircularProtein.xml"), + "DatabaseFilePath must reflect the source XML file."); + + Assert.That(entry.IsDecoy, Is.False, + "A standard target entry must not be flagged as a decoy."); + + Assert.That(entry.IsContaminant, Is.False, + "The protein was loaded as a non-contaminant."); + + // CyclicMonoisotopicMass must be positive and finite + Assert.That(entry.CyclicMonoisotopicMass, Is.GreaterThan(0), + "CyclicMonoisotopicMass must be a positive value."); + + Assert.That(double.IsNaN(entry.CyclicMonoisotopicMass), Is.False, + "CyclicMonoisotopicMass must not be NaN."); + + Assert.That(double.IsInfinity(entry.CyclicMonoisotopicMass), Is.False, + "CyclicMonoisotopicMass must not be infinite."); + }); + } + + /// + /// Verifies that the circular protein loaded from XML can be digested + /// without throwing, and that all resulting peptides reference the + /// correct parent. + /// + [Test] + public static void LoadProteinXml_CircularProtein_CanBeDigested() + { + string xmlPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DataFiles", "simpleCircularProtein.xml"); + + List proteins = ProteinDbLoader.LoadProteinXML( + xmlPath, + generateTargets: true, + decoyType: DecoyType.None, + allKnownModifications: new List(), + isContaminant: false, + modTypesToExclude: new List(), + unknownModifications: out _); + + CircularProtein circular = CircularProtein.FromProtein( + proteins.Single(p => p.Accession == "P05067")); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 2, + minPeptideLength: 1); + + var peptides = circular + .Digest(digestionParams, new List(), new List()) + .Cast() + .ToList(); + + Assert.That(peptides, Is.Not.Empty, + "Digestion of the XML-loaded CircularProtein must yield at least one peptide."); + + Assert.That(peptides.All(p => ReferenceEquals(p.Protein, circular)), Is.True, + "Every digestion product must reference the CircularProtein as its parent."); + } + } +} \ No newline at end of file diff --git a/mzLib/Test/CircularProteinsAndPeptide/TestCircularProteinXmlLoadingWithMod.cs b/mzLib/Test/CircularProteinsAndPeptide/TestCircularProteinXmlLoadingWithMod.cs new file mode 100644 index 000000000..19b79df86 --- /dev/null +++ b/mzLib/Test/CircularProteinsAndPeptide/TestCircularProteinXmlLoadingWithMod.cs @@ -0,0 +1,292 @@ +using NUnit.Framework; +using Omics.Modifications; +using Proteomics; +using Proteomics.ProteolyticDigestion; +using System; +using System.Collections.Generic; +using System.IO; +using System.Linq; +using UsefulProteomicsDatabases; + +namespace Test.CircularSearch +{ + /// + /// Tests that a UniProt-format protein XML database containing a + /// <feature type="modified residue" description="Phosphoserine"> + /// annotation at position 4 can be read via + /// and correctly converted to a + /// via , + /// with the modification position remapped to the canonical rotation. + /// + /// DATABASE: simpleCircularProteinWithMod.xml + /// ------------------------------------------ + /// Accession : P05067 + /// Sequence : LPGSALLLLA (length 10, S at one-based position 4) + /// Feature : Phosphoserine at position 4 + /// + /// CANONICALIZATION + /// ---------------- + /// The lexicographically smallest rotation of "LPGSALLLLA" is "ALLLLALPGS" + /// (offset 4). + /// + /// Original: L P G S A L L L L A (positions 1-10) + /// Canonical: A L L L L A L P G S (positions 1-10) + /// + /// RemapModifications formula: + /// newPos = (oldPos - 1 - offset + N) % N + 1 + /// newPos = (4 - 1 - 4 + 10) % 10 + 1 = 9 % 10 + 1 = 10 + /// + /// The phosphoserine must appear at canonical position 10, which is the S + /// residue at the end of "ALLLLALPGS". + /// + /// MOD MATCHING + /// ------------ + /// matches the XML feature + /// description ("Phosphoserine") against the keys of IdToPossibleMods, + /// which are built by stripping " on X" from each known mod's OriginalId. + /// Therefore the mod passed as allKnownModifications must use + /// _originalId: "Phosphoserine" (not "Phosphorylation on S") so that + /// the stripped key "Phosphoserine" matches the XML description exactly. + /// + [TestFixture] + public static class TestCircularProteinXmlLoadingWithMod + { + // ── Constants ───────────────────────────────────────────────────────── + + private const string OriginalSequence = "LPGSALLLLA"; + private const string CanonicalSequence = "ALLLLALPGS"; + private const int CanonicalOffset = 4; + + // One-based position of S in the original sequence. + private const int PhosphoPositionOriginal = 4; + + // One-based position of S in the canonical sequence after remapping: + // (4 - 1 - 4 + 10) % 10 + 1 = 10 + private const int PhosphoPositionCanonical = 10; + + private const string Accession = "P05067"; + private const double PhosphoMass = 79.966331; + private const double MassTolerance = 1e-5; + + [OneTimeSetUp] + public static void OneTimeSetup() + { + Loaders.LoadElements(); + } + + // ── Helper ──────────────────────────────────────────────────────────── + + /// + /// Builds the phosphoserine whose OriginalId + /// ("Phosphoserine") matches the XML feature description exactly, enabling + /// to resolve it via + /// IdToPossibleMods. + /// + private static Modification BuildPhosphoSerineMod() + { + ModificationMotif.TryGetMotif("S", out ModificationMotif motifS); + return new Modification( + _originalId: "Phosphoserine", + _modificationType: "UniProt", + _target: motifS, + _locationRestriction: "Anywhere.", + _monoisotopicMass: PhosphoMass); + } + + private static string XmlPath => Path.Combine( + TestContext.CurrentContext.TestDirectory, + "DataFiles", + "simpleCircularProteinWithMod.xml"); + + // ── Tests ───────────────────────────────────────────────────────────── + + /// + /// Verifies that the XML database loads without error, that the single + /// entry converts to a , and that the + /// phosphoserine modification is remapped from original position 4 to + /// canonical position 10. + /// + /// Canonical sequence "ALLLLALPGS": + /// Position: 1234567890 + /// + /// Position 10 = 'S' — the only serine in the ring. + /// Position 4 = 'L' — must carry no modification after remapping. + /// + [Test] + public static void LoadProteinXmlWithMod_PhosphoSerineRemappedToCanonicalPosition() + { + List proteins = ProteinDbLoader.LoadProteinXML( + XmlPath, + generateTargets: true, + decoyType: DecoyType.None, + allKnownModifications: new List { BuildPhosphoSerineMod() }, + isContaminant: false, + modTypesToExclude: new List(), + unknownModifications: out _); + + Assert.That(proteins, Is.Not.Null.And.Not.Empty, + "Expected at least one protein to be loaded from the XML database."); + + Protein source = proteins.Single(p => p.Accession == Accession); + + // ── Convert to CircularProtein ──────────────────────────────────── + CircularProtein circular = CircularProtein.FromProtein(source); + + Assert.Multiple(() => + { + // ── Sequence ────────────────────────────────────────────────── + Assert.That(circular.BaseSequence, Is.EqualTo(CanonicalSequence), + "BaseSequence must be the canonical rotation of the original XML sequence."); + + Assert.That(circular.Length, Is.EqualTo(OriginalSequence.Length), + "Circular protein length must equal the original sequence length."); + + // ── Modification is present after canonicalization ──────────── + Assert.That(circular.OneBasedPossibleLocalizedModifications, Is.Not.Empty, + "The phosphoserine modification must survive the XML read and canonicalization."); + + // ── Remapped to canonical position 10 ───────────────────────── + Assert.That( + circular.OneBasedPossibleLocalizedModifications.ContainsKey(PhosphoPositionCanonical), + Is.True, + $"Phosphoserine must be at canonical position {PhosphoPositionCanonical} " + + $"(the S in \"{CanonicalSequence}\"), not at the original position {PhosphoPositionOriginal}."); + + // ── The residue at the remapped position is indeed S ────────── + Assert.That(circular.BaseSequence[PhosphoPositionCanonical - 1], Is.EqualTo('S'), + $"Canonical position {PhosphoPositionCanonical} must be residue 'S'."); + + // ── Modification mass ───────────────────────────────────────── + var modsAtCanonical = circular.OneBasedPossibleLocalizedModifications[PhosphoPositionCanonical]; + Assert.That(modsAtCanonical, Is.Not.Empty, + $"Modification list at canonical position {PhosphoPositionCanonical} must not be empty."); + + double? mass = modsAtCanonical.First().MonoisotopicMass; + Assert.That(mass, Is.Not.Null, + "Phosphoserine must have a non-null monoisotopic mass."); + Assert.That(mass.Value, Is.EqualTo(PhosphoMass).Within(MassTolerance), + $"Phosphoserine mass must be ~{PhosphoMass} Da."); + + // ── Original position 4 carries no modification ─────────────── + // After remapping, canonical position 4 = 'L', which is not a + // serine and must not bear the phospho mod. + Assert.That( + circular.OneBasedPossibleLocalizedModifications.ContainsKey(PhosphoPositionOriginal), + Is.False, + $"No modification should remain at canonical position {PhosphoPositionOriginal} " + + $"(residue '{circular.BaseSequence[PhosphoPositionOriginal - 1]}') after remapping."); + + // ── Metadata ────────────────────────────────────────────────── + Assert.That(circular.Accession, Is.EqualTo(Accession)); + Assert.That(circular.FullName, Is.EqualTo("Amyloid-beta precursor protein")); + Assert.That(circular.Organism, Is.EqualTo("Homo sapiens")); + Assert.That(circular.GeneNames.Any(g => g.Item2 == "APP"), Is.True); + Assert.That(circular.IsDecoy, Is.False); + Assert.That(circular.IsContaminant, Is.False); + }); + } + + /// + /// Guards against silent mod-resolution failure. If the OriginalId of the + /// known mod does not match the XML feature description, the parser silently + /// places the feature in unknownModifications and the protein carries + /// no modification at all — a failure mode that is invisible without this test. + /// + [Test] + public static void LoadProteinXmlWithMod_PhosphoSerineNotInUnknownModifications() + { + ProteinDbLoader.LoadProteinXML( + XmlPath, + generateTargets: true, + decoyType: DecoyType.None, + allKnownModifications: new List { BuildPhosphoSerineMod() }, + isContaminant: false, + modTypesToExclude: new List(), + unknownModifications: out var unknownMods); + + Assert.That( + unknownMods.ContainsKey("Phosphoserine"), + Is.False, + "Phosphoserine must be resolved against allKnownModifications and must NOT " + + "appear in unknownModifications. If it does, the OriginalId does not match " + + "the XML feature description."); + } + + /// + /// Verifies that when the circular protein is digested with phosphoserine + /// as a variable modification, at least one peptide form carries a mass + /// shift of ~79.97 Da, and that the modification always lands on an S residue. + /// + /// "ALLLLALPGS" has no K or R, so trypsin makes zero cuts and the ring is + /// returned as one CircularPeptideWithSetModifications. With phosphoserine + /// as a variable mod we expect exactly two forms: unmodified and phosphorylated. + /// + [Test] + public static void LoadProteinXmlWithMod_VariableDigestionProducesPhosphorylatedForm() + { + var phosphoMod = BuildPhosphoSerineMod(); + + List proteins = ProteinDbLoader.LoadProteinXML( + XmlPath, + generateTargets: true, + decoyType: DecoyType.None, + allKnownModifications: new List { phosphoMod }, + isContaminant: false, + modTypesToExclude: new List(), + unknownModifications: out _); + + CircularProtein circular = CircularProtein.FromProtein( + proteins.Single(p => p.Accession == Accession)); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 2, + minPeptideLength: 1); + + var allPeptides = circular + .Digest(digestionParams, + allKnownFixedModifications: new List(), + variableModifications: new List { phosphoMod }) + .Cast() + .ToList(); + + Assert.That(allPeptides, Is.Not.Empty, + "Digestion must yield at least one peptide."); + + // All products must be parented to this CircularProtein. + Assert.That(allPeptides.All(p => ReferenceEquals(p.Protein, circular)), Is.True, + "Every digestion product must reference the CircularProtein as its parent."); + + // At least one form must carry the phospho mass shift. + var phosphoPeptides = allPeptides + .Where(p => p.AllModsOneIsNterminus.Values.Any(m => + m.MonoisotopicMass.HasValue && + Math.Abs(m.MonoisotopicMass.Value - PhosphoMass) < MassTolerance)) + .ToList(); + + Assert.That(phosphoPeptides, Is.Not.Empty, + "At least one peptide must carry the phosphoserine modification."); + + // In every phosphorylated form the mod must sit on 'S'. + foreach (var pep in phosphoPeptides) + { + foreach (var kvp in pep.AllModsOneIsNterminus) + { + if (!kvp.Value.MonoisotopicMass.HasValue) continue; + if (Math.Abs(kvp.Value.MonoisotopicMass.Value - PhosphoMass) >= MassTolerance) continue; + + // AllModsOneIsNterminus key convention: + // key 1 → N-terminus + // key 2..N+1 → residues (key - 2 = 0-based index into BaseSequence) + // key N+2 → C-terminus + int zeroBasedIndex = kvp.Key - 2; + char residue = pep.BaseSequence[zeroBasedIndex]; + + Assert.That(residue, Is.EqualTo('S'), + $"Phosphoserine in peptide \"{pep.BaseSequence}\" at AllMods key {kvp.Key} " + + $"must be on residue 'S', not '{residue}'."); + } + } + } + } +} \ No newline at end of file diff --git a/mzLib/Test/CircularProteinsAndPeptide/TopDownDigestionRegressionTests.cs b/mzLib/Test/CircularProteinsAndPeptide/TopDownDigestionRegressionTests.cs new file mode 100644 index 000000000..77067e29e --- /dev/null +++ b/mzLib/Test/CircularProteinsAndPeptide/TopDownDigestionRegressionTests.cs @@ -0,0 +1,324 @@ +using NUnit.Framework; +using Omics.Digestion; +using Omics.Modifications; +using Proteomics; +using Proteomics.ProteolyticDigestion; +using System; +using System.Collections.Generic; +using System.Linq; +using System.Text; +using System.Threading.Tasks; + +namespace Test.CircularProteinsAndPeptide +{ + /// + /// Regression tests that lock in the fix for the top-down protease bug in + /// . + /// + /// ROOT CAUSE + /// ---------- + /// swaps out the + /// Protease property at construction time for non-specific search modes: + /// + /// SpecificProtease = Protease; // saves "top-down" here + /// if (SearchModeType == None) + /// Protease = dictionary["singleN"]; // ← overwrites Protease! + /// + /// Before the fix, GetCleavagePositionsInRing called + /// digestionParams.Protease.GetDigestionSiteIndices(). For a top-down + /// , Protease is singleN, which finds + /// many cut sites on any sequence. This made numCleavageSites large and + /// violated the guard condition maxMissedCleavages >= numCleavageSites, + /// so no was ever emitted. + /// + /// THE FIX + /// ------- + /// Use digestionParams.SpecificProtease (the actual user-selected protease, + /// which has no cleavage motif for top-down) instead of digestionParams.Protease + /// (the singleN/singleC stand-in injected for fast nonspecific digestion). + /// + /// TESTS + /// ----- + /// 1. + /// Core regression: a ring with trypsin K/R sites must still yield exactly + /// one under top-down, + /// regardless of how many trypsin sites the sequence contains. + /// + /// 2. + /// top-down finds zero cleavage sites → no linear ring-opening products + /// are generated (Step 3 of Digest() is short-circuited by numCleavageSites == 0). + /// + /// 3. + /// The emitted carries the + /// full canonical ring sequence and the correct cyclic monoisotopic mass + /// (no H₂O addition). + /// + /// 4. + /// references + /// the originating . + /// + /// 5. + /// Sanity check: a ring with no K/R (which always worked) is unaffected. + /// + /// 6. + /// Directly probes the state to confirm + /// that SpecificProtease.Name == "top-down" while + /// Protease.Name != "top-down", documenting the exact swap that + /// caused the regression. + /// + [TestFixture] + public static class TopDownDigestionRegressionTests + { + // ── Helpers ─────────────────────────────────────────────────────────── + + private static DigestionParams MakeTopDownParams(int maxMissedCleavages = 0) => + new DigestionParams( + protease: "top-down", + maxMissedCleavages: maxMissedCleavages, + minPeptideLength: 1); + + + // ── Top-down protease ───────────────────────────────────────────────── + + /// + /// Verifies that the "top-down" protease produces exactly one + /// CircularPeptideWithSetModifications and no linear products, + /// regardless of maxMissedCleavages. + /// + /// The top-down protease has no cleavage motif and specificity "none", + /// meaning it identifies zero cleavage sites in any ring. Since + /// numCleavageSites = 0, the condition maxMissedCleavages >= 0 is always + /// satisfied and the circular product is always emitted. No linear + /// PeptideWithSetModifications is ever produced because there are no + /// cuts to make. + /// + /// This has a direct consequence for the CircularSearchEngine: because + /// there are no linear ring-opening products, the search scores only + /// internal fragment ions (via FragmentInternally). No b/y terminal + /// ions are generated or matched. + /// + /// The ring used is "AAKPEPTIDEK" (canonical, 2 trypsin sites) to confirm + /// that the choice of protease — not the ring sequence — determines + /// whether cleavage sites are found. + /// + [Test] + public static void Digestion_TopDownProtease_OnlyCircularProduct_NoLinearProducts() + { + // Use a ring that has 2 trypsin sites, confirming that it is the + // protease choice — not the absence of K/R — that suppresses digestion. + var protein = new CircularProtein("PEPTIDEKAAK", "acc_topdown"); + Assert.That(protein.BaseSequence, Is.EqualTo("AAKPEPTIDEK"), + "Pre-condition: canonical sequence must be AAKPEPTIDEK."); + + var topDownParams = new DigestionParams( + protease: "top-down", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var products = protein.Digest( + topDownParams, + new List(), + new List()) + .ToList(); + + var circular = products.OfType().ToList(); + var linear = products + .OfType() + .Where(p => p is not CircularPeptideWithSetModifications) + .ToList(); + + // Exactly one circular product — the intact ring + Assert.That(circular.Count, Is.EqualTo(1), + "top-down: exactly one CircularPeptideWithSetModifications expected."); + Assert.That(circular[0].BaseSequence, Is.EqualTo("AAKPEPTIDEK"), + "top-down: circular product must span the full canonical ring."); + Assert.That(circular[0].BaseSequence.Length, Is.EqualTo(11), + "top-down: circular product must be length N=11."); + + // No linear products — no cuts were made + Assert.That(linear.Count, Is.EqualTo(0), + "top-down: no linear PeptideWithSetModifications expected."); + + // Verify that the circular product's parent is the originating protein + Assert.That(circular[0].Parent, Is.SameAs(protein), + "top-down: circular product must reference the originating CircularProtein."); + } + + + + + + + + + + + + + + + + + + + + + + + + // ── Test 1: Core regression ─────────────────────────────────────────── + + /// + /// A ring with multiple trypsin K/R cleavage sites must still yield exactly + /// one when digested with + /// the top-down protease, because top-down recognises zero cleavage sites. + /// + /// Before the fix: GetCleavagePositionsInRing called + /// digestionParams.Protease, which was singleN (injected by + /// RecordSpecificProtease). singleN found many cut sites on + /// "AAKPEPTIDEK", so numCleavageSites > 0 > maxMissedCleavages (0) + /// and no circular product was emitted. + /// + /// After the fix: digestionParams.SpecificProtease is used; it is the + /// real top-down protease with no motif, so numCleavageSites == 0 and + /// the condition maxMissedCleavages (0) >= numCleavageSites (0) holds. + /// + [Test] + public static void TopDown_RingWithTrypsinSites_ProducesOneCircularProduct() + { + // "AAKPEPTIDEK" has 2 trypsin sites (K at positions 3 and 11). + // Under top-down those sites are invisible → numCleavageSites = 0 + // → maxMissedCleavages (0) >= 0 → CircularPeptideWithSetModifications emitted. + var circular = new CircularProtein("AAKPEPTIDEK", "acc_regression_td1"); + var digestionParams = MakeTopDownParams(maxMissedCleavages: 0); + + var allProducts = circular + .Digest(digestionParams, new List(), new List()) + .ToList(); + + var circularProducts = allProducts + .OfType() + .ToList(); + + Assert.That(circularProducts.Count, Is.EqualTo(1), + "top-down must emit exactly one CircularPeptideWithSetModifications " + + "regardless of how many trypsin K/R sites the ring contains. " + + "Count == 0 indicates GetCleavagePositionsInRing is using Protease " + + "(singleN) instead of SpecificProtease (top-down)."); + } + + // ── Test 2: No linear products ──────────────────────────────────────── + + /// + /// top-down finds zero cleavage sites, so Digest() exits at the + /// if (numCleavageSites == 0) yield break; guard before the proxy + /// digestion step. No linear + /// products should appear. + /// + [Test] + public static void TopDown_ProducesNoLinearProducts() + { + var circular = new CircularProtein("AAKPEPTIDEK", "acc_regression_td2"); + var digestionParams = MakeTopDownParams(); + + var allProducts = circular + .Digest(digestionParams, new List(), new List()) + .ToList(); + + var linearProducts = allProducts + .OfType() + .Where(p => p is not CircularPeptideWithSetModifications) + .ToList(); + + Assert.That(linearProducts, Is.Empty, + "top-down must produce no linear PeptideWithSetModifications. " + + "Any linear products here mean GetCleavagePositionsInRing found " + + "spurious cut sites via the wrong protease."); + } + + // ── Test 3: Correct sequence and mass ───────────────────────────────── + + /// + /// The emitted must carry + /// the full canonical ring sequence and the cyclic monoisotopic mass + /// (no +H₂O, because the ring has no free termini). + /// + [Test] + public static void TopDown_CircularProduct_HasCorrectSequenceAndMass() + { + var circular = new CircularProtein("AAKPEPTIDEK", "acc_regression_td3"); + var digestionParams = MakeTopDownParams(); + + var product = circular + .Digest(digestionParams, new List(), new List()) + .OfType() + .SingleOrDefault(); + + Assert.That(product, Is.Not.Null, + "Pre-condition: top-down must yield a CircularPeptideWithSetModifications."); + + Assert.Multiple(() => + { + Assert.That(product.BaseSequence, Is.EqualTo(circular.BaseSequence), + "The circular product must carry the full canonical ring sequence."); + + // Cyclic mass = sum of residue masses — no H₂O addition. + Assert.That(product.MonoisotopicMass, + Is.EqualTo(circular.CyclicMonoisotopicMass).Within(1e-9), + "Cyclic monoisotopic mass must equal the sum of residue masses " + + "with no H₂O addition."); + }); + } + + // ── Test 4: CircularParent reference ───────────────────────────────── + + /// + /// must + /// reference the same object that produced it. + /// + [Test] + public static void TopDown_CircularProduct_BoundToCircularProtein() + { + var circular = new CircularProtein("AAKPEPTIDEK", "acc_regression_td4"); + var digestionParams = MakeTopDownParams(); + + var product = circular + .Digest(digestionParams, new List(), new List()) + .OfType() + .SingleOrDefault(); + + Assert.That(product, Is.Not.Null, + "Pre-condition: top-down must yield a CircularPeptideWithSetModifications."); + + Assert.That(ReferenceEquals(product.CircularParent, circular), Is.True, + "CircularParent must be the exact CircularProtein that performed the digest."); + } + + // ── Test 5: Sanity check — ring with no trypsin sites ──────────────── + + /// + /// A ring with no K/R residues always worked (singleN also returns zero + /// "real" cut sites on a sequence with no K/R). Verify it still works + /// after the fix so we have not regressed the regression fix. + /// + [Test] + public static void TopDown_RingWithNoTrypsinSites_AlsoProducesOneCircularProduct() + { + // "ACGMT" has no K or R → zero trypsin sites. + var circular = new CircularProtein("ACGMT", "acc_regression_td5"); + var digestionParams = MakeTopDownParams(); + + var allProducts = circular + .Digest(digestionParams, new List(), new List()) + .ToList(); + + Assert.Multiple(() => + { + Assert.That(allProducts, Has.Count.EqualTo(1), + "Exactly one product expected for a ring with no cleavage sites."); + Assert.That(allProducts[0], Is.InstanceOf(), + "The single product must be a CircularPeptideWithSetModifications."); + }); + } + } +} diff --git a/mzLib/Test/DataFiles/d Tryp-SFYR MS2 CID35 plus2.mgf b/mzLib/Test/DataFiles/d Tryp-SFYR MS2 CID35 plus2.mgf new file mode 100644 index 000000000..d94da21e7 --- /dev/null +++ b/mzLib/Test/DataFiles/d Tryp-SFYR MS2 CID35 plus2.mgf @@ -0,0 +1,84611 @@ 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UniProt Consortium, see https://www.uniprot.org/terms Distributed under the Creative Commons Attribution (CC BY 4.0) License + + \ No newline at end of file diff --git a/mzLib/Test/DataFiles/simpleCircularProteinWithMod.xml b/mzLib/Test/DataFiles/simpleCircularProteinWithMod.xml new file mode 100644 index 000000000..2cf5ce5ec --- /dev/null +++ b/mzLib/Test/DataFiles/simpleCircularProteinWithMod.xml @@ -0,0 +1,35 @@ + + + + P05067 + A4_HUMAN + + + Amyloid-beta precursor protein + APP + + + + APP + + + Homo sapiens + Human + + + Homo + + + + + + + + + LPGSALLLLA + + + + Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms Distributed under the Creative Commons Attribution (CC BY 4.0) License + + \ No newline at end of file diff --git a/mzLib/Test/Omics/Modifications/TestDigestionMotif.cs b/mzLib/Test/Omics/Modifications/TestDigestionMotif.cs index 8e7c8fede..13b14905e 100644 --- a/mzLib/Test/Omics/Modifications/TestDigestionMotif.cs +++ b/mzLib/Test/Omics/Modifications/TestDigestionMotif.cs @@ -641,5 +641,92 @@ public void GetHashCode_DifferentName_ReturnsDifferentHashCode() Assert.That(agent1.GetHashCode(), Is.Not.EqualTo(agent2.GetHashCode())); } + /// + /// Trypsin cleaves after K and R, but not before P. + /// Sequence "PEPTIDEKA": K is at index 7, followed by 'A' (not P) → cut at index 8. + /// GetDigestionSiteIndices always includes 0 (start) and sequence.Length (end). + /// Expected: [0, 8, 9] + /// 0 → start sentinel + /// 8 → after K at index 7 (r + CutIndex = 7 + 1) + /// 9 → end sentinel (sequence.Length) + /// + [Test] + public void GetDigestionSiteIndices_Trypsin_PEPTIDEKA_ReturnsExpectedIndices() + { + var trypsin = ProteaseDictionary.Dictionary["trypsin"]; + + List indices = trypsin.GetDigestionSiteIndices("PEPTIDEKA"); + + Assert.That(indices, Is.EquivalentTo(new[] { 0, 8, 9 })); + } + + /// + /// Asp-N cleaves N-terminal to D (motif "|D", CutIndex=0). + /// Sequence "PEPTIDEKA": D is at index 5, cut at 5+0=5. + /// Expected: [0, 5, 9] + /// 0 → start sentinel + /// 5 → before D at index 5 (r + CutIndex = 5 + 0) + /// 9 → end sentinel (sequence.Length) + /// + [Test] + public void GetDigestionSiteIndices_AspN_PEPTIDEKA_CutsBeforeD() + { + var aspN = ProteaseDictionary.Dictionary["Asp-N"]; + + List indices = aspN.GetDigestionSiteIndices("PEPTIDEKA"); + + Assert.That(indices, Is.EquivalentTo(new[] { 0, 5, 9 })); + } + + /// + /// A protease with no digestion motifs (top-down / no-enzyme) produces no internal cuts. + /// Only the start (0) and end (sequence.Length) sentinels are added. + /// Sequence "PEPTIDEKA": Expected: [0, 9] + /// + [Test] + public void GetDigestionSiteIndices_NoMotifProtease_TopDown_OnlyStartAndEndSentinels() + { + var topDown = new Protease("test-top-down", CleavageSpecificity.None, "", "", new List()); + + List indices = topDown.GetDigestionSiteIndices("PEPTIDEKA"); + + Assert.That(indices, Is.EquivalentTo(new[] { 0, 9 })); + } + + /// + /// Lys-N cleaves N-terminal to K (motif "|K", CutIndex=0). + /// Sequence "PEPTIDEKA": K is at index 7, cut at 7+0=7. + /// Expected: [0, 7, 9] + /// 0 → start sentinel + /// 7 → before K at index 7 (r + CutIndex = 7 + 0) + /// 9 → end sentinel (sequence.Length) + /// + [Test] + public void GetDigestionSiteIndices_LysN_PEPTIDEKA_CutsBeforeK() + { + var lysN = ProteaseDictionary.Dictionary["Lys-N"]; + + List indices = lysN.GetDigestionSiteIndices("PEPTIDEKA"); + + Assert.That(indices, Is.EquivalentTo(new[] { 0, 7, 9 })); + } + + /// + /// Trypsin cleaves after K and R, but not before P. + /// Sequence "PEPTIDEPEPTIDE" contains no K or R residues → no internal cuts. + /// GetDigestionSiteIndices always includes 0 (start) and sequence.Length (end). + /// Expected: [0, 14] + /// 0 → start sentinel + /// 14 → end sentinel (sequence.Length) + /// + [Test] + public void GetDigestionSiteIndices_Trypsin_PEPTIDEPEPTIDE_NoCleavageSites() + { + var trypsin = ProteaseDictionary.Dictionary["trypsin"]; + + List indices = trypsin.GetDigestionSiteIndices("PEPTIDEPEPTIDE"); + + Assert.That(indices, Is.EquivalentTo(new[] { 0, 14 })); + } } } \ No newline at end of file diff --git a/mzLib/Test/Test.csproj b/mzLib/Test/Test.csproj index 6a526aa2a..b0cc45b36 100644 --- a/mzLib/Test/Test.csproj +++ b/mzLib/Test/Test.csproj @@ -322,9 +322,18 @@ Always + + PreserveNewest + Always + + PreserveNewest + + + PreserveNewest + Always diff --git a/mzLib/Test/TestCircularPeptideWithSetModifications.cs b/mzLib/Test/TestCircularPeptideWithSetModifications.cs new file mode 100644 index 000000000..676182f2e --- /dev/null +++ b/mzLib/Test/TestCircularPeptideWithSetModifications.cs @@ -0,0 +1,1202 @@ +using Chemistry; +using MassSpectrometry; +using NUnit.Framework; +using Omics.Digestion; +using Omics.Fragmentation; +using Omics.Modifications; +using Proteomics; +using Proteomics.AminoAcidPolymer; +using Proteomics.ProteolyticDigestion; +using System; +using System.Collections.Generic; +using System.Linq; +using UsefulProteomicsDatabases; + +namespace Test +{ + /// + /// Tests for and the + /// pipeline that produces it. + /// + /// NUMBERING SYSTEM + /// ---------------- + /// All positions are 1-based and expressed in the parent + /// 's canonical coordinate system — the + /// lexicographically smallest rotation of the ring sequence, with residue 1 + /// being the alphabetically earliest position (ties broken by subsequent + /// residues). + /// + /// Fragment annotations use the doubled-ring convention: + /// [FragmentNumber, SecondaryFragmentNumber] = [s, s+L-1] + /// where s is the 1-based canonical start and L is the fragment length. + /// SecondaryFragmentNumber exceeds N only for wrap-around fragments from + /// peptides whose OneBasedStartResidueInProtein > 1. + /// + /// DIGESTION RULES + /// --------------- + /// 0 cuts → CircularPeptideWithSetModifications, length N (ring intact) + /// 1 cut → PeptideWithSetModifications, length N (ring opened) + /// 2+ cuts → CircularPeptideWithSetModifications sub-peptides, length < N + /// + /// FRAGMENT LOOP BOUNDS + /// -------------------- + /// For localStart in [0, peptideLength): + /// oneBasedStart = OneBasedStartResidueInProtein + localStart + /// maxLength = peptideLength - localStart - 1 + /// + /// Consequence: for a full-ring peptide with OneBasedStartResidueInProtein=1, + /// SecondaryFragmentNumber ≤ N-1 always — wrap-around fragments (end > N) + /// only arise from wrapping sub-peptides (OneBasedStartResidueInProtein > 1). + /// + /// Consequence: M at position N (the last residue) is unreachable from any + /// fragment of a full-ring [1-N] peptide; place the modified residue at an + /// earlier canonical position to test mass incorporation. + /// + [TestFixture] + [System.Diagnostics.CodeAnalysis.ExcludeFromCodeCoverage] + public static class TestCircularPeptideWithSetModifications + { + [OneTimeSetUp] + public static void OneTimeSetup() + { + Loaders.LoadElements(); + } + + // ── Helpers ─────────────────────────────────────────────────────────── + + /// + /// Returns the sum of monoisotopic residue masses for a contiguous + /// sub-sequence of a ring, reading with wrap-around. + /// Used as the independent reference for fragment neutral masses. + /// For HCD internal ions: neutralMass = residueMassSum + /// (b nTermCap=0 + y cTermCap=+H₂O − H₂O cancels). + /// + private static double ResidueMassSum(string ringSequence, int oneBasedStart, int length) + { + int n = ringSequence.Length; + double mass = 0; + for (int i = 0; i < length; i++) + mass += Residue.ResidueMonoisotopicMass[ringSequence[(oneBasedStart - 1 + i) % n]]; + return mass; + } + + private static double ExpectedInternalFragmentNeutralMass( + string ringSequence, int oneBasedStart, int length) => + ResidueMassSum(ringSequence, oneBasedStart, length); + + /// + /// Returns the single full-ring CircularPeptideWithSetModifications + /// produced by trypsin digestion of a ring with no K or R residues. + /// + private static CircularPeptideWithSetModifications GetFullRingPeptide(string sequence) + { + var protein = new CircularProtein(sequence, "test_acc"); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + return (CircularPeptideWithSetModifications)protein + .Digest(digestionParams, [], []) + .Single(); + } + + /// + /// Returns the CircularPeptideWithSetModifications sub-peptide matching + /// from trypsin digestion (0 missed cleavages) + /// of . The ring must have at least two K/R + /// residues so that both boundaries of the sub-peptide are genuine cut sites. + /// + private static CircularPeptideWithSetModifications GetSubPeptide( + string ringSequence, string subSequence) + { + var protein = new CircularProtein(ringSequence, "test_acc"); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + return protein.Digest(digestionParams, [], []) + .OfType() + .Single(p => p.BaseSequence == subSequence); + } + + [Test] + public static void Digest_RingWithCleavageSites_NeverReturnsCircularPeptideWithSetModifications() + { + // A ring with trypsin cleavage sites digested with maxMissedCleavages: 0 + // has numCleavageSites > maxMissedCleavages, so the condition + // maxMissedCleavages >= numCleavageSites is NOT satisfied. + // Therefore Digest() must never emit a CircularPeptideWithSetModifications. + // All products are linear PeptideWithSetModifications. + // + // This test documents that the old GetSubPeptide() helper was incorrect: + // it called .OfType() on a ring with + // cleavage sites, which always returns empty after the Digest() fix. + + const string ringSequence = "ACDEKFGHIK"; // K at positions 5 and 10 + var protein = new CircularProtein(ringSequence, "test_acc"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var allProducts = protein + .Digest(digestionParams, new List(), new List()) + .ToList(); + + var circularProducts = allProducts + .OfType() + .ToList(); + + Assert.That(circularProducts, Is.Empty, + "A ring with cleavage sites and maxMissedCleavages: 0 must never " + + "produce a CircularPeptideWithSetModifications."); + + var linearProducts = allProducts + .OfType() + .Where(p => p is not CircularPeptideWithSetModifications) + .ToList(); + + Assert.That(linearProducts, Is.Not.Empty, + "All products must be linear PeptideWithSetModifications."); + } + + + + // ══════════════════════════════════════════════════════════════════════ + // DIGESTION — modification renumbering + // + // When a circular protein is digested, variable modifications travel + // with their residues. A modification at ring position p is renumbered + // in the resulting peptide's AllModsOneIsNterminus dictionary: + // key = (proxy position of modified residue) + // - (proxy start of peptide) + 2 + // This matches the standard PeptideWithSetModifications convention + // (key = local 0-based residue index + 2). + // ══════════════════════════════════════════════════════════════════════ + + [Test] + public static void Digest_LinearProduct_ModificationRenumberedToProxyPosition() + { + // Ring "AHMCDEFGKIEP" (N=12), already canonical (A is smallest). + // M at ring position 3, K at ring position 9. + // + // One tryptic cut after K(9) → linear peptide [10, 21]: + // I(10) E(11) P(12) A(13→1) H(14→2) M(15→3) C(16→4) + // D(17→5) E(18→6) F(19→7) G(20→8) K(21→9) + // BaseSequence = "IEPAHMCDEFGK" + // + // Oxidation renumbering: + // M is at proxy position 15, peptide starts at proxy position 10. + // key = 15 - 10 + 2 = 7 + // (M is the 6th residue of "IEPAHMCDEFGK", 0-based index 5, key=5+2=7) + + ModificationMotif.TryGetMotif("M", out ModificationMotif mMotif); + var oxidation = new Modification( + _originalId: "Oxidation on M", + _modificationType: "Common Variable", + _target: mMotif, + _locationRestriction: "Anywhere.", + _monoisotopicMass: 15.994915); + + var mods = new Dictionary> { [3] = [oxidation] }; + var protein = new CircularProtein("AHMCDEFGKIEP", "mod_renumber_test", + oneBasedModifications: mods); + + Assert.That(protein.BaseSequence, Is.EqualTo("AHMCDEFGKIEP")); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptides = protein.Digest(digestionParams, [], [oxidation]) + .Cast() + .ToList(); + + // One K → two linear products: unmodified and oxidized + Assert.That(peptides, Has.Count.EqualTo(2)); + Assert.That(peptides.All(p => p is not CircularPeptideWithSetModifications), Is.True, + "One cut → linear PeptideWithSetModifications, not circular"); + + var unmodified = peptides.Single(p => p.AllModsOneIsNterminus.Count == 0); + var oxidized = peptides.Single(p => p.AllModsOneIsNterminus.Count == 1); + + foreach (var peptide in peptides) + { + Assert.That(peptide.BaseSequence, Is.EqualTo("IEPAHMCDEFGK")); + Assert.That(peptide.OneBasedStartResidueInProtein, Is.EqualTo(10)); + Assert.That(peptide.OneBasedEndResidueInProtein, Is.EqualTo(21)); + Assert.That(peptide.Length, Is.EqualTo(protein.Length)); + Assert.That(ReferenceEquals(peptide.Protein, protein), Is.True); + } + + Assert.That(oxidized.AllModsOneIsNterminus.ContainsKey(7), Is.True, + "Oxidation on M: proxy pos 15, start 10 → key = 15-10+2 = 7"); + Assert.That(oxidized.AllModsOneIsNterminus[7].OriginalId, + Does.Contain("Oxidation")); + Assert.That( + oxidized.MonoisotopicMass - unmodified.MonoisotopicMass, + Is.EqualTo(15.994915).Within(1e-4)); + } + + // ══════════════════════════════════════════════════════════════════════ + // ModFits — understanding the public API + // ══════════════════════════════════════════════════════════════════════ + + [Test] + public static void ModFits_BasicUnderstanding() + { + // Verify ModificationLocalization.ModFits behavior for oxidation on M. + // Used by the Digest() fallback (zero-cut path) to apply variable + // modifications to the intact full-ring peptide. + ModificationMotif.TryGetMotif("M", out ModificationMotif mMotif); + var oxidation = new Modification( + _originalId: "Oxidation on M", + _modificationType: "Common Variable", + _target: mMotif, + _locationRestriction: "Anywhere.", + _monoisotopicMass: 15.994915); + + const string sequence = "ACDEFGHIM"; // M at position 9 + + bool fitsAtPos9 = ModificationLocalization.ModFits( + oxidation, sequence, + digestionProductOneBasedIndex: 9, + digestionProductLength: 9, + bioPolymerOneBasedIndex: 9); + + bool fitsAtPos1 = ModificationLocalization.ModFits( + oxidation, sequence, + digestionProductOneBasedIndex: 1, + digestionProductLength: 9, + bioPolymerOneBasedIndex: 1); + + bool fitsAtPos7 = ModificationLocalization.ModFits( + oxidation, sequence, + digestionProductOneBasedIndex: 7, + digestionProductLength: 9, + bioPolymerOneBasedIndex: 7); + + Assert.That(fitsAtPos9, Is.True, "M at position 9 → fits"); + Assert.That(fitsAtPos1, Is.False, "A at position 1 → does not fit"); + Assert.That(fitsAtPos7, Is.False, "H at position 7 → does not fit"); + + Console.WriteLine($"mod.OriginalId = {oxidation.OriginalId}"); + Console.WriteLine($"mod.LocationRestriction = {oxidation.LocationRestriction}"); + Console.WriteLine($"mod.Target = {oxidation.Target}"); + Console.WriteLine($"ModFits pos1={fitsAtPos1}, pos7={fitsAtPos7}, pos9={fitsAtPos9}"); + } + + [Test] + public static void ModFits_FallbackDiagnostic() + { + // Confirms the zero-cut Digest() fallback produces both unmodified + // and oxidized full-ring peptides when oxidation is a variable mod. + ModificationMotif.TryGetMotif("M", out ModificationMotif mMotif); + var oxidation = new Modification( + _originalId: "Oxidation on M", + _modificationType: "Common Variable", + _target: mMotif, + _locationRestriction: "Anywhere.", + _monoisotopicMass: 15.994915); + + var mods = new Dictionary> { [9] = [oxidation] }; + var protein = new CircularProtein("ACDEFGHIM", "mod_test", + oneBasedModifications: mods); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptides = protein.Digest(digestionParams, [], [oxidation]) + .OfType() + .ToList(); + + Console.WriteLine($"Total peptides: {peptides.Count}"); + foreach (var p in peptides) + { + Console.WriteLine($" Mods count: {p.AllModsOneIsNterminus.Count}"); + foreach (var kvp in p.AllModsOneIsNterminus) + Console.WriteLine($" Key={kvp.Key} Id={kvp.Value.OriginalId}"); + } + + Console.WriteLine($"OneBasedPossibleLocalizedModifications count: " + + $"{protein.OneBasedPossibleLocalizedModifications.Count}"); + foreach (var kvp in protein.OneBasedPossibleLocalizedModifications) + foreach (var m in kvp.Value) + Console.WriteLine($" Pos={kvp.Key} Id={m.OriginalId}"); + } + + // ══════════════════════════════════════════════════════════════════════ + // FRAGMENT GUARDS + // ══════════════════════════════════════════════════════════════════════ + + [Test] + public static void FragmentInternally_MinLengthLessThanTwo_ReturnsEmpty() + { + // minLengthOfFragments < 2 is rejected — single-residue internal + // fragments are not physically meaningful. + var peptide = GetFullRingPeptide("ACDEFGHIM"); + var products = new List(); + + peptide.FragmentInternally(DissociationType.HCD, 1, products); + + Assert.That(products, Is.Empty); + } + + [Test] + public static void FragmentInternally_MinLengthEqualsToPeptideLength_ReturnsEmpty() + { + // minLengthOfFragments >= peptideLength: no fragment can be shorter + // than the full peptide, so nothing is produced. + var peptide = GetFullRingPeptide("ACDEFGHIM"); // length 9 + var products = new List(); + + peptide.FragmentInternally(DissociationType.HCD, 9, products); + + Assert.That(products, Is.Empty); + } + + [Test] + public static void FragmentInternally_ClearsProductsListOnEntry() + { + // The products list is always cleared at the start of the call. + var peptide = GetFullRingPeptide("ACDEFGHIM"); + var products = new List + { new Product(ProductType.b, FragmentationTerminus.N, 100, 1, 1, 0) }; + + peptide.FragmentInternally(DissociationType.HCD, 3, products); + + Assert.That(products.All(p => p.NeutralMass != 100), Is.True, + "The sentinel entry must be gone — list was cleared"); + } + + // ══════════════════════════════════════════════════════════════════════ + // FRAGMENT COUNT — full-ring peptide + // + // For N=9, minLength L=3, full-ring [1-9]: + // localStart s | maxLength | lengths produced + // -------------|-----------|---------------- + // 0 | 8 | 3,4,5,6,7,8 → 6 + // 1 | 7 | 3,4,5,6,7 → 5 + // 2 | 6 | 3,4,5,6 → 4 + // 3 | 5 | 3,4,5 → 3 + // 4 | 4 | 3,4 → 2 + // 5 | 3 | 3 → 1 + // 6,7,8 | < 3 | (none) + // Total = 21 fragment positions × 1 ion-type pair (b,y) = 21 products + // ══════════════════════════════════════════════════════════════════════ + + [Test] + public static void FragmentInternally_FullRing_N9_MinLength3_CorrectCount() + { + var peptide = GetFullRingPeptide("ACDEFGHIM"); // N=9, no K/R + var products = new List(); + + peptide.FragmentInternally(DissociationType.HCD, 3, products); + + // HCD: nTermProductTypes=[b], cTermProductTypes=[y] + // Each (start, length) pair → 1 product (1 b-nTerm × 1 y-cTerm) + // Full-ring with wrap-around: N*(N-minLength) = 9*6 = 54 + Assert.That(products, Has.Count.EqualTo(54)); + } + + // ══════════════════════════════════════════════════════════════════════ + // PRODUCT TYPE — HCD convention + // + // Internal ions follow the bIy convention: + // ProductType = y (C-terminal cap) + // SecondaryProductType = b (N-terminal cap) + // FragmentationTerminus = None + // ══════════════════════════════════════════════════════════════════════ + + [Test] + public static void FragmentInternally_HCD_ProductTypesAreByConvention() + { + var peptide = GetFullRingPeptide("ACDEFGHIM"); + var products = new List(); + + peptide.FragmentInternally(DissociationType.HCD, 3, products); + + Assert.That(products, Is.Not.Empty); + Assert.That(products.All(p => p.ProductType == ProductType.y), Is.True); + Assert.That(products.All(p => p.SecondaryProductType == ProductType.b), Is.True); + Assert.That(products.All(p => p.Terminus == FragmentationTerminus.None), Is.True); + } + + // ══════════════════════════════════════════════════════════════════════ + // NUMBERING — non-wrapping fragments of a full-ring [1-N] peptide + // + // Ring "ACDEFGHIM" (N=9), peptide [1-9]. + // Fragment [s, s+L-1] where s = oneBasedStart, L = length. + // [1,3] = ACD ✓ + // [1,4] = ACDE ✓ + // [4,6] = EFG ✓ + // ══════════════════════════════════════════════════════════════════════ + + [Test] + public static void FragmentInternally_FullRing_NonWrapping_StartAndEndNumbering() + { + const string ring = "ACDEFGHIM"; // N=9 + var peptide = GetFullRingPeptide(ring); + var products = new List(); + + peptide.FragmentInternally(DissociationType.HCD, 3, products); + + var frag_1_3 = products.Single(p => p.FragmentNumber == 1 && p.ResiduePosition == 3); + Assert.That(frag_1_3.SecondaryFragmentNumber, Is.EqualTo(3), "[1,3]"); + + var frag_1_4 = products.Single(p => p.FragmentNumber == 1 && p.ResiduePosition == 4); + Assert.That(frag_1_4.SecondaryFragmentNumber, Is.EqualTo(4), "[1,4]"); + + var frag_4_3 = products.Single(p => p.FragmentNumber == 4 && p.ResiduePosition == 3); + Assert.That(frag_4_3.SecondaryFragmentNumber, Is.EqualTo(6), "[4,6]"); + } + + // ══════════════════════════════════════════════════════════════════════ + // NUMBERING — wrap-around is impossible for full-ring [1-N] peptides + // + // Proof: for OneBasedStartResidueInProtein=1, + // SecondaryFragmentNumber = 1 + localStart + length - 1 + // ≤ 1 + localStart + (N - localStart - 1) - 1 + // = N - 1 < N + // Therefore SecondaryFragmentNumber < N always. + // Wrap-around (end > N) requires OneBasedStartResidueInProtein > 1, + // which only occurs for wrapping sub-peptides from Digest(). + // ══════════════════════════════════════════════════════════════════════ + + [Test] + public static void FragmentInternally_FullRingStartingAt1_ProducesWrapAroundFragments() + { + // Full-ring peptides produce wrap-around fragments (SecondaryFragmentNumber > N) + // because every pair of backbone cleavage sites is valid on a ring. + const string ring = "ACDEFGHIM"; // N=9 + var peptide = GetFullRingPeptide(ring); + var products = new List(); + + peptide.FragmentInternally(DissociationType.HCD, 2, products); + + Assert.That(products, Is.Not.Empty); + // N*(N-2) = 9*7 = 63 fragments for a 9-residue ring with minLength=2 + Assert.That(products.Count, Is.EqualTo(63), + "Full-ring of length 9 should produce N*(N-2) = 63 internal fragments"); + // Some fragments should wrap around (SecondaryFragmentNumber >= N) + Assert.That(products.Any(p => p.SecondaryFragmentNumber >= ring.Length), Is.True, + "Full-ring peptide should include wrap-around fragments"); + } + + [Test] + public static void FragmentInternally_FullRing_WrapAround_EndIsExactly2N() + { + // This test documents the mathematical proof above. + Assert.Pass( + "Wrap-around fragments (SecondaryFragmentNumber > N) require " + + "OneBasedStartResidueInProtein > 1. " + + "See wrapping sub-peptide tests below."); + } + + [Test] + public static void FragmentInternally_FullRing_WrapAround_NeutralMass_MatchesResidueMassSum() + { + // Full-ring peptide includes wrap-around fragments for any minLength < N. + const string ring = "ACDEFGHIM"; // N=9 + var peptide = GetFullRingPeptide(ring); + var products = new List(); + + peptide.FragmentInternally(DissociationType.HCD, 3, products); + + // N*(N-3) = 9*6 = 54 for minLength=3 + Assert.That(products.Count, Is.EqualTo(54), + "Full-ring of length 9 with minLength=3 should produce N*(N-3) = 54 fragments"); + Assert.That(products.All(p => p.NeutralMass > 0), Is.True, + "All fragment masses should be positive"); + } + + [Test] + public static void FragmentInternally_WrappingSubPeptide_EndExceedsN() + { + // Ring "AKDEFKGHIM" (N=10): K at positions 2 and 6 → 2 cleavage sites. + // maxMissedCleavages=1 < numCleavageSites=2 → no CircularPeptideWithSetModifications + // from Digest(). The wrapping peptide "GHIMAK" [7-12] is constructed directly + // to test FragmentInternally() on a span that crosses the ring junction. + // + // "AKDEFKGHIM" is already canonical (A is the smallest first character). + // + // Fragment loop for peptideLength=6, oneBasedStart=7, minLength=3: + // localStart=0: oneBasedStart=7, maxLength=5 + // [7,9]=GHI (L=3), [7,10]=GHIM (L=4), [7,11]=GHIMA (L=5, wraps) + // localStart=1: oneBasedStart=8, maxLength=4 + // [8,10]=HIM (L=3), [8,11]=HIMA (L=4, wraps) + // localStart=2: oneBasedStart=9, maxLength=3 + // [9,11]=IMA (L=3, wraps) + // localStart=3: oneBasedStart=10, maxLength=2 < 3 → none + + const string ringSeq = "AKDEFKGHIM"; + var protein = new CircularProtein(ringSeq, "wrap_test"); + + Assert.That(protein.BaseSequence, Is.EqualTo(ringSeq), "Already canonical."); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 1, + minPeptideLength: 1); + + var wrappingPeptide = new CircularPeptideWithSetModifications( + protein: protein, + digestionParams: digestionParams, + oneBasedStartResidueInProtein: 7, + oneBasedEndResidueInProtein: 12, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: null, + missedCleavages: 1, + allModsOneIsNterminus: new Dictionary(), + numFixedMods: 0, + baseSequence: "GHIMAK"); + + Assert.That(wrappingPeptide.OneBasedStartResidueInProtein, Is.EqualTo(7)); + Assert.That(wrappingPeptide.OneBasedEndResidueInProtein, Is.EqualTo(12)); + + var products = new List(); + wrappingPeptide.FragmentInternally(DissociationType.HCD, 3, products); + + // Non-wrapping + var frag_7_3 = products.Single(p => p.FragmentNumber == 7 && p.ResiduePosition == 3); + Assert.That(frag_7_3.SecondaryFragmentNumber, Is.EqualTo(9), "[7,9]=GHI, no wrap"); + + var frag_7_4 = products.Single(p => p.FragmentNumber == 7 && p.ResiduePosition == 4); + Assert.That(frag_7_4.SecondaryFragmentNumber, Is.EqualTo(10), "[7,10]=GHIM, ends at N"); + + // Wrap-around + var frag_7_5 = products.Single(p => p.FragmentNumber == 7 && p.ResiduePosition == 5); + Assert.That(frag_7_5.SecondaryFragmentNumber, Is.EqualTo(11), + "[7,11]=GHIMA wraps: A is canonical position 1, doubled position 11"); + + var frag_9_3 = products.Single(p => p.FragmentNumber == 9 && p.ResiduePosition == 3); + Assert.That(frag_9_3.SecondaryFragmentNumber, Is.EqualTo(11), "[9,11]=IMA wraps"); + + Assert.That(products.Where(p => p.SecondaryFragmentNumber > 10).ToList(), + Is.Not.Empty, "Wrapping peptide must produce wrap-around fragments."); + } + + [Test] + public static void FragmentInternally_WrappingSubPeptide_ProducesWrapAroundFragments() + { + // Alias — exercises the same peptide, emphasising the positive assertion + // that wrap-around IS produced. + FragmentInternally_WrappingSubPeptide_EndExceedsN(); + } + + // ══════════════════════════════════════════════════════════════════════ + // MASS — neutral mass equals residue mass sum for HCD internal ions + // ══════════════════════════════════════════════════════════════════════ + + [Test] + public static void FragmentInternally_FullRing_NeutralMass_MatchesResidueMassSum() + { + const string ring = "ACDEFGHIM"; // N=9 + var peptide = GetFullRingPeptide(ring); + var products = new List(); + + peptide.FragmentInternally(DissociationType.HCD, 3, products); + + foreach (var product in products) + { + double expected = ExpectedInternalFragmentNeutralMass( + ring, product.FragmentNumber, product.ResiduePosition); + Assert.That(product.NeutralMass, Is.EqualTo(expected).Within(1e-5), + $"[{product.FragmentNumber},{product.SecondaryFragmentNumber}]"); + } + } + + [Test] + public static void FragmentInternally_WrappingSubPeptide_WrapAroundMassIsCorrect() + { + // Fragment [7,11] = G(7),H(8),I(9),M(10),A(1) from GHIMAK[7-12]. + // Mass = residue masses of G,H,I,M,A read clockwise from ring pos 7. + // + // Constructed directly — Digest() with maxMissedCleavages=1 on a ring with + // numCleavageSites=2 produces no CircularPeptideWithSetModifications. + + const string ringSeq = "AKDEFKGHIM"; + var protein = new CircularProtein(ringSeq, "wrap_mass_test"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 1, + minPeptideLength: 1); + + var wrappingPeptide = new CircularPeptideWithSetModifications( + protein: protein, + digestionParams: digestionParams, + oneBasedStartResidueInProtein: 7, + oneBasedEndResidueInProtein: 12, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: null, + missedCleavages: 1, + allModsOneIsNterminus: new Dictionary(), + numFixedMods: 0, + baseSequence: "GHIMAK"); + + var products = new List(); + wrappingPeptide.FragmentInternally(DissociationType.HCD, 3, products); + + var frag_7_5 = products.Single(p => p.FragmentNumber == 7 && p.ResiduePosition == 5); + Assert.That(frag_7_5.NeutralMass, + Is.EqualTo(ExpectedInternalFragmentNeutralMass(ringSeq, 7, 5)).Within(1e-5), + "[7,11]=GHIMA mass = G+H+I+M+A residue masses"); + } + + [Test] + public static void FragmentInternally_SubPeptide_N5_MinLength2_CorrectCount() + { + // "ACDEK" [1-5] from ring "ACDEKFGHIK" (N=10), length 5, minLength 2. + // + // Fragment count for peptideLength=5, minLength=2: + // localStart=0: maxLength=4 → lengths 2,3,4 → 3 fragments + // localStart=1: maxLength=3 → lengths 2,3 → 2 fragments + // localStart=2: maxLength=2 → length 2 → 1 fragment + // localStart=3: maxLength=1 < 2 → 0 + // localStart=4: maxLength=0 < 2 → 0 + // Total = 6 fragments + // + // Note: CircularPeptideWithSetModifications for this span is constructed + // directly because Digest() with maxMissedCleavages=0 on a ring with two + // cleavage sites produces linear PeptideWithSetModifications, not circular. + + var protein = new CircularProtein("ACDEKFGHIK", "test_acc"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptide = new CircularPeptideWithSetModifications( + protein: protein, + digestionParams: digestionParams, + oneBasedStartResidueInProtein: 1, + oneBasedEndResidueInProtein: 5, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: null, + missedCleavages: 0, + allModsOneIsNterminus: new Dictionary(), + numFixedMods: 0, + baseSequence: "ACDEK"); + + var products = new List(); + peptide.FragmentInternally(DissociationType.HCD, 2, products); + + Assert.That(products, Has.Count.EqualTo(6)); + } + + [Test] + public static void FragmentInternally_SubPeptide_AtRingStart_NumberingIsCanonical() + { + // "ACDEK" [1-5] from ring "ACDEKFGHIK" (N=10). + // Fragment numbers must be in parent ring coordinates. + // + // Constructed directly — see FragmentInternally_SubPeptide_N5_MinLength2_CorrectCount + // for why GetSubPeptide() cannot be used here. + + var protein = new CircularProtein("ACDEKFGHIK", "test_acc"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptide = new CircularPeptideWithSetModifications( + protein: protein, + digestionParams: digestionParams, + oneBasedStartResidueInProtein: 1, + oneBasedEndResidueInProtein: 5, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: null, + missedCleavages: 0, + allModsOneIsNterminus: new Dictionary(), + numFixedMods: 0, + baseSequence: "ACDEK"); + + var products = new List(); + peptide.FragmentInternally(DissociationType.HCD, 3, products); + + var frag_1_3 = products.Single(p => p.FragmentNumber == 1 && p.ResiduePosition == 3); + Assert.That(frag_1_3.SecondaryFragmentNumber, Is.EqualTo(3), "[1,3]=ACD"); + + var frag_1_4 = products.Single(p => p.FragmentNumber == 1 && p.ResiduePosition == 4); + Assert.That(frag_1_4.SecondaryFragmentNumber, Is.EqualTo(4), "[1,4]=ACDE"); + + var frag_2_3 = products.Single(p => p.FragmentNumber == 2 && p.ResiduePosition == 3); + Assert.That(frag_2_3.SecondaryFragmentNumber, Is.EqualTo(4), "[2,4]=CDE"); + } + + [Test] + public static void FragmentInternally_SubPeptide_NotAtRingStart_NumberingIsCanonical() + { + // "FGHIK" [6-10] from ring "ACDEKFGHIK" (N=10). + // All fragment numbers must be ≥ 6 (parent ring coordinates). + // + // Constructed directly — see FragmentInternally_SubPeptide_N5_MinLength2_CorrectCount + // for why GetSubPeptide() cannot be used here. + + var protein = new CircularProtein("ACDEKFGHIK", "test_acc"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptide = new CircularPeptideWithSetModifications( + protein: protein, + digestionParams: digestionParams, + oneBasedStartResidueInProtein: 6, + oneBasedEndResidueInProtein: 10, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: null, + missedCleavages: 0, + allModsOneIsNterminus: new Dictionary(), + numFixedMods: 0, + baseSequence: "FGHIK"); + + var products = new List(); + peptide.FragmentInternally(DissociationType.HCD, 3, products); + + var frag_6_3 = products.Single(p => p.FragmentNumber == 6 && p.ResiduePosition == 3); + Assert.That(frag_6_3.SecondaryFragmentNumber, Is.EqualTo(8), "[6,8]=FGH"); + + var frag_6_4 = products.Single(p => p.FragmentNumber == 6 && p.ResiduePosition == 4); + Assert.That(frag_6_4.SecondaryFragmentNumber, Is.EqualTo(9), "[6,9]=FGHI"); + + var frag_7_3 = products.Single(p => p.FragmentNumber == 7 && p.ResiduePosition == 3); + Assert.That(frag_7_3.SecondaryFragmentNumber, Is.EqualTo(9), "[7,9]=GHI"); + } + + [Test] + public static void FragmentInternally_SubPeptide_NoFragmentsStartAtParentPosition1() + { + // "FGHIK" [6-10] from ring "ACDEKFGHIK" (N=10). + // Starts at canonical position 6 — no fragment may have FragmentNumber < 6. + // + // Constructed directly — see FragmentInternally_SubPeptide_N5_MinLength2_CorrectCount + // for why GetSubPeptide() cannot be used here. + + var protein = new CircularProtein("ACDEKFGHIK", "test_acc"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptide = new CircularPeptideWithSetModifications( + protein: protein, + digestionParams: digestionParams, + oneBasedStartResidueInProtein: 6, + oneBasedEndResidueInProtein: 10, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: null, + missedCleavages: 0, + allModsOneIsNterminus: new Dictionary(), + numFixedMods: 0, + baseSequence: "FGHIK"); + + var products = new List(); + peptide.FragmentInternally(DissociationType.HCD, 2, products); + + Assert.That(products.All(p => p.FragmentNumber >= 6), Is.True); + } + + [Test] + public static void FragmentInternally_SubPeptide_NeutralMass_MatchesResidueMassSum() + { + // "FGHIK" [6-10] from ring "ACDEKFGHIK" (N=10). + // All fragment neutral masses must equal the sum of parent ring residue masses + // for the corresponding sub-sequence. + // + // Constructed directly — see FragmentInternally_SubPeptide_N5_MinLength2_CorrectCount + // for why GetSubPeptide() cannot be used here. + + const string ring = "ACDEKFGHIK"; + + var protein = new CircularProtein(ring, "test_acc"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptide = new CircularPeptideWithSetModifications( + protein: protein, + digestionParams: digestionParams, + oneBasedStartResidueInProtein: 6, + oneBasedEndResidueInProtein: 10, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: null, + missedCleavages: 0, + allModsOneIsNterminus: new Dictionary(), + numFixedMods: 0, + baseSequence: "FGHIK"); + + var products = new List(); + peptide.FragmentInternally(DissociationType.HCD, 3, products); + + foreach (var product in products) + { + double expected = ExpectedInternalFragmentNeutralMass( + ring, product.FragmentNumber, product.ResiduePosition); + Assert.That(product.NeutralMass, Is.EqualTo(expected).Within(1e-5), + $"[{product.FragmentNumber},{product.SecondaryFragmentNumber}]"); + } + } + + [Test] + public static void FragmentInternally_SubPeptide_NoFragmentExceedsSpan() + { + // "ACDEK" [1-5] from ring "ACDEKFGHIK" (N=10). + // No fragment end may reach position 5 (the K boundary). + // maxLength at localStart=0 is 4, so max end = 1+4-1 = 4 < 5. ✓ + // + // Constructed directly — see FragmentInternally_SubPeptide_N5_MinLength2_CorrectCount + // for why GetSubPeptide() cannot be used here. + + var protein = new CircularProtein("ACDEKFGHIK", "test_acc"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptide = new CircularPeptideWithSetModifications( + protein: protein, + digestionParams: digestionParams, + oneBasedStartResidueInProtein: 1, + oneBasedEndResidueInProtein: 5, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: null, + missedCleavages: 0, + allModsOneIsNterminus: new Dictionary(), + numFixedMods: 0, + baseSequence: "ACDEK"); + + var products = new List(); + peptide.FragmentInternally(DissociationType.HCD, 2, products); + + Assert.That(products.All(p => p.SecondaryFragmentNumber < 5), Is.True, + "ACDEK[1-5]: SecondaryFragmentNumber must be < 5."); + } + + [Test] + public static void FragmentInternally_SubPeptide_NoWrapAroundFragments() + { + // "FGHIK" [6-10] from ring "ACDEKFGHIK" (N=10). + // Sub-peptides (length < N) never produce wrap-around fragments. + // Both cleavage sites lie within the ring, so no fragment can extend + // beyond the C-terminal boundary of the sub-peptide. + // + // Max SecondaryFragmentNumber: localStart=0, length=4 → 6+4-1=9 ≤ N=10. ✓ + // + // Constructed directly — see FragmentInternally_SubPeptide_N5_MinLength2_CorrectCount + // for why GetSubPeptide() cannot be used here. + + var protein = new CircularProtein("ACDEKFGHIK", "test_acc"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptide = new CircularPeptideWithSetModifications( + protein: protein, + digestionParams: digestionParams, + oneBasedStartResidueInProtein: 6, + oneBasedEndResidueInProtein: 10, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: null, + missedCleavages: 0, + allModsOneIsNterminus: new Dictionary(), + numFixedMods: 0, + baseSequence: "FGHIK"); + + var products = new List(); + peptide.FragmentInternally(DissociationType.HCD, 2, products); + + Assert.That(products.All(p => p.SecondaryFragmentNumber <= 10), Is.True, + "FGHIK[6-10]: SecondaryFragmentNumber must be ≤ N=10."); + } + + // ══════════════════════════════════════════════════════════════════════ + // MODIFICATION MASS — oxidation must shift fragment masses correctly + // + // KEY CONSTRAINT: a modified residue at canonical position p is only + // reachable by fragments from a full-ring [1-N] peptide if + // oneBasedStart + length - 1 ≥ p + // ⟺ localStart + length ≥ p - 1 + 1 = p + // But maxLength = N - localStart - 1, so the maximum reachable position is: + // oneBasedStart + maxLength - 1 = 1 + localStart + (N-localStart-1) - 1 = N-1 + // Therefore M at position N (the last residue) is NEVER reachable. + // + // Test A: ring "ACDEFGHIM", M at position 9 (=N). + // No fragment contains M → oxidation has zero effect on all fragment masses. + // + // Test B: ring "ACMDEFGHI", M at position 3 (well inside the ring). + // Fragments [1,3]=ACM and [2,3]=CM contain M → masses shift by +15.994915. + // Fragment [1,2]=AC does not contain M → mass unchanged. + // ══════════════════════════════════════════════════════════════════════ + + [Test] + public static void FragmentInternally_ModifiedResidue_IncludedInFragmentMass() + { + // TEST A: M at position 9 = N → no fragment reaches it. + // Verifies that the fallback Digest() path correctly produces both + // unmodified and oxidized full-ring peptides (key=10 for pos 9), + // and that all fragment masses are identical between the two forms. + ModificationMotif.TryGetMotif("M", out ModificationMotif mMotif); + var oxidation = new Modification( + _originalId: "Oxidation on M", + _modificationType: "Common Variable", + _target: mMotif, + _locationRestriction: "Anywhere.", + _monoisotopicMass: 15.994915); + + var mods = new Dictionary> { [9] = [oxidation] }; + var protein = new CircularProtein("ACDEFGHIM", "mod_test", + oneBasedModifications: mods); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptides = protein.Digest(digestionParams, [], [oxidation]) + .OfType() + .ToList(); + + var unmodified = peptides.Single(p => p.AllModsOneIsNterminus.Count == 0); + var oxidized = peptides.Single(p => p.AllModsOneIsNterminus.Count == 1); + + // Modification key: position 9 + 1 = 10 + Assert.That(oxidized.AllModsOneIsNterminus.ContainsKey(10), Is.True); + Assert.That(oxidized.AllModsOneIsNterminus[10].OriginalId, + Does.Contain("Oxidation")); + + var unmodProducts = new List(); + var oxProducts = new List(); + unmodified.FragmentInternally(DissociationType.HCD, 2, unmodProducts); + oxidized.FragmentInternally(DissociationType.HCD, 2, oxProducts); + + // [7,8]=HI exists (localStart=6, length=2) — does NOT span position 9 + var unmod_7_2 = unmodProducts.Single(p => p.FragmentNumber == 7 && p.ResiduePosition == 2); + var ox_7_2 = oxProducts.Single(p => p.FragmentNumber == 7 && p.ResiduePosition == 2); + Assert.That(ox_7_2.NeutralMass, + Is.EqualTo(unmod_7_2.NeutralMass).Within(1e-4), + "[7,8]=HI: does not span position 9, so no mass shift"); + + // With wrap-around, some fragments DO span position 9. + // Fragments that include residue 9 should show a mass shift equal to the oxidation mass. + Assert.That(unmodProducts.Count, Is.EqualTo(oxProducts.Count)); + + // Fragments NOT spanning position 9 should have identical masses. + // Fragments spanning position 9 should differ by the oxidation mass. + var unmodOrdered = unmodProducts.OrderBy(p => p.FragmentNumber) + .ThenBy(p => p.ResiduePosition).ToList(); + var oxOrdered = oxProducts.OrderBy(p => p.FragmentNumber) + .ThenBy(p => p.ResiduePosition).ToList(); + + bool foundModifiedFragment = false; + for (int i = 0; i < unmodOrdered.Count; i++) + { + double diff = Math.Abs(oxOrdered[i].NeutralMass - unmodOrdered[i].NeutralMass); + if (diff > 1e-4) + { + // Fragment spans the modified residue — mass difference should be ~15.995 + Assert.That(diff, Is.EqualTo(15.994915).Within(1e-3), + $"Fragment [{unmodOrdered[i].FragmentNumber},{unmodOrdered[i].SecondaryFragmentNumber}]: " + + "mass difference should equal oxidation mass"); + foundModifiedFragment = true; + } + } + Assert.That(foundModifiedFragment, Is.True, + "At least one fragment should span the modified position 9 via wrap-around"); + } + + [Test] + public static void FragmentInternally_ModifiedResidue_MidRing_IncludedInFragmentMass() + { + // TEST B: M at position 3 (well inside the ring) → fragments CAN reach it. + // Ring "ACMDEFGHI" (N=9), M at canonical position 3, no K/R → full-ring [1-9]. + // + // Fragments containing M (end ≥ 3 and start ≤ 3): + // [1,3]=ACM (L=3, localStart=0, maxLength=8 ✓) + // [2,3]=CM (L=2, localStart=1, maxLength=7 ✓) + // [3,4]=MD (L=2, localStart=2, maxLength=6 ✓) ← starts at M + // Fragments NOT containing M: + // [1,2]=AC (L=2, end=2 < 3) + + ModificationMotif.TryGetMotif("M", out ModificationMotif mMotif); + var oxidation = new Modification( + _originalId: "Oxidation on M", + _modificationType: "Common Variable", + _target: mMotif, + _locationRestriction: "Anywhere.", + _monoisotopicMass: 15.994915); + + var mods = new Dictionary> { [3] = [oxidation] }; + var protein = new CircularProtein("ACMDEFGHI", "mod_mid_test", + oneBasedModifications: mods); + + Assert.That(protein.BaseSequence, Is.EqualTo("ACMDEFGHI"), + "Already canonical (A is smallest)"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptides = protein.Digest(digestionParams, [], [oxidation]) + .OfType() + .ToList(); + + var unmodified = peptides.Single(p => p.AllModsOneIsNterminus.Count == 0); + var oxidized = peptides.Single(p => p.AllModsOneIsNterminus.Count == 1); + + // Modification key: position 3 + 1 = 4 + Assert.That(oxidized.AllModsOneIsNterminus.ContainsKey(4), Is.True, + "Oxidation on M at position 3 → key = 4"); + + const string ring = "ACMDEFGHI"; + double oxMass = 15.994915; + + var unmodProducts = new List(); + var oxProducts = new List(); + unmodified.FragmentInternally(DissociationType.HCD, 2, unmodProducts); + oxidized.FragmentInternally(DissociationType.HCD, 2, oxProducts); + + // [1,2]=AC — does NOT contain M → same mass in both forms + var unmod_1_2 = unmodProducts.Single(p => p.FragmentNumber == 1 && p.ResiduePosition == 2); + var ox_1_2 = oxProducts.Single(p => p.FragmentNumber == 1 && p.ResiduePosition == 2); + Assert.That(ox_1_2.NeutralMass, Is.EqualTo(unmod_1_2.NeutralMass).Within(1e-4), + "[1,2]=AC: no M → no oxidation shift"); + Assert.That(ox_1_2.NeutralMass, + Is.EqualTo(ExpectedInternalFragmentNeutralMass(ring, 1, 2)).Within(1e-4)); + + // [2,3]=CM — contains M → mass shifts by +oxMass + var unmod_2_2 = unmodProducts.Single(p => p.FragmentNumber == 2 && p.ResiduePosition == 2); + var ox_2_2 = oxProducts.Single(p => p.FragmentNumber == 2 && p.ResiduePosition == 2); + Assert.That(ox_2_2.NeutralMass, + Is.EqualTo(ExpectedInternalFragmentNeutralMass(ring, 2, 2) + oxMass).Within(1e-4), + "[2,3]=CM: M in fragment → +oxMass"); + Assert.That(ox_2_2.NeutralMass - unmod_2_2.NeutralMass, + Is.EqualTo(oxMass).Within(1e-4), + "Mass difference for [2,3]=CM = oxMass"); + + // [1,3]=ACM (L=3) — contains M → mass shifts by +oxMass + var unmod_1_3 = unmodProducts.Single(p => p.FragmentNumber == 1 && p.ResiduePosition == 3); + var ox_1_3 = oxProducts.Single(p => p.FragmentNumber == 1 && p.ResiduePosition == 3); + Assert.That(ox_1_3.NeutralMass, + Is.EqualTo(ExpectedInternalFragmentNeutralMass(ring, 1, 3) + oxMass).Within(1e-4), + "[1,3]=ACM: M in fragment → +oxMass"); + Assert.That(ox_1_3.NeutralMass - unmod_1_3.NeutralMass, + Is.EqualTo(oxMass).Within(1e-4), + "Mass difference for [1,3]=ACM = oxMass"); + } + + // ── Constructor guards: terminal mods are invalid on a circular peptide ── + + private static DigestionParams SimpleDigestionParams() => + new DigestionParams(protease: "trypsin", maxMissedCleavages: 0, minPeptideLength: 1); + + private static Modification BuildAnyAnywhereMod() + { + ModificationMotif.TryGetMotif("M", out ModificationMotif motif); + return new Modification( + _originalId: "TestMod", + _modificationType: "Test", + _target: motif, + _locationRestriction: "Anywhere.", + _monoisotopicMass: 10.0); + } + + /// + /// A circular peptide has no free N-terminus, so a modification at the + /// N-terminal key (1) must be rejected by the constructor. + /// + [Test] + public static void Constructor_NTerminalMod_ThrowsArgumentException() + { + var protein = new CircularProtein("ACDEFGHIM", "test_acc"); // N = 9 + var mod = BuildAnyAnywhereMod(); + + Assert.Throws(() => new CircularPeptideWithSetModifications( + protein: protein, + digestionParams: SimpleDigestionParams(), + oneBasedStartResidueInProtein: 1, + oneBasedEndResidueInProtein: 9, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: null, + missedCleavages: 0, + allModsOneIsNterminus: new Dictionary { { 1, mod } }, + numFixedMods: 0, + baseSequence: "ACDEFGHIM")); + } + + /// + /// A circular peptide has no free C-terminus, so a modification at the + /// C-terminal key (peptideLength + 2 = 11) must be rejected by the constructor. + /// + [Test] + public static void Constructor_CTerminalMod_ThrowsArgumentException() + { + var protein = new CircularProtein("ACDEFGHIM", "test_acc"); // N = 9 + var mod = BuildAnyAnywhereMod(); + + Assert.Throws(() => new CircularPeptideWithSetModifications( + protein: protein, + digestionParams: SimpleDigestionParams(), + oneBasedStartResidueInProtein: 1, + oneBasedEndResidueInProtein: 9, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: null, + missedCleavages: 0, + allModsOneIsNterminus: new Dictionary { { 11, mod } }, + numFixedMods: 0, + baseSequence: "ACDEFGHIM")); + } + + /// + /// FragmentInternally caches the ring-mass and doubled-prefix arrays after the + /// first call (the peptide is immutable). A second call must hit the cache and + /// return identical fragments. + /// + [Test] + public static void FragmentInternally_CalledTwice_ReturnsIdenticalProducts() + { + var peptide = GetFullRingPeptide("ACDEFGHIM"); + var first = new List(); + var second = new List(); + + peptide.FragmentInternally(DissociationType.HCD, 3, first); + peptide.FragmentInternally(DissociationType.HCD, 3, second); + + Assert.That(first, Is.Not.Empty, "First fragmentation should produce internal fragments."); + Assert.That(second.Count, Is.EqualTo(first.Count), + "Repeated fragmentation must produce the same number of fragments."); + Assert.That(second.Select(p => p.NeutralMass).ToList(), + Is.EqualTo(first.Select(p => p.NeutralMass).ToList()), + "Cached fragmentation must yield identical neutral masses."); + } + + /// + /// FragmentInternally enforces its documented contract: a minimum fragment + /// length below 1 is invalid. + /// + [Test] + public static void FragmentInternally_MinLengthBelowOne_Throws() + { + var peptide = GetFullRingPeptide("ACDEFGHIM"); + var products = new List(); + + Assert.Throws(() => + peptide.FragmentInternally(DissociationType.HCD, 0, products)); + } + } +} \ No newline at end of file diff --git a/mzLib/Test/TestCircularProtein.cs b/mzLib/Test/TestCircularProtein.cs new file mode 100644 index 000000000..626797803 --- /dev/null +++ b/mzLib/Test/TestCircularProtein.cs @@ -0,0 +1,1410 @@ +using Chemistry; +using MassSpectrometry; +using NUnit.Framework; +using Omics.Digestion; +using Omics.Fragmentation; +using Omics.Modifications; +using Proteomics; +using Proteomics.ProteolyticDigestion; +using System; +using System.Collections.Generic; +using System.Linq; +using UsefulProteomicsDatabases; + +namespace Test +{ + [TestFixture] + [System.Diagnostics.CodeAnalysis.ExcludeFromCodeCoverage] + public static class TestCircularProtein + { + [OneTimeSetUp] + public static void OneTimeSetup() + { + Loaders.LoadElements(); + } + + // ────────────────────────────────────────────────────────────────────── + // GetCanonicalRotation + // ────────────────────────────────────────────────────────────────────── + + [TestCase("ACGT", "ACGT", TestName = "AlreadyCanonical")] + [TestCase("CGTA", "ACGT", TestName = "RotationByOne")] + [TestCase("GTAC", "ACGT", TestName = "RotationByTwo")] + [TestCase("TACG", "ACGT", TestName = "RotationByThree")] + [TestCase("A", "A", TestName = "SingleCharacter")] + [TestCase("", "", TestName = "EmptyString")] + public static void GetCanonicalRotation_ReturnsSmallestRotation(string input, string expected) + { + Assert.That(CircularProtein.GetCanonicalRotation(input), Is.EqualTo(expected)); + } + + // ────────────────────────────────────────────────────────────────────── + // Constructor + // ────────────────────────────────────────────────────────────────────── + + [Test] + public static void Constructor_CanonicalizesInputSequence() + { + // "TACG" is not the smallest rotation; "ACGT" is + var circular = new CircularProtein("TACG", "acc1"); + + Assert.Multiple(() => + { + Assert.That(circular.BaseSequence, Is.EqualTo("ACGT")); + Assert.That(circular.CircularSequence, Is.EqualTo(circular.BaseSequence)); + Assert.That(circular.Length, Is.EqualTo(4)); + }); + } + + [Test] + public static void Constructor_PreservesMetadata() + { + var geneNames = new List> { Tuple.Create("primary", "CYCA") }; + var circular = new CircularProtein( + sequence: "ACGT", + accession: "ACC001", + organism: "Homo sapiens", + geneNames: geneNames, + name: "cyclic test", + fullName: "cyclic test protein", + isDecoy: false, + isContaminant: true); + + Assert.Multiple(() => + { + Assert.That(circular.Accession, Is.EqualTo("ACC001")); + Assert.That(circular.Organism, Is.EqualTo("Homo sapiens")); + Assert.That(circular.Name, Is.EqualTo("cyclic test")); + Assert.That(circular.FullName, Is.EqualTo("cyclic test protein")); + Assert.That(circular.IsDecoy, Is.False); + Assert.That(circular.IsContaminant, Is.True); + Assert.That(circular.GeneNames, Has.Count.EqualTo(1)); + }); + } + + // ────────────────────────────────────────────────────────────────────── + // CyclicMonoisotopicMass + // ────────────────────────────────────────────────────────────────────── + + [Test] + public static void CyclicMonoisotopicMass_IsLinearMassMinusWater() + { + // A=Ala C=Cys G=Gly T=Thr — all standard residues, already canonical + const string sequence = "ACGT"; + var circular = new CircularProtein(sequence, "acc1"); + + var linearPeptide = new PeptideWithSetModifications(sequence, new Dictionary()); + double waterMass = PeriodicTable.GetElement("H").PrincipalIsotope.AtomicMass * 2 + + PeriodicTable.GetElement("O").PrincipalIsotope.AtomicMass; + + Assert.That(circular.CyclicMonoisotopicMass, + Is.EqualTo(linearPeptide.MonoisotopicMass - waterMass).Within(1e-5)); + } + + // ────────────────────────────────────────────────────────────────────── + // FromProtein + // ────────────────────────────────────────────────────────────────────── + + [Test] + public static void FromProtein_CanonicalizesAndPreservesMetadata() + { + var source = new Protein( + "TACG", + "ACC002", + organism: "Mus musculus", + name: "source protein", + isDecoy: true); + + var circular = CircularProtein.FromProtein(source); + + Assert.Multiple(() => + { + Assert.That(circular, Is.InstanceOf()); + Assert.That(circular.BaseSequence, Is.EqualTo("ACGT")); + Assert.That(circular.Accession, Is.EqualTo("ACC002")); + Assert.That(circular.Organism, Is.EqualTo("Mus musculus")); + Assert.That(circular.Name, Is.EqualTo("source protein")); + Assert.That(circular.IsDecoy, Is.True); + }); + } + + // ────────────────────────────────────────────────────────────────────── + // Digest + // + // Sequences are designed so the reasoning is auditable by inspection: + // + // "ACDEFK" N=6, one K at the last position. + // Proxy = "ACDEFKACDEF" → K only at proxy pos 6. + // One cut → one linearised full-circle peptide "ACDEFK". + // + // "ACDEKFGHIK" N=10, K at positions 5 and 10 (last). + // Proxy = "ACDEKFGHIKACDEKFGHI" → K at proxy pos 5, 10, 15. + // 0 MC: arcs [1-5]="ACDEK" and [6-10]="FGHIK". + // 1 MC: adds [1-10]="ACDEKFGHIK" (end=N, non-wrapping) + // and [6-15]="FGHIKACDEK" (end>N, wrapping). + // ────────────────────────────────────────────────────────────────────── + + [Test] + public static void Digest_OneLysine_ProducesOnePeptideOfFullLength() + { + var circular = new CircularProtein("ACDEFK", "acc_digest1"); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptides = circular.Digest(digestionParams, [], []) + .Cast().ToList(); + + Assert.Multiple(() => + { + Assert.That(peptides, Has.Count.EqualTo(1)); + Assert.That(peptides[0].BaseSequence, Is.EqualTo("ACDEFK")); + Assert.That(peptides[0].Length, Is.EqualTo(circular.Length)); + }); + } + + [Test] + public static void Digest_TwoLysines_ZeroMissedCleavages_ReturnsTwoShortPeptides() + { + var circular = new CircularProtein("ACDEKFGHIK", "acc_digest2"); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptides = circular.Digest(digestionParams, [], []) + .Cast() + .OrderBy(p => p.BaseSequence) + .ToList(); + + Assert.Multiple(() => + { + Assert.That(peptides, Has.Count.EqualTo(2)); + Assert.That(peptides[0].BaseSequence, Is.EqualTo("ACDEK")); + Assert.That(peptides[1].BaseSequence, Is.EqualTo("FGHIK")); + Assert.That(peptides.All(p => p.Length < circular.Length), Is.True); + }); + } + + [Test] + public static void Digest_TwoLysines_OneMissedCleavage_ReturnsFourPeptides() + { + // 0 MC: "ACDEK", "FGHIK" + // 1 MC: "ACDEKFGHIK" (full-length, non-wrapping) + // "FGHIKACDEK" (full-length, wrapping — starts at position 6 of circle) + var circular = new CircularProtein("ACDEKFGHIK", "acc_digest3"); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 1, + minPeptideLength: 1); + + var sequences = circular.Digest(digestionParams, [], []) + .Cast() + .Select(p => p.BaseSequence) + .ToHashSet(); + + Assert.Multiple(() => + { + Assert.That(sequences, Has.Count.EqualTo(4)); + Assert.That(sequences, Does.Contain("ACDEK")); + Assert.That(sequences, Does.Contain("FGHIK")); + Assert.That(sequences, Does.Contain("ACDEKFGHIK")); + Assert.That(sequences, Does.Contain("FGHIKACDEK")); + }); + } + + [Test] + public static void Digest_WrappingPeptide_HasEndResidueGreaterThanN() + { + // "FGHIKACDEK" spans the circular junction: + // proxy positions [6, 15], end=15 > N=10. + var circular = new CircularProtein("ACDEKFGHIK", "acc_digest4"); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 1, + minPeptideLength: 1); + + var peptides = circular.Digest(digestionParams, [], []) + .Cast().ToList(); + + var wrapping = peptides.Single(p => p.BaseSequence == "FGHIKACDEK"); + Assert.Multiple(() => + { + Assert.That(wrapping.OneBasedStartResidueInProtein, Is.LessThanOrEqualTo(circular.Length)); + Assert.That(wrapping.OneBasedEndResidueInProtein, Is.GreaterThan(circular.Length)); + }); + } + + [Test] + public static void Digest_AllPeptidesAreBoundToCircularProtein() + { + // Rebinding replaces the transient proxy Protein with `this`. + var circular = new CircularProtein("ACDEKFGHIK", "acc_digest5"); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 1, + minPeptideLength: 1); + + var peptides = circular.Digest(digestionParams, [], []) + .Cast().ToList(); + + Assert.That(peptides, Is.Not.Empty); + Assert.That(peptides.All(p => ReferenceEquals(p.Protein, circular)), Is.True); + } + + // ────────────────────────────────────────────────────────────────────── + // Modification localization + // + // Sequence: "ACDKEPGHIK" (N=10, K at 4 and 10, P at 6) + // Proxy: "ACDKEPGHIKACDKEPGHI" (2N-1=19 residues) + // P is at proxy position 6 (first copy, ≤ N → in mod dict). + // + // Trypsin 1 MC peptides that span the proline: + // "EPGHIK" proxy [5-10] → allModsKey = 6-5+2 = 3 + // "ACDKEPGHIK" proxy [1-10] → allModsKey = 6-1+2 = 7 ← same P, different key! + // "EPGHIKACDK" proxy [5-14] → allModsKey = 6-5+2 = 3 (wrapping, same start) + // ────────────────────────────────────────────────────────────────────── + + [Test] + public static void Digest_HydroxyprolineLocalization_DiffersByCleavageSite() + { + ModificationMotif.TryGetMotif("P", out ModificationMotif pMotif); + var hydroxyproline = new Modification( + _originalId: "Oxidation on P", + _modificationType: "Common Variable", + _target: pMotif, + _locationRestriction: "Anywhere.", + _monoisotopicMass: 15.994915); + + // P is at position 6 in "ACDKEPGHIK" (K at 4 and 10) + var mods = new Dictionary> { [6] = [hydroxyproline] }; + var circular = new CircularProtein("ACDKEPGHIK", "acc_mod", oneBasedModifications: mods); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 1, + minPeptideLength: 1); + + // Only keep peptides that actually carry the modification + var modifiedPeptides = circular.Digest(digestionParams, [], []) + .Cast() + .Where(p => p.AllModsOneIsNterminus.Count > 0) + .ToList(); + + var modEpghik = modifiedPeptides.Single(p => p.BaseSequence == "EPGHIK"); + var modFullLength = modifiedPeptides.Single(p => p.BaseSequence == "ACDKEPGHIK"); + var modWrapping = modifiedPeptides.Single(p => p.BaseSequence == "EPGHIKACDK"); + + Assert.Multiple(() => + { + // "EPGHIK" starts at proxy pos 5 → key = 6-5+2 = 3 + Assert.That(modEpghik.AllModsOneIsNterminus.Keys.Single(), Is.EqualTo(3)); + + // "ACDKEPGHIK" starts at proxy pos 1 → key = 6-1+2 = 7 (same physical P, different key!) + Assert.That(modFullLength.AllModsOneIsNterminus.Keys.Single(), Is.EqualTo(7)); + + // "EPGHIKACDK" starts at proxy pos 5 → key = 6-5+2 = 3 (wrapping, same start as "EPGHIK") + Assert.That(modWrapping.AllModsOneIsNterminus.Keys.Single(), Is.EqualTo(3)); + + // All three carry the same modification identity + Assert.That(modEpghik.AllModsOneIsNterminus.Values.Single().OriginalId, Is.EqualTo("Oxidation")); + Assert.That(modFullLength.AllModsOneIsNterminus.Values.Single().OriginalId, Is.EqualTo("Oxidation")); + Assert.That(modWrapping.AllModsOneIsNterminus.Values.Single().OriginalId, Is.EqualTo("Oxidation")); + }); + } + + [Test] + public static void Digest_NoCleavageSites_YieldsCircularPeptideWithSetModifications() + { + // "ACGMT" contains no K or R — trypsin finds no cleavage sites. + // Digest() must still yield the full-length ring as a + // CircularPeptideWithSetModifications. + var circular = new CircularProtein("ACGMT", "acc_type1"); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptides = circular.Digest(digestionParams, [], []).ToList(); + + Assert.Multiple(() => + { + Assert.That(peptides, Has.Count.EqualTo(1)); + Assert.That(peptides[0], Is.InstanceOf(), + "Digest() must yield CircularPeptideWithSetModifications when no cleavage sites exist"); + Assert.That(((PeptideWithSetModifications)peptides[0]).BaseSequence, + Is.EqualTo(circular.BaseSequence), + "The yielded peptide must be the full-length canonical ring sequence"); + }); + } + + [Test] + public static void Digest_NoCleavageSites_CircularParentReferenceIsCorrect() + { + var circular = new CircularProtein("ACGMT", "acc_type5"); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptide = circular.Digest(digestionParams, [], []) + .Cast() + .Single(); + + Assert.Multiple(() => + { + Assert.That(peptide, Is.InstanceOf()); + Assert.That(ReferenceEquals(peptide.CircularParent, circular), Is.True, + "CircularParent must reference the originating CircularProtein"); + Assert.That(peptide.CircularParent.CyclicMonoisotopicMass, + Is.EqualTo(circular.CyclicMonoisotopicMass).Within(1e-9)); + }); + } + [Test] + public static void Digest_TwoKs_MaxMissedCleavagesTwo_ProducesCorrectMixOfTypes() + { + // Ring "ACDEKFGHIK" (N=10): K at positions 5 and 10 → 2 cleavage sites. + // maxMissedCleavages: 2 >= numCleavageSites: 2 + // → CircularPeptideWithSetModifications IS emitted (Step 2, full ring intact). + // + // Step 3 (proxy digestion, maxMissedCleavages=2) produces linear products: + // 0 missed cleavages (two cuts, length < N): + // "ACDEK" [1-5] → PeptideWithSetModifications + // "FGHIK" [6-10] → PeptideWithSetModifications + // 1 missed cleavage (one cut, length == N): + // "ACDEKFGHIK" [1-10] → PeptideWithSetModifications + // "FGHIKACDEK" [6-15] → PeptideWithSetModifications + // 2 missed cleavages: length 15 > N → discarded. + // + // Total: 1 circular + 4 linear = 5 products. + + var circular = new CircularProtein("ACDEKFGHIK", "acc_type2"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 2, + minPeptideLength: 1); + + var peptides = circular.Digest(digestionParams, [], []) + .Cast() + .ToList(); + + var circularProducts = peptides.OfType().ToList(); + var linearProducts = peptides.Where(p => p is not CircularPeptideWithSetModifications).ToList(); + var subPeptides = linearProducts.Where(p => p.Length < circular.Length).ToList(); + var fullLengthLinear = linearProducts.Where(p => p.Length == circular.Length).ToList(); + + Assert.Multiple(() => + { + Assert.That(peptides, Has.Count.EqualTo(5)); + + // Circular product: full ring intact, length == N + Assert.That(circularProducts, Has.Count.EqualTo(1), + "maxMissedCleavages (2) >= numCleavageSites (2): exactly one circular product."); + Assert.That(circularProducts[0].BaseSequence, Is.EqualTo("ACDEKFGHIK")); + Assert.That(circularProducts[0].Length, Is.EqualTo(circular.Length)); + + // Sub-peptides: two cuts, length < N, linear + Assert.That(subPeptides, Has.Count.EqualTo(2)); + Assert.That(subPeptides.All(p => p is not CircularPeptideWithSetModifications), Is.True, + "Sub-peptides (length < N) are linear PeptideWithSetModifications."); + Assert.That(subPeptides.Select(p => p.BaseSequence), + Is.EquivalentTo(new[] { "ACDEK", "FGHIK" })); + + // Full-length linear products: one cut, length == N + Assert.That(fullLengthLinear, Has.Count.EqualTo(2)); + Assert.That(fullLengthLinear.All(p => p is not CircularPeptideWithSetModifications), Is.True, + "Full-length linear products (one cut) are PeptideWithSetModifications."); + Assert.That(fullLengthLinear.Select(p => p.BaseSequence), + Is.EquivalentTo(new[] { "ACDEKFGHIK", "FGHIKACDEK" })); + Assert.That(fullLengthLinear.All(p => p.Length == circular.Length), Is.True); + + // All bound to the CircularProtein parent + Assert.That(peptides.All(p => ReferenceEquals(p.Protein, circular)), Is.True); + }); + } + + [Test] + public static void Digest_AllPeptidesAreBoundToCircularProteinParent() + { + // Every peptide yielded by CircularProtein.Digest() — regardless of type — + // must be bound to the originating CircularProtein as its parent. + // + // Ring "ACDEKFGHIK" (N=10): K at positions 5 and 10 → 2 cleavage sites. + // maxMissedCleavages: 1 < numCleavageSites: 2 → NO CircularPeptideWithSetModifications. + // All products are linear PeptideWithSetModifications. + // + // Expected products (trypsin, maxMissedCleavages=1, minPeptideLength=1): + // 0 missed cleavages: ACDEK [1-5], FGHIK [6-10] (length < N) + // 1 missed cleavage: ACDEKFGHIK [1-10], FGHIKACDEK [6-15] (length == N) + + var circular = new CircularProtein("ACDEKFGHIK", "acc_type3"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 1, + minPeptideLength: 1); + + var peptides = circular.Digest(digestionParams, [], []) + .Cast() + .ToList(); + + var subPeptides = peptides.Where(p => p.Length < circular.Length).ToList(); + var fullLengthPeptides = peptides.Where(p => p.Length == circular.Length).ToList(); + + Assert.Multiple(() => + { + Assert.That(peptides, Is.Not.Empty); + + // No CircularPeptideWithSetModifications: maxMissedCleavages (1) < numCleavageSites (2) + Assert.That(peptides.All(p => p is not CircularPeptideWithSetModifications), Is.True, + "maxMissedCleavages (1) < numCleavageSites (2): no circular product expected."); + + // Sub-peptides (length < N) are linear PeptideWithSetModifications — two cuts opened the ring + Assert.That(subPeptides, Is.Not.Empty); + Assert.That(subPeptides.All(p => p is not CircularPeptideWithSetModifications), Is.True, + "Sub-peptides (length < N) are linear PeptideWithSetModifications, never circular."); + + // Full-length products (length == N) are single-cut ring-opening linear products + Assert.That(fullLengthPeptides, Is.Not.Empty); + Assert.That(fullLengthPeptides.All(p => p is not CircularPeptideWithSetModifications), Is.True, + "Full-length products (length == N, one cut) are linear PeptideWithSetModifications."); + + // All products are bound to the CircularProtein parent + Assert.That(peptides.All(p => ReferenceEquals(p.Protein, circular)), Is.True, + "Every product from CircularProtein.Digest() must reference the CircularProtein parent."); + }); + } + + [Test] + public static void Digest_CircularPeptide_CircularParentIsTheSameInstance() + { + // The CircularParent property of every CircularPeptideWithSetModifications + // must reference the exact same CircularProtein instance that was digested. + // Linear products (PeptideWithSetModifications) must also reference the same + // CircularProtein instance via their Protein property. + // + // Ring "ACDEKFGHIK" (N=10): K at positions 5 and 10 → 2 cleavage sites. + // maxMissedCleavages: 2 >= numCleavageSites: 2 → CircularPeptideWithSetModifications IS emitted. + // + // Expected products: + // Circular: ACDEKFGHIK [1-10] (maxMissedCleavages absorbs both sites) + // Linear: ACDEK [1-5] (0 missed cleavages) + // Linear: FGHIK [6-10] (0 missed cleavages) + // Linear: ACDEKFGHIK [1-10] (1 missed cleavage, length == N) + // Linear: FGHIKACDEK [6-15] (1 missed cleavage, wraps, length == N) + + var circular = new CircularProtein("ACDEKFGHIK", "acc_type4"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 2, + minPeptideLength: 1); + + var peptides = circular.Digest(digestionParams, [], []) + .Cast() + .ToList(); + + var circularPeptides = peptides.OfType().ToList(); + var linearPeptides = peptides.Where(p => p is not CircularPeptideWithSetModifications).ToList(); + + Assert.Multiple(() => + { + Assert.That(peptides, Is.Not.Empty); + + // CircularPeptideWithSetModifications: CircularParent must be this instance + Assert.That(circularPeptides, Is.Not.Empty, + "maxMissedCleavages (2) >= numCleavageSites (2): circular product must be emitted."); + Assert.That(circularPeptides.All(p => ReferenceEquals(p.CircularParent, circular)), Is.True, + "CircularParent must be the same instance as the digested CircularProtein."); + + // Linear products: Protein must be this instance + Assert.That(linearPeptides, Is.Not.Empty); + Assert.That(linearPeptides.All(p => ReferenceEquals(p.Protein, circular)), Is.True, + "All linear products must also reference the CircularProtein as their Protein."); + }); + } + + [Test] + public static void Digest_CircularPeptideMonoisotopicMass_IsLinearMassMinusWater() + { + // "ACDEFGHIM" has no K or R — trypsin makes zero cuts — the ring is + // intact and yields a CircularPeptideWithSetModifications of length N. + // Its mass must equal the linear peptide mass minus one water molecule. + const string sequence = "ACDEFGHIM"; + var circular = new CircularProtein(sequence, "acc_mass"); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptide = circular.Digest(digestionParams, [], []) + .OfType() + .Single(); + + var linearPeptide = new PeptideWithSetModifications( + sequence, new Dictionary()); + + double waterMass = PeriodicTable.GetElement("H").PrincipalIsotope.AtomicMass * 2 + + PeriodicTable.GetElement("O").PrincipalIsotope.AtomicMass; + + Assert.Multiple(() => + { + Assert.That(peptide.MonoisotopicMass, + Is.EqualTo(linearPeptide.MonoisotopicMass - waterMass).Within(1e-5), + "Circular peptide mass must equal linear peptide mass minus H₂O"); + + Assert.That(peptide.MonoisotopicMass, + Is.EqualTo(circular.CyclicMonoisotopicMass).Within(1e-5), + "Circular peptide mass must equal parent CyclicMonoisotopicMass"); + }); + } + // ────────────────────────────────────────────────────────────────────── + // Single cleavage site — linear ring-opening product + // ────────────────────────────────────────────────────────────────────── + + [Test] + public static void Digest_OneLysine_ZeroMissedCleavages_ProducesLinearPeptide() + { + // One K at position 6: a single tryptic cut opens the ring, producing + // a linear PeptideWithSetModifications, NOT a CircularPeptideWithSetModifications. + // The ring-opening ion is mass-equivalent to the precursor and carries + // no additional circular identity. + var circular = new CircularProtein("ACDEFK", "acc_linear1"); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptides = circular.Digest(digestionParams, [], []) + .Cast().ToList(); + + Assert.Multiple(() => + { + Assert.That(peptides, Has.Count.EqualTo(1)); + Assert.That(peptides[0].BaseSequence, Is.EqualTo("ACDEFK")); + Assert.That(peptides[0].Length, Is.EqualTo(circular.Length)); + + // Must be a plain linear peptide, not circular + Assert.That(peptides[0], Is.Not.InstanceOf(), + "A single-cut ring-opening product must be a linear PeptideWithSetModifications"); + + // But it must still be bound to the CircularProtein parent + // so that canonical numbering is preserved + Assert.That(ReferenceEquals(peptides[0].Protein, circular), Is.True, + "Linear ring-opening product must reference the CircularProtein parent"); + }); + } + + [Test] + public static void Digest_OneLysine_ZeroMissedCleavages_NumberingIsCanonical() + { + // The single K is at position 6 (last residue) in the canonical sequence "ACDEFK". + // The ring-opening product spans the entire canonical sequence [1, 6]. + var circular = new CircularProtein("ACDEFK", "acc_linear2"); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptide = circular.Digest(digestionParams, [], []) + .Cast() + .Single(); + + Assert.Multiple(() => + { + Assert.That(peptide.OneBasedStartResidueInProtein, Is.EqualTo(1), + "Start residue must be 1 in the canonical ring numbering"); + Assert.That(peptide.OneBasedEndResidueInProtein, Is.EqualTo(circular.Length), + "End residue must equal N in the canonical ring numbering"); + }); + } + + [Test] + public static void Digest_OneLysine_ZeroMissedCleavages_NumberingReflectsCleavageSitePosition() + { + // "KACDEF" canonicalizes to "ACDEFK" (A < K). + // The K moves from position 1 (input) to position 6 (canonical). + // The ring-opening product must start at canonical position 1. + var circular = new CircularProtein("KACDEF", "acc_linear3"); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptide = circular.Digest(digestionParams, [], []) + .Cast() + .Single(); + + Assert.Multiple(() => + { + // After canonicalization, the sequence is "ACDEFK" + Assert.That(circular.BaseSequence, Is.EqualTo("ACDEFK")); + // The product spans the full canonical sequence + Assert.That(peptide.BaseSequence, Is.EqualTo("ACDEFK")); + Assert.That(peptide.OneBasedStartResidueInProtein, Is.EqualTo(1)); + Assert.That(peptide.OneBasedEndResidueInProtein, Is.EqualTo(6)); + // Not circular + Assert.That(peptide, Is.Not.InstanceOf()); + }); + } + + [Test] + public static void Digest_TwoLysines_ZeroMissedCleavages_ProducesOnlyLinearSubPeptides() + { + // Ring "ACDEKFGHIK" (N=10): K at positions 5 and 10 → 2 cleavage sites. + // maxMissedCleavages: 0 < numCleavageSites: 2 + // → no CircularPeptideWithSetModifications emitted. + // → two cuts produce two linear sub-peptides, both length < N. + // + // Sub-peptides are PeptideWithSetModifications — the ring has been opened + // and they are linear fragments with free termini. They are NOT circular. + + var circular = new CircularProtein("ACDEKFGHIK", "acc_linear4"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptides = circular.Digest(digestionParams, [], []) + .Cast() + .ToList(); + + Assert.Multiple(() => + { + Assert.That(peptides, Has.Count.EqualTo(2)); + + Assert.That(peptides.All(p => p is not CircularPeptideWithSetModifications), Is.True, + "Sub-peptides from two cuts are linear PeptideWithSetModifications, not circular."); + + Assert.That(peptides.All(p => p.Length < circular.Length), Is.True, + "Both sub-peptides must be shorter than the full ring length N."); + }); + } + + [Test] + public static void Digest_ZeroCuts_NoCleavageSites_YieldsCircularPeptideOfLengthN() + { + // "ACDEFG" has no K or R — trypsin makes zero cuts. + // The ring is intact → CircularPeptideWithSetModifications of length N. + // This is the correct way to obtain a full-length CircularPeptideWithSetModifications: + // not via missed cleavages, but via absence of cleavage sites entirely. + var circular = new CircularProtein("ACDEFGM", "acc_zero_cuts"); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptides = circular.Digest(digestionParams, [], []).ToList(); + + Assert.Multiple(() => + { + Assert.That(peptides, Has.Count.EqualTo(1)); + Assert.That(peptides[0], Is.InstanceOf(), + "Zero cuts → ring intact → CircularPeptideWithSetModifications"); + Assert.That(((PeptideWithSetModifications)peptides[0]).Length, + Is.EqualTo(circular.Length)); + Assert.That(((PeptideWithSetModifications)peptides[0]).BaseSequence, + Is.EqualTo(circular.BaseSequence)); + }); + } + // ────────────────────────────────────────────────────────────────────── + // Zero cuts: no cleavage sites → CircularPeptideWithSetModifications, length N + // ────────────────────────────────────────────────────────────────────── + + [Test] + public static void Digest_ZeroCuts_YieldsCircularPeptideOfLengthN() + { + // No K or R → trypsin makes zero cuts → ring is intact. + var circular = new CircularProtein("ACDEFGHIM", "acc_cuts0"); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptides = circular.Digest(digestionParams, [], []).ToList(); + + Assert.Multiple(() => + { + Assert.That(peptides, Has.Count.EqualTo(1)); + Assert.That(peptides[0], Is.InstanceOf(), + "Zero cuts → ring intact → CircularPeptideWithSetModifications"); + Assert.That(((PeptideWithSetModifications)peptides[0]).Length, + Is.EqualTo(circular.Length)); + Assert.That(((PeptideWithSetModifications)peptides[0]).OneBasedStartResidueInProtein, + Is.EqualTo(1)); + Assert.That(((PeptideWithSetModifications)peptides[0]).OneBasedEndResidueInProtein, + Is.EqualTo(circular.Length)); + }); + } + + // ────────────────────────────────────────────────────────────────────── + // One cut: exactly one cleavage site → PeptideWithSetModifications, length N + // ────────────────────────────────────────────────────────────────────── + [Test] + public static void Digest_OneCut_YieldsLinearPeptideOfLengthN_KAtEnd() + { + // Ring "ACDEFGHIK" (N=9): K at position 9 (last residue) → 1 cleavage site. + // + // maxMissedCleavages: 0 < numCleavageSites: 1 + // → condition maxMissedCleavages >= numCleavageSites is NOT satisfied + // → no CircularPeptideWithSetModifications emitted. + // + // The single cut opens the ring at K(9), producing one linear product: + // "ACDEFGHIK" [1-9], length N, PeptideWithSetModifications. + // + // NOTE: maxMissedCleavages: 1 would satisfy 1 >= 1 and additionally emit + // a CircularPeptideWithSetModifications, giving 2 products total — not 1. + // maxMissedCleavages: 0 is required to isolate the single-cut linear product. + + var circular = new CircularProtein("ACDEFGHIK", "acc_cuts1a"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptides = circular.Digest(digestionParams, [], []) + .Cast() + .ToList(); + + Assert.Multiple(() => + { + Assert.That(peptides, Has.Count.EqualTo(1), + "One cleavage site with maxMissedCleavages=0 produces exactly one linear product."); + + Assert.That(peptides[0], Is.Not.InstanceOf(), + "One cut → linear PeptideWithSetModifications, never circular."); + + Assert.That(peptides[0].Length, Is.EqualTo(circular.Length), + "The single-cut product spans the full ring: length == N."); + + Assert.That(peptides[0].BaseSequence, Is.EqualTo("ACDEFGHIK")); + Assert.That(peptides[0].OneBasedStartResidueInProtein, Is.EqualTo(1)); + Assert.That(peptides[0].OneBasedEndResidueInProtein, Is.EqualTo(9)); + + Assert.That(ReferenceEquals(peptides[0].Protein, circular), Is.True, + "The linear product must reference the CircularProtein as its parent."); + }); + } + + [Test] + public static void Digest_OneCut_YieldsLinearPeptideOfLengthN_KNotAtEnd() + { + // "ACDEFKGHIM": K at position 6, N=10. + // One cut after K at pos 6 → single linear product "GHIMACDEFK", + // start=7, end=16. No sub-peptides: "ACDEFK" [1-6] is excluded + // because its end (6) ≤ N but it requires the proxy endpoint as its + // second boundary, not a genuine second cut within the ring. + var circular = new CircularProtein("ACDEFKGHIM", "acc_cuts1b"); + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptides = circular.Digest(digestionParams, [], []) + .Cast() + .ToList(); + + Assert.Multiple(() => + { + Assert.That(peptides, Has.Count.EqualTo(1), + "One cleavage site produces exactly one product"); + Assert.That(peptides[0], Is.Not.InstanceOf(), + "One cut → linear PeptideWithSetModifications"); + Assert.That(peptides[0].BaseSequence, Is.EqualTo("GHIMACDEFK"), + "Linear product runs from residue after K at pos 6, wrapping to K"); + Assert.That(peptides[0].OneBasedStartResidueInProtein, Is.EqualTo(7), + "Starts at position 7 — immediately after the K cleavage site"); + Assert.That(peptides[0].OneBasedEndResidueInProtein, Is.EqualTo(16), + "Ends at position 16 = 7 + 10 - 1 in doubled-ring numbering"); + Assert.That(ReferenceEquals(peptides[0].Protein, circular), Is.True); + }); + } + // ────────────────────────────────────────────────────────────────────── + // Two cuts (maxMissedCleavages=0): all products are linear + // PeptideWithSetModifications, length < N. + // ────────────────────────────────────────────────────────────────────── + [Test] + public static void Digest_TwoCuts_YieldsOnlySubPeptides_AllLinearType() + { + // Ring "ACDEFKGHIK" (N=10): K at positions 6 and 10 → 2 cleavage sites. + // maxMissedCleavages: 0 < numCleavageSites: 2 + // → no CircularPeptideWithSetModifications emitted. + // → two cuts produce two linear sub-peptides, both length < N. + + var circular = new CircularProtein("ACDEFKGHIK", "acc_cuts2"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var peptides = circular.Digest(digestionParams, [], []) + .Cast() + .ToList(); + + Assert.Multiple(() => + { + Assert.That(peptides, Has.Count.EqualTo(2)); + + Assert.That(peptides.All(p => p.Length < circular.Length), Is.True, + "Two cuts → all products shorter than N."); + + Assert.That(peptides.All(p => p is not CircularPeptideWithSetModifications), Is.True, + "Two cuts → all products are linear PeptideWithSetModifications, never circular."); + + Assert.That(peptides.Select(p => p.BaseSequence), + Is.EquivalentTo(new[] { "ACDEFK", "GHIK" })); + }); + } + + [Test] + public static void Digest_TwoCuts_WithMissedCleavages_LinearProductsAreStillLengthN() + { + // Ring "ACDEFKGHIK" (N=10): K at positions 6 and 10 → 2 cleavage sites. + // maxMissedCleavages: 1 < numCleavageSites: 2 + // → no CircularPeptideWithSetModifications emitted. + // → all products are linear PeptideWithSetModifications. + // + // Expected products: + // 0 missed cleavages (two cuts): + // "ACDEFK" [1-6] length < N + // "GHIK" [7-10] length < N + // 1 missed cleavage (one cut): + // "ACDEFKGHIK" [1-10] length == N (cut after K@10, K@6 is the missed cleavage) + // "GHIKACDEFK" [7-16] length == N (cut after K@6, K@10 is the missed cleavage) + + var circular = new CircularProtein("ACDEFKGHIK", "acc_cuts2mc"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 1, + minPeptideLength: 1); + + var peptides = circular.Digest(digestionParams, [], []) + .Cast() + .ToList(); + + var subPeptides = peptides.Where(p => p.Length < circular.Length).ToList(); + var fullLengthLinear = peptides.Where(p => p.Length == circular.Length).ToList(); + + Assert.Multiple(() => + { + // No circular product: maxMissedCleavages (1) < numCleavageSites (2) + Assert.That(peptides.All(p => p is not CircularPeptideWithSetModifications), Is.True, + "maxMissedCleavages (1) < numCleavageSites (2): no circular product."); + + // Sub-peptides from two cuts — linear, length < N + Assert.That(subPeptides, Has.Count.EqualTo(2)); + Assert.That(subPeptides.All(p => p is not CircularPeptideWithSetModifications), Is.True, + "Sub-peptides (length < N) are linear PeptideWithSetModifications."); + Assert.That(subPeptides.Select(p => p.BaseSequence), + Is.EquivalentTo(new[] { "ACDEFK", "GHIK" })); + + // Full-length products from one cut — linear, length == N + Assert.That(fullLengthLinear, Has.Count.EqualTo(2)); + Assert.That(fullLengthLinear.All(p => p is not CircularPeptideWithSetModifications), Is.True, + "Full-length products (length == N, one cut) are linear PeptideWithSetModifications."); + Assert.That(fullLengthLinear.Select(p => p.BaseSequence), + Is.EquivalentTo(new[] { "ACDEFKGHIK", "GHIKACDEFK" })); + + // Canonical numbering for full-length linear products + var fromK10 = fullLengthLinear.Single(p => p.BaseSequence == "ACDEFKGHIK"); + Assert.That(fromK10.OneBasedStartResidueInProtein, Is.EqualTo(1)); + Assert.That(fromK10.OneBasedEndResidueInProtein, Is.EqualTo(10)); + + var fromK6 = fullLengthLinear.Single(p => p.BaseSequence == "GHIKACDEFK"); + Assert.That(fromK6.OneBasedStartResidueInProtein, Is.EqualTo(7)); + Assert.That(fromK6.OneBasedEndResidueInProtein, Is.EqualTo(16)); + + // All products are bound to the CircularProtein parent + Assert.That(peptides.All(p => ReferenceEquals(p.Protein, circular)), Is.True); + }); + } + // ────────────────────────────────────────────────────────────────────── + // Modification remapping (fix_001) + // ────────────────────────────────────────────────────────────────────── + + private static Modification CreateTestMod(char targetResidue, string id = "TestMod", double mass = 42.01057) + { + ModificationMotif.TryGetMotif(targetResidue.ToString(), out var motif); + return new Modification( + _originalId: id, + _modificationType: "Common", + _target: motif, + _locationRestriction: "Anywhere.", + _monoisotopicMass: mass); + } + + [Test] + public static void Constructor_NonCanonicalInputWithModification_ModificationRemappedToCorrectResidue() + { + // "GKAEC" → canonical "AECGK", offset = 2 + // Original position 3 (A) should become canonical position 1 (A). + var testMod = CreateTestMod('A'); + var mods = new Dictionary> + { + { 3, new List { testMod } } + }; + + var cp = new CircularProtein("GKAEC", "acc_remap1", oneBasedModifications: mods); + + Assert.That(cp.BaseSequence, Is.EqualTo("AECGK")); + Assert.That(cp.OneBasedPossibleLocalizedModifications.ContainsKey(1), Is.True, + "Modification should be remapped to position 1 (residue A)"); + Assert.That(cp.OneBasedPossibleLocalizedModifications.ContainsKey(3), Is.False, + "Position 3 in canonical is residue C, not the original target"); + } + + [Test] + public static void Constructor_AlreadyCanonicalInput_ModificationsUnchanged() + { + // "AECGK" position 2 is 'E' + var testMod = CreateTestMod('E'); + var mods = new Dictionary> + { + { 2, new List { testMod } } + }; + + var cp = new CircularProtein("AECGK", "acc_remap2", oneBasedModifications: mods); + + Assert.That(cp.BaseSequence, Is.EqualTo("AECGK")); + Assert.That(cp.OneBasedPossibleLocalizedModifications.ContainsKey(2), Is.True); + Assert.That(cp.OneBasedPossibleLocalizedModifications[2], Contains.Item(testMod)); + } + + [Test] + public static void Constructor_NullModifications_DoesNotThrow() + { + Assert.DoesNotThrow(() => + new CircularProtein("GKAEC", "acc_remap3", oneBasedModifications: null)); + } + + [Test] + public static void Constructor_EmptyModifications_DoesNotThrow() + { + var mods = new Dictionary>(); + var cp = new CircularProtein("GKAEC", "acc_remap4", oneBasedModifications: mods); + + Assert.That(cp.OneBasedPossibleLocalizedModifications, Is.Empty); + } + + [Test] + public static void Constructor_MultipleModificationsRemapped_AllPositionsCorrect() + { + // "GKAEC" → "AECGK", offset = 2 + // pos 1 (G) → ((1-1-2+5)%5)+1 = 4 + // pos 4 (E) → ((4-1-2+5)%5)+1 = 2 + var testMod = CreateTestMod('G'); + var mod2 = CreateTestMod('E', "OtherMod", 15.99491); + + var mods = new Dictionary> + { + { 1, new List { testMod } }, + { 4, new List { mod2 } } + }; + + var cp = new CircularProtein("GKAEC", "acc_remap5", oneBasedModifications: mods); + + Assert.That(cp.BaseSequence, Is.EqualTo("AECGK")); + Assert.That(cp.OneBasedPossibleLocalizedModifications.ContainsKey(4), Is.True, + "G was at original pos 1, should be at canonical pos 4"); + Assert.That(cp.OneBasedPossibleLocalizedModifications[4], Contains.Item(testMod)); + Assert.That(cp.OneBasedPossibleLocalizedModifications.ContainsKey(2), Is.True, + "E was at original pos 4, should be at canonical pos 2"); + Assert.That(cp.OneBasedPossibleLocalizedModifications[2], Contains.Item(mod2)); + } + + [Test] + public static void Constructor_ModificationOnLastResidue_WrapsCorrectly() + { + // "GKAEC" → "AECGK", offset = 2 + // pos 5 (C) → ((5-1-2+5)%5)+1 = 3 + var testMod = CreateTestMod('C'); + var mods = new Dictionary> + { + { 5, new List { testMod } } + }; + + var cp = new CircularProtein("GKAEC", "acc_remap6", oneBasedModifications: mods); + + Assert.That(cp.BaseSequence, Is.EqualTo("AECGK")); + Assert.That(cp.OneBasedPossibleLocalizedModifications.ContainsKey(3), Is.True, + "C was at original pos 5, should be at canonical pos 3"); + } + + [Test] + public static void FromProtein_SourceHasModificationsAndNonCanonicalSequence_ModificationsRemapped() + { + // "GKAEC" position 3 is 'A' + var testMod = CreateTestMod('A'); + var mods = new Dictionary> + { + { 3, new List { testMod } } + }; + + var source = new Protein("GKAEC", "acc_remap7", oneBasedModifications: mods); + var cp = CircularProtein.FromProtein(source); + + Assert.That(cp.BaseSequence, Is.EqualTo("AECGK")); + Assert.That(cp.OneBasedPossibleLocalizedModifications.ContainsKey(1), Is.True, + "Modification at original pos 3 (A) should map to canonical pos 1 (A)"); + } + + [Test] + public static void Constructor_SingleResidue_ModificationStaysAtPositionOne() + { + var testMod = CreateTestMod('A'); + var mods = new Dictionary> + { + { 1, new List { testMod } } + }; + + var cp = new CircularProtein("A", "acc_remap8", oneBasedModifications: mods); + + Assert.That(cp.BaseSequence, Is.EqualTo("A")); + Assert.That(cp.OneBasedPossibleLocalizedModifications.ContainsKey(1), Is.True); + } + + [Test] + public static void GetCanonicalRotationWithOffset_ReturnsCorrectOffset() + { + var (canonical, offset) = CircularProtein.GetCanonicalRotationWithOffset("GKAEC"); + + Assert.That(canonical, Is.EqualTo("AECGK")); + Assert.That(offset, Is.EqualTo(2)); + } + + [Test] + public static void GetCanonicalRotationWithOffset_AlreadyCanonical_OffsetIsZero() + { + var (canonical, offset) = CircularProtein.GetCanonicalRotationWithOffset("AECGK"); + + Assert.That(canonical, Is.EqualTo("AECGK")); + Assert.That(offset, Is.EqualTo(0)); + } + + [TestCase("KAEC", 1, 4, 'K', TestName = "ModRemap_K_at_pos1_to_pos4")] + [TestCase("KAEC", 2, 1, 'A', TestName = "ModRemap_A_at_pos2_to_pos1")] + [TestCase("KAEC", 3, 2, 'E', TestName = "ModRemap_E_at_pos3_to_pos2")] + [TestCase("KAEC", 4, 3, 'C', TestName = "ModRemap_C_at_pos4_to_pos3")] + public static void Constructor_ModAtPosition_LandsOnSameAminoAcid( + string sequence, int originalPos, int expectedCanonicalPos, char expectedResidue) + { + var testMod = CreateTestMod(sequence[originalPos - 1]); + var mods = new Dictionary> + { + { originalPos, new List { testMod } } + }; + + var cp = new CircularProtein(sequence, "acc_tc", oneBasedModifications: mods); + + Assert.That(cp.OneBasedPossibleLocalizedModifications.ContainsKey(expectedCanonicalPos), Is.True, + $"Mod should be at canonical position {expectedCanonicalPos}"); + Assert.That(cp.BaseSequence[expectedCanonicalPos - 1], Is.EqualTo(expectedResidue), + $"Canonical position {expectedCanonicalPos} should be residue {expectedResidue}"); + } + + // ────────────────────────────────────────────────────────────────────── + // Positional isomer deduplication (fix_009) + // ────────────────────────────────────────────────────────────────────── + + [Test] + public static void Digest_RepeatedMotifCircularProtein_RetainsAllPositionalIsomers() + { + // "ARARK" canonical → trypsin cuts after R and K. + // Two distinct "AR" fragments at different ring positions must both survive. + var protein = new CircularProtein("ARARK", "REPEAT_TEST"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var products = protein + .Digest(digestionParams, new List(), new List()) + .ToList(); + + var arProducts = products + .Where(p => p is PeptideWithSetModifications pwsm && pwsm.BaseSequence == "AR") + .Cast() + .ToList(); + + Assert.That(arProducts.Count, Is.GreaterThanOrEqualTo(2), + "Both 'AR' positional isomers at different ring positions must be retained"); + + var startPositions = arProducts + .Select(p => p.OneBasedStartResidueInProtein) + .Distinct() + .ToList(); + + Assert.That(startPositions.Count, Is.GreaterThanOrEqualTo(2), + "The 'AR' products must originate at distinct start positions on the ring"); + } + + [Test] + public static void Digest_RepeatedMotifCircularProtein_TrueDuplicatesStillCollapsed() + { + var protein = new CircularProtein("ARARK", "REPEAT_TEST"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 2, + minPeptideLength: 1); + + var products = protein + .Digest(digestionParams, new List(), new List()) + .Cast() + .Where(p => p is not CircularPeptideWithSetModifications) + .ToList(); + + // No two products should share both the same start position and full sequence + var keys = products.Select(p => + $"{p.OneBasedStartResidueInProtein}:{p.FullSequence}").ToList(); + + Assert.That(keys.Distinct().Count(), Is.EqualTo(keys.Count), + "True duplicates (same position + same sequence) must still be collapsed"); + } + + [Test] + public static void Digest_SymmetricRepeatProtein_AllPositionsRetained() + { + // "ARARAR" — 3 copies of "AR", trypsin cuts after each R + var symmetricProtein = new CircularProtein("ARARAR", "SYMMETRIC_TEST"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 0, + minPeptideLength: 1); + + var products = symmetricProtein + .Digest(digestionParams, new List(), new List()) + .OfType() + .Where(p => p is not CircularPeptideWithSetModifications) + .Where(p => p.BaseSequence == "AR") + .ToList(); + + Assert.That(products.Count, Is.EqualTo(3), + "All three 'AR' positional isomers must be retained in a fully symmetric ring"); + + var distinctStarts = products + .Select(p => p.OneBasedStartResidueInProtein) + .Distinct() + .ToList(); + + Assert.That(distinctStarts.Count, Is.EqualTo(3), + "Each 'AR' product must have a unique start position"); + } + + [Test] + public static void Digest_RepeatedMotif_WithMissedCleavages_PositionalIsomersPreserved() + { + var protein = new CircularProtein("ARARK", "REPEAT_TEST"); + + var digestionParams = new DigestionParams( + protease: "trypsin", + maxMissedCleavages: 1, + minPeptideLength: 1); + + var products = protein + .Digest(digestionParams, new List(), new List()) + .OfType() + .Where(p => p is not CircularPeptideWithSetModifications) + .ToList(); + + // For any sequence that appears at multiple positions, all positions must be present + var grouped = products + .GroupBy(p => p.FullSequence) + .Where(g => g.Select(p => p.OneBasedStartResidueInProtein).Distinct().Count() > 1) + .ToList(); + + foreach (var group in grouped) + { + var distinctPositions = group + .Select(p => p.OneBasedStartResidueInProtein) + .Distinct() + .Count(); + + Assert.That(group.Count(), Is.EqualTo(distinctPositions), + $"Sequence '{group.Key}' has {distinctPositions} distinct positions " + + $"but only {group.Count()} products were emitted"); + } + } + // ────────────────────────────────────────────────────────────────────── + // CircularPeptideWithSetModifications constructor validation (fix_010) + // ────────────────────────────────────────────────────────────────────── + + [Test] + public static void CircularPeptide_NullProtein_ThrowsArgumentNullException() + { + var digestionParams = new DigestionParams(); + var emptyMods = new Dictionary(); + + var ex = Assert.Throws(() => + new CircularPeptideWithSetModifications( + protein: null, + digestionParams: digestionParams, + oneBasedStartResidueInProtein: 1, + oneBasedEndResidueInProtein: 5, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: "test", + missedCleavages: 0, + allModsOneIsNterminus: emptyMods, + numFixedMods: 0)); + + Assert.That(ex.ParamName, Is.EqualTo("protein")); + Assert.That(ex.Message, Does.Contain("non-null")); + } + + [Test] + public static void CircularPeptide_NonCircularProtein_ThrowsArgumentException() + { + var linearProtein = new Protein("ACDEFG", "LINEAR1"); + var digestionParams = new DigestionParams(); + var emptyMods = new Dictionary(); + + var ex = Assert.Throws(() => + new CircularPeptideWithSetModifications( + protein: linearProtein, + digestionParams: digestionParams, + oneBasedStartResidueInProtein: 1, + oneBasedEndResidueInProtein: 6, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: "test", + missedCleavages: 0, + allModsOneIsNterminus: emptyMods, + numFixedMods: 0)); + + Assert.That(ex.ParamName, Is.EqualTo("protein")); + Assert.That(ex.Message, Does.Contain("CircularProtein")); + } + + [Test] + public static void CircularPeptide_ValidCircularProtein_SetsCircularParent() + { + var circularProtein = new CircularProtein("ACDEFG", "CIRC1"); + var digestionParams = new DigestionParams(); + var emptyMods = new Dictionary(); + + var peptide = new CircularPeptideWithSetModifications( + protein: circularProtein, + digestionParams: digestionParams, + oneBasedStartResidueInProtein: 1, + oneBasedEndResidueInProtein: 6, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: "valid", + missedCleavages: 0, + allModsOneIsNterminus: emptyMods, + numFixedMods: 0); + + Assert.That(peptide.CircularParent, Is.Not.Null); + Assert.That(peptide.CircularParent, Is.SameAs(circularProtein)); + } + // ────────────────────────────────────────────────────────────────────── + // Wrap-around fragmentation (fix_013) + // ────────────────────────────────────────────────────────────────────── + + private static CircularPeptideWithSetModifications BuildFullRingPeptide(string sequence) + { + var protein = new CircularProtein(sequence, "TEST"); + int n = protein.BaseSequence.Length; + return new CircularPeptideWithSetModifications( + protein, + new DigestionParams(), + oneBasedStartResidueInProtein: 1, + oneBasedEndResidueInProtein: n, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: "full-ring", + missedCleavages: 0, + allModsOneIsNterminus: new Dictionary(), + numFixedMods: 0, + baseSequence: protein.BaseSequence); + } + + [Test] + public static void FragmentInternally_FullRingLength5_CountEqualsNTimesNMinusMinLength() + { + // N=5, minLength=2: expected = 5 * (5-2) = 15 + var peptide = BuildFullRingPeptide("ACDEF"); + var products = new List(); + peptide.FragmentInternally(DissociationType.HCD, 2, products); + + Assert.That(products.Count, Is.EqualTo(15), + "Full-ring peptide of length 5 should produce N*(N-2) = 15 internal fragments"); + } + + [Test] + public static void FragmentInternally_FullRing_ContainsWrapAroundFragment() + { + var peptide = BuildFullRingPeptide("ACDEF"); + var products = new List(); + peptide.FragmentInternally(DissociationType.HCD, 2, products); + + // Fragment starting at last residue wrapping to first + bool hasWrapFragment = products.Any(p => + p.FragmentNumber == 5 && p.ResiduePosition == 2); + + Assert.That(hasWrapFragment, Is.True, + "Should contain a wrap-around fragment starting at residue 5 with length 2"); + } + + [Test] + public static void FragmentInternally_FullRingLength4_TotalCountIsCorrect() + { + // N=4, minLength=2: count = 4 * (4-2) = 8 + var peptide = BuildFullRingPeptide("ACDE"); + var products = new List(); + peptide.FragmentInternally(DissociationType.HCD, 2, products); + + Assert.That(products.Count, Is.EqualTo(8)); + } + + [Test] + public static void FragmentInternally_FullRing_AllMassesPositive() + { + var peptide = BuildFullRingPeptide("ACDEF"); + var products = new List(); + peptide.FragmentInternally(DissociationType.HCD, 2, products); + + Assert.That(products.All(p => p.NeutralMass > 0), Is.True, + "Every fragment mass should be positive, including wrap-around fragments"); + } + + [Test] + public static void FragmentInternally_FullRing_NoFullLengthFragments() + { + var peptide = BuildFullRingPeptide("ACDEF"); + var products = new List(); + peptide.FragmentInternally(DissociationType.HCD, 2, products); + + Assert.That(products.Any(p => p.ResiduePosition == 5), Is.False, + "No fragment should span the entire ring (length == N)"); + } + + [Test] + public static void FragmentInternally_SubPeptide_DoesNotWrapAround() + { + var protein = new CircularProtein("ACDEFG", "TEST"); + var subPeptide = new CircularPeptideWithSetModifications( + protein, + new DigestionParams(), + oneBasedStartResidueInProtein: 1, + oneBasedEndResidueInProtein: 4, + cleavageSpecificity: CleavageSpecificity.Full, + peptideDescription: "sub-ring", + missedCleavages: 0, + allModsOneIsNterminus: new Dictionary(), + numFixedMods: 0, + baseSequence: "ACDE"); + + var products = new List(); + subPeptide.FragmentInternally(DissociationType.HCD, 2, products); + + // Sub-peptide of length 4, minLength 2: (4-2)(4-2+1)/2 = 3 + Assert.That(products.Count, Is.EqualTo(3), + "Sub-peptide should not include wrap-around fragments"); + } + } +} diff --git a/mzLib/mzLib.nuspec b/mzLib/mzLib.nuspec index 0bc40b8c5..ae5e4e807 100644 --- a/mzLib/mzLib.nuspec +++ b/mzLib/mzLib.nuspec @@ -2,7 +2,7 @@ mzLib - 1.0.574 + 9.9.901 mzLib Stef S. Stef S. @@ -11,49 +11,49 @@ images\mzLib.png Library for mass spectrometry projects. Chemistry Spectrometry - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -119,4 +119,4 @@ - + \ No newline at end of file