p2s_mapper 1.0.0

package/esm/pairwiseAlignment.js

@@ -0,0 +1,328 @@
+// BLOSUM62 scoring matrix — standard 20 amino acids + B, Z, X, *
+// prettier-ignore
+const AMINO_ACIDS = ['A', 'R', 'N', 'D', 'C', 'Q', 'E', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V', 'B', 'Z', 'X', '*'];
+// prettier-ignore
+const BLOSUM62_RAW = [
+    //  A   R   N   D   C   Q   E   G   H   I   L   K   M   F   P   S   T   W   Y   V   B   Z   X   *
+    [4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0, -4], // A
+    [-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1, -4], // R
+    [-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1, -4], // N
+    [-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1, -4], // D
+    [0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2, -4], // C
+    [-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1, -4], // Q
+    [-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4], // E
+    [0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1, -4], // G
+    [-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1, -4], // H
+    [-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1, -4], // I
+    [-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1, -4], // L
+    [-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1, -4], // K
+    [-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1, -4], // M
+    [-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1, -4], // F
+    [-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2, -4], // P
+    [1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0, -4], // S
+    [0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0, -4], // T
+    [-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2, -4], // W
+    [-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1, -4], // Y
+    [0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1, -4], // V
+    [-2, -1, 3, 4, -3, 0, 1, -1, 0, -3, -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1, -4], // B
+    [-1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3, 1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1, -4], // Z
+    [0, -1, -1, -1, -2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1, -4], // X
+    [-4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, -4, 1], // *
+];
+// Score of a residue pair that isn't in the matrix at all.
+const UNKNOWN_PAIR_SCORE = -4;
+// The DP reads the matrix once per cell, so both the residue→row lookup and the
+// matrix itself are flat typed arrays keyed by char code: charCodeToRow maps
+// 'a'/'A' to the same row, and unknown residues to -1 (scored as unknown).
+const N_AA = AMINO_ACIDS.length;
+const charCodeToRow = new Int8Array(128).fill(-1);
+for (let i = 0; i < N_AA; i++) {
+    const aa = AMINO_ACIDS[i];
+    charCodeToRow[aa.charCodeAt(0)] = i;
+    charCodeToRow[aa.toLowerCase().charCodeAt(0)] = i;
+}
+const BLOSUM62 = new Int8Array(N_AA * N_AA);
+for (let i = 0; i < N_AA; i++) {
+    for (let j = 0; j < N_AA; j++) {
+        BLOSUM62[i * N_AA + j] = BLOSUM62_RAW[i][j];
+    }
+}
+const rowOf = (c) => {
+    const code = c.charCodeAt(0);
+    return code < 128 ? charCodeToRow[code] : -1;
+};
+function getScore(a, b) {
+    const i = rowOf(a);
+    const j = rowOf(b);
+    return i < 0 || j < 0 ? UNKNOWN_PAIR_SCORE : BLOSUM62[i * N_AA + j];
+}
+// Default gap penalties (matching EMBOSS defaults)
+const GAP_OPEN = -10;
+const GAP_EXTEND = -0.5;
+/**
+ * Ceiling on the dynamic-programming table, in cells. Both algorithms are
+ * O(m*n) time and hold one byte of traceback per cell, so this bounds the
+ * alignment at ~40 MB and roughly a second of main-thread work. Without it a
+ * titin-sized transcript or a long nucleic-acid chain locks up or OOMs the tab.
+ * Callers that have several candidates to align should check `alignmentTooLarge`
+ * and skip the oversized ones rather than let this throw.
+ */
+export const MAX_ALIGNMENT_CELLS = 40_000_000;
+export function alignmentTooLarge(len1, len2) {
+    return (len1 + 1) * (len2 + 1) > MAX_ALIGNMENT_CELLS;
+}
+function assertAlignable(len1, len2) {
+    if (alignmentTooLarge(len1, len2)) {
+        throw new Error(`Sequences too long to align (${len1} x ${len2} residues exceeds the ${MAX_ALIGNMENT_CELLS} cell limit)`);
+    }
+}
+// Traceback states. Each cell stores, for each of the three matrices, which
+// matrix its best predecessor came from — 2 bits per matrix, packed into one
+// byte. Storing pointers instead of re-deriving them by comparing scores keeps
+// traceback exact under Float32 rounding and lets the score matrices collapse
+// to two rows.
+const FROM_M = 0;
+const FROM_IX = 1;
+const FROM_IY = 2;
+// Smith-Waterman only: the local alignment restarts here, so traceback stops.
+const FROM_NONE = 3;
+const M_SHIFT = 0;
+const IX_SHIFT = 2;
+const IY_SHIFT = 4;
+const readPointer = (trace, at, shift) => ((trace[at] >> shift) & 0b11);
+/**
+ * Fill the affine-gap DP tables for both algorithms; `local` switches
+ * Needleman-Wunsch (global, ends at the corner) to Smith-Waterman (restarts at
+ * 0, ends at the best-scoring cell). Only the previous and current score rows
+ * are kept — the full traceback lives in the packed `trace` byte array.
+ */
+function fillMatrices(seq1, seq2, gapOpen, gapExtend, local) {
+    const m = seq1.length;
+    const n = seq2.length;
+    assertAlignable(m, n);
+    const width = n + 1;
+    const trace = new Uint8Array((m + 1) * width);
+    // Row 0. Global: only M[0][0] is reachable and Iy[0][j] is the leading-gap
+    // base case. Local: M starts at 0 everywhere, gaps are unreachable.
+    let prevM = new Float32Array(width);
+    let prevIx = new Float32Array(width).fill(-Infinity);
+    let prevIy = new Float32Array(width).fill(-Infinity);
+    let curM = new Float32Array(width);
+    let curIx = new Float32Array(width);
+    let curIy = new Float32Array(width);
+    if (!local) {
+        prevM.fill(-Infinity);
+        prevM[0] = 0;
+        for (let j = 1; j <= n; j++) {
+            prevIy[j] = gapOpen + (j - 1) * gapExtend;
+        }
+    }
+    let bestScore = local ? 0 : -Infinity;
+    let bestI = 0;
+    let bestJ = 0;
+    let bestMatrix = FROM_M;
+    // Resolve seq2 to matrix rows once instead of once per cell.
+    const cols = new Int8Array(n);
+    for (let j = 0; j < n; j++) {
+        cols[j] = rowOf(seq2[j]);
+    }
+    for (let i = 1; i <= m; i++) {
+        // Column 0, mirroring row 0.
+        curM[0] = local ? 0 : -Infinity;
+        curIx[0] = local ? -Infinity : gapOpen + (i - 1) * gapExtend;
+        curIy[0] = -Infinity;
+        const rowBase = i * width;
+        const scoreRow = rowOf(seq1[i - 1]);
+        const scoreBase = scoreRow * N_AA;
+        for (let j = 1; j <= n; j++) {
+            const col = cols[j - 1];
+            const matchScore = scoreRow < 0 || col < 0
+                ? UNKNOWN_PAIR_SCORE
+                : BLOSUM62[scoreBase + col];
+            const dM = prevM[j - 1];
+            const dIx = prevIx[j - 1];
+            const dIy = prevIy[j - 1];
+            // Ties resolve M > Ix > Iy, matching the previous implementation.
+            const bestDiag = Math.max(dM, dIx, dIy);
+            const diagFrom = bestDiag === dM ? FROM_M : bestDiag === dIx ? FROM_IX : FROM_IY;
+            const mScore = bestDiag + matchScore;
+            const restart = local && mScore <= 0;
+            curM[j] = restart ? 0 : mScore;
+            const openIx = prevM[j] + gapOpen;
+            const extendIx = prevIx[j] + gapExtend;
+            curIx[j] = Math.max(openIx, extendIx);
+            const openIy = curM[j - 1] + gapOpen;
+            const extendIy = curIy[j - 1] + gapExtend;
+            curIy[j] = Math.max(openIy, extendIy);
+            trace[rowBase + j] =
+                ((restart ? FROM_NONE : diagFrom) << M_SHIFT) |
+                    ((openIx >= extendIx ? FROM_M : FROM_IX) << IX_SHIFT) |
+                    ((openIy >= extendIy ? FROM_M : FROM_IY) << IY_SHIFT);
+            if (local) {
+                const cellMax = Math.max(curM[j], curIx[j], curIy[j]);
+                if (cellMax > bestScore) {
+                    bestScore = cellMax;
+                    bestI = i;
+                    bestJ = j;
+                    bestMatrix =
+                        cellMax === curM[j]
+                            ? FROM_M
+                            : cellMax === curIx[j]
+                                ? FROM_IX
+                                : FROM_IY;
+                }
+            }
+        }
+        ;
+        [prevM, curM] = [curM, prevM];
+        [prevIx, curIx] = [curIx, prevIx];
+        [prevIy, curIy] = [curIy, prevIy];
+    }
+    if (local) {
+        return {
+            trace,
+            width,
+            score: bestScore,
+            startI: bestI,
+            startJ: bestJ,
+            startMatrix: bestMatrix,
+        };
+    }
+    // prev* now holds row m.
+    const finalM = prevM[n];
+    const finalIx = prevIx[n];
+    const finalIy = prevIy[n];
+    const score = Math.max(finalM, finalIx, finalIy);
+    return {
+        trace,
+        width,
+        score,
+        startI: m,
+        startJ: n,
+        startMatrix: score === finalM ? FROM_M : score === finalIx ? FROM_IX : FROM_IY,
+    };
+}
+/**
+ * Walk the packed traceback back to an edge. Rows are built back-to-front into
+ * arrays and reversed once, rather than prepending onto a string per residue
+ * (which is quadratic in the alignment length).
+ */
+function traceback(seq1, seq2, filled) {
+    const { trace, width, startI, startJ, score } = filled;
+    // Reversed: pushing here is prepending to the final string.
+    const out1 = [];
+    const out2 = [];
+    // Residues past the aligned region (the whole sequences when the local
+    // alignment is empty) hang off the end as gaps.
+    for (let k = seq1.length; k > startI; k--) {
+        out1.push(seq1[k - 1]);
+        out2.push('-');
+    }
+    for (let k = seq2.length; k > startJ; k--) {
+        out1.push('-');
+        out2.push(seq2[k - 1]);
+    }
+    let i = startI;
+    let j = startJ;
+    let matrix = filled.startMatrix;
+    while (i > 0 && j > 0) {
+        const at = i * width + j;
+        if (matrix === FROM_M) {
+            const next = readPointer(trace, at, M_SHIFT);
+            if (next === FROM_NONE) {
+                break;
+            }
+            out1.push(seq1[i - 1]);
+            out2.push(seq2[j - 1]);
+            matrix = next;
+            i--;
+            j--;
+        }
+        else if (matrix === FROM_IX) {
+            out1.push(seq1[i - 1]);
+            out2.push('-');
+            matrix = readPointer(trace, at, IX_SHIFT);
+            i--;
+        }
+        else {
+            out1.push('-');
+            out2.push(seq2[j - 1]);
+            matrix = readPointer(trace, at, IY_SHIFT);
+            j--;
+        }
+    }
+    // Whatever is left runs into an edge, so it can only be gaps.
+    while (i > 0) {
+        out1.push(seq1[i - 1]);
+        out2.push('-');
+        i--;
+    }
+    while (j > 0) {
+        out1.push('-');
+        out2.push(seq2[j - 1]);
+        j--;
+    }
+    return {
+        alignedSeq1: out1.reverse().join(''),
+        alignedSeq2: out2.reverse().join(''),
+        score,
+    };
+}
+/**
+ * Needleman-Wunsch global alignment algorithm
+ * Aligns entire sequences end-to-end
+ */
+export function needlemanWunsch(seq1, seq2, gapOpen = GAP_OPEN, gapExtend = GAP_EXTEND) {
+    return traceback(seq1, seq2, fillMatrices(seq1, seq2, gapOpen, gapExtend, false));
+}
+/**
+ * Smith-Waterman local alignment algorithm
+ * Finds the best local alignment between subsequences
+ */
+export function smithWaterman(seq1, seq2, gapOpen = GAP_OPEN, gapExtend = GAP_EXTEND) {
+    return traceback(seq1, seq2, fillMatrices(seq1, seq2, gapOpen, gapExtend, true));
+}
+function buildConsensus(alignedSeq1, alignedSeq2) {
+    const chars = [];
+    for (let i = 0; i < alignedSeq1.length; i++) {
+        const a = alignedSeq1[i];
+        const b = alignedSeq2[i];
+        if (a !== '-' && b !== '-' && a.toUpperCase() === b.toUpperCase()) {
+            chars.push('|');
+        }
+        else if (a !== '-' && b !== '-' && getScore(a, b) > 0) {
+            chars.push(':');
+        }
+        else {
+            chars.push(' ');
+        }
+    }
+    return chars.join('');
+}
+/** The score of a sequence aligned to itself with no gaps. */
+export function selfScore(seq) {
+    let score = 0;
+    for (const c of seq) {
+        score += getScore(c, c);
+    }
+    return score;
+}
+export function scoredAlignment(seq1, seq2, algorithm) {
+    const { alignedSeq1, alignedSeq2, score } = algorithm === 'smith_waterman'
+        ? smithWaterman(seq1, seq2)
+        : needlemanWunsch(seq1, seq2);
+    return {
+        alignment: {
+            consensus: buildConsensus(alignedSeq1, alignedSeq2),
+            alns: [
+                { id: 'a', seq: alignedSeq1 },
+                { id: 'b', seq: alignedSeq2 },
+            ],
+        },
+        score,
+    };
+}
+export function runLocalAlignment(seq1, seq2, algorithm) {
+    return scoredAlignment(seq1, seq2, algorithm).alignment;
+}
+//# sourceMappingURL=pairwiseAlignment.js.map

package/esm/pairwiseAlignment.js.map

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package/esm/pdbUniProtMapping.d.ts

@@ -0,0 +1,75 @@
+import type { FetchOptions } from './fetchUtils.ts';
+/** One contiguous UniProt <-> structure correspondence for a single entity.
+ * `unp*` are 1-based UniProt positions; `struct*` are 0-based inclusive
+ * structure-sequence positions, this plugin's native coordinate. */
+export interface UniProtStructureSegment {
+    entityId: string;
+    /** author chain id, when the response names it */
+    chainId?: string;
+    unpStart: number;
+    unpEnd: number;
+    structStart: number;
+    structEnd: number;
+    /** the endpoints' author residue numbers, the numbering a paper cites and a
+     * Mol* hover shows; absent when the response omits them */
+    authorStart?: number;
+    authorEnd?: number;
+}
+export interface UniProtStructureMapping {
+    accession: string;
+    /** UniProt entry name, e.g. "P53_HUMAN" */
+    name?: string;
+    segments: UniProtStructureSegment[];
+}
+/**
+ * Maps a 1-based UniProt position to a 0-based structure-sequence position.
+ * Returns undefined for positions outside the modeled region, so callers drop
+ * the feature instead of drawing it somewhere misleading.
+ */
+export type MapUniProtPosition = (uniprotPos: number) => number | undefined;
+export declare function pdbeSiftsUrl(pdbId: string): string;
+/** SIFTS for an entry, retried twice: one failed request would otherwise
+ * leave a fusion construct mapped onto its partner for the whole session. */
+export declare function fetchUniProtStructureMappings(pdbId: string, opts?: FetchOptions): Promise<UniProtStructureMapping[]>;
+/**
+ * Parses a PDBe `mappings/uniprot/{pdbId}` response into one entry per UniProt
+ * accession. Unparseable segments are skipped rather than failing the whole
+ * response — a chimera with one malformed segment still maps its other chains.
+ * The response is keyed by pdb id, so the single entry is taken whatever its key.
+ */
+export declare function parseUniProtStructureMappings(json: unknown): UniProtStructureMapping[];
+/** The entity a SIFTS segment is matched against: its mmCIF id and the author
+ * chains carrying it. */
+export interface SegmentEntity {
+    entityId: string;
+    chains: readonly string[];
+}
+/**
+ * Picks the UniProt entry that describes a given entity, with its segments
+ * narrowed to that entity. Only the entity the plugin has mapped to the
+ * transcript is relevant — a heteromer maps each of its chains to a different
+ * accession, and using the wrong one would silently annotate the wrong protein.
+ * When several accessions cover the same entity (a chimeric construct) the one
+ * contributing the most residues wins.
+ */
+export declare function chooseUniProtMappingForEntity(mappings: UniProtStructureMapping[], entity: SegmentEntity | undefined): UniProtStructureMapping | undefined;
+/**
+ * Mapped structure positions that SIFTS assigns to a protein other than the
+ * transcript's, on a chain that fuses two. Local alignment bridges a fusion
+ * boundary, and on every GPCR fusion construct checked it scattered receptor
+ * residues onto the partner, 33 of them onto T4 lysozyme in 2RH1.
+ *
+ * `mapped` is each mapped structure position and whether its pair is
+ * identical. The transcript's own accession is the one whose covered positions
+ * are most often identical, plus a pseudocount, as the chain picker scores
+ * chains. A count of covered positions would not do: TP53's 11-residue peptide
+ * fused to CDK2 covers 11 positions against 224 chance hits on the kinase, and
+ * counting unmapped the peptide. Unless that accession reaches half identity
+ * the transcript is taken to be neither protein, and nothing is unmapped.
+ * Residues SIFTS assigns to no accession, such as tags, stay mapped.
+ */
+export declare function fusionPartnerPositions(mappings: UniProtStructureMapping[], entity: SegmentEntity | undefined, mapped: ReadonlyMap<number, boolean>): Set<number>;
+/** 1-based UniProt position -> 0-based structure position, for an AlphaFold
+ * model whose sequence is the UniProt sequence. */
+export declare const identityUniProtPositionMap: MapUniProtPosition;
+export declare function makeUniProtPositionMap(segments: UniProtStructureSegment[]): MapUniProtPosition;

package/esm/pdbUniProtMapping.js

@@ -0,0 +1,231 @@
+// SIFTS UniProt <-> PDB residue mapping.
+//
+// UniProt feature coordinates are positions in the UniProt canonical sequence.
+// For an AlphaFold model that *is* the structure's own sequence, so a feature at
+// UniProt position p sits at structure position p - 1. For an experimental PDB
+// entry it is not: the deposited construct is usually a fragment, often with
+// tags or engineered residues, so the two numberings differ by a per-segment
+// offset (1TUP's p53 chain starts at UniProt 94; 6VXX's spike SEQRES 33 is
+// UniProt 14). SIFTS is the authoritative alignment between the two, published
+// per entity/chain by PDBe.
+//
+// `residue_number` in the PDBe response is the 1-based index into the entity's
+// SEQRES, i.e. label_seq_id, which is exactly this plugin's structure-sequence
+// position + 1 (see applyLociInteractivity.ts for the other place that boundary
+// is crossed).
+import { jsonfetch, timeout } from "./fetchUtils.js";
+export function pdbeSiftsUrl(pdbId) {
+    return `https://www.ebi.ac.uk/pdbe/api/mappings/uniprot/${pdbId.toLowerCase()}`;
+}
+const SIFTS_RETRY_DELAYS_MS = [1000, 3000];
+// bounded, since a view reports itself loading until SIFTS answers
+const SIFTS_TIMEOUT_MS = 20_000;
+/** SIFTS for an entry, retried twice: one failed request would otherwise
+ * leave a fusion construct mapped onto its partner for the whole session. */
+export async function fetchUniProtStructureMappings(pdbId, opts) {
+    const { signal: caller, ...rest } = opts ?? {};
+    const signal = caller ?? undefined;
+    const deadline = () => signal
+        ? AbortSignal.any([signal, AbortSignal.timeout(SIFTS_TIMEOUT_MS)])
+        : AbortSignal.timeout(SIFTS_TIMEOUT_MS);
+    for (let attempt = 0;; attempt++) {
+        try {
+            return parseUniProtStructureMappings(await jsonfetch(pdbeSiftsUrl(pdbId), { ...rest, signal: deadline() }));
+        }
+        catch (e) {
+            const delay = SIFTS_RETRY_DELAYS_MS[attempt];
+            if (delay === undefined) {
+                throw e;
+            }
+            await timeout(delay, signal);
+        }
+    }
+}
+function isRecord(value) {
+    return typeof value === 'object' && value !== null && !Array.isArray(value);
+}
+function finiteNumber(value) {
+    return typeof value === 'number' && Number.isFinite(value) ? value : undefined;
+}
+function residueNumber(endpoint) {
+    return isRecord(endpoint) ? finiteNumber(endpoint.residue_number) : undefined;
+}
+function authorResidueNumber(endpoint) {
+    return isRecord(endpoint)
+        ? finiteNumber(endpoint.author_residue_number)
+        : undefined;
+}
+function parseSegment(mapping) {
+    if (!isRecord(mapping)) {
+        return undefined;
+    }
+    const entityId = finiteNumber(mapping.entity_id);
+    const unpStart = finiteNumber(mapping.unp_start);
+    const unpEnd = finiteNumber(mapping.unp_end);
+    const structStart = residueNumber(mapping.start);
+    const structEnd = residueNumber(mapping.end);
+    const authorStart = authorResidueNumber(mapping.start);
+    const authorEnd = authorResidueNumber(mapping.end);
+    return entityId === undefined ||
+        unpStart === undefined ||
+        unpEnd === undefined ||
+        structStart === undefined ||
+        structEnd === undefined
+        ? undefined
+        : {
+            entityId: String(entityId),
+            ...(typeof mapping.chain_id === 'string'
+                ? { chainId: mapping.chain_id }
+                : {}),
+            unpStart,
+            unpEnd,
+            // SEQRES/label_seq_id is 1-based, structure positions are 0-based
+            structStart: structStart - 1,
+            structEnd: structEnd - 1,
+            ...(authorStart === undefined ? {} : { authorStart }),
+            ...(authorEnd === undefined ? {} : { authorEnd }),
+        };
+}
+/**
+ * Parses a PDBe `mappings/uniprot/{pdbId}` response into one entry per UniProt
+ * accession. Unparseable segments are skipped rather than failing the whole
+ * response — a chimera with one malformed segment still maps its other chains.
+ * The response is keyed by pdb id, so the single entry is taken whatever its key.
+ */
+export function parseUniProtStructureMappings(json) {
+    const entry = isRecord(json) ? Object.values(json)[0] : undefined;
+    const uniprot = isRecord(entry) ? entry.UniProt : undefined;
+    if (!isRecord(uniprot)) {
+        return [];
+    }
+    const result = [];
+    for (const [accession, value] of Object.entries(uniprot)) {
+        const mappings = isRecord(value) ? value.mappings : undefined;
+        const segments = Array.isArray(mappings)
+            ? mappings.map(parseSegment).filter(s => s !== undefined)
+            : [];
+        if (segments.length > 0) {
+            result.push({
+                accession,
+                name: isRecord(value) && typeof value.name === 'string'
+                    ? value.name
+                    : undefined,
+                segments,
+            });
+        }
+    }
+    return result;
+}
+function coveredResidues(segments) {
+    return segments.reduce((a, s) => a + (s.structEnd - s.structStart + 1), 0);
+}
+/**
+ * The segments of one accession that describe this entity. SIFTS numbers
+ * entities as the mmCIF does, and a PDB-format file loaded through Mol* numbers
+ * them per chain (1H26.pdb's chain C is entity 2, which in SIFTS is cyclin A),
+ * so a segment naming its chain is matched by chain.
+ */
+function segmentsForEntity(mapping, entity) {
+    return dedupeSegments(mapping.segments.filter(s => s.chainId === undefined
+        ? s.entityId === entity.entityId
+        : entity.chains.includes(s.chainId)));
+}
+/**
+ * Picks the UniProt entry that describes a given entity, with its segments
+ * narrowed to that entity. Only the entity the plugin has mapped to the
+ * transcript is relevant — a heteromer maps each of its chains to a different
+ * accession, and using the wrong one would silently annotate the wrong protein.
+ * When several accessions cover the same entity (a chimeric construct) the one
+ * contributing the most residues wins.
+ */
+export function chooseUniProtMappingForEntity(mappings, entity) {
+    if (entity === undefined) {
+        return undefined;
+    }
+    let best;
+    for (const mapping of mappings) {
+        const segments = segmentsForEntity(mapping, entity);
+        if (segments.length > 0 &&
+            (!best || coveredResidues(segments) > coveredResidues(best.segments))) {
+            best = { ...mapping, segments };
+        }
+    }
+    return best;
+}
+const OWN_PSEUDOCOUNT = 5;
+const MIN_OWN_IDENTITY = 0.5;
+/**
+ * Mapped structure positions that SIFTS assigns to a protein other than the
+ * transcript's, on a chain that fuses two. Local alignment bridges a fusion
+ * boundary, and on every GPCR fusion construct checked it scattered receptor
+ * residues onto the partner, 33 of them onto T4 lysozyme in 2RH1.
+ *
+ * `mapped` is each mapped structure position and whether its pair is
+ * identical. The transcript's own accession is the one whose covered positions
+ * are most often identical, plus a pseudocount, as the chain picker scores
+ * chains. A count of covered positions would not do: TP53's 11-residue peptide
+ * fused to CDK2 covers 11 positions against 224 chance hits on the kinase, and
+ * counting unmapped the peptide. Unless that accession reaches half identity
+ * the transcript is taken to be neither protein, and nothing is unmapped.
+ * Residues SIFTS assigns to no accession, such as tags, stay mapped.
+ */
+export function fusionPartnerPositions(mappings, entity, mapped) {
+    const partners = new Set();
+    const byAccession = entity
+        ? mappings
+            .map(m => segmentsForEntity(m, entity))
+            .filter(segments => segments.length > 0)
+        : [];
+    if (byAccession.length < 2) {
+        return partners;
+    }
+    const covers = (segments, pos) => segments.some(s => pos >= s.structStart && pos <= s.structEnd);
+    const identity = byAccession.map(segments => {
+        let covered = 0;
+        let identical = 0;
+        for (const [pos, same] of mapped) {
+            if (covers(segments, pos)) {
+                covered++;
+                identical += same ? 1 : 0;
+            }
+        }
+        return identical / (covered + OWN_PSEUDOCOUNT);
+    });
+    const ownIdentity = Math.max(...identity);
+    if (ownIdentity < MIN_OWN_IDENTITY) {
+        return partners;
+    }
+    const own = byAccession[identity.indexOf(ownIdentity)];
+    for (const pos of mapped.keys()) {
+        if (!covers(own, pos) &&
+            byAccession.some(segments => segments !== own && covers(segments, pos))) {
+            partners.add(pos);
+        }
+    }
+    return partners;
+}
+// SIFTS lists one mapping per *chain*, so the several chains of a homodimer
+// repeat the same entity-level correspondence. They collapse to one segment.
+function dedupeSegments(segments) {
+    const seen = new Set();
+    return segments.filter(s => {
+        const key = `${s.unpStart}-${s.unpEnd}-${s.structStart}-${s.structEnd}`;
+        const isNew = !seen.has(key);
+        seen.add(key);
+        return isNew;
+    });
+}
+/** 1-based UniProt position -> 0-based structure position, for an AlphaFold
+ * model whose sequence is the UniProt sequence. */
+export const identityUniProtPositionMap = uniprotPos => uniprotPos - 1;
+export function makeUniProtPositionMap(segments) {
+    return uniprotPos => {
+        const segment = segments.find(s => uniprotPos >= s.unpStart && uniprotPos <= s.unpEnd);
+        if (!segment) {
+            return undefined;
+        }
+        const pos = segment.structStart + (uniprotPos - segment.unpStart);
+        return pos <= segment.structEnd ? pos : undefined;
+    };
+}
+//# sourceMappingURL=pdbUniProtMapping.js.map