p2s_mapper 1.0.0

package/esm/fetchUtils.js

@@ -0,0 +1,82 @@
+function hostOf(url) {
+    try {
+        return new URL(url).host;
+    }
+    catch {
+        return url;
+    }
+}
+const MAX_DETAIL = 200;
+function firstLine(body) {
+    const line = body.split('\n', 1)[0]?.trim() ?? '';
+    return line.length > MAX_DETAIL ? `${line.slice(0, MAX_DETAIL)}…` : line;
+}
+/**
+ * The error a failed response deserves: status and host, plus at most the first
+ * line of the body. A whole body is an HTML error page or a megabyte of JSON,
+ * and pasting it into the dialog buries the one line that says what went wrong.
+ */
+export async function httpError(response, url) {
+    const detail = firstLine(await response.text().catch(() => ''));
+    const status = `HTTP ${response.status}${response.statusText ? ` ${response.statusText}` : ''} from ${hostOf(url)}`;
+    return new Error(detail ? `${status}: ${detail}` : status);
+}
+/**
+ * `fetch` rejects with a bare `TypeError: Failed to fetch` for a DNS failure,
+ * an offline browser and a refused cross-origin request alike, naming neither
+ * the host nor the cause. Anything else — an abort, most notably — passes
+ * through untouched.
+ */
+export function networkError(url, cause) {
+    return cause instanceof TypeError
+        ? new Error(`Could not reach ${hostOf(url)}. Check your network connection; the server may also be refusing cross-origin requests from this page.`, { cause })
+        : cause;
+}
+export async function rawfetch(url, args) {
+    const { fetch: f = globalThis.fetch, ...init } = args ?? {};
+    try {
+        return await f(url, init);
+    }
+    catch (e) {
+        throw networkError(url, e);
+    }
+}
+export async function myfetch(url, args) {
+    const response = await rawfetch(url, args);
+    if (!response.ok) {
+        throw await httpError(response, url);
+    }
+    return response;
+}
+export async function jsonfetch(url, args) {
+    // The caller names the shape it expects; `Response.json` promises `any`, and
+    // narrowing it here rather than at the return keeps the body free of casts.
+    const response = await myfetch(url, args);
+    return response.json();
+}
+/**
+ * An AbortSignal's reason as a real Error. `signal.reason` is `any` — usually a
+ * DOMException, but a caller can abort with anything at all — and throwing a
+ * non-Error loses the stack and breaks `instanceof Error` checks in the UI's
+ * error rendering. Normalize at every throw site.
+ */
+export function abortError(signal) {
+    return signal.reason instanceof Error
+        ? signal.reason
+        : new Error('Aborted', { cause: signal.reason });
+}
+export function timeout(time, signal) {
+    return new Promise((resolve, reject) => {
+        if (signal?.aborted) {
+            reject(abortError(signal));
+        }
+        else {
+            const id = setTimeout(resolve, time);
+            signal?.addEventListener('abort', () => {
+                clearTimeout(id);
+                reject(abortError(signal));
+            }, { once: true });
+        }
+    });
+}
+//# sourceMappingURL=fetchUtils.js.map

package/esm/fetchUtils.js.map

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package/esm/index.d.ts

@@ -0,0 +1,23 @@
+export * from './types.ts';
+export * from './mappings.ts';
+export * from './pairwiseAlignment.ts';
+export * from './alignmentQuality.ts';
+export * from './coordinates.ts';
+export * from './invertMap.ts';
+export * from './stripStopCodon.ts';
+export * from './chooseMappedEntity.ts';
+export * from './extractStructureSequences.ts';
+export * from './extractPerResidueConfidence.ts';
+export * from './isoformRanking.ts';
+export * from './pdbUniProtMapping.ts';
+export * from './siftsNumbering.ts';
+export * from './alphaFoldModels.ts';
+export * from './pdbeBestStructures.ts';
+export * from './pdbeEntryMolecules.ts';
+export * from './structureSources.ts';
+export * from './uniProtSearch.ts';
+export * from './dbIds.ts';
+export * from './structureUrls.ts';
+export * from './structureFormat.ts';
+export * from './caCoordsToPdb.ts';
+export * from './fetchUtils.ts';

package/esm/index.js

@@ -0,0 +1,30 @@
+// Alignment
+export * from "./types.js";
+export * from "./mappings.js";
+export * from "./pairwiseAlignment.js";
+export * from "./alignmentQuality.js";
+// Coordinates
+export * from "./coordinates.js";
+export * from "./invertMap.js";
+export * from "./stripStopCodon.js";
+// Chain choice
+export * from "./chooseMappedEntity.js";
+export * from "./extractStructureSequences.js";
+export * from "./extractPerResidueConfidence.js";
+export * from "./isoformRanking.js";
+// SIFTS
+export * from "./pdbUniProtMapping.js";
+export * from "./siftsNumbering.js";
+// Structure sources
+export * from "./alphaFoldModels.js";
+export * from "./pdbeBestStructures.js";
+export * from "./pdbeEntryMolecules.js";
+export * from "./structureSources.js";
+export * from "./uniProtSearch.js";
+export * from "./dbIds.js";
+// Urls and formats
+export * from "./structureUrls.js";
+export * from "./structureFormat.js";
+export * from "./caCoordsToPdb.js";
+export * from "./fetchUtils.js";
+//# sourceMappingURL=index.js.map

package/esm/index.js.map

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package/esm/invertMap.d.ts

@@ -0,0 +1,2 @@
+/** Swap keys and values of a numeric map, for reading a position map backwards. */
+export declare function invertMap(arg: Record<number, number>): Record<number, number>;

package/esm/invertMap.js

@@ -0,0 +1,5 @@
+/** Swap keys and values of a numeric map, for reading a position map backwards. */
+export function invertMap(arg) {
+    return Object.fromEntries(Object.entries(arg).map(([a, b]) => [b, +a]));
+}
+//# sourceMappingURL=invertMap.js.map

package/esm/invertMap.js.map

@@ -0,0 +1 @@
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package/esm/isoformRanking.d.ts

@@ -0,0 +1,47 @@
+/** A transcript isoform, named by whatever id the caller ranks by. `seq` is its
+ * translation, absent when none could be computed. */
+export interface Isoform {
+    id: string;
+    seq?: string;
+}
+export interface RankedIsoform {
+    id: string;
+    length: number;
+    /** identical residues against the structure, for an isoform that does not
+     * match it exactly; undefined with no structure to compare to */
+    identical?: number;
+    /** that alignment's score, which is what ranks non-matching isoforms */
+    score?: number;
+}
+export interface ClassifiedIsoforms {
+    matches: RankedIsoform[];
+    nonMatches: RankedIsoform[];
+    noData: string[];
+}
+/**
+ * The single rule for ranking transcript isoforms against a structure, shared
+ * by a picker UI and an auto-selection. An isoform whose translation is the
+ * structure's sequence wins outright. Among the rest, the best alignment score
+ * comes first, then the most identical residues, then length.
+ *
+ * The score has to lead: an isoform carrying an exon the structure lacks
+ * aligns every structure residue too, across a gap, so it ties on identical
+ * residues with the isoform the structure was made from (1MH1 against Rac1
+ * and Rac1b).
+ */
+export declare function classifyIsoforms({ isoforms, structureSequence, }: {
+    isoforms: readonly Isoform[];
+    structureSequence?: string;
+}): ClassifiedIsoforms;
+/** The id of the isoform to open, by the ranking above. */
+export declare function selectBestTranscript(args: {
+    isoforms: readonly Isoform[];
+    structureSequence?: string;
+}): string | undefined;
+/**
+ * Which of a structure's protein chains isoforms are compared against: one some
+ * isoform translates to exactly, else the chain `chooseMappedEntity` would map
+ * the longest isoform to, never simply the first (CDK2, on 1H26).
+ * `structureSequences` must hold protein chains only.
+ */
+export declare function pickStructureSequence(structureSequences: string[] | undefined, isoforms: readonly Isoform[] | undefined): string | undefined;

package/esm/isoformRanking.js

@@ -0,0 +1,86 @@
+import { stripStopCodon } from "./stripStopCodon.js";
+import { alignTranscriptToEntity, chooseMappedEntity, } from "./chooseMappedEntity.js";
+// The picker re-ranks on every render and each non-exact isoform costs an
+// O(len²) alignment, so results are cached by sequence pair: a titin-sized
+// isoform against a long chain is a second of main-thread work each time.
+const alignmentCache = new Map();
+const ALIGNMENT_CACHE_LIMIT = 200;
+function alignToStructure(isoform, structure) {
+    const key = `${isoform}\n${structure}`;
+    let result = alignmentCache.get(key);
+    if (result === undefined) {
+        const scored = alignTranscriptToEntity(isoform, structure, 'smith_waterman');
+        result = { identical: scored?.matches ?? 0, score: scored?.score ?? 0 };
+        if (alignmentCache.size >= ALIGNMENT_CACHE_LIMIT) {
+            alignmentCache.clear();
+        }
+        alignmentCache.set(key, result);
+    }
+    return result;
+}
+/**
+ * The single rule for ranking transcript isoforms against a structure, shared
+ * by a picker UI and an auto-selection. An isoform whose translation is the
+ * structure's sequence wins outright. Among the rest, the best alignment score
+ * comes first, then the most identical residues, then length.
+ *
+ * The score has to lead: an isoform carrying an exon the structure lacks
+ * aligns every structure residue too, across a gap, so it ties on identical
+ * residues with the isoform the structure was made from (1MH1 against Rac1
+ * and Rac1b).
+ */
+export function classifyIsoforms({ isoforms, structureSequence, }) {
+    const matches = [];
+    const nonMatches = [];
+    const noData = [];
+    const structure = structureSequence
+        ? stripStopCodon(structureSequence)
+        : undefined;
+    for (const { id, seq } of isoforms) {
+        if (seq === undefined) {
+            noData.push(id);
+        }
+        else if (structure && stripStopCodon(seq) === structure) {
+            matches.push({ id, length: seq.length });
+        }
+        else {
+            nonMatches.push({
+                id,
+                length: seq.length,
+                ...(structure ? alignToStructure(seq, structure) : {}),
+            });
+        }
+    }
+    const byLengthDesc = (a, b) => b.length - a.length;
+    const byAlignmentThenLength = (a, b) => (b.score ?? 0) - (a.score ?? 0) ||
+        (b.identical ?? 0) - (a.identical ?? 0) ||
+        byLengthDesc(a, b);
+    return {
+        matches: matches.toSorted(byLengthDesc),
+        nonMatches: nonMatches.toSorted(byAlignmentThenLength),
+        noData,
+    };
+}
+/** The id of the isoform to open, by the ranking above. */
+export function selectBestTranscript(args) {
+    const { matches, nonMatches } = classifyIsoforms(args);
+    return (matches[0] ?? nonMatches[0])?.id;
+}
+/**
+ * Which of a structure's protein chains isoforms are compared against: one some
+ * isoform translates to exactly, else the chain `chooseMappedEntity` would map
+ * the longest isoform to, never simply the first (CDK2, on 1H26).
+ * `structureSequences` must hold protein chains only.
+ */
+export function pickStructureSequence(structureSequences, isoforms) {
+    const translations = (isoforms ?? []).flatMap(({ seq }) => seq === undefined ? [] : [stripStopCodon(seq)]);
+    const translated = new Set(translations);
+    const exact = structureSequences?.find(s => translated.has(stripStopCodon(s)));
+    const longest = translations.reduce((a, b) => (a !== undefined && a.length >= b.length ? a : b), undefined);
+    const aligned = structureSequences && longest
+        ? chooseMappedEntity(longest, structureSequences, 'smith_waterman')
+        : undefined;
+    return (exact ??
+        (aligned ? structureSequences?.[aligned.index] : structureSequences?.[0]));
+}
+//# sourceMappingURL=isoformRanking.js.map

package/esm/isoformRanking.js.map

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package/esm/mappings.d.ts

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+export interface AlignmentRow {
+    id: string;
+    seq: string;
+}
+/**
+ * A two-row alignment whose ROW ORDER IS A CONTRACT: row 0 is the transcript,
+ * row 1 is the structure. Every producer honors it — runLocalAlignment is
+ * always called as (transcript, structure), and the manual-import dialog tells
+ * the user to paste them in that order — and every consumer depends on it, but
+ * nothing in the type can enforce it, and swapping the two silently inverts
+ * every coordinate map. Read the rows through the accessors below rather than
+ * indexing, so a call site states which sequence it means.
+ */
+export interface PairwiseAlignment {
+    consensus: string;
+    alns: readonly [AlignmentRow, AlignmentRow];
+}
+export declare const transcriptAlignedSeq: (pa: PairwiseAlignment) => string;
+export declare const structureAlignedSeq: (pa: PairwiseAlignment) => string;
+/** Number of columns, gaps included. Both rows have this length by definition;
+ * `pairwiseAlignmentProblem` is what guarantees it. */
+export declare const alignmentLength: (pa: PairwiseAlignment) => number;
+/**
+ * Why a pairwise alignment can't be used, or undefined if it's usable. The two
+ * rows must be the same non-zero length — every coordinate map walks them in
+ * lockstep, so a ragged pair would map positions to nonsense. Callers that
+ * accept alignments from outside (the manual-import dialog) check this and
+ * report it; the internal map builders assert on it.
+ */
+export declare function pairwiseAlignmentProblem(pa: PairwiseAlignment): string | undefined;
+/**
+ * Why an externally supplied alignment does not describe these two sequences,
+ * or undefined if it does. The coordinate maps index the transcript and the
+ * structure by counting residues along each row, so a row whose residues are
+ * not the sequence being mapped (an alignment made against UniProt canonical
+ * for a different isoform, or against another chain) shifts every position
+ * after the first difference without any map noticing.
+ */
+export declare function pairwiseAlignmentSequenceProblem(pa: PairwiseAlignment, transcript: string, structure: string): string | undefined;
+export declare function structureSeqVsTranscriptSeqMap(pairwiseAlignment: PairwiseAlignment): {
+    structureSeqToTranscriptSeqPosition: Record<number, number>;
+    transcriptSeqToStructureSeqPosition: Record<number, number>;
+};
+/** Each 0-based structure position opposite a transcript residue, and whether
+ * the two residues are identical. */
+export declare function mappedStructureIdentity(pa: PairwiseAlignment): Map<number, boolean>;
+/**
+ * The alignment with each listed structure position taken out of its column,
+ * so both rows still spell their sequences and those residues map to nothing.
+ * An unmapped region, including the gap columns inside it, becomes its
+ * transcript residues against gaps, then gaps against its structure residues,
+ * rather than alternating column by column. Returns `pa` itself when nothing
+ * changes.
+ */
+export declare function unmapStructurePositions(pa: PairwiseAlignment, positions: ReadonlySet<number>): PairwiseAlignment;
+export declare function structurePositionToAlignmentMap(pairwiseAlignment: PairwiseAlignment): Record<number, number>;
+export declare function transcriptPositionToAlignmentMap(pairwiseAlignment: PairwiseAlignment): Record<number, number>;
+export declare function codonGenomeSpan(p2gCodon: Record<number, number[]>, proteinPos: number): readonly [number, number] | undefined;

package/esm/mappings.js

@@ -0,0 +1,179 @@
+import { getCodonRanges } from 'g2p_mapper';
+export const transcriptAlignedSeq = (pa) => pa.alns[0].seq;
+export const structureAlignedSeq = (pa) => pa.alns[1].seq;
+/** Number of columns, gaps included. Both rows have this length by definition;
+ * `pairwiseAlignmentProblem` is what guarantees it. */
+export const alignmentLength = (pa) => transcriptAlignedSeq(pa).length;
+/**
+ * Why a pairwise alignment can't be used, or undefined if it's usable. The two
+ * rows must be the same non-zero length — every coordinate map walks them in
+ * lockstep, so a ragged pair would map positions to nonsense. Callers that
+ * accept alignments from outside (the manual-import dialog) check this and
+ * report it; the internal map builders assert on it.
+ */
+export function pairwiseAlignmentProblem(pa) {
+    const transcript = transcriptAlignedSeq(pa);
+    const structure = structureAlignedSeq(pa);
+    if (transcript.length === 0 || structure.length === 0) {
+        return 'The aligned sequences must not be empty';
+    }
+    if (transcript.length !== structure.length) {
+        return `The two aligned sequences must be the same length (got ${transcript.length} and ${structure.length})`;
+    }
+    return undefined;
+}
+const ungapped = (row) => row.replaceAll('-', '').toUpperCase();
+/**
+ * Why an externally supplied alignment does not describe these two sequences,
+ * or undefined if it does. The coordinate maps index the transcript and the
+ * structure by counting residues along each row, so a row whose residues are
+ * not the sequence being mapped (an alignment made against UniProt canonical
+ * for a different isoform, or against another chain) shifts every position
+ * after the first difference without any map noticing.
+ */
+export function pairwiseAlignmentSequenceProblem(pa, transcript, structure) {
+    const t = ungapped(transcriptAlignedSeq(pa));
+    const s = ungapped(structureAlignedSeq(pa));
+    if (t !== transcript.toUpperCase()) {
+        return `The first sequence is not this transcript's translation (${t.length} vs ${transcript.length} residues)`;
+    }
+    if (s !== structure.toUpperCase()) {
+        return `The second sequence is not the mapped chain's sequence (${s.length} vs ${structure.length} residues)`;
+    }
+    return undefined;
+}
+export function structureSeqVsTranscriptSeqMap(pairwiseAlignment) {
+    const problem = pairwiseAlignmentProblem(pairwiseAlignment);
+    if (problem) {
+        throw new Error(problem);
+    }
+    const structureSeq = structureAlignedSeq(pairwiseAlignment);
+    const transcriptSeq = transcriptAlignedSeq(pairwiseAlignment);
+    let j = 0;
+    let k = 0;
+    const structureSeqToTranscriptSeqPosition = {};
+    const transcriptSeqToStructureSeqPosition = {};
+    for (let i = 0; i < structureSeq.length; i++) {
+        const inStructure = structureSeq[i] !== '-';
+        const inTranscript = transcriptSeq[i] !== '-';
+        if (inStructure && inTranscript) {
+            structureSeqToTranscriptSeqPosition[j] = k;
+            transcriptSeqToStructureSeqPosition[k] = j;
+        }
+        if (inStructure) {
+            j++;
+        }
+        if (inTranscript) {
+            k++;
+        }
+    }
+    return {
+        structureSeqToTranscriptSeqPosition,
+        transcriptSeqToStructureSeqPosition,
+    };
+}
+/** Each 0-based structure position opposite a transcript residue, and whether
+ * the two residues are identical. */
+export function mappedStructureIdentity(pa) {
+    const transcript = transcriptAlignedSeq(pa);
+    const structure = structureAlignedSeq(pa);
+    const mapped = new Map();
+    for (let i = 0, j = 0; i < structure.length; i++) {
+        if (structure[i] !== '-') {
+            if (transcript[i] !== '-') {
+                mapped.set(j, transcript[i].toUpperCase() === structure[i].toUpperCase());
+            }
+            j++;
+        }
+    }
+    return mapped;
+}
+/**
+ * The alignment with each listed structure position taken out of its column,
+ * so both rows still spell their sequences and those residues map to nothing.
+ * An unmapped region, including the gap columns inside it, becomes its
+ * transcript residues against gaps, then gaps against its structure residues,
+ * rather than alternating column by column. Returns `pa` itself when nothing
+ * changes.
+ */
+export function unmapStructurePositions(pa, positions) {
+    const transcript = transcriptAlignedSeq(pa);
+    const structure = structureAlignedSeq(pa);
+    const t = [];
+    const s = [];
+    const c = [];
+    const runT = [];
+    const runS = [];
+    const flushRun = () => {
+        t.push(...runT, ...runS.map(() => '-'));
+        s.push(...runT.map(() => '-'), ...runS);
+        c.push(...runT.map(() => ' '), ...runS.map(() => ' '));
+        runT.length = 0;
+        runS.length = 0;
+    };
+    let j = 0;
+    let changed = false;
+    for (let i = 0; i < structure.length; i++) {
+        const inStructure = structure[i] !== '-';
+        const inTranscript = transcript[i] !== '-';
+        if (inStructure && inTranscript && positions.has(j)) {
+            runT.push(transcript[i]);
+            runS.push(structure[i]);
+            changed = true;
+        }
+        else if (runT.length > 0 && !(inStructure && inTranscript)) {
+            if (inTranscript) {
+                runT.push(transcript[i]);
+            }
+            if (inStructure) {
+                runS.push(structure[i]);
+            }
+        }
+        else {
+            flushRun();
+            t.push(transcript[i]);
+            s.push(structure[i]);
+            c.push(pa.consensus[i] ?? ' ');
+        }
+        if (inStructure) {
+            j++;
+        }
+    }
+    flushRun();
+    return changed
+        ? {
+            consensus: c.join(''),
+            alns: [
+                { ...pa.alns[0], seq: t.join('') },
+                { ...pa.alns[1], seq: s.join('') },
+            ],
+        }
+        : pa;
+}
+function seqPositionToAlignmentMap(seq) {
+    const map = {};
+    for (let i = 0, j = 0; i < seq.length; i++) {
+        if (seq[i] !== '-') {
+            map[j] = i;
+            j++;
+        }
+    }
+    return map;
+}
+export function structurePositionToAlignmentMap(pairwiseAlignment) {
+    return seqPositionToAlignmentMap(structureAlignedSeq(pairwiseAlignment));
+}
+export function transcriptPositionToAlignmentMap(pairwiseAlignment) {
+    return seqPositionToAlignmentMap(transcriptAlignedSeq(pairwiseAlignment));
+}
+// Enclosing 0-based half-open [start, end) genome span for a codon. getCodonRanges
+// returns the codon's separate genomic pieces (multiple when it straddles an
+// exon/intron boundary); this collapses them to the outer span for navigation
+// and highlighting. undefined when the protein position isn't mapped.
+export function codonGenomeSpan(p2gCodon, proteinPos) {
+    const ranges = getCodonRanges(p2gCodon, proteinPos);
+    return ranges && ranges.length > 0
+        ? [Math.min(...ranges.map(r => r[0])), Math.max(...ranges.map(r => r[1]))]
+        : undefined;
+}
+//# sourceMappingURL=mappings.js.map

package/esm/mappings.js.map

@@ -0,0 +1 @@
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package/esm/pairwiseAlignment.d.ts

@@ -0,0 +1,35 @@
+import type { PairwiseAlignment } from './mappings.ts';
+import type { AlignmentAlgorithm } from './types.ts';
+interface AlignmentResult {
+    alignedSeq1: string;
+    alignedSeq2: string;
+    score: number;
+}
+/**
+ * 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 declare const MAX_ALIGNMENT_CELLS = 40000000;
+export declare function alignmentTooLarge(len1: number, len2: number): boolean;
+/**
+ * Needleman-Wunsch global alignment algorithm
+ * Aligns entire sequences end-to-end
+ */
+export declare function needlemanWunsch(seq1: string, seq2: string, gapOpen?: number, gapExtend?: number): AlignmentResult;
+/**
+ * Smith-Waterman local alignment algorithm
+ * Finds the best local alignment between subsequences
+ */
+export declare function smithWaterman(seq1: string, seq2: string, gapOpen?: number, gapExtend?: number): AlignmentResult;
+/** The score of a sequence aligned to itself with no gaps. */
+export declare function selfScore(seq: string): number;
+export declare function scoredAlignment(seq1: string, seq2: string, algorithm: AlignmentAlgorithm): {
+    alignment: PairwiseAlignment;
+    score: number;
+};
+export declare function runLocalAlignment(seq1: string, seq2: string, algorithm: AlignmentAlgorithm): PairwiseAlignment;
+export {};