p2s_mapper 1.0.0

package/esm/pdbUniProtMapping.js.map

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

@@ -0,0 +1,23 @@
+export interface PdbStructureEntry {
+    pdbId: string;
+    experimentalMethod: string;
+    /** Å; absent for NMR and some EM entries */
+    resolution?: number;
+    /** 1-based inclusive UniProt positions the entry covers */
+    unpStart: number;
+    unpEnd: number;
+    /** share of the UniProt sequence the entry covers, 0..1 */
+    coverage: number;
+    chains: string[];
+}
+export declare function pdbeBestStructuresUrl(uniprotId: string): string;
+export declare function isPdbId(value: string): boolean;
+export declare function rcsbEntryUrl(pdbId: string): string;
+/**
+ * Groups the per-chain rows into one entry per PDB id, keeping PDBe's order.
+ * An entry whose chains cover different UniProt ranges (a construct
+ * crystallised beside a different fragment of itself) keeps its first row's
+ * range, which is the one PDBe ranked it by. The response is keyed by
+ * accession, so the single entry is taken whatever its key.
+ */
+export declare function parseBestStructures(json: unknown): PdbStructureEntry[];

package/esm/pdbeBestStructures.js

@@ -0,0 +1,73 @@
+// PDBe's SIFTS-derived list of the experimental structures covering a UniProt
+// entry, one row per chain, ranked by PDBe (coverage, then resolution). The
+// dialog shows one row per entry, so the chains of a homomer collapse into it.
+export function pdbeBestStructuresUrl(uniprotId) {
+    return `https://www.ebi.ac.uk/pdbe/api/mappings/best_structures/${uniprotId}`;
+}
+// A PDB id is four characters, the first a digit: 1TUP, 6ZIO. Checked before
+// a typed one reaches a fetch, so three characters on the way to four are not
+// a 404 apiece.
+export function isPdbId(value) {
+    return /^[1-9][A-Za-z0-9]{3}$/.test(value);
+}
+export function rcsbEntryUrl(pdbId) {
+    return `https://www.rcsb.org/structure/${pdbId.toUpperCase()}`;
+}
+function isRecord(value) {
+    return typeof value === 'object' && value !== null && !Array.isArray(value);
+}
+function finiteNumber(value) {
+    return typeof value === 'number' && Number.isFinite(value) ? value : undefined;
+}
+/**
+ * Groups the per-chain rows into one entry per PDB id, keeping PDBe's order.
+ * An entry whose chains cover different UniProt ranges (a construct
+ * crystallised beside a different fragment of itself) keeps its first row's
+ * range, which is the one PDBe ranked it by. The response is keyed by
+ * accession, so the single entry is taken whatever its key.
+ */
+export function parseBestStructures(json) {
+    const rows = isRecord(json) ? Object.values(json)[0] : undefined;
+    if (!Array.isArray(rows)) {
+        return [];
+    }
+    const byId = new Map();
+    for (const row of rows) {
+        if (!isRecord(row)) {
+            continue;
+        }
+        const pdbId = typeof row.pdb_id === 'string' ? row.pdb_id : undefined;
+        const chain = typeof row.chain_id === 'string' ? row.chain_id : undefined;
+        const unpStart = finiteNumber(row.unp_start);
+        const unpEnd = finiteNumber(row.unp_end);
+        const coverage = finiteNumber(row.coverage);
+        if (pdbId === undefined ||
+            chain === undefined ||
+            unpStart === undefined ||
+            unpEnd === undefined ||
+            coverage === undefined) {
+            continue;
+        }
+        const existing = byId.get(pdbId);
+        if (existing) {
+            if (!existing.chains.includes(chain)) {
+                existing.chains.push(chain);
+            }
+            continue;
+        }
+        const resolution = finiteNumber(row.resolution);
+        byId.set(pdbId, {
+            pdbId,
+            experimentalMethod: typeof row.experimental_method === 'string'
+                ? row.experimental_method
+                : 'unknown',
+            ...(resolution === undefined ? {} : { resolution }),
+            unpStart,
+            unpEnd,
+            coverage,
+            chains: [chain],
+        });
+    }
+    return [...byId.values()];
+}
+//# sourceMappingURL=pdbeBestStructures.js.map

package/esm/pdbeBestStructures.js.map

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

@@ -0,0 +1,7 @@
+export declare function pdbeEntryMoleculesUrl(pdbId: string): string;
+/**
+ * One sequence per protein entity, in entity order. Nucleic-acid entities are
+ * left out: A, C, G, T and U are amino-acid letters too, so a DNA chain scores
+ * as a candidate rather than losing honestly.
+ */
+export declare function parseEntryMolecules(json: unknown): string[];

package/esm/pdbeEntryMolecules.js

@@ -0,0 +1,35 @@
+// The polymer entities of a PDB entry, as PDBe already knows them. The dialog
+// wants the entry's residues only to annotate the isoform list, and reading
+// them out of the structure file meant downloading and parsing the whole
+// mmCIF — minutes for a ribosome, for a label. This is a few kB of JSON, and
+// the view downloads the file itself when the user actually launches.
+export function pdbeEntryMoleculesUrl(pdbId) {
+    return `https://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/${pdbId.toLowerCase()}`;
+}
+function isRecord(value) {
+    return typeof value === 'object' && value !== null && !Array.isArray(value);
+}
+/**
+ * One sequence per protein entity, in entity order. Nucleic-acid entities are
+ * left out: A, C, G, T and U are amino-acid letters too, so a DNA chain scores
+ * as a candidate rather than losing honestly.
+ */
+export function parseEntryMolecules(json) {
+    const entities = isRecord(json) ? Object.values(json)[0] : undefined;
+    if (!Array.isArray(entities)) {
+        return [];
+    }
+    return entities.flatMap(entity => {
+        if (!isRecord(entity)) {
+            return [];
+        }
+        const { molecule_type: type, sequence } = entity;
+        return typeof type === 'string' &&
+            type.startsWith('polypeptide') &&
+            typeof sequence === 'string' &&
+            sequence.length > 0
+            ? [sequence]
+            : [];
+    });
+}
+//# sourceMappingURL=pdbeEntryMolecules.js.map

package/esm/pdbeEntryMolecules.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"pdbeEntryMolecules.js","sourceRoot":"","sources":["../src/pdbeEntryMolecules.ts"],"names":[],"mappings":"AAAA,8EAA8E;AAC9E,4EAA4E;AAC5E,yEAAyE;AACzE,6EAA6E;AAC7E,sEAAsE;AAEtE,MAAM,UAAU,qBAAqB,CAAC,KAAa;IACjD,OAAO,sDAAsD,KAAK,CAAC,WAAW,EAAE,EAAE,CAAA;AACpF,CAAC;AAED,SAAS,QAAQ,CAAC,KAAc;IAC9B,OAAO,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;AAC7E,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,mBAAmB,CAAC,IAAa;IAC/C,MAAM,QAAQ,GAAG,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACpE,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE,CAAC;QAC7B,OAAO,EAAE,CAAA;IACX,CAAC;IACD,OAAO,QAAQ,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;QAC/B,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,EAAE,CAAC;YACtB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,EAAE,aAAa,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,CAAA;QAChD,OAAO,OAAO,IAAI,KAAK,QAAQ;YAC7B,IAAI,CAAC,UAAU,CAAC,aAAa,CAAC;YAC9B,OAAO,QAAQ,KAAK,QAAQ;YAC5B,QAAQ,CAAC,MAAM,GAAG,CAAC;YACnB,CAAC,CAAC,CAAC,QAAQ,CAAC;YACZ,CAAC,CAAC,EAAE,CAAA;IACR,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/esm/siftsNumbering.d.ts

@@ -0,0 +1,23 @@
+import type { UniProtStructureSegment } from './pdbUniProtMapping.ts';
+export interface AuthorRange {
+    start: number;
+    end: number;
+    chain: string;
+    /** author number minus UniProt number in the chosen segment */
+    shift: number;
+}
+/** The segments SIFTS gives one accession, chain ids and author numbers
+ * included, out of a whole entry's mappings. */
+export declare function segmentsForAccession(mappings: readonly {
+    accession: string;
+    segments: UniProtStructureSegment[];
+}[], accession: string): UniProtStructureSegment[];
+/**
+ * The author-numbered range a UniProt range is cited by in the entry: the
+ * segment overlapping most of the range decides the shift. Undefined when no
+ * chain of the entry covers any of it, or when SIFTS named no author numbers.
+ */
+export declare function toAuthorRange(segments: readonly UniProtStructureSegment[], range: {
+    start: number;
+    end: number;
+}): AuthorRange | undefined;

package/esm/siftsNumbering.js

@@ -0,0 +1,40 @@
+// How a PDB entry numbers the residues of a UniProt sequence. Author numbering
+// is what a paper cites and what a viewer lights a named residue by, and it is
+// not the UniProt numbering for every entry: haemoglobin's chains number from
+// the mature protein, so author residue 1 is UniProt residue 2 (2HHB, measured
+// 2026-09-12). SIFTS records the correspondence per chain segment, and
+// `fetchUniProtStructureMappings` is what asks PDBe for it.
+/** The segments SIFTS gives one accession, chain ids and author numbers
+ * included, out of a whole entry's mappings. */
+export function segmentsForAccession(mappings, accession) {
+    return mappings.find(m => m.accession === accession)?.segments ?? [];
+}
+/**
+ * The author-numbered range a UniProt range is cited by in the entry: the
+ * segment overlapping most of the range decides the shift. Undefined when no
+ * chain of the entry covers any of it, or when SIFTS named no author numbers.
+ */
+export function toAuthorRange(segments, range) {
+    const overlap = (s) => Math.min(s.unpEnd, range.end) - Math.max(s.unpStart, range.start) + 1;
+    const best = segments
+        .flatMap(s => {
+        const { chainId, authorStart, unpStart, unpEnd } = s;
+        return chainId !== undefined &&
+            authorStart !== undefined &&
+            overlap(s) > 0
+            ? [{ chainId, authorStart, unpStart, unpEnd, overlap: overlap(s) }]
+            : [];
+    })
+        .toSorted((a, b) => b.overlap - a.overlap)[0];
+    if (!best) {
+        return undefined;
+    }
+    const shift = best.authorStart - best.unpStart;
+    return {
+        start: Math.max(range.start, best.unpStart) + shift,
+        end: Math.min(range.end, best.unpEnd) + shift,
+        chain: best.chainId,
+        shift,
+    };
+}
+//# sourceMappingURL=siftsNumbering.js.map

package/esm/siftsNumbering.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"siftsNumbering.js","sourceRoot":"","sources":["../src/siftsNumbering.ts"],"names":[],"mappings":"AAAA,+EAA+E;AAC/E,+EAA+E;AAC/E,8EAA8E;AAC9E,+EAA+E;AAC/E,uEAAuE;AACvE,4DAA4D;AAY5D;gDACgD;AAChD,MAAM,UAAU,oBAAoB,CAClC,QAGG,EACH,SAAiB;IAEjB,OAAO,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,SAAS,KAAK,SAAS,CAAC,EAAE,QAAQ,IAAI,EAAE,CAAA;AACtE,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,aAAa,CAC3B,QAA4C,EAC5C,KAAqC;IAErC,MAAM,OAAO,GAAG,CAAC,CAA0B,EAAE,EAAE,CAC7C,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,MAAM,EAAE,KAAK,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,KAAK,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IACvE,MAAM,IAAI,GAAG,QAAQ;SAClB,OAAO,CAAC,CAAC,CAAC,EAAE;QACX,MAAM,EAAE,OAAO,EAAE,WAAW,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,CAAC,CAAA;QACpD,OAAO,OAAO,KAAK,SAAS;YAC1B,WAAW,KAAK,SAAS;YACzB,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC;YACd,CAAC,CAAC,CAAC,EAAE,OAAO,EAAE,WAAW,EAAE,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC;YACnE,CAAC,CAAC,EAAE,CAAA;IACR,CAAC,CAAC;SACD,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;IAC/C,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,KAAK,GAAG,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,QAAQ,CAAA;IAC9C,OAAO;QACL,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,IAAI,CAAC,QAAQ,CAAC,GAAG,KAAK;QACnD,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,GAAG,KAAK;QAC7C,KAAK,EAAE,IAAI,CAAC,OAAO;QACnB,KAAK;KACN,CAAA;AACH,CAAC"}

package/esm/stripStopCodon.d.ts

@@ -0,0 +1,15 @@
+/**
+ * Drop the terminal stop codon(s) from a translated protein sequence.
+ *
+ * Only trailing `*` go: an interior stop (mis-annotated CDS, selenoprotein
+ * read-through) occupies a real codon position, and deleting it would shift
+ * every later residue out of step with g2p's codon-indexed transcript
+ * coordinates — offsetting every genome↔structure hover past that point.
+ */
+export declare function stripStopCodon(seq: string): string;
+/**
+ * Strip every stop codon, including interior ones. Only for sequences handed to
+ * an external similarity search (Foldseek, AlphaFold), where `*` is not a valid
+ * query character and no coordinate depends on the result's positions.
+ */
+export declare function stripAllStopCodons(seq: string): string;

package/esm/stripStopCodon.js

@@ -0,0 +1,20 @@
+/**
+ * Drop the terminal stop codon(s) from a translated protein sequence.
+ *
+ * Only trailing `*` go: an interior stop (mis-annotated CDS, selenoprotein
+ * read-through) occupies a real codon position, and deleting it would shift
+ * every later residue out of step with g2p's codon-indexed transcript
+ * coordinates — offsetting every genome↔structure hover past that point.
+ */
+export function stripStopCodon(seq) {
+    return seq.replace(/\*+$/, '');
+}
+/**
+ * Strip every stop codon, including interior ones. Only for sequences handed to
+ * an external similarity search (Foldseek, AlphaFold), where `*` is not a valid
+ * query character and no coordinate depends on the result's positions.
+ */
+export function stripAllStopCodons(seq) {
+    return seq.replaceAll('*', '');
+}
+//# sourceMappingURL=stripStopCodon.js.map

package/esm/stripStopCodon.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"stripStopCodon.js","sourceRoot":"","sources":["../src/stripStopCodon.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AACH,MAAM,UAAU,cAAc,CAAC,GAAW;IACxC,OAAO,GAAG,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAA;AAChC,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,kBAAkB,CAAC,GAAW;IAC5C,OAAO,GAAG,CAAC,UAAU,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;AAChC,CAAC"}

package/esm/structureFormat.d.ts

@@ -0,0 +1,40 @@
+/**
+ * Which molstar trajectory parser a structure needs.
+ *
+ * Getting this wrong is not a graceful failure in either direction: parsing a
+ * PDB file as mmCIF throws ("Unexpected token. Expected data_, loop_, or data
+ * name"), and — worse — parsing an mmCIF as PDB *succeeds* and yields a model
+ * with zero polymer entities and thousands of misread atoms, so the view loads
+ * with no sequence, no alignment and no genome mapping, and nothing reports an
+ * error.
+ *
+ * So detection lives here and is applied as the default at every entry point,
+ * rather than at one of them.
+ *
+ * The two names are the subset of molstar's `BuiltInTrajectoryFormat` a
+ * structure loaded from a file or a url can be, spelled out rather than
+ * imported so nothing here depends on molstar.
+ */
+export type StructureFormat = 'pdb' | 'mmcif';
+/** Trailing extension of a filename or URL, lowercased, ignoring any query or
+ * fragment and any `.gz` wrapper (`…/pdb1tup.ent.gz` -> `ent`). */
+export declare function structureFileExtension(nameOrUrl: string): string;
+/**
+ * Format for a filename or URL. Unknown extensions fall back to mmCIF, which is
+ * what every URL this plugin generates itself serves (AlphaFold and RCSB both
+ * hand out `.cif`).
+ */
+export declare function structureFormatFromName(nameOrUrl: string): StructureFormat;
+/** Whether a URL points at a binary-encoded structure, which molstar must be
+ * told to download as bytes rather than text. */
+export declare function isBinaryStructureUrl(url: string): boolean;
+/**
+ * Format for structure text that arrived without a filename — an inline `data`
+ * snapshot, a pasted file, or the PDB the plugin synthesizes from Foldseek Cα
+ * coordinates. Sniffs the content, which is strictly more reliable than a name
+ * and is the only signal available here.
+ *
+ * mmCIF is line-oriented and its first meaningful line is a `data_` block
+ * header (comments and blank lines may precede it); PDB has none.
+ */
+export declare function structureFormatFromContent(data: string): StructureFormat;

package/esm/structureFormat.js

@@ -0,0 +1,48 @@
+// Only the PDB set is enumerated: mmCIF is the fallback (see below), so listing
+// its extensions would be a second source of truth that could disagree.
+const PDB_EXTENSIONS = new Set(['pdb', 'ent', 'pdb1', 'pdb2', 'pdb3']);
+/** Trailing extension of a filename or URL, lowercased, ignoring any query or
+ * fragment and any `.gz` wrapper (`…/pdb1tup.ent.gz` -> `ent`). */
+export function structureFileExtension(nameOrUrl) {
+    const path = nameOrUrl.split(/[?#]/)[0] ?? '';
+    const name = path.split('/').pop() ?? '';
+    const parts = name.toLowerCase().split('.');
+    if (parts.at(-1) === 'gz') {
+        parts.pop();
+    }
+    return parts.length > 1 ? (parts.at(-1) ?? '') : '';
+}
+/**
+ * Format for a filename or URL. Unknown extensions fall back to mmCIF, which is
+ * what every URL this plugin generates itself serves (AlphaFold and RCSB both
+ * hand out `.cif`).
+ */
+export function structureFormatFromName(nameOrUrl) {
+    return PDB_EXTENSIONS.has(structureFileExtension(nameOrUrl)) ? 'pdb' : 'mmcif';
+}
+/** Whether a URL points at a binary-encoded structure, which molstar must be
+ * told to download as bytes rather than text. */
+export function isBinaryStructureUrl(url) {
+    return structureFileExtension(url) === 'bcif';
+}
+/**
+ * Format for structure text that arrived without a filename — an inline `data`
+ * snapshot, a pasted file, or the PDB the plugin synthesizes from Foldseek Cα
+ * coordinates. Sniffs the content, which is strictly more reliable than a name
+ * and is the only signal available here.
+ *
+ * mmCIF is line-oriented and its first meaningful line is a `data_` block
+ * header (comments and blank lines may precede it); PDB has none.
+ */
+export function structureFormatFromContent(data) {
+    // a data_ header can only appear in the first few lines; don't scan a 30MB
+    // structure to find out
+    for (const line of data.slice(0, 4096).split('\n')) {
+        const trimmed = line.trim();
+        if (trimmed !== '' && !trimmed.startsWith('#')) {
+            return trimmed.toLowerCase().startsWith('data_') ? 'mmcif' : 'pdb';
+        }
+    }
+    return 'pdb';
+}
+//# sourceMappingURL=structureFormat.js.map

package/esm/structureFormat.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"structureFormat.js","sourceRoot":"","sources":["../src/structureFormat.ts"],"names":[],"mappings":"AAmBA,gFAAgF;AAChF,wEAAwE;AACxE,MAAM,cAAc,GAAG,IAAI,GAAG,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,CAAC,CAAA;AAEtE;mEACmE;AACnE,MAAM,UAAU,sBAAsB,CAAC,SAAiB;IACtD,MAAM,IAAI,GAAG,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;IAC7C,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,IAAI,EAAE,CAAA;IACxC,MAAM,KAAK,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;IAC3C,IAAI,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,CAAC;QAC1B,KAAK,CAAC,GAAG,EAAE,CAAA;IACb,CAAC;IACD,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;AACrD,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,uBAAuB,CAAC,SAAiB;IACvD,OAAO,cAAc,CAAC,GAAG,CAAC,sBAAsB,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,OAAO,CAAA;AAChF,CAAC;AAED;iDACiD;AACjD,MAAM,UAAU,oBAAoB,CAAC,GAAW;IAC9C,OAAO,sBAAsB,CAAC,GAAG,CAAC,KAAK,MAAM,CAAA;AAC/C,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,0BAA0B,CAAC,IAAY;IACrD,2EAA2E;IAC3E,wBAAwB;IACxB,KAAK,MAAM,IAAI,IAAI,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;QACnD,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAA;QAC3B,IAAI,OAAO,KAAK,EAAE,IAAI,CAAC,OAAO,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YAC/C,OAAO,OAAO,CAAC,WAAW,EAAE,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAAA;QACpE,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAA;AACd,CAAC"}

package/esm/structureSources.d.ts

@@ -0,0 +1,28 @@
+import type { FetchOptions } from './fetchUtils.ts';
+export interface ExperimentalStructure {
+    pdbId: string;
+    method: string;
+    /** Å; absent for NMR and some EM entries */
+    resolution?: number;
+    /** 1-based inclusive UniProt residues the entry covers */
+    start: number;
+    end: number;
+    /** fraction of the UniProt sequence the entry covers, 0..1 */
+    coverage: number;
+}
+export declare function beaconsSummaryUrl(uniprotId: string): string;
+/**
+ * PDBe entries only, best-covering first and sharpest within a tie.
+ *
+ * Predicted entries (AlphaFold, SWISS-MODEL, AlphaFill) are left out because a
+ * prediction comes from AlphaFold's own API, which answers per model. And
+ * 3D-Beacons files SASBDB's small-angle-scattering fits under "experimentally
+ * determined" too, with numeric ids and near-full coverage — dystrophin's best
+ * "structure" by coverage was SASBDB 436 — which are not entries a residue
+ * mapping exists for. Hence the `provider === 'PDBe'` gate rather than the
+ * category alone.
+ */
+export declare function parseExperimentalStructures(json: unknown): ExperimentalStructure[];
+/** Best-effort: an unreachable API reads as "no entries", which costs a
+ * structure suggestion and nothing else. */
+export declare function fetchExperimentalStructures(uniprotId: string, opts?: FetchOptions): Promise<ExperimentalStructure[]>;

package/esm/structureSources.js

@@ -0,0 +1,71 @@
+// The experimental structures 3D-Beacons knows for a UniProt entry: every PDBe
+// entry mapped to the accession, with the UniProt range it covers and its
+// resolution, in one CORS-enabled call. That is what lets a page offer a
+// crystal structure beside a prediction without a PDB search of its own; take
+// the entry id from here and ask `fetchUniProtStructureMappings` for its
+// residue mapping.
+import { rawfetch } from "./fetchUtils.js";
+export function beaconsSummaryUrl(uniprotId) {
+    return `https://www.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/${encodeURIComponent(uniprotId)}.json?provider=pdbe`;
+}
+function isRecord(value) {
+    return typeof value === 'object' && value !== null && !Array.isArray(value);
+}
+function finiteNumber(value) {
+    return typeof value === 'number' && Number.isFinite(value) ? value : undefined;
+}
+/**
+ * PDBe entries only, best-covering first and sharpest within a tie.
+ *
+ * Predicted entries (AlphaFold, SWISS-MODEL, AlphaFill) are left out because a
+ * prediction comes from AlphaFold's own API, which answers per model. And
+ * 3D-Beacons files SASBDB's small-angle-scattering fits under "experimentally
+ * determined" too, with numeric ids and near-full coverage — dystrophin's best
+ * "structure" by coverage was SASBDB 436 — which are not entries a residue
+ * mapping exists for. Hence the `provider === 'PDBe'` gate rather than the
+ * category alone.
+ */
+export function parseExperimentalStructures(json) {
+    const structures = isRecord(json) ? json.structures : undefined;
+    if (!Array.isArray(structures)) {
+        return [];
+    }
+    return structures
+        .flatMap(entry => {
+        const s = isRecord(entry) ? entry.summary : undefined;
+        if (!isRecord(s)) {
+            return [];
+        }
+        const start = finiteNumber(s.uniprot_start);
+        const end = finiteNumber(s.uniprot_end);
+        const coverage = finiteNumber(s.coverage);
+        return typeof s.model_identifier === 'string' &&
+            s.provider === 'PDBe' &&
+            s.model_category === 'EXPERIMENTALLY DETERMINED' &&
+            start !== undefined &&
+            end !== undefined &&
+            coverage !== undefined
+            ? [
+                {
+                    pdbId: s.model_identifier.toLowerCase(),
+                    method: typeof s.experimental_method === 'string'
+                        ? s.experimental_method
+                        : 'experimental',
+                    resolution: finiteNumber(s.resolution),
+                    start,
+                    end,
+                    coverage,
+                },
+            ]
+            : [];
+    })
+        .sort((a, b) => b.coverage - a.coverage ||
+        (a.resolution ?? Infinity) - (b.resolution ?? Infinity));
+}
+/** Best-effort: an unreachable API reads as "no entries", which costs a
+ * structure suggestion and nothing else. */
+export async function fetchExperimentalStructures(uniprotId, opts) {
+    const res = await rawfetch(beaconsSummaryUrl(uniprotId), opts).catch(() => undefined);
+    return res?.ok ? parseExperimentalStructures(await res.json()) : [];
+}
+//# sourceMappingURL=structureSources.js.map

package/esm/structureSources.js.map

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

@@ -0,0 +1,54 @@
+export declare function uniprotGffUrl(uniprotId: string): string;
+export declare function uniprotFastaUrl(uniprotId: string): string;
+export declare function uniprotEntryUrl(uniprotId: string): string;
+/**
+ * The guessed filename of an accession's canonical AlphaFold model. A guess:
+ * the F1 fragment does not exist past the length cap and the version moves, so
+ * this is the last resort when the prediction API cannot be reached. Ask
+ * `fetchAlphaFoldModels` for the real files.
+ */
+export declare function getAlphaFoldStructureUrl(uniprotId: string, version?: string): string;
+export declare function getPdbStructureUrl(pdbId: string): string;
+/**
+ * Resolve the `{ pdbId }` shorthand to a concrete structure URL, so a
+ * hand-authored snapshot or a short launch URL doesn't have to know RCSB's
+ * filename format. An explicit `url` (or inline `data`) always wins.
+ * Idempotent: re-resolving an already-resolved spec returns the same url.
+ *
+ * `uniprotId` deliberately resolves to no url here, and still outranks a
+ * `pdbId`. An accession's files are whatever AlphaFold DB currently holds — an
+ * isoform model, several fragments, a new model version — so the structure
+ * keeps the accession and the structure loader asks the prediction API which
+ * file to open.
+ *
+ * Shared by the Structure model's snapshot preprocessor and the
+ * LaunchView-ProteinView extension point, which would otherwise each carry
+ * their own copy of the same precedence rule.
+ */
+export declare function resolveStructureUrl({ url, data, uniprotId, pdbId, }: {
+    url?: string;
+    data?: string;
+    uniprotId?: string;
+    pdbId?: string;
+}): string | undefined;
+/**
+ * The PDB id of a structure URL from the PDB archive, lowercased, or undefined
+ * for any other URL. Accepts the filename forms those hosts serve, e.g.
+ * `1TUP.cif`, `pdb1tup.ent.gz`, `1tup_updated.cif`.
+ */
+export declare function getPdbIdFromUrl(url: string): string | undefined;
+/** The accession of an AlphaFold model id or url, with its isoform suffix:
+ * `AF-P16442-F1-model_v6` gives P16442, `AF-P04637-2-F1-model_v6` P04637-2. */
+export declare function getUniprotIdFromAlphaFoldTarget(target: string): string | undefined;
+export declare function getStructureUrlFromTarget(target: string, db: string): string | undefined;
+export declare function getConfidenceUrlFromTarget(target: string): string | undefined;
+/**
+ * What a structure is called in the UI: its PDB id, its AlphaFold accession,
+ * else the file's name. Shared by the view title, the alignment panel heading
+ * and the hover readout, so one structure reads the same everywhere.
+ */
+export declare function structureDisplayLabel({ url, data, uniprotId, }: {
+    url?: string;
+    data?: string;
+    uniprotId?: string;
+}): string;