@cyanheads/protein-mcp-server 0.2.0 → 0.3.0

package/dist/mcp-server/tools/definitions/track-ligands.tool.js.map

@@ -1 +1 @@
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package/dist/services/rcsb/rcsb-service.d.ts

@@ -11,7 +11,7 @@ import type { Context } from '@cyanheads/mcp-ts-core';
 import type { AppConfig } from '@cyanheads/mcp-ts-core/config';
 import type { StorageService } from '@cyanheads/mcp-ts-core/storage';
 import type { ServerConfig } from '../../config/server-config.js';
-import type { BindingSite, ChemComp, ContentType, EntryMeta, FacetDimension, SearchResult, StructureSearchParams } from './types.js';
+import type { BindingSite, ChemComp, ContentType, EntryMeta, FacetDimension, SearchResult, StructureSearchParams, UniProtXref } from './types.js';
 /** RCSB return types relevant to this server. */
 export type ReturnType = 'entry' | 'polymer_entity' | 'mol_definition';
 /** A facet dimension request: friendly name + how RCSB should aggregate it. */
@@ -56,8 +56,14 @@ export declare class RcsbService {
     }>;
     /** Batched entry metadata for up to N PDB IDs in one GraphQL call. */
     getEntries(ids: string[], ctx: Context): Promise<EntryMeta[]>;
-    /** Resolve a PDB entry to its cross-referenced UniProt accession(s). */
-    resolveUniprot(pdbId: string, ctx: Context): Promise<string[]>;
+    /**
+     * Resolve a PDB entry to its UniProt-cross-referenced polymer entities. Each
+     * returned entry carries the author chain IDs it covers, the mapped UniProt
+     * accession, and the polymer description — entity-grained so a caller can
+     * disambiguate a multi-chain entry by chain. One entry per polymer entity that
+     * carries a UniProt xref; entities without one are skipped. Single round trip.
+     */
+    resolveUniprotEntities(pdbId: string, ctx: Context): Promise<UniProtXref[]>;
     /** First polymer entity's one-letter sequence for a PDB entry. */
     getSequence(pdbId: string, ctx: Context): Promise<{
         entityId: string;

package/dist/services/rcsb/rcsb-service.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"rcsb-service.d.ts","sourceRoot":"","sources":["../../../src/services/rcsb/rcsb-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,+BAA+B,CAAC;AAE/D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AACrE,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAE9D,OAAO,KAAK,EAEV,WAAW,EACX,QAAQ,EACR,WAAW,EACX,SAAS,EAET,cAAc,EAId,YAAY,EACZ,qBAAqB,EACrB,WAAW,EACZ,MAAM,YAAY,CAAC;AAEpB,iDAAiD;AACjD,MAAM,MAAM,UAAU,GAAG,OAAO,GAAG,gBAAgB,GAAG,gBAAgB,CAAC;AAEvE,+EAA+E;AAC/E,MAAM,WAAW,SAAS;IACxB,wBAAwB;IACxB,WAAW,EAAE,OAAO,GAAG,WAAW,GAAG,gBAAgB,CAAC;IACtD,mCAAmC;IACnC,SAAS,EAAE,MAAM,CAAC;IAClB,iDAAiD;IACjD,KAAK,CAAC,EAAE,SAAS,CAAC;IAClB,qDAAqD;IACrD,SAAS,EAAE,MAAM,CAAC;IAClB,gGAAgG;IAChG,QAAQ,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;CAC5B;AA6BD,qBAAa,WAAW;IACtB,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAS;IACnC,OAAO,CAAC,QAAQ,CAAC,UAAU,CAAS;IACpC,OAAO,CAAC,QAAQ,CAAC,YAAY,CAAS;IACtC,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAS;gBAEvB,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,cAAc,EAAE,YAAY,EAAE,YAAY;IASpF,gFAAgF;IAC1E,MAAM,CACV,MAAM,EAAE,qBAAqB,EAC7B,GAAG,EAAE,OAAO,EACZ,MAAM,CAAC,EAAE,SAAS,EAAE,GACnB,OAAO,CAAC,YAAY,CAAC;IAqBxB,uEAAuE;IACjE,cAAc,CAClB,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE;QAAE,SAAS,CAAC,EAAE,MAAM,CAAC;QAAC,WAAW,CAAC,EAAE,MAAM,CAAC;QAAC,KAAK,CAAC,EAAE,MAAM,CAAC;QAAC,WAAW,CAAC,EAAE,WAAW,CAAA;KAAE,EAC7F,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,YAAY,CAAC;IAuBxB,4EAA4E;IACtE,cAAc,CAClB,MAAM,EAAE,MAAM,EACd,IAAI,EAAE;QAAE,KAAK,CAAC,EAAE,MAAM,CAAC;QAAC,WAAW,CAAC,EAAE,WAAW,CAAA;KAAE,EACnD,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,YAAY,CAAC;IAqBxB,yEAAyE;IACnE,aAAa,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAuBlF,2EAA2E;IACrE,aAAa,CACjB,MAAM,EAAE,qBAAqB,EAC7B,MAAM,EAAE,SAAS,EAAE,EACnB,GAAG,EAAE,OAAO,GACX,OAAO,CAAC;QAAE,KAAK,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,cAAc,EAAE,CAAA;KAAE,CAAC;IAgBvD,sEAAsE;IAChE,UAAU,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,SAAS,EAAE,CAAC;IAWnE;;;;;;OAMG;IACG,sBAAsB,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,WAAW,EAAE,CAAC;IAyBjF,kEAAkE;IAC5D,WAAW,CACf,KAAK,EAAE,MAAM,EACb,GAAG,EAAE,OAAO,GACX,OAAO,CAAC;QAAE,QAAQ,EAAE,MAAM,CAAC;QAAC,QAAQ,EAAE,MAAM,CAAA;KAAE,GAAG,IAAI,CAAC;IAezD,oFAAoF;IAC9E,eAAe,CACnB,KAAK,EAAE,MAAM,EACb,MAAM,EAAE,MAAM,GAAG,SAAS,EAC1B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,WAAW,EAAE,CAAC;IAmCzB,uEAAuE;IACjE,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,QAAQ,GAAG,IAAI,CAAC;IAsBzE,gEAAgE;IAChE,iBAAiB,CAAC,KAAK,EAAE,MAAM,EAAE,MAAM,EAAE,KAAK,GAAG,KAAK,GAAG,MAAM,GAAG,MAAM;IAMxE,OAAO,CAAC,UAAU;YAeJ,OAAO;CAwBtB;AAID,yFAAyF;AACzF,wBAAgB,UAAU,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAqCjE;AAWD,sFAAsF;AACtF,wBAAgB,WAAW,CAAC,IAAI,EAAE,SAAS,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAUpE;AA+PD,wBAAgB,eAAe,CAC7B,MAAM,EAAE,SAAS,EACjB,OAAO,EAAE,cAAc,EACvB,YAAY,EAAE,YAAY,GACzB,IAAI,CAEN;AAED,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}

package/dist/services/rcsb/rcsb-service.js

@@ -137,19 +137,30 @@ export class RcsbService {
         const data = await this.graphql(ENTRIES_QUERY, { ids: ids.map((id) => id.toUpperCase()) }, ctx, 'RcsbService.getEntries');
         return (data.entries ?? []).filter((e) => e != null).map(normalizeEntry);
     }
-    /** Resolve a PDB entry to its cross-referenced UniProt accession(s). */
-    async resolveUniprot(pdbId, ctx) {
-        const data = await this.graphql(XREF_QUERY, { id: pdbId.toUpperCase() }, ctx, 'RcsbService.resolveUniprot');
-        const accessions = new Set();
+    /**
+     * Resolve a PDB entry to its UniProt-cross-referenced polymer entities. Each
+     * returned entry carries the author chain IDs it covers, the mapped UniProt
+     * accession, and the polymer description — entity-grained so a caller can
+     * disambiguate a multi-chain entry by chain. One entry per polymer entity that
+     * carries a UniProt xref; entities without one are skipped. Single round trip.
+     */
+    async resolveUniprotEntities(pdbId, ctx) {
+        const data = await this.graphql(XREF_QUERY, { id: pdbId.toUpperCase() }, ctx, 'RcsbService.resolveUniprotEntities');
+        const xrefs = [];
         for (const entity of data.entry?.polymer_entities ?? []) {
-            for (const ref of entity.rcsb_polymer_entity_container_identifiers
-                ?.reference_sequence_identifiers ?? []) {
-                if (/uniprot/i.test(ref.database_name ?? '') && ref.database_accession) {
-                    accessions.add(ref.database_accession.toUpperCase());
-                }
-            }
+            const container = entity.rcsb_polymer_entity_container_identifiers;
+            const accession = container?.reference_sequence_identifiers?.find((ref) => /uniprot/i.test(ref.database_name ?? '') && ref.database_accession)?.database_accession;
+            if (!accession)
+                continue;
+            xrefs.push({
+                accession: accession.toUpperCase(),
+                chains: container?.auth_asym_ids ?? [],
+                ...(entity.rcsb_polymer_entity?.pdbx_description
+                    ? { proteinName: entity.rcsb_polymer_entity.pdbx_description }
+                    : {}),
+            });
         }
-        return [...accessions];
+        return xrefs;
     }
     /** First polymer entity's one-letter sequence for a PDB entry. */
     async getSequence(pdbId, ctx) {
@@ -439,7 +450,9 @@ const ENTRIES_QUERY = `query Entries($ids: [String!]!) {
 const XREF_QUERY = `query Xref($id: String!) {
   entry(entry_id: $id) {
     polymer_entities {
+      rcsb_polymer_entity { pdbx_description }
       rcsb_polymer_entity_container_identifiers {
+        auth_asym_ids
         reference_sequence_identifiers { database_accession database_name }
       }
     }

package/dist/services/rcsb/rcsb-service.js.map

@@ -1 +1 @@
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package/dist/services/rcsb/types.d.ts

@@ -55,6 +55,15 @@ export interface PolymerEntityMeta {
     /** Residue count of the sample sequence. */
     sequenceLength?: number;
 }
+/** One polymer entity's UniProt cross-reference: the chains it covers and the mapped accession. */
+export interface UniProtXref {
+    /** UniProt accession this entity maps to. */
+    accession: string;
+    /** Author chain IDs (auth_asym_id) this entity covers (e.g. ["A", "C"]). */
+    chains: string[];
+    /** Polymer entity description (e.g. "Hemoglobin subunit alpha"). */
+    proteinName?: string;
+}
 /** A bound non-polymer (ligand) component within an entry. */
 export interface LigandMeta {
     /** Chemical component ID (e.g. `HEM`, `STI`). */

package/dist/services/rcsb/types.d.ts.map

@@ -1 +1 @@
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package/dist/services/shared/attribution.d.ts

@@ -0,0 +1,42 @@
+/**
+ * @fileoverview Upstream data-source attribution — the license and citation each
+ * contributing database asks to travel with its data. `protein_get_structure` and
+ * `protein_get_annotations` project the sources that actually contributed to a
+ * response into a deduped attribution array, so the obligation rides with the data
+ * to every downstream consumer rather than living only in repo docs. Curated
+ * strings are verified against each source's primary license/citation page.
+ * `best_available` structures are federated through 3D-Beacons, an open set of
+ * model providers (AlphaFold DB, SWISS-MODEL, BFVD, AlphaFill, …), so an uncurated
+ * provider gets an honest fallback entry that asserts no license rather than a
+ * fabricated one. Pure data + a projection helper; the Zod output schema and
+ * renderer live in the tools' shared `_schemas.ts`.
+ * @module services/shared/attribution
+ */
+/**
+ * Curated data-source display names (verified license + citation), in canonical
+ * render order. The structure sources come first (RCSB PDB, then the federated
+ * predicted providers), followed by the annotation trio.
+ */
+export declare const CURATED_SOURCES: readonly ["RCSB PDB", "AlphaFold DB", "SWISS-MODEL", "BFVD", "UniProt", "InterPro", "GO"];
+/** A curated data-source display name with a verified license + citation. */
+export type CuratedSource = (typeof CURATED_SOURCES)[number];
+/** License, citation, and homepage for one contributing data source. */
+export interface Attribution {
+    /** Primary-literature citation the source asks consumers to cite. */
+    citation: string;
+    /** Source homepage. */
+    homepage: string;
+    /** License the source's data is released under (e.g. "CC BY 4.0"). */
+    license: string;
+    /** Data-source display name (a curated name, or a federated provider string). */
+    source: string;
+}
+/**
+ * Project the source names that contributed to a response into a deduped
+ * attribution array. Curated names render first in {@link CURATED_SOURCES} order;
+ * any uncurated provider follows, alphabetized, each with an honest fallback entry.
+ * The ordering is caller-insertion-independent, so an identical contributing set
+ * always renders identically.
+ */
+export declare function attributionsFor(sources: Iterable<string>): Attribution[];
+//# sourceMappingURL=attribution.d.ts.map

package/dist/services/shared/attribution.d.ts.map

@@ -0,0 +1 @@
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package/dist/services/shared/attribution.js

@@ -0,0 +1,111 @@
+/**
+ * @fileoverview Upstream data-source attribution — the license and citation each
+ * contributing database asks to travel with its data. `protein_get_structure` and
+ * `protein_get_annotations` project the sources that actually contributed to a
+ * response into a deduped attribution array, so the obligation rides with the data
+ * to every downstream consumer rather than living only in repo docs. Curated
+ * strings are verified against each source's primary license/citation page.
+ * `best_available` structures are federated through 3D-Beacons, an open set of
+ * model providers (AlphaFold DB, SWISS-MODEL, BFVD, AlphaFill, …), so an uncurated
+ * provider gets an honest fallback entry that asserts no license rather than a
+ * fabricated one. Pure data + a projection helper; the Zod output schema and
+ * renderer live in the tools' shared `_schemas.ts`.
+ * @module services/shared/attribution
+ */
+/**
+ * Curated data-source display names (verified license + citation), in canonical
+ * render order. The structure sources come first (RCSB PDB, then the federated
+ * predicted providers), followed by the annotation trio.
+ */
+export const CURATED_SOURCES = [
+    'RCSB PDB',
+    'AlphaFold DB',
+    'SWISS-MODEL',
+    'BFVD',
+    'UniProt',
+    'InterPro',
+    'GO',
+];
+/**
+ * Canonical license + citation strings, keyed by source. Verified against each
+ * source's primary license/citation page. CC BY / CC BY-SA sources require
+ * attribution to travel with redistributed data; CC0 sources are citation-only
+ * (attribution encouraged, not required) but carried here so the obligation is
+ * legible either way. InterPro's own domain/family data is CC0 — the CC BY 4.0 GO
+ * terms carried alongside it are a separate, independently-gated source.
+ */
+const ATTRIBUTIONS = {
+    'RCSB PDB': {
+        source: 'RCSB PDB',
+        license: 'CC0 1.0 Universal',
+        citation: 'H.M. Berman et al., "The Protein Data Bank," Nucleic Acids Research 28:235–242 (2000). DOI: 10.1093/nar/28.1.235',
+        homepage: 'https://www.rcsb.org/',
+    },
+    'AlphaFold DB': {
+        source: 'AlphaFold DB',
+        license: 'CC BY 4.0',
+        citation: 'Jumper et al., "Highly accurate protein structure prediction with AlphaFold," Nature 596:583–589 (2021). DOI: 10.1038/s41586-021-03819-2; Bertoni et al., "AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage," Nucleic Acids Research 54(D1):D358–D362 (2025). DOI: 10.1093/nar/gkaf1226',
+        homepage: 'https://alphafold.ebi.ac.uk/',
+    },
+    'SWISS-MODEL': {
+        source: 'SWISS-MODEL',
+        license: 'CC BY-SA 4.0',
+        citation: 'Waterhouse et al., "SWISS-MODEL: homology modelling of protein structures and complexes," Nucleic Acids Research 46(W1):W296–W303 (2018). DOI: 10.1093/nar/gky427; Bienert et al., "The SWISS-MODEL Repository—new features and functionality," Nucleic Acids Research 45(D1):D313–D319 (2017). DOI: 10.1093/nar/gkw1132',
+        homepage: 'https://swissmodel.expasy.org/',
+    },
+    BFVD: {
+        source: 'BFVD',
+        license: 'CC BY 4.0',
+        citation: 'Kim et al., "BFVD—a large repository of predicted viral protein structures," Nucleic Acids Research 53(D1):D340–D347 (2025). DOI: 10.1093/nar/gkae1119',
+        homepage: 'https://bfvd.steineggerlab.workers.dev/',
+    },
+    UniProt: {
+        source: 'UniProt',
+        license: 'CC BY 4.0',
+        citation: 'The UniProt Consortium, "UniProt: the Universal Protein Knowledgebase in 2025," Nucleic Acids Research 53(D1):D609–D617 (2025). DOI: 10.1093/nar/gkae1010',
+        homepage: 'https://www.uniprot.org/',
+    },
+    InterPro: {
+        source: 'InterPro',
+        license: 'CC0 1.0 Universal',
+        citation: 'Blum et al., "InterPro: the protein sequence classification resource in 2025," Nucleic Acids Research 53(D1):D444–D456 (2025). DOI: 10.1093/nar/gkae1082',
+        homepage: 'https://www.ebi.ac.uk/interpro/',
+    },
+    GO: {
+        source: 'GO',
+        license: 'CC BY 4.0',
+        citation: 'Ashburner et al., "Gene Ontology: tool for the unification of biology," Nature Genetics 25:25–29 (2000). DOI: 10.1038/75556; Gene Ontology Consortium, "The Gene Ontology knowledgebase in 2026," Nucleic Acids Research 54(D1):D1779–D1792 (2026). DOI: 10.1093/nar/gkaf1292',
+        homepage: 'https://geneontology.org/',
+    },
+};
+const CURATED_NAMES = new Set(CURATED_SOURCES);
+/**
+ * Honest fallback for an uncurated federated provider (AlphaFill, or any 3D-Beacons
+ * provider without a verified license entry). Asserts no license — better to point
+ * the consumer at the provider's own terms than to fabricate one.
+ */
+function fallbackAttribution(source) {
+    return {
+        source,
+        license: 'See provider terms',
+        citation: 'Federated via 3D-Beacons — consult the provider for citation and license terms.',
+        homepage: 'https://3d-beacons.org/',
+    };
+}
+/**
+ * Project the source names that contributed to a response into a deduped
+ * attribution array. Curated names render first in {@link CURATED_SOURCES} order;
+ * any uncurated provider follows, alphabetized, each with an honest fallback entry.
+ * The ordering is caller-insertion-independent, so an identical contributing set
+ * always renders identically.
+ */
+export function attributionsFor(sources) {
+    const wanted = new Set(sources);
+    const curated = CURATED_SOURCES.filter((s) => wanted.has(s)).map((s) => ATTRIBUTIONS[s]);
+    const uncurated = [...wanted]
+        .filter((s) => !CURATED_NAMES.has(s))
+        .sort()
+        .map(fallbackAttribution);
+    return [...curated, ...uncurated];
+}
+//# sourceMappingURL=attribution.js.map

package/dist/services/shared/attribution.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/protein-mcp-server",
-  "version": "0.2.0",
+  "version": "0.3.0",
   "mcpName": "io.github.cyanheads/protein-mcp-server",
   "description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
   "type": "module",

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/protein-mcp-server",
     "source": "github"
   },
-  "version": "0.2.0",
+  "version": "0.3.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.2.0",
+      "version": "0.3.0",
       "packageArguments": [
         {
           "type": "positional",
@@ -48,7 +48,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.2.0",
+      "version": "0.3.0",
       "packageArguments": [
         {
           "type": "positional",