@cyanheads/protein-mcp-server 0.8.3 → 0.8.5

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

@@ -106,6 +106,10 @@ export class RcsbService {
      * match therefore falls through to the name/synonym search rather than ending
      * the resolution, which keeps those IDs reaching the path that can resolve
      * them. The extra call happens only when the formula terminal matched nothing.
+     *
+     * Returns the first `limit` candidate IDs in RCSB's order alongside the
+     * upstream `total` for the search that produced them, so a caller can tell a
+     * complete match set from a truncated one.
      */
     async findChemComps(query, limit, ctx) {
         const search = async (query_) => {
@@ -114,12 +118,12 @@ export class RcsbService {
                 return_type: 'mol_definition',
                 request_options: { paginate: { start: 0, rows: limit } },
             }, ctx, 'RcsbService.findChemComps');
-            return normalizeHits(raw.result_set).map((h) => h.id);
+            return { ids: normalizeHits(raw.result_set).map((h) => h.id), total: raw.total_count ?? 0 };
         };
         if (!isChemicalFormula(query))
             return search(chemNameQuery(query));
         const byFormula = await search(formulaQuery(query));
-        return byFormula.length > 0 ? byFormula : search(chemNameQuery(query));
+        return byFormula.ids.length > 0 ? byFormula : search(chemNameQuery(query));
     }
     /** Facet-only aggregation over an optional scoping query (no row pull). */
     async analyzeFacets(params, facets, ctx) {
@@ -177,9 +181,26 @@ export class RcsbService {
             return null;
         return { entityId: entity.rcsb_id ?? pdbId, sequence: seq.replace(/\s+/g, '') };
     }
-    /** Ligand binding-site residues for an entry, optionally filtered to one ligand. */
+    /**
+     * Ligand binding-site residues for an entry, optionally filtered to one ligand.
+     * Each pocket residue carries both numbering namespaces: `rcsb_target_neighbors`
+     * reports the mmCIF label chain and position plus the author residue number,
+     * and the author chain comes from the entry's own per-instance
+     * `asym_id`/`auth_asym_id` pairs.
+     */
     async getBindingSites(pdbId, compId, ctx) {
         const data = await this.graphql(BINDING_SITE_QUERY, { id: pdbId.toUpperCase() }, ctx, 'RcsbService.getBindingSites');
+        // Label → author chain, one pair per polymer instance. The entity-level
+        // `asym_ids`/`auth_asym_ids` arrays are each sorted independently (6QNR_9:
+        // ["I","OB"] vs ["82","8E"], where I is 8E), so they cannot be zipped.
+        const authChainByLabel = new Map();
+        for (const poly of data.entry?.polymer_entities ?? []) {
+            for (const inst of poly.polymer_entity_instances ?? []) {
+                const ids = inst.rcsb_polymer_entity_instance_container_identifiers;
+                if (ids?.asym_id && ids.auth_asym_id)
+                    authChainByLabel.set(ids.asym_id, ids.auth_asym_id);
+            }
+        }
         const sites = [];
         const want = compId?.toUpperCase();
         for (const nonpoly of data.entry?.nonpolymer_entities ?? []) {
@@ -190,15 +211,14 @@ export class RcsbService {
                 const neighbors = inst.rcsb_target_neighbors ?? [];
                 if (neighbors.length === 0)
                     continue;
+                const ids = inst.rcsb_nonpolymer_entity_instance_container_identifiers;
+                const ligandAuthSeqId = parseAuthSeqId(ids?.auth_seq_id);
                 sites.push({
                     ligandCompId: ligand,
-                    ...(inst.rcsb_nonpolymer_entity_instance_container_identifiers?.auth_asym_id
-                        ? {
-                            ligandAsymId: inst.rcsb_nonpolymer_entity_instance_container_identifiers.auth_asym_id,
-                        }
-                        : {}),
+                    ...(ids?.auth_asym_id ? { ligandAsymId: ids.auth_asym_id } : {}),
+                    ...(ligandAuthSeqId !== undefined ? { ligandAuthSeqId } : {}),
                     residues: neighbors
-                        .map(normalizeNeighbor)
+                        .map((n) => normalizeNeighbor(n, authChainByLabel))
                         .filter((r) => r != null)
                         .sort((a, b) => (a.distance ?? Infinity) - (b.distance ?? Infinity)),
                 });
@@ -594,16 +614,29 @@ function normalizeLigand(raw) {
         ...(chem?.formula ? { formula: chem.formula } : {}),
     };
 }
-function normalizeNeighbor(raw) {
+function normalizeNeighbor(raw, authChainByLabel) {
     if (!raw.target_comp_id || !raw.target_asym_id)
         return;
+    const authAsymId = authChainByLabel.get(raw.target_asym_id);
     return {
         residueCompId: raw.target_comp_id,
         asymId: raw.target_asym_id,
         ...(typeof raw.target_seq_id === 'number' ? { seqId: raw.target_seq_id } : {}),
+        ...(authAsymId ? { authAsymId } : {}),
+        ...(typeof raw.target_auth_seq_id === 'number' ? { authSeqId: raw.target_auth_seq_id } : {}),
         ...(typeof raw.distance === 'number' ? { distance: raw.distance } : {}),
     };
 }
+/**
+ * The instance container reports `auth_seq_id` as a string ("201"); keep it only
+ * when it is an integer, the form every author residue number in the archive takes.
+ */
+function parseAuthSeqId(raw) {
+    if (!raw?.trim())
+        return;
+    const n = Number(raw);
+    return Number.isInteger(n) ? n : undefined;
+}
 function normalizeChemComp(id, raw) {
     const descriptors = raw.rcsb_chem_comp_descriptor;
     const smiles = descriptors?.SMILES_stereo ??
@@ -668,11 +701,16 @@ const SEQUENCE_QUERY = `query Sequence($id: String!) {
 }`;
 const BINDING_SITE_QUERY = `query BindingSite($id: String!) {
   entry(entry_id: $id) {
+    polymer_entities {
+      polymer_entity_instances {
+        rcsb_polymer_entity_instance_container_identifiers { asym_id auth_asym_id }
+      }
+    }
     nonpolymer_entities {
       rcsb_nonpolymer_entity_container_identifiers { nonpolymer_comp_id }
       nonpolymer_entity_instances {
-        rcsb_nonpolymer_entity_instance_container_identifiers { auth_asym_id }
-        rcsb_target_neighbors { target_asym_id target_comp_id target_seq_id distance }
+        rcsb_nonpolymer_entity_instance_container_identifiers { auth_asym_id auth_seq_id }
+        rcsb_target_neighbors { target_asym_id target_comp_id target_seq_id target_auth_seq_id distance }
       }
     }
   }

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

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

@@ -150,26 +150,44 @@ export interface CoordinateUrls {
     /** Legacy PDB format. */
     pdb?: string;
 }
-/** One protein residue lining a ligand's binding pocket. */
+/**
+ * One protein residue lining a ligand's binding pocket, in both numbering
+ * namespaces. `asymId`/`seqId` are mmCIF label identifiers; `authAsymId`/
+ * `authSeqId` are the depositor's (author) identifiers. The two are related by
+ * no fixed offset — 1IEP label THR93 is author THR315.
+ */
 export interface BindingResidue {
-    /** Author/asym chain ID the residue belongs to. */
+    /** mmCIF `label_asym_id` of the residue's chain. */
     asymId: string;
+    /** Author chain ID (`auth_asym_id`), from the entry's per-instance chain pairs. */
+    authAsymId?: string;
+    /** Author residue number (`auth_seq_id`). */
+    authSeqId?: number;
     /** Contact distance to the ligand in Å. */
     distance?: number;
     /** Residue chemical component ID (e.g. `ASP`). */
     residueCompId: string;
-    /** Sequence position of the residue. */
+    /** mmCIF `label_seq_id` — position in the entity sequence. */
     seqId?: number;
 }
 /** A ligand instance and the residues lining its pocket. */
 export interface BindingSite {
-    /** Ligand instance chain (asym) ID. */
+    /** Ligand instance author chain ID (`auth_asym_id`). */
     ligandAsymId?: string;
+    /** Ligand instance author residue number (`auth_seq_id`). */
+    ligandAuthSeqId?: number;
     /** Ligand chemical component ID. */
     ligandCompId: string;
     /** Interacting protein residues, nearest first. */
     residues: BindingResidue[];
 }
+/** Candidate chemical components for a name or formula search. */
+export interface ChemCompMatches {
+    /** Candidate component IDs pulled from the search, in upstream order. */
+    ids: string[];
+    /** Total components upstream matched, which can exceed `ids.length`. */
+    total: number;
+}
 /** Chemical-component metadata for a ligand. */
 export interface ChemComp {
     /** Component ID (e.g. `STI`). */

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

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

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/protein-mcp-server",
-  "version": "0.8.3",
+  "version": "0.8.5",
   "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": "0.8.3",
+  "version": "0.8.5",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.8.3",
+      "version": "0.8.5",
       "packageArguments": [
         {
           "type": "positional",
@@ -48,7 +48,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.8.3",
+      "version": "0.8.5",
       "packageArguments": [
         {
           "type": "positional",