@cyanheads/protein-mcp-server 0.6.0 → 0.8.0

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

@@ -91,28 +91,33 @@ export class RcsbService {
         const raw = await this.postSearch(ligandContainmentQuery(compId, undefined, 0, 0, false), ctx, 'RcsbService.countEntriesWithLigand');
         return raw.total_count ?? 0;
     }
-    /** Resolve a ligand name/synonym to candidate chemical component IDs. */
+    /**
+     * Resolve a ligand name, synonym, or molecular formula to candidate chemical
+     * component IDs. A formula-shaped query routes to RCSB's `chemical` service,
+     * which matches composition; anything else runs the name/synonym search, where
+     * a formula would only match components whose *name* contains formula-like
+     * tokens.
+     *
+     * Formula detection is a shape heuristic, so it can claim a string that is
+     * really a component ID — an all-caps ID built only from single-letter element
+     * symbols and a digit (`SF4`, `H4B`) tokenizes as a formula. An empty formula
+     * 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.
+     */
     async findChemComps(query, limit, ctx) {
-        // Match the term against both the formal component name and its synonyms:
-        // common names ("heme", "aspirin") live in synonyms, not the formal name
-        // ("PROTOPORPHYRIN IX CONTAINING FE"). A plain full_text search over
-        // mol_definition matches far too broadly and buries the intended component.
-        const chemTerm = (attribute) => ({
-            type: 'terminal',
-            service: 'text_chem',
-            parameters: { attribute, operator: 'contains_words', value: query },
-        });
-        const body = {
-            query: {
-                type: 'group',
-                logical_operator: 'or',
-                nodes: [chemTerm('chem_comp.name'), chemTerm('rcsb_chem_comp_synonyms.name')],
-            },
-            return_type: 'mol_definition',
-            request_options: { paginate: { start: 0, rows: limit } },
+        const search = async (query_) => {
+            const raw = await this.postSearch({
+                query: query_,
+                return_type: 'mol_definition',
+                request_options: { paginate: { start: 0, rows: limit } },
+            }, ctx, 'RcsbService.findChemComps');
+            return normalizeHits(raw.result_set).map((h) => h.id);
         };
-        const raw = await this.postSearch(body, ctx, 'RcsbService.findChemComps');
-        return normalizeHits(raw.result_set).map((h) => h.id);
+        if (!isChemicalFormula(query))
+            return search(chemNameQuery(query));
+        const byFormula = await search(formulaQuery(query));
+        return byFormula.length > 0 ? byFormula : search(chemNameQuery(query));
     }
     /** Facet-only aggregation over an optional scoping query (no row pull). */
     async analyzeFacets(params, facets, ctx) {
@@ -248,10 +253,20 @@ export class RcsbService {
             label: 'RCSB GraphQL API',
             baseDelayMs: 400,
         });
+        // GraphQL reports field-level failures in `errors` while still returning the
+        // sub-selections that succeeded, so `errors` is evaluated before `data`: a
+        // partial payload is indistinguishable from a genuinely sparse record, and
+        // every metadata consumer of this helper treats a metadata-request failure as
+        // a whole-call failure. An empty `errors` array is not a failure.
+        if (body.errors && body.errors.length > 0) {
+            const message = body.errors[0]?.message ?? 'unknown error';
+            throw new McpError(JsonRpcErrorCode.InternalError, `RCSB GraphQL error: ${message}`, {
+                retryable: false,
+            });
+        }
         if (body.data)
             return body.data;
-        const message = body.errors?.[0]?.message ?? 'unknown error';
-        throw new McpError(JsonRpcErrorCode.InternalError, `RCSB GraphQL error: ${message}`, {
+        throw new McpError(JsonRpcErrorCode.InternalError, 'RCSB GraphQL error: unknown error', {
             retryable: false,
         });
     }
@@ -293,6 +308,82 @@ export function buildQuery(params) {
 function textNode(attribute, operator, value) {
     return { type: 'terminal', service: 'text', parameters: { attribute, operator, value } };
 }
+/**
+ * Name/synonym chemical-dictionary query. Matches the term against both the
+ * formal component name and its synonyms: common names ("heme", "aspirin") live
+ * in synonyms, not the formal name ("PROTOPORPHYRIN IX CONTAINING FE"). A plain
+ * full_text search over mol_definition matches far too broadly and buries the
+ * intended component.
+ */
+function chemNameQuery(query) {
+    const chemTerm = (attribute) => ({
+        type: 'terminal',
+        service: 'text_chem',
+        parameters: { attribute, operator: 'contains_words', value: query },
+    });
+    return {
+        type: 'group',
+        logical_operator: 'or',
+        nodes: [chemTerm('chem_comp.name'), chemTerm('rcsb_chem_comp_synonyms.name')],
+    };
+}
+/**
+ * Composition query against RCSB's `chemical` service. The formula terminal
+ * accepts both CCD Hill notation (`C29 H31 N7 O`) and the unspaced form
+ * (`C29H31N7O`), so the value is passed through unnormalized. `match_subset` is
+ * left unset for an exact-composition match: the callers that consume the
+ * resolved ID (`structures_with_ligand`, `binding_site`) expect a single
+ * canonical component, which subset matching would dilute with supersets.
+ * The `text_chem` attribute `chem_comp.formula` is not an alternative — RCSB
+ * rejects it with "search is not enabled on [ chem_comp.formula ] attribute".
+ */
+function formulaQuery(query) {
+    return {
+        type: 'terminal',
+        service: 'chemical',
+        parameters: { type: 'formula', value: query.trim() },
+    };
+}
+/**
+ * Element symbols in canonical casing — the token vocabulary formula detection
+ * accepts. Token shape alone is not enough: an all-caps chemical name can
+ * tokenize as element-shaped letters (`VITAMIN B12` → V·I·T·A·M·I·N·B12), and
+ * mis-routing a name to the formula terminal returns an empty match set rather
+ * than an error, so the miss would be silent.
+ */
+const ELEMENT_SYMBOLS = new Set(`H He Li Be B C N O F Ne Na Mg Al Si P S Cl Ar K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se
+   Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb
+   Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Th Pa U Np Pu Am Cm
+   Bk Cf Es Fm Md No Lr Rf Db Sg Bh Hs Mt Ds Rg Cn Nh Fl Mc Lv Ts Og`.split(/\s+/));
+/** One formula token: an element symbol plus an optional count (`C29`, `Fe`). */
+const FORMULA_TOKEN_RE = /[A-Z][a-z]?\d*/g;
+/**
+ * True when `query` is a molecular formula rather than a chemical name or a
+ * component ID. Whitespace is insignificant — both the spaced CCD Hill notation
+ * and the unspaced form resolve upstream — but every remaining character must
+ * belong to an element-symbol token, and at least one element count must be
+ * present. The digit requirement carries most of the discrimination: Hill
+ * notation omits an implicit `1` only for the leading element, never for all of
+ * them, so `STI` (S·Ti) and `HEM` (H·E·M) are IDs, not formulas.
+ *
+ * It is a shape test, not a decision about what the string means, and it cannot
+ * separate every component ID from a formula: an all-caps ID built only from
+ * single-letter element symbols plus a digit (`SF4`, `H4B`, `BU1`) satisfies
+ * every rule here. `findChemComps` absorbs that by retrying the name/synonym
+ * search when the formula terminal matches nothing, so a claimed ID still
+ * resolves.
+ */
+export function isChemicalFormula(query) {
+    const compact = query.trim().replace(/\s+/g, '');
+    if (!/\d/.test(compact))
+        return false;
+    const tokens = compact.match(FORMULA_TOKEN_RE) ?? [];
+    // Anything the tokenizer skipped (punctuation, a lowercase-leading word, a
+    // digit-leading component ID) leaves the rejoined tokens shorter than the input.
+    if (tokens.join('') !== compact)
+        return false;
+    return tokens.every((token) => ELEMENT_SYMBOLS.has(token.replace(/\d+$/, '')));
+}
 /**
  * Emit the `results_content_type` request option for a content scope. Omitting
  * the option is not a union — RCSB defaults to experimental only — so a caller
@@ -443,14 +534,21 @@ function normalizeEntry(raw) {
 }
 function normalizePolymerEntity(raw) {
     const organism = raw.rcsb_entity_source_organism?.find((o) => o.ncbi_scientific_name)?.ncbi_scientific_name;
-    const chains = raw.rcsb_polymer_entity_container_identifiers?.auth_asym_ids;
+    // Two distinct chain namespaces, never interchangeable: `auth_asym_ids` are the
+    // depositor's labels (what protein_get_annotations.chain takes), `asym_ids` the
+    // mmCIF label_asym_ids (what protein_compare_structures.chain takes). For many
+    // entries they coincide; for 6QNR_9 they are ["82","8E"] vs ["I","OB"].
+    const container = raw.rcsb_polymer_entity_container_identifiers;
+    const authAsymIds = container?.auth_asym_ids;
+    const labelAsymIds = container?.asym_ids;
     return {
         entityId: raw.rcsb_id ?? '',
+        ...(authAsymIds && authAsymIds.length > 0 ? { authAsymIds } : {}),
         ...(raw.rcsb_polymer_entity?.pdbx_description
             ? { description: raw.rcsb_polymer_entity.pdbx_description }
             : {}),
+        ...(labelAsymIds && labelAsymIds.length > 0 ? { labelAsymIds } : {}),
         ...(organism ? { organism } : {}),
-        ...(chains && chains.length > 0 ? { chains } : {}),
         ...(typeof raw.entity_poly?.rcsb_sample_sequence_length === 'number'
             ? { sequenceLength: raw.entity_poly.rcsb_sample_sequence_length }
             : {}),
@@ -509,7 +607,7 @@ const ENTRIES_QUERY = `query Entries($ids: [String!]!) {
     polymer_entities {
       rcsb_id
       rcsb_polymer_entity { pdbx_description }
-      rcsb_polymer_entity_container_identifiers { auth_asym_ids }
+      rcsb_polymer_entity_container_identifiers { auth_asym_ids asym_ids }
       entity_poly { rcsb_sample_sequence_length }
       rcsb_entity_source_organism { ncbi_scientific_name }
     }

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

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

@@ -61,12 +61,21 @@ export interface SearchResult {
 }
 /** A modeled polymer (protein/nucleic) entity within an entry. */
 export interface PolymerEntityMeta {
-    /** Author-assigned chain IDs for this entity. */
-    chains?: string[];
+    /**
+     * Author-assigned chain IDs (`auth_asym_id`) for this entity — the namespace
+     * `protein_get_annotations.chain` consumes. Absent when upstream omits it.
+     */
+    authAsymIds?: string[];
     /** Free-text description (e.g. "Hemoglobin subunit alpha"). */
     description?: string;
     /** Entity identifier (e.g. `4HHB_1`). */
     entityId: string;
+    /**
+     * mmCIF `label_asym_id` chain IDs for this entity — the namespace
+     * `protein_compare_structures.chain` consumes. Unrelated to `authAsymIds` by any
+     * transformation, though the two coincide for many entries.
+     */
+    labelAsymIds?: string[];
     /** Source organism scientific name. */
     organism?: string;
     /** One-letter canonical sequence (present only when explicitly requested). */

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": "0.6.0",
+  "version": "0.8.0",
   "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": "0.6.0",
+  "version": "0.8.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.6.0",
+      "version": "0.8.0",
       "packageArguments": [
         {
           "type": "positional",
@@ -48,7 +48,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.6.0",
+      "version": "0.8.0",
       "packageArguments": [
         {
           "type": "positional",