@cyanheads/protein-mcp-server 0.6.0 → 0.8.0

package/dist/mcp-server/tools/definitions/get-structure.tool.js

@@ -2,9 +2,12 @@
  * @fileoverview protein_get_structure — fetch experimental, predicted, or
  * best-available structures by ID. Batches up to N experimental IDs in one RCSB
  * GraphQL call with per-ID partial success (`failed[]`). Optionally inlines
- * coordinate-file content; when that overflows a byte budget it returns a
- * per-structure section outline for targeted re-call instead of truncating.
- * Carries upstream data attribution (RCSB PDB / AlphaFold DB) per response.
+ * coordinate-file content; when that overflows a byte budget the content is
+ * withheld from both surfaces and a per-structure size outline is returned
+ * instead of truncating. Every success-path advisory — batch cap, partial
+ * failure, overflow, failed inlining — accumulates into one notice, since the
+ * framework's `notice` field is last-write-wins. Carries upstream data
+ * attribution (RCSB PDB / AlphaFold DB) per response.
  * @module mcp-server/tools/definitions/get-structure.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -18,7 +21,7 @@ import { mapWithConcurrency } from '../../../services/shared/async.js';
 import { attributionsFor } from '../../../services/shared/attribution.js';
 import { fetchText } from '../../../services/shared/http.js';
 import { isAlphaFoldEntryId, isPdbId, isUniProtAccession } from '../../../services/shared/identifiers.js';
-import { attributionSchema, renderAttribution } from './_schemas.js';
+import { attributionSchema, ligandSchema, polymerEntitySchema, renderAttribution, } from './_schemas.js';
 const confidenceBucketsSchema = z.object({
     veryLow: z.number().describe('Fraction of residues with pLDDT < 50.'),
     low: z.number().describe('Fraction with pLDDT 50–70.'),
@@ -39,6 +42,22 @@ const structureRecordSchema = z
     method: z.string().optional().describe('Experimental method(s).'),
     resolution: z.number().optional().describe('Resolution in Å (experimental).'),
     organism: z.string().optional().describe('Source organism.'),
+    molecularWeight: z
+        .number()
+        .optional()
+        .describe('Deposited structure molecular weight in kDa, from the RCSB entry record. Omitted when the record does not report one.'),
+    releaseDate: z
+        .string()
+        .optional()
+        .describe('Initial release date (ISO 8601), from the RCSB entry record. Omitted when the record does not report one.'),
+    polymerEntities: z
+        .array(polymerEntitySchema)
+        .optional()
+        .describe('Modeled polymer entities, each with both chain namespaces — authAsymIds for protein_get_annotations.chain, labelAsymIds for protein_compare_structures.chain. Present for records served by the RCSB entry endpoint (source experimental, computed models included); omitted for predicted / best_available records and for entries with none.'),
+    ligands: z
+        .array(ligandSchema)
+        .optional()
+        .describe('Bound non-polymer components. Present for records served by the RCSB entry endpoint; omitted when the entry binds none or the record carries no ligand data.'),
     provider: z.string().optional().describe('Model provider (predicted / best_available).'),
     confidence: z
         .number()
@@ -78,16 +97,7 @@ const structureRecordSchema = z
     .describe('A resolved structure with metadata and coordinate-file URLs.');
 export const getStructure = tool('protein_get_structure', {
     title: 'protein-mcp-server: get structure',
-    description: 'Fetch structures with metadata and coordinate-file URLs. source "experimental" takes PDB entry IDs ' +
-        '(batched in one call), and also resolves the computed-model IDs protein_search_structures returns ' +
-        '(AF_*/MA_*), which come back marked source "predicted" with their modelling provider; ' +
-        '"predicted" takes UniProt accessions (AlphaFold, with pLDDT/PAE confidence); ' +
-        '"best_available" takes UniProt accessions and returns the top federated model — the highest-resolution ' +
-        'experimental structure if one exists (optimizing resolution, not biological representativeness, so it can ' +
-        'return an engineered mutant over the wild-type entry), else the best prediction. Resolves up to the ' +
-        'configured batch cap per call with per-ID partial success — missed IDs are listed in failed[]. Set ' +
-        'include_coords to inline coordinate content; if that overflows, a section outline is returned — re-call ' +
-        'with sections:[ids] to inline specific structures.',
+    description: `Fetch structures with metadata and coordinate-file URLs. source "experimental" takes PDB entry IDs (batched in one call), and also resolves the computed-model IDs protein_search_structures returns (AF_*/MA_*), which come back marked source "predicted" with their modelling provider; "predicted" takes UniProt accessions (AlphaFold, with pLDDT/PAE confidence); "best_available" takes UniProt accessions and returns the top federated model — the highest-resolution experimental structure if one exists (optimizing resolution, not biological representativeness, so it can return an engineered mutant over the wild-type entry), else the best prediction. Records served by the RCSB entry endpoint also carry polymer entities with both chain namespaces (labelAsymIds for protein_compare_structures, authAsymIds for protein_get_annotations), bound ligands, molecular weight, and release date. Resolves up to the configured batch cap per call with per-ID partial success — missed IDs are listed in failed[], and IDs beyond the cap are reported in the notice. Set include_coords to inline coordinate content; if the inlined bytes exceed the response budget the content is withheld and overflow lists each structure's size — re-call with sections:[ids] for specific structures, or for a single oversized file download it from that record's coordinateUrls.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -154,15 +164,26 @@ export const getStructure = tool('protein_get_structure', {
             .describe('Present only when inlined coordinates across the batch exceeded the response budget.'),
     }),
     enrichment: {
-        requested: z.number().describe('Number of IDs requested.'),
-        resolved: z.number().describe('Number of IDs resolved.'),
-        notice: z.string().optional().describe('Advisory note (partial failures, overflow guidance).'),
+        requested: z
+            .number()
+            .describe('Number of IDs in the original request (input.ids.length), before the batch cap was applied.'),
+        processed: z
+            .number()
+            .describe('Number of IDs actually processed after the batch cap. Lower than requested means the excess IDs were ignored and never looked up — re-submit them in a follow-up call.'),
+        resolved: z.number().describe('Number of processed IDs that resolved to a structure.'),
+        notice: z
+            .string()
+            .optional()
+            .describe('Every applicable advisory joined into one string: batch cap, partial failures, coordinate-budget overflow, and failed coordinate inlining.'),
     },
     async handler(input, ctx) {
         const cfg = getServerConfig();
         const ids = input.ids.slice(0, cfg.maxBatchIds).map((s) => s.trim());
+        // `ctx.enrich.notice` is last-write-wins, so a second call erases the first.
+        // Every advisory this handler can raise accumulates here and is written once.
+        const notices = [];
         if (input.ids.length > cfg.maxBatchIds) {
-            ctx.enrich.notice(`Batch capped at ${cfg.maxBatchIds} IDs; ${input.ids.length - cfg.maxBatchIds} ignored.`);
+            notices.push(`Batch capped at ${cfg.maxBatchIds} IDs; ${input.ids.length - cfg.maxBatchIds} ignored.`);
         }
         if (input.source === 'experimental') {
             if (ids.some((id) => isUniProtAccession(id) && !isPdbId(id))) {
@@ -178,6 +199,9 @@ export const getStructure = tool('protein_get_structure', {
         if (structures.length === 0) {
             throw ctx.fail('all_failed', `None of the ${ids.length} requested IDs resolved to a structure.`, { ...ctx.recoveryFor('all_failed') });
         }
+        if (failed.length > 0) {
+            notices.push(`${failed.length} of ${ids.length} IDs did not resolve: ${failed.map((f) => f.id).join(', ')}.`);
+        }
         // Inline coordinates when requested (all, or only the re-called sections).
         const inlineSet = input.sections?.length
             ? new Set(input.sections.map((s) => s.toUpperCase()))
@@ -185,34 +209,44 @@ export const getStructure = tool('protein_get_structure', {
                 ? 'all'
                 : null;
         if (inlineSet) {
-            await inlineCoordinates(structures, inlineSet, cfg.fanoutConcurrency, ctx);
+            const inlineFailures = await inlineCoordinates(structures, inlineSet, cfg.fanoutConcurrency, ctx);
+            if (inlineFailures.length > 0) {
+                notices.push(`Coordinate inlining failed for ${inlineFailures.join(', ')}; the metadata is complete but the coordinate content is missing — retry, or download the file from that structure's coordinateUrls.`);
+            }
         }
-        // Overflow guard: inlining several coordinate files at once can blow the
-        // response budget. A single structure always inlines (re-calling for the lone
-        // section would return the same bytes); 2+ over budget collapse to a size index.
+        // Overflow guard: one coordinate file can blow the response budget on its own
+        // (4HHB.cif is ~30× it), so the budget applies to the inlined total however few
+        // files it spans. Over budget the payload is withheld from both surfaces and
+        // `overflow` carries the per-structure size index. A lone withheld file is
+        // pointed at its own coordinateUrls — a `sections` re-call would return the
+        // identical bytes — while a batch keeps the targeted re-call. A `sections`
+        // re-call is not itself re-gated: the caller has already named the exact bytes.
         let overflow;
         if (inlineSet === 'all') {
             const withCoords = structures.filter((s) => s.coordinates);
             const total = withCoords.reduce((n, s) => n + (s.coordinates?.length ?? 0), 0);
-            if (withCoords.length > 1 && total > DEFAULT_OUTLINE_BUDGET_BYTES) {
+            if (total > DEFAULT_OUTLINE_BUDGET_BYTES) {
                 const sections = withCoords.map((s) => ({ id: s.id, bytes: s.coordinates?.length ?? 0 }));
                 for (const s of structures) {
                     delete s.coordinates;
                     delete s.coordinateFormat;
                 }
-                overflow = {
-                    sections,
-                    notice: `Inlined coordinates (${total} bytes across ${sections.length} structures) exceeded the ` +
-                        `${DEFAULT_OUTLINE_BUDGET_BYTES}-byte budget. Re-call with sections:["${sections[0]?.id}"] ` +
-                        `(add more IDs as needed) to inline specific structures.`,
-                };
-                ctx.enrich.notice('Coordinates exceeded the inline budget; re-call with sections for specific structures.');
+                // One string for `overflow.notice` and the enrichment accumulator, so the
+                // structured and text surfaces cannot describe the withheld state differently.
+                const overflowNotice = sections.length === 1
+                    ? `Inlined coordinates for ${sections[0]?.id} (${total} bytes) exceeded the ${DEFAULT_OUTLINE_BUDGET_BYTES}-byte budget and were withheld. Download the file from that structure's coordinateUrls — re-calling for the lone section would return the same bytes.`
+                    : `Inlined coordinates (${total} bytes across ${sections.length} structures) exceeded the ${DEFAULT_OUTLINE_BUDGET_BYTES}-byte budget. Re-call with sections:["${sections[0]?.id}"] (add more IDs as needed) to inline specific structures.`;
+                overflow = { sections, notice: overflowNotice };
+                notices.push(overflowNotice);
             }
         }
-        ctx.enrich({ requested: ids.length, resolved: structures.length });
-        if (failed.length > 0) {
-            ctx.enrich.notice(`${failed.length} of ${ids.length} IDs did not resolve: ${failed.map((f) => f.id).join(', ')}.`);
-        }
+        ctx.enrich({
+            requested: input.ids.length,
+            processed: ids.length,
+            resolved: structures.length,
+        });
+        if (notices.length > 0)
+            ctx.enrich.notice(notices.join(' '));
         // Attribution is a per-response union of the sources actually present, keyed
         // off each record's real provider. Experimental data is fetched from RCSB
         // regardless of the beacon's provider label. best_available federates predicted
@@ -234,6 +268,11 @@ export const getStructure = tool('protein_get_structure', {
         };
     },
     format: (result) => {
+        // Structures whose payload the batch-overflow gate already purged from the
+        // structured surface. Their `coordinates` is gone, so the per-structure
+        // length check below reads 0 and cannot recognize them — this set is what
+        // still earns them the withheld marker instead of silent omission.
+        const withheld = new Set(result.overflow?.sections.map((s) => s.id) ?? []);
         const lines = [`## Structures (${result.structures.length})`];
         for (const s of result.structures) {
             lines.push(`\n### ${s.id} _(${s.source})_`);
@@ -244,6 +283,8 @@ export const getStructure = tool('protein_get_structure', {
                 s.method ? `**Method:** ${s.method}` : null,
                 typeof s.resolution === 'number' ? `**Resolution:** ${s.resolution} Å` : null,
                 s.organism ? `**Organism:** ${s.organism}` : null,
+                typeof s.molecularWeight === 'number' ? `**MW:** ${s.molecularWeight} kDa` : null,
+                s.releaseDate ? `**Released:** ${s.releaseDate}` : null,
                 s.provider ? `**Provider:** ${s.provider}` : null,
                 typeof s.confidence === 'number'
                     ? `**Confidence:** ${s.confidence}${s.confidenceType ? ` (${s.confidenceType})` : ''}`
@@ -256,6 +297,27 @@ export const getStructure = tool('protein_get_structure', {
                 const b = s.confidenceBuckets;
                 lines.push(`**Confidence:** veryHigh ${pct(b.veryHigh)} · confident ${pct(b.confident)} · low ${pct(b.low)} · veryLow ${pct(b.veryLow)}`);
             }
+            if (s.polymerEntities && s.polymerEntities.length > 0) {
+                lines.push('**Polymer entities:**');
+                for (const e of s.polymerEntities) {
+                    const parts = [
+                        e.description,
+                        e.organism,
+                        // Both namespaces are labelled, never merged — they are not interchangeable.
+                        e.authAsymIds ? `auth_asym_id: ${e.authAsymIds.join(', ')}` : null,
+                        e.labelAsymIds ? `label_asym_id: ${e.labelAsymIds.join(', ')}` : null,
+                        typeof e.sequenceLength === 'number' ? `${e.sequenceLength} residues` : null,
+                    ].filter(Boolean);
+                    lines.push(`- **${e.entityId}** — ${parts.join(' · ')}`);
+                }
+            }
+            if (s.ligands && s.ligands.length > 0) {
+                lines.push('**Ligands:**');
+                for (const l of s.ligands) {
+                    const parts = [l.name, l.formula].filter(Boolean);
+                    lines.push(`- **${l.compId}**${parts.length > 0 ? ` — ${parts.join(' · ')}` : ''}`);
+                }
+            }
             const urls = [
                 s.coordinateUrls.cif ? `[cif](${s.coordinateUrls.cif})` : null,
                 s.coordinateUrls.pdb ? `[pdb](${s.coordinateUrls.pdb})` : null,
@@ -265,9 +327,20 @@ export const getStructure = tool('protein_get_structure', {
                 lines.push(`**Coordinates:** ${urls.join(' · ')}`);
             if (s.paeDocUrl)
                 lines.push(`**PAE:** ${s.paeDocUrl}`);
-            if (s.coordinates) {
+            // One length rule for every structure carrying coordinates, whether or not
+            // the overflow index names it: whole under the budget, otherwise the
+            // withheld marker plus the URL pointer above — never a truncated prefix.
+            // A `sections` re-call is deliberately not re-gated on the structured
+            // surface (the caller named the exact bytes), so this is the one path where
+            // the two surfaces carry different payloads; they still agree on *state*,
+            // because the token-bounded text surface discloses the omission and points
+            // at a working retrieval route instead of silently cutting the content off.
+            if (withheld.has(s.id) || (s.coordinates?.length ?? 0) > DEFAULT_OUTLINE_BUDGET_BYTES) {
+                lines.push('**Coordinates withheld** — over the inline budget; see the URLs above.');
+            }
+            else if (s.coordinates) {
                 lines.push(`**Inlined ${s.coordinateFormat ?? 'coordinates'} (${s.coordinates.length} bytes):**`);
-                lines.push('```', s.coordinates.slice(0, 2000), s.coordinates.length > 2000 ? '… (truncated in text view)' : '', '```');
+                lines.push('```', s.coordinates, '```');
             }
         }
         if (result.failed.length > 0) {
@@ -315,7 +388,15 @@ async function fetchExperimental(ids, ctx) {
             ...(meta.title ? { title: meta.title } : {}),
             ...(meta.methods && meta.methods.length > 0 ? { method: meta.methods.join(', ') } : {}),
             ...(typeof meta.resolution === 'number' ? { resolution: meta.resolution } : {}),
+            ...(typeof meta.molecularWeight === 'number'
+                ? { molecularWeight: meta.molecularWeight }
+                : {}),
+            ...(meta.releaseDate ? { releaseDate: meta.releaseDate } : {}),
             ...(meta.organisms.length > 0 ? { organism: meta.organisms[0] } : {}),
+            // Already on EntryMeta from the same getEntries() call — omitted rather than
+            // emitted empty, so a sparse entry does not read as "this entry has none".
+            ...(meta.polymerEntities.length > 0 ? { polymerEntities: meta.polymerEntities } : {}),
+            ...(meta.ligands.length > 0 ? { ligands: meta.ligands } : {}),
             coordinateUrls: {
                 cif: rcsb.coordinateFileUrl(meta.id, 'cif'),
                 pdb: rcsb.coordinateFileUrl(meta.id, 'pdb'),
@@ -436,9 +517,15 @@ function coordinateUrlFor(url) {
         return { pdb: url };
     return { cif: url };
 }
-/** Fetch and inline coordinate content for the requested structures. */
+/**
+ * Fetch and inline coordinate content for the requested structures. Returns the
+ * IDs whose fetch failed — a record that silently lacks `coordinates` is
+ * indistinguishable from one that was never asked to inline, so the caller needs
+ * the failure named in the response rather than only in the log.
+ */
 async function inlineCoordinates(structures, inline, concurrency, ctx) {
     const targets = structures.filter((s) => inline === 'all' || inline.has(s.id.toUpperCase()));
+    const failures = [];
     await mapWithConcurrency(targets, concurrency, async (s) => {
         const pick = s.coordinateUrls.cif
             ? ['cif', s.coordinateUrls.cif]
@@ -461,7 +548,9 @@ async function inlineCoordinates(structures, inline, concurrency, ctx) {
                 id: s.id,
                 error: err instanceof Error ? err.message : err,
             });
+            failures.push(s.id);
         }
     });
+    return failures;
 }
 //# sourceMappingURL=get-structure.tool.js.map

package/dist/mcp-server/tools/definitions/get-structure.tool.js.map

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

@@ -2,7 +2,9 @@
  * @fileoverview Foldseek service — wraps the public Foldseek structural-search
  * ticket API (`/api/ticket` → poll `/api/ticket/{id}` → `/api/result/{id}/{n}`).
  * Submits a query coordinate file against experimental + predicted databases and
- * returns fold-similarity hits. Backs `protein_find_similar` (`by: structure`).
+ * returns a page of fold-similarity hits alongside the full hit count, so a
+ * completed ticket can be re-paged instead of resubmitted. Backs
+ * `protein_find_similar` (`by: structure`).
  * Async: the ticket status field drives completion, not the HTTP code.
  * @module services/foldseek/foldseek-service
  */
@@ -40,6 +42,7 @@ export type FoldseekOutcome = {
     status: 'complete';
     ticketId: string;
     hits: FoldseekHit[];
+    total: number;
 } | {
     status: 'computing';
     ticketId: string;
@@ -63,6 +66,7 @@ export declare class FoldseekService {
         databases: string[];
         mode: string;
         limit: number;
+        start: number;
         timeoutMs: number;
     }, ctx: Context): Promise<FoldseekOutcome>;
     /**
@@ -74,10 +78,17 @@ export declare class FoldseekService {
     resume(params: {
         ticketId: string;
         limit: number;
+        start: number;
         timeoutMs: number;
     }, ctx: Context): Promise<FoldseekOutcome>;
     private submit;
     private pollTicket;
+    /**
+     * Read a completed ticket's full alignment set and return the requested page.
+     * The whole list is parsed before slicing so the caller learns the real hit
+     * count — a page with no total leaves an agent unable to tell a complete result
+     * from a truncated one, and unable to ask for the rest.
+     */
     private fetchResults;
 }
 export declare function initFoldseekService(config: AppConfig, storage: StorageService, serverConfig: ServerConfig): void;

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

@@ -1 +1 @@
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package/dist/services/foldseek/foldseek-service.js

@@ -2,7 +2,9 @@
  * @fileoverview Foldseek service — wraps the public Foldseek structural-search
  * ticket API (`/api/ticket` → poll `/api/ticket/{id}` → `/api/result/{id}/{n}`).
  * Submits a query coordinate file against experimental + predicted databases and
- * returns fold-similarity hits. Backs `protein_find_similar` (`by: structure`).
+ * returns a page of fold-similarity hits alongside the full hit count, so a
+ * completed ticket can be re-paged instead of resubmitted. Backs
+ * `protein_find_similar` (`by: structure`).
  * Async: the ticket status field drives completion, not the HTTP code.
  * @module services/foldseek/foldseek-service
  */
@@ -28,14 +30,14 @@ export class FoldseekService {
         }
         try {
             const outcome = await withAsyncPoll({
-                step: () => this.pollTicket(ticketId, params.limit, ctx),
+                step: () => this.pollTicket(ticketId, params.start, params.limit, ctx),
                 timeoutMs: params.timeoutMs,
                 ctx,
                 intervalMs: 1500,
                 maxIntervalMs: 2500,
             });
             return outcome.status === 'complete'
-                ? { status: 'complete', ticketId, hits: outcome.value }
+                ? { status: 'complete', ticketId, ...outcome.value }
                 : { status: 'computing', ticketId };
         }
         catch (err) {
@@ -51,14 +53,14 @@ export class FoldseekService {
     async resume(params, ctx) {
         try {
             const outcome = await withAsyncPoll({
-                step: () => this.pollTicket(params.ticketId, params.limit, ctx),
+                step: () => this.pollTicket(params.ticketId, params.start, params.limit, ctx),
                 timeoutMs: params.timeoutMs,
                 ctx,
                 intervalMs: 1500,
                 maxIntervalMs: 2500,
             });
             return outcome.status === 'complete'
-                ? { status: 'complete', ticketId: params.ticketId, hits: outcome.value }
+                ? { status: 'complete', ticketId: params.ticketId, ...outcome.value }
                 : { status: 'computing', ticketId: params.ticketId };
         }
         catch (err) {
@@ -90,7 +92,7 @@ export class FoldseekService {
             throw new Error('Foldseek did not return a ticket ID');
         return raw.id;
     }
-    async pollTicket(ticketId, limit, ctx) {
+    async pollTicket(ticketId, start, limit, ctx) {
         const ticket = await fetchJson(`${this.baseUrl}/api/ticket/${encodeURIComponent(ticketId)}`, ctx, {
             operation: 'FoldseekService.pollTicket',
             label: 'Foldseek',
@@ -102,10 +104,15 @@ export class FoldseekService {
             throw new Error('Foldseek reported an error processing the structure');
         if (status !== 'COMPLETE')
             return { ready: false };
-        const hits = await this.fetchResults(ticketId, limit, ctx);
-        return { ready: true, value: hits };
+        return { ready: true, value: await this.fetchResults(ticketId, start, limit, ctx) };
     }
-    async fetchResults(ticketId, limit, ctx) {
+    /**
+     * Read a completed ticket's full alignment set and return the requested page.
+     * The whole list is parsed before slicing so the caller learns the real hit
+     * count — a page with no total leaves an agent unable to tell a complete result
+     * from a truncated one, and unable to ask for the rest.
+     */
+    async fetchResults(ticketId, start, limit, ctx) {
         const raw = await fetchJson(`${this.baseUrl}/api/result/${encodeURIComponent(ticketId)}/0`, ctx, { operation: 'FoldseekService.fetchResults', label: 'Foldseek', baseDelayMs: 400 });
         const hits = [];
         for (const dbResult of raw.results ?? []) {
@@ -115,12 +122,10 @@ export class FoldseekService {
                     if (!aln.target)
                         continue;
                     hits.push(normalizeHit(aln, db));
-                    if (hits.length >= limit)
-                        return hits;
                 }
             }
         }
-        return hits;
+        return { total: hits.length, hits: hits.slice(start, start + limit) };
     }
 }
 // ─── Normalizers ──────────────────────────────────────────────────────────────

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

@@ -61,7 +61,20 @@ export declare class RcsbService {
      * surfaces first — a count-only query (rows 0), no rows or sort pulled.
      */
     countEntriesWithLigand(compId: string, ctx: Context): Promise<number>;
-    /** 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.
+     */
     findChemComps(query: string, limit: number, ctx: Context): Promise<string[]>;
     /** Facet-only aggregation over an optional scoping query (no row pull). */
     analyzeFacets(params: StructureSearchParams, facets: FacetSpec[], ctx: Context): Promise<{
@@ -94,6 +107,23 @@ export declare class RcsbService {
 }
 /** Build the RCSB query node from search params (match-all when no constraint given). */
 export declare function buildQuery(params: StructureSearchParams): unknown;
+/**
+ * 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 declare function isChemicalFormula(query: string): boolean;
 /** Translate a friendly FacetSpec into the RCSB facet request shape (recursively). */
 export declare function toRcsbFacet(spec: FacetSpec): Record<string, unknown>;
 export declare function initRcsbService(config: AppConfig, storage: StorageService, serverConfig: ServerConfig): void;

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

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