@cyanheads/protein-mcp-server 0.8.3 → 0.8.5

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

@@ -27,22 +27,42 @@ const chemCompSchema = z
 const bindingSiteSchema = z
     .object({
     ligandCompId: z.string().describe('Bound ligand chemical component ID.'),
-    ligandAsymId: z.string().optional().describe('Ligand instance chain (asym) ID.'),
+    ligandAsymId: z
+        .string()
+        .optional()
+        .describe('Author chain ID (auth_asym_id) of the ligand instance — the author namespace, unlike residues[].asymId.'),
+    ligandAuthSeqId: z
+        .number()
+        .optional()
+        .describe('Author residue number (auth_seq_id) of the ligand instance.'),
     residues: z
         .array(z
         .object({
         residueCompId: z.string().describe('Interacting residue type (e.g. ASP).'),
-        asymId: z.string().describe('Chain ID the residue belongs to.'),
-        seqId: z.number().optional().describe('Residue sequence position.'),
+        asymId: z
+            .string()
+            .describe("mmCIF label_asym_id of the residue's chain (label namespace, paired with seqId). Can differ from authAsymId."),
+        seqId: z
+            .number()
+            .optional()
+            .describe('mmCIF label_seq_id: position in the entity sequence (label namespace). Not the deposited residue number; see authSeqId.'),
+        authAsymId: z
+            .string()
+            .optional()
+            .describe("Author chain ID (auth_asym_id) of the residue's chain, as deposited and as most structure viewers label it."),
+        authSeqId: z
+            .number()
+            .optional()
+            .describe('Author residue number (auth_seq_id), as deposited and as most literature and viewers number it. Related to seqId by no fixed offset; insertion codes are not reported.'),
         distance: z.number().optional().describe('Contact distance to the ligand in Å.'),
     })
-        .describe('A pocket residue in contact with the ligand.'))
+        .describe('A pocket residue in contact with the ligand, in both numbering namespaces.'))
         .describe('Protein residues lining the pocket, nearest first.'),
 })
     .describe('A ligand instance and the protein residues lining its pocket.');
 export const trackLigands = tool('protein_track_ligands', {
     title: 'protein-mcp-server: track ligands',
-    description: `Ligand discovery and binding-site analysis across the PDB. mode "find_ligand" resolves a name or formula to chemical component IDs with metadata (formula, weight, SMILES), ranked by deposition frequency — most-deposited component first, so the top hit is the most common match for the name, not necessarily an exact name-string match. mode "structures_with_ligand" returns PDB entries containing a ligand (by exact component ID — get the ID from find_ligand first), highest-resolution first, each with its resolution in Å. mode "binding_site" returns the protein residues lining a ligand's pocket in a given structure, with contact distances. Binding sites are experimental-only (computed from deposited coordinates; predicted models carry no bound ligands).`,
+    description: `Ligand discovery and binding-site analysis across the PDB. mode "find_ligand" resolves a name or formula to chemical component IDs with metadata (formula, weight, SMILES), ranked by deposition frequency — most-deposited component first, so the top hit is the most common match for the name, not necessarily an exact name-string match. The ranking covers a bounded candidate pool; totalCount and candidatesConsidered report how many components matched and how many were ranked. mode "structures_with_ligand" returns PDB entries containing a ligand (by exact component ID — get the ID from find_ligand first), highest-resolution first, each with its resolution in Å. mode "binding_site" returns the protein residues lining a ligand's pocket in a given structure, with contact distances, each numbered in both the mmCIF label namespace (asymId, seqId) and the author namespace (authAsymId, authSeqId) used by deposited coordinates and most literature. Binding sites are experimental-only (computed from deposited coordinates; predicted models carry no bound ligands).`,
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -80,7 +100,7 @@ export const trackLigands = tool('protein_track_ligands', {
             .int()
             .min(0)
             .default(0)
-            .describe('Zero-based result offset (mode structures_with_ligand only).'),
+            .describe('Zero-based result offset (modes structures_with_ligand and binding_site; binding_site pages ligand instances).'),
     }),
     output: z.object({
         mode: z
@@ -111,20 +131,24 @@ export const trackLigands = tool('protein_track_ligands', {
         totalCount: z
             .number()
             .optional()
-            .describe('Total upstream matches before pagination (structures_with_ligand).'),
+            .describe('Total upstream matches before any local narrowing: PDB entries containing the component (structures_with_ligand), chemical components matching the query (find_ligand), or ligand instances with pocket contacts (binding_site).'),
+        candidatesConsidered: z
+            .number()
+            .optional()
+            .describe('Chemical components pulled into the deposition-frequency ranking (find_ligand). Below totalCount when the candidate pool was truncated; the ranking then covers only these candidates.'),
         start: z
             .number()
             .optional()
-            .describe('Zero-based offset of the structures_with_ligand result page.'),
+            .describe('Zero-based offset of the structures_with_ligand or binding_site result page.'),
         nextStart: z
             .number()
             .optional()
-            .describe('Offset for the next structures_with_ligand page; absent on the final or past-end page.'),
+            .describe('Offset for the next structures_with_ligand or binding_site page; absent on the final or past-end page.'),
         resolvedCompId: z.string().optional().describe('The chemical component ID used to query.'),
         notice: z
             .string()
             .optional()
-            .describe('Advisory note: a structures_with_ligand page that is empty because no entry contains the component or because start is past the end, or binding-site instances beyond limit that were left out.'),
+            .describe('Advisory note: a find_ligand candidate pool smaller than the upstream match count, a structures_with_ligand page that is empty because no entry contains the component or because start is past the end, or a binding_site page that leaves instances for a later start or starts past the last instance.'),
     },
     async handler(input, ctx) {
         const rcsb = getRcsbService();
@@ -138,10 +162,18 @@ export const trackLigands = tool('protein_track_ligands', {
             // deposition frequency and slice to the limit. The canonical component (e.g.
             // HEM for "heme") is the most-deposited but RCSB name-ranks it low, so a small
             // `limit` would never fetch it — the count re-rank can only reorder what it
-            // pulls. Re-rank, never filter. RCSB returns a bounded candidate set per name,
-            // so a pool of ~25 stays cheap while still covering low-name-ranked canonicals.
+            // pulls. Re-rank, never filter. Specific names match a handful of components
+            // ("ATP": 7), which a pool of ~25 covers cheaply; broad words match far more
+            // ("iron": 119), so the pool can truncate.
             const candidatePool = Math.max(input.limit, 25);
-            const ids = await rcsb.findChemComps(input.query, candidatePool, ctx);
+            const { ids, total } = await rcsb.findChemComps(input.query, candidatePool, ctx);
+            // A name with more matches than the pool holds ranks only the pool, so a
+            // more-deposited match beyond it can be missing — disclose that.
+            ctx.enrich.total(total);
+            ctx.enrich({ candidatesConsidered: ids.length });
+            if (ids.length < total) {
+                ctx.enrich.notice(`${ids.length} of ${total} components matching "${input.query}" were ranked by deposition frequency; the ranking covers only those ${ids.length}, so a more-deposited match can be missing. Narrow the query (a more specific name, a synonym, or a formula) to rank the full match set.`);
+            }
             const resolved = await mapWithConcurrency(ids, cfg.fanoutConcurrency, async (id) => {
                 const [chem, depositionCount] = await Promise.all([
                     rcsb.getChemComp(id, ctx),
@@ -216,14 +248,24 @@ export const trackLigands = tool('protein_track_ligands', {
                 },
             });
         }
-        // Cap binding-site INSTANCES to the shared limit (mode-consistent top-N; the
-        // other two modes already bound their results). Disclose the drop via notice.
-        const bindingSites = sites.slice(0, input.limit);
-        if (sites.length > input.limit) {
-            ctx.enrich.notice(`Showing ${input.limit} of ${sites.length} binding-site instances in ${input.pdb_id.toUpperCase()}${compId ? ` for ${compId}` : ''}; raise limit to see more.`);
+        // Page binding-site INSTANCES with the shared start/limit. An entry can hold
+        // more instances of one ligand than the limit ceiling (6QNR: 994 MG), so start
+        // is the only way to reach the tail.
+        const bindingSites = sites.slice(input.start, input.start + input.limit);
+        const nextStart = input.start + bindingSites.length;
+        const where = `${input.pdb_id.toUpperCase()}${compId ? ` for ${compId}` : ''}`;
+        ctx.enrich.total(sites.length);
+        ctx.enrich({
+            start: input.start,
+            ...(nextStart < sites.length ? { nextStart } : {}),
+            ...(compId ? { resolvedCompId: compId } : {}),
+        });
+        if (bindingSites.length === 0) {
+            ctx.enrich.notice(`start ${input.start} is past the end of the ${sites.length} binding-site instances in ${where}. Re-call with a lower start to read a populated page.`);
+        }
+        else if (nextStart < sites.length) {
+            ctx.enrich.notice(`Showing ${bindingSites.length} of ${sites.length} binding-site instances in ${where}; re-call with start ${nextStart} for the next page.`);
         }
-        if (compId)
-            ctx.enrich({ resolvedCompId: compId });
         return { mode: input.mode, bindingSites };
     },
     format: (result) => {
@@ -251,12 +293,23 @@ export const trackLigands = tool('protein_track_ligands', {
                     lines.push(`- ${s.id} — ${s.resolution.toFixed(2)} Å`);
             }
         }
+        if (result.bindingSites?.length) {
+            lines.push('\nResidues are numbered as label_seq_id (chain = label_asym_id); the author numbering follows as auth_seq_id (chain = auth_asym_id) where reported.');
+        }
         for (const site of result.bindingSites ?? []) {
-            lines.push(`\n### Ligand ${site.ligandCompId}${site.ligandAsymId ? ` (chain ${site.ligandAsymId})` : ''}`);
+            const ligandIds = [
+                site.ligandAsymId ? `author chain ${site.ligandAsymId}` : null,
+                site.ligandAuthSeqId != null ? `residue ${site.ligandAuthSeqId}` : null,
+            ].filter(Boolean);
+            lines.push(`\n### Ligand ${site.ligandCompId}${ligandIds.length > 0 ? ` (${ligandIds.join(', ')})` : ''}`);
             for (const r of site.residues) {
                 const pos = r.seqId != null ? `${r.residueCompId}${r.seqId}` : r.residueCompId;
+                const author = [
+                    r.authSeqId != null ? `author ${r.residueCompId}${r.authSeqId}` : null,
+                    r.authAsymId ? `${r.authSeqId != null ? '' : 'author '}chain ${r.authAsymId}` : null,
+                ].filter(Boolean);
                 const dist = r.distance != null ? ` — ${r.distance.toFixed(2)} Å` : '';
-                lines.push(`- ${pos} (chain ${r.asymId})${dist}`);
+                lines.push(`- ${pos} (chain ${r.asymId}${author.length > 0 ? `; ${author.join(', ')}` : ''})${dist}`);
             }
         }
         return [{ type: 'text', text: lines.join('\n') }];

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

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

@@ -1,10 +1,13 @@
 /**
  * @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 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`).
+ * ticket API (`/api/ticket` → poll `/api/ticket/{id}` → `/api/result/queries/{id}/…`
+ * + `/api/result/{id}/{query}`). Submits a query coordinate file against
+ * experimental + predicted databases; Foldseek splits a multichain file into one
+ * query per chain, so a completed ticket is read one query at a time. Returns a
+ * page of that query's fold-similarity hits, ranked by score across databases,
+ * alongside the full hit count and the ticket's query count, so a completed
+ * ticket can be re-paged or re-read at another query 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
  */
@@ -41,8 +44,17 @@ export interface FoldseekHit {
 export type FoldseekOutcome = {
     status: 'complete';
     ticketId: string;
+    /** Zero-based query index the hits belong to. */
+    query: number;
+    /** Number of queries (one per chain of the submitted file) the ticket holds. */
+    queryCount: number;
     hits: FoldseekHit[];
     total: number;
+} | {
+    status: 'query_out_of_range';
+    ticketId: string;
+    query: number;
+    queryCount: number;
 } | {
     status: 'computing';
     ticketId: string;
@@ -66,6 +78,8 @@ export declare class FoldseekService {
         databases: string[];
         mode: string;
         limit: number;
+        /** Zero-based query index to read; defaults to 0. */
+        query?: number;
         start: number;
         timeoutMs: number;
     }, ctx: Context): Promise<FoldseekOutcome>;
@@ -78,16 +92,21 @@ export declare class FoldseekService {
     resume(params: {
         ticketId: string;
         limit: number;
+        query?: number;
         start: number;
         timeoutMs: number;
     }, ctx: Context): Promise<FoldseekOutcome>;
     private submit;
+    /** Bounded-poll a ticket and map the read to an outcome. Throws on poll failure. */
+    private pollToOutcome;
     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.
+     * Read one query of a completed ticket and return the requested page of its
+     * hits. The query index is range-checked against the ticket's query list first:
+     * Foldseek answers an out-of-range index with HTTP 200 and empty blocks, which
+     * would read as a search with no matches. The whole hit list is parsed and
+     * ranked before slicing, so the caller learns the real hit count and pages walk
+     * one stable ordering.
      */
     private fetchResults;
 }

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

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

@@ -1,16 +1,26 @@
 /**
  * @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 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`).
+ * ticket API (`/api/ticket` → poll `/api/ticket/{id}` → `/api/result/queries/{id}/…`
+ * + `/api/result/{id}/{query}`). Submits a query coordinate file against
+ * experimental + predicted databases; Foldseek splits a multichain file into one
+ * query per chain, so a completed ticket is read one query at a time. Returns a
+ * page of that query's fold-similarity hits, ranked by score across databases,
+ * alongside the full hit count and the ticket's query count, so a completed
+ * ticket can be re-paged or re-read at another query 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
  */
 import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
 import { withAsyncPoll } from '../shared/async.js';
 import { fetchJson } from '../shared/http.js';
+/**
+ * Page size for the query-list request. The endpoint's `limit`/`offset` paging
+ * is off by one upstream (a limit of N returns at most N−1 entries, and
+ * `hasNext` can read false while entries remain), so the whole list is read in
+ * a single oversized request rather than walked.
+ */
+const QUERY_LIST_LIMIT = 10_000;
 export class FoldseekService {
     baseUrl;
     constructor(_config, _storage, serverConfig) {
@@ -29,16 +39,7 @@ export class FoldseekService {
             return { status: 'failed', error: err instanceof Error ? err.message : String(err) };
         }
         try {
-            const outcome = await withAsyncPoll({
-                step: () => this.pollTicket(ticketId, params.start, params.limit, ctx),
-                timeoutMs: params.timeoutMs,
-                ctx,
-                intervalMs: 1500,
-                maxIntervalMs: 2500,
-            });
-            return outcome.status === 'complete'
-                ? { status: 'complete', ticketId, ...outcome.value }
-                : { status: 'computing', ticketId };
+            return await this.pollToOutcome(ticketId, params, ctx);
         }
         catch (err) {
             return { status: 'failed', error: err instanceof Error ? err.message : String(err) };
@@ -52,16 +53,7 @@ export class FoldseekService {
      */
     async resume(params, ctx) {
         try {
-            const outcome = await withAsyncPoll({
-                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, ...outcome.value }
-                : { status: 'computing', ticketId: params.ticketId };
+            return await this.pollToOutcome(params.ticketId, params, ctx);
         }
         catch (err) {
             // A 400 from the ticket/result endpoint is Foldseek's "invalid ID" — the
@@ -92,7 +84,31 @@ export class FoldseekService {
             throw new Error('Foldseek did not return a ticket ID');
         return raw.id;
     }
-    async pollTicket(ticketId, start, limit, ctx) {
+    /** Bounded-poll a ticket and map the read to an outcome. Throws on poll failure. */
+    async pollToOutcome(ticketId, page, ctx) {
+        const query = page.query ?? 0;
+        const outcome = await withAsyncPoll({
+            step: () => this.pollTicket(ticketId, query, page.start, page.limit, ctx),
+            timeoutMs: page.timeoutMs,
+            ctx,
+            intervalMs: 1500,
+            maxIntervalMs: 2500,
+        });
+        if (outcome.status !== 'complete')
+            return { status: 'computing', ticketId };
+        const read = outcome.value;
+        return read.kind === 'query_out_of_range'
+            ? { status: 'query_out_of_range', ticketId, query, queryCount: read.queryCount }
+            : {
+                status: 'complete',
+                ticketId,
+                query,
+                queryCount: read.queryCount,
+                hits: read.hits,
+                total: read.total,
+            };
+    }
+    async pollTicket(ticketId, query, start, limit, ctx) {
         const ticket = await fetchJson(`${this.baseUrl}/api/ticket/${encodeURIComponent(ticketId)}`, ctx, {
             operation: 'FoldseekService.pollTicket',
             label: 'Foldseek',
@@ -104,16 +120,23 @@ export class FoldseekService {
             throw new Error('Foldseek reported an error processing the structure');
         if (status !== 'COMPLETE')
             return { ready: false };
-        return { ready: true, value: await this.fetchResults(ticketId, start, limit, ctx) };
+        return { ready: true, value: await this.fetchResults(ticketId, query, start, 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.
+     * Read one query of a completed ticket and return the requested page of its
+     * hits. The query index is range-checked against the ticket's query list first:
+     * Foldseek answers an out-of-range index with HTTP 200 and empty blocks, which
+     * would read as a search with no matches. The whole hit list is parsed and
+     * ranked before slicing, so the caller learns the real hit count and pages walk
+     * one stable ordering.
      */
-    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 });
+    async fetchResults(ticketId, query, start, limit, ctx) {
+        const ticket = encodeURIComponent(ticketId);
+        const list = await fetchJson(`${this.baseUrl}/api/result/queries/${ticket}/${QUERY_LIST_LIMIT}/0`, ctx, { operation: 'FoldseekService.fetchQueries', label: 'Foldseek', baseDelayMs: 400 });
+        const queryCount = list.lookup?.length ?? 0;
+        if (query >= queryCount)
+            return { kind: 'query_out_of_range', queryCount };
+        const raw = await fetchJson(`${this.baseUrl}/api/result/${ticket}/${query}`, ctx, { operation: 'FoldseekService.fetchResults', label: 'Foldseek', baseDelayMs: 400 });
         const hits = [];
         for (const dbResult of raw.results ?? []) {
             const db = dbResult.db ?? 'unknown';
@@ -125,9 +148,29 @@ export class FoldseekService {
                 }
             }
         }
-        return { total: hits.length, hits: hits.slice(start, start + limit) };
+        hits.sort(compareHits);
+        return { kind: 'page', queryCount, total: hits.length, hits: hits.slice(start, start + limit) };
     }
 }
+/**
+ * Best-first order across databases: `score` descending, a hit with no score
+ * last, ties broken by database then target so every page of a ticket walks the
+ * same sequence. Each database block already arrives score-sorted upstream;
+ * `score` is the one field comparable across them.
+ */
+function compareHits(a, b) {
+    if (a.score !== b.score) {
+        if (a.score === undefined)
+            return 1;
+        if (b.score === undefined)
+            return -1;
+        return b.score - a.score;
+    }
+    return compareText(a.database, b.database) || compareText(a.target, b.target);
+}
+function compareText(a, b) {
+    return a < b ? -1 : a > b ? 1 : 0;
+}
 // ─── Normalizers ──────────────────────────────────────────────────────────────
 function normalizeHit(aln, database) {
     const target = aln.target;
@@ -148,12 +191,16 @@ function normalizeHit(aln, database) {
         hit.score = aln.score;
     return hit;
 }
-/** Resolve a Foldseek target header to an addressable identifier. */
+/**
+ * Resolve a Foldseek target header to an addressable identifier. PDB targets
+ * arrive either bare (`1abc_A`) or as assembly files (`1abc-assembly1.cif.gz_A`);
+ * the chain is the segment after the underscore in both.
+ */
 function parseTarget(target) {
     const af = /^AF-([A-Za-z0-9]+)-F\d+/.exec(target);
     if (af)
         return { targetType: 'alphafold', uniprotAccession: af[1] };
-    const pdb = /^(\d[A-Za-z0-9]{3})[_-]([A-Za-z0-9]+)/.exec(target);
+    const pdb = /^(\d[A-Za-z0-9]{3})(?:-assembly\d+\.cif(?:\.gz)?)?[_-]([A-Za-z0-9]+)/.exec(target);
     if (pdb)
         return { targetType: 'pdb', pdbId: pdb[1].toUpperCase(), chain: pdb[2] };
     return { targetType: 'other' };

package/dist/services/foldseek/foldseek-service.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, CoordinateUrls, EntryMeta, FacetDimension, SearchResult, StructureSearchParams, UniProtXref } from './types.js';
+import type { BindingSite, ChemComp, ChemCompMatches, ContentType, CoordinateUrls, 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. */
@@ -75,8 +75,12 @@ export declare 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.
      */
-    findChemComps(query: string, limit: number, ctx: Context): Promise<string[]>;
+    findChemComps(query: string, limit: number, ctx: Context): Promise<ChemCompMatches>;
     /** Facet-only aggregation over an optional scoping query (no row pull). */
     analyzeFacets(params: StructureSearchParams, facets: FacetSpec[], ctx: Context): Promise<{
         total: number;
@@ -97,7 +101,13 @@ export declare class RcsbService {
         entityId: string;
         sequence: string;
     } | null>;
-    /** 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.
+     */
     getBindingSites(pdbId: string, compId: string | undefined, ctx: Context): Promise<BindingSite[]>;
     /** Chemical-component metadata (formula, weight, SMILES, InChIKey). */
     getChemComp(compId: string, ctx: Context): Promise<ChemComp | null>;

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

@@ -1 +1 @@
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