@cyanheads/protein-mcp-server 0.8.2 → 0.8.4

package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts

@@ -5,8 +5,9 @@
  * poll → bounded timeout, returning "still computing" rather than blocking).
  * Both modes page their results the same way (totalCount / start / nextStart),
  * and a completed structure job returns its ticket so it can be re-paged instead
- * of resubmitted. Fields the selected mode cannot consume are rejected, not
- * ignored.
+ * of resubmitted. A structure response covers one Foldseek query (one chain of a
+ * multichain file), selected by `query` and disclosed with `queryCount`. Fields
+ * the selected mode cannot consume are rejected, not ignored.
  * @module mcp-server/tools/definitions/find-similar.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -21,6 +22,7 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
     uniprot: z.ZodOptional<z.ZodString>;
     ticket_id: z.ZodOptional<z.ZodString>;
     databases: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    query: z.ZodOptional<z.ZodNumber>;
     max_evalue: z.ZodOptional<z.ZodNumber>;
     min_identity: z.ZodOptional<z.ZodNumber>;
     limit: z.ZodDefault<z.ZodNumber>;
@@ -36,6 +38,8 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
         computing: "computing";
     }>;
     ticketId: z.ZodOptional<z.ZodString>;
+    query: z.ZodOptional<z.ZodNumber>;
+    queryCount: z.ZodOptional<z.ZodNumber>;
     hits: z.ZodArray<z.ZodObject<{
         id: z.ZodString;
         entityId: z.ZodOptional<z.ZodString>;
@@ -60,8 +64,8 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
 }, {
     readonly reason: "mode_mismatched_field";
     readonly code: JsonRpcErrorCode.InvalidParams;
-    readonly when: "An input field only the other by mode consumes was supplied: sequence, max_evalue or min_identity under by:\"structure\"; ticket_id or a non-empty databases list under by:\"sequence\".";
-    readonly recovery: "Drop the field, or switch by to the mode that reads it — sequence, max_evalue and min_identity apply to by:\"sequence\"; ticket_id and databases apply to by:\"structure\".";
+    readonly when: "An input field only the other by mode consumes was supplied: sequence, max_evalue or min_identity under by:\"structure\"; ticket_id, query or a non-empty databases list under by:\"sequence\".";
+    readonly recovery: "Drop the field, or switch by to the mode that reads it — sequence, max_evalue and min_identity apply to by:\"sequence\"; ticket_id, databases and query apply to by:\"structure\".";
     readonly thrownBy: "service";
 }, {
     readonly reason: "no_sequence";
@@ -69,6 +73,12 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
     readonly when: "A sequence could not be resolved from the given PDB ID or UniProt accession.";
     readonly recovery: "Verify the identifier, or pass a raw one-letter sequence directly via the sequence parameter.";
     readonly thrownBy: "service";
+}, {
+    readonly reason: "query_out_of_range";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "The requested query index is not below the number of queries the completed Foldseek job holds.";
+    readonly recovery: "Re-call with the ticket_id from the error and a query index below the reported query count; the job is already complete.";
+    readonly thrownBy: "service";
 }, {
     readonly reason: "search_failed";
     readonly code: JsonRpcErrorCode.ServiceUnavailable;

package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"find-similar.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-similar.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAA6B,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8HjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsFtB,CAAC"}
+{"version":3,"file":"find-similar.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-similar.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EAA6B,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA4JjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkGtB,CAAC"}

package/dist/mcp-server/tools/definitions/find-similar.tool.js

@@ -5,8 +5,9 @@
  * poll → bounded timeout, returning "still computing" rather than blocking).
  * Both modes page their results the same way (totalCount / start / nextStart),
  * and a completed structure job returns its ticket so it can be re-paged instead
- * of resubmitted. Fields the selected mode cannot consume are rejected, not
- * ignored.
+ * of resubmitted. A structure response covers one Foldseek query (one chain of a
+ * multichain file), selected by `query` and disclosed with `queryCount`. Fields
+ * the selected mode cannot consume are rejected, not ignored.
  * @module mcp-server/tools/definitions/find-similar.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -38,6 +39,12 @@ const inputSchema = z.object({
         .array(z.string())
         .optional()
         .describe('Foldseek target databases (by:structure). Default pdb100 + afdb50. e.g. afdb-swissprot, BFVD.'),
+    query: z
+        .number()
+        .int()
+        .min(0)
+        .optional()
+        .describe('Zero-based Foldseek query index (by:structure). Default 0. Foldseek splits a multichain structure into one query per chain, in file order; queryCount in the response says how many the job holds. Pass the same value with ticket_id to resume or re-page that query.'),
     max_evalue: z
         .number()
         .positive()
@@ -67,6 +74,14 @@ const outputSchema = z.object({
         .string()
         .optional()
         .describe('Async job ticket ID (by:structure). Present while status is computing, and also on a complete response — re-call with ticket_id plus a different start/limit to page the same finished job instead of resubmitting.'),
+    query: z
+        .number()
+        .optional()
+        .describe('Zero-based Foldseek query index the hits belong to (by:structure).'),
+    queryCount: z
+        .number()
+        .optional()
+        .describe('Number of queries the Foldseek job holds, one per chain of the submitted structure (by:structure, complete). Valid query values run from 0 to queryCount - 1.'),
     hits: z
         .array(z
         .object({
@@ -98,7 +113,7 @@ const outputSchema = z.object({
             .describe('UniProt accession (predicted structure hits).'),
     })
         .describe('A similar protein, with alignment scores when available.'))
-        .describe('Similar proteins, best first.'),
+        .describe('Similar proteins, best first. Structure hits are ranked by score across all searched databases (hits without a score last, ties by database then target).'),
 });
 const enrichmentShape = {
     totalCount: z.number().optional().describe('Total upstream matches before pagination.'),
@@ -107,11 +122,14 @@ const enrichmentShape = {
         .number()
         .optional()
         .describe('Offset for the next result page; absent on the final or past-end page.'),
-    notice: z.string().optional().describe('Advisory note (still computing, empty results).'),
+    notice: z
+        .string()
+        .optional()
+        .describe('Advisory note: a structure job still computing (with how to resume it), no matches, a start past the end of the results, or other queries in a multichain structure job.'),
 };
 export const findSimilar = tool('protein_find_similar', {
     title: 'protein-mcp-server: find similar',
-    description: `Find structurally or evolutionarily related proteins. by:"sequence" runs an RCSB mmseqs2 sequence-similarity search (synchronous) over a sequence — supplied directly, or pulled from a PDB ID or UniProt accession. by:"structure" runs a Foldseek fold-similarity search (asynchronous) against experimental and predicted databases; if the job is still computing when the poll budget elapses, the response reports status "computing" with a ticket — re-call with ticket_id set to that value to resume the same job instead of resubmitting, and a complete response carries the same ticket so a finished job can be re-paged with a different start. Each mode reads only its own controls: sequence, max_evalue and min_identity belong to by:"sequence"; ticket_id and databases belong to by:"structure"; pdb_id, uniprot, start and limit are shared. A field the selected mode cannot consume is rejected rather than silently ignored. Output names the engine and database each hit came from.`,
+    description: `Find structurally or evolutionarily related proteins. by:"sequence" runs an RCSB mmseqs2 sequence-similarity search (synchronous) over a sequence — supplied directly, or pulled from a PDB ID or UniProt accession. by:"structure" runs a Foldseek fold-similarity search (asynchronous) against experimental and predicted databases; if the job is still computing when the poll budget elapses, the response reports status "computing" with a ticket — re-call with ticket_id set to that value to resume the same job instead of resubmitting, and a complete response carries the same ticket so a finished job can be re-paged with a different start. Foldseek searches each chain of a multichain structure as its own query: a response covers one query (query, default 0), reports queryCount, and ranks that query's hits by score across all searched databases. Each mode reads only its own controls: sequence, max_evalue and min_identity belong to by:"sequence"; ticket_id, databases and query belong to by:"structure"; pdb_id, uniprot, start and limit are shared. A field the selected mode cannot consume is rejected rather than silently ignored. Output names the engine and database each hit came from.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
     // Every reason is thrown by a helper below the handler, hence thrownBy on each entry.
     errors: [
@@ -125,8 +143,8 @@ export const findSimilar = tool('protein_find_similar', {
         {
             reason: 'mode_mismatched_field',
             code: JsonRpcErrorCode.InvalidParams,
-            when: 'An input field only the other by mode consumes was supplied: sequence, max_evalue or min_identity under by:"structure"; ticket_id or a non-empty databases list under by:"sequence".',
-            recovery: 'Drop the field, or switch by to the mode that reads it — sequence, max_evalue and min_identity apply to by:"sequence"; ticket_id and databases apply to by:"structure".',
+            when: 'An input field only the other by mode consumes was supplied: sequence, max_evalue or min_identity under by:"structure"; ticket_id, query or a non-empty databases list under by:"sequence".',
+            recovery: 'Drop the field, or switch by to the mode that reads it — sequence, max_evalue and min_identity apply to by:"sequence"; ticket_id, databases and query apply to by:"structure".',
             thrownBy: 'service',
         },
         {
@@ -136,6 +154,13 @@ export const findSimilar = tool('protein_find_similar', {
             recovery: 'Verify the identifier, or pass a raw one-letter sequence directly via the sequence parameter.',
             thrownBy: 'service',
         },
+        {
+            reason: 'query_out_of_range',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: 'The requested query index is not below the number of queries the completed Foldseek job holds.',
+            recovery: 'Re-call with the ticket_id from the error and a query index below the reported query count; the job is already complete.',
+            thrownBy: 'service',
+        },
         {
             reason: 'search_failed',
             code: JsonRpcErrorCode.ServiceUnavailable,
@@ -167,8 +192,12 @@ export const findSimilar = tool('protein_find_similar', {
     },
     format: (result) => {
         const lines = [`## ${result.engine} (by:${result.by}) — ${result.status}`];
-        if (result.ticketId)
-            lines.push(`**Ticket:** ${result.ticketId} — re-call with ticket_id to resume or re-page this job.`);
+        if (result.ticketId) {
+            const withQuery = result.query ? ` and query ${result.query}` : '';
+            lines.push(`**Ticket:** ${result.ticketId} — re-call with ticket_id${withQuery} to resume or re-page this job.`);
+        }
+        if (typeof result.queryCount === 'number')
+            lines.push(`**Query:** ${result.query ?? 0} of ${result.queryCount} (0-based)`);
         for (const h of result.hits) {
             lines.push(`\n### ${h.id} _(${h.source})_`);
             if (h.title)
@@ -209,8 +238,12 @@ async function runSequence(input, ctx) {
         start: input.start,
         ...(nextStart < result.total ? { nextStart } : {}),
     });
+    // Same two empty-page causes runStructure separates: nothing matched, or an
+    // offset past the end of a populated result set.
     if (result.hits.length === 0)
-        ctx.enrich.notice('No sequence-similar entries found. Lower min_identity or raise max_evalue.');
+        ctx.enrich.notice(result.total === 0
+            ? 'No sequence-similar entries found. Lower min_identity or raise max_evalue.'
+            : `start ${input.start} is past the end of the ${result.total} matches. Re-call with a lower start to read a populated page.`);
     return {
         by: 'sequence',
         engine: 'RCSB mmseqs2',
@@ -234,12 +267,13 @@ async function runSequence(input, ctx) {
 }
 async function runStructure(input, timeoutMs, ctx) {
     const foldseek = getFoldseekService();
+    const query = input.query ?? 0;
     let outcome;
     if (input.ticket_id) {
         // Resume path: poll the existing ticket, skipping coordinate resolution +
         // submit. A completed ticket is idempotent upstream, so a re-call with a new
-        // start/limit pages the same finished job instead of running a second search.
-        outcome = await foldseek.resume({ ticketId: input.ticket_id, limit: input.limit, start: input.start, timeoutMs }, ctx);
+        // start/limit/query pages the same finished job instead of running a second search.
+        outcome = await foldseek.resume({ ticketId: input.ticket_id, query, limit: input.limit, start: input.start, timeoutMs }, ctx);
     }
     else {
         const { content, fileName } = await resolveCoordinateFile(input, ctx);
@@ -248,11 +282,22 @@ async function runStructure(input, timeoutMs, ctx) {
             fileName,
             databases: input.databases && input.databases.length > 0 ? input.databases : DEFAULT_FOLDSEEK_DBS,
             mode: FOLDSEEK_MODE,
+            query,
             limit: input.limit,
             start: input.start,
             timeoutMs,
         }, ctx);
     }
+    if (outcome.status === 'query_out_of_range') {
+        const { ticketId, queryCount } = outcome;
+        throw ctx.fail('query_out_of_range', `query ${query} is out of range: Foldseek ticket ${ticketId} holds ${queryCount} ${queryCount === 1 ? 'query' : 'queries'}.`, {
+            recovery: {
+                hint: queryCount > 0
+                    ? `Re-call with ticket_id "${ticketId}" and query between 0 and ${queryCount - 1}; the job is already complete, so nothing is resubmitted.`
+                    : 'Foldseek read no chains from the submitted structure; confirm it has protein coordinates via protein_get_structure.',
+            },
+        });
+    }
     if (outcome.status === 'not_found') {
         throw ctx.fail('ticket_not_found', `Foldseek ticket ${outcome.ticketId} is invalid or expired.`, { ...ctx.recoveryFor('ticket_not_found') });
     }
@@ -264,12 +309,14 @@ async function runStructure(input, timeoutMs, ctx) {
         });
     }
     if (outcome.status === 'computing') {
-        ctx.enrich.notice(`Foldseek job still computing (ticket ${outcome.ticketId}). Re-call protein_find_similar with ticket_id set to "${outcome.ticketId}" to resume.`);
+        const withQuery = query > 0 ? ` and query ${query}` : '';
+        ctx.enrich.notice(`Foldseek job still computing (ticket ${outcome.ticketId}). Re-call protein_find_similar with ticket_id set to "${outcome.ticketId}"${withQuery} to resume.`);
         return {
             by: 'structure',
             engine: 'Foldseek',
             status: 'computing',
             ticketId: outcome.ticketId,
+            query,
             hits: [],
         };
     }
@@ -284,17 +331,27 @@ async function runStructure(input, timeoutMs, ctx) {
     });
     // An empty page has two unrelated causes now that `start` pages a completed
     // job, and they need opposite next moves: no hits at all means widen the
-    // databases, while a start past the end means ask for a lower offset.
+    // databases, while a start past the end means ask for a lower offset. A
+    // multichain job adds a third note — this page covers one query of several.
+    // `notice` is last-wins, so the applicable notes are joined into one string.
+    const notes = [];
     if (outcome.hits.length === 0) {
-        ctx.enrich.notice(outcome.total === 0
+        notes.push(outcome.total === 0
             ? 'Foldseek returned no fold-similar hits in the selected databases.'
             : `start ${input.start} is past the end of this job's ${outcome.total} hits. Re-call with a lower start to read a populated page.`);
     }
+    if (outcome.queryCount > 1) {
+        notes.push(`This job holds ${outcome.queryCount} queries, one per chain Foldseek read from the submitted structure in file order; these hits are for query ${outcome.query}. Re-call with ticket_id "${outcome.ticketId}" and a different query (0–${outcome.queryCount - 1}) to read another chain's hits.`);
+    }
+    if (notes.length > 0)
+        ctx.enrich.notice(notes.join(' '));
     return {
         by: 'structure',
         engine: 'Foldseek',
         status: 'complete',
         ticketId: outcome.ticketId,
+        query: outcome.query,
+        queryCount: outcome.queryCount,
         hits: outcome.hits.map((h) => ({
             id: h.pdbId ?? h.uniprotAccession ?? h.target,
             source: h.targetType === 'alphafold' ? 'predicted' : 'experimental',
@@ -309,7 +366,7 @@ async function runStructure(input, timeoutMs, ctx) {
 /**
  * Reject an input field the selected `by` mode cannot consume. Each branch reads
  * only its own subset — `runSequence` alone reads sequence/max_evalue/
- * min_identity, `runStructure` alone reads ticket_id/databases — so a field
+ * min_identity, `runStructure` alone reads ticket_id/databases/query — so a field
  * supplied for the other mode would be dropped silently, making an unfiltered
  * search look filtered or an unscoped one look scoped. Guarded here rather than
  * by a Zod refine so the rejection carries `data.reason` and a recovery hint
@@ -327,6 +384,7 @@ function rejectModeMismatchedFields(input, ctx) {
         : [
             typeof input.ticket_id === 'string' ? 'ticket_id' : null,
             input.databases && input.databases.length > 0 ? 'databases' : null,
+            typeof input.query === 'number' ? 'query' : null,
         ]).filter((field) => field !== null);
     if (offenders.length === 0)
         return;
@@ -358,13 +416,14 @@ async function resolveSequence(input, ctx) {
         ...ctx.recoveryFor('missing_query'),
     });
 }
-/** Resolve a query coordinate file (PDB-format text) from a PDB ID or UniProt accession. */
+/** Resolve a query coordinate file (mmCIF or PDB-format text) from a PDB ID or UniProt accession. */
 async function resolveCoordinateFile(input, ctx) {
-    const rcsb = getRcsbService();
     if (input.pdb_id && isPdbId(input.pdb_id)) {
+        // mmCIF, not PDB format: every entry has an mmCIF file, while large entries
+        // are archived without a PDB-format one, and Foldseek reads either.
         const id = input.pdb_id.toUpperCase();
-        const content = await fetchCoordinateText(rcsb.coordinateFileUrl(id, 'pdb'), ctx);
-        return { content, fileName: `${id}.pdb` };
+        const content = await fetchCoordinateText(getRcsbService().mmcifUrl(id), ctx);
+        return { content, fileName: `${id}.cif` };
     }
     if (input.uniprot && isUniProtAccession(input.uniprot)) {
         const model = await getAlphaFoldService().getPrediction(input.uniprot, ctx);

package/dist/mcp-server/tools/definitions/find-similar.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map

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