npm - @cyanheads/protein-mcp-server - Versions diffs - 0.8.1 → 0.8.3 - Mend

@cyanheads/protein-mcp-server 0.8.1 → 0.8.3

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Files changed (51) hide show

package/dist/mcp-server/tools/definitions/compare-structures.tool.js CHANGED Viewed

@@ -57,7 +57,7 @@ const inputSchema = z.object({
     })
         .describe('A prior pair to resume by UUID instead of resubmitting.'))
         .optional()
-        .describe("Resume tickets from a prior call: for each pair whose labels match an entry here, poll the existing UUID instead of submitting a new alignment job. Copy a, b, and uuid verbatim from a prior response's pairs[]; keep structures and reference unchanged."),
+        .describe("Resume tickets from a prior call: for each pair whose labels match an entry here, poll the existing UUID instead of submitting a new alignment job. Copy a, b, and uuid verbatim from a prior response's pairs[]; keep structures, reference, and method unchanged. The order of structures may change — a resumed pair keeps the orientation its job was submitted in."),
 });
 const outputSchema = z.object({
     method: z.string().describe('Alignment method used.'),
@@ -65,16 +65,15 @@ const outputSchema = z.object({
     pairs: z
         .array(z
         .object({
-        a: z.string().describe('First structure of the pair (entry[.chain]).'),
+        a: z
+            .string()
+            .describe("First structure of the pair (entry[.chain]), as the alignment job was submitted — for a resumed pair that can differ from this call's structures[] order."),
         b: z.string().describe('Second structure of the pair (entry[.chain]).'),
         status: z.enum(['complete', 'computing', 'failed']).describe('Outcome for this pair.'),
         tmScore: z
             .number()
             .optional()
-            .describe('TM-score (0–1; higher is more similar). Length-normalized, so it can be sensitive to ' +
-            'terminal length differences between the two structures — a one-residue overhang can flip ' +
-            'the greedy superposition into a worse local optimum, dropping the score sharply. Cross-check ' +
-            'rmsd and alignedResidues to spot such cases.'),
+            .describe("TM-score (0–1; higher is more similar). Length-normalized by structure a's modeled length, so the same pair aligned b-first can score very differently (0.17 vs 0.40 for a 141- vs a 46-residue chain). It can also be sensitive to terminal length differences between the two structures — a one-residue overhang can flip the greedy superposition into a worse local optimum, dropping the score sharply. Cross-check rmsd and alignedResidues to spot such cases."),
         rmsd: z.number().optional().describe('RMSD in Å over aligned residues.'),
         alignedResidues: z.number().optional().describe('Number of aligned residue pairs.'),
         modeledResidues: z
@@ -98,17 +97,7 @@ const outputSchema = z.object({
 });
 export const compareStructures = tool('protein_compare_structures', {
     title: 'protein-mcp-server: compare structures',
-    description: 'Structurally align multiple structures (up to the configured batch cap) via the RCSB Structural ' +
-        'Comparison service (TM-align / jFATCAT). reference:"first" aligns every structure to the first; ' +
-        'reference:"all_pairs" computes the full pairwise matrix. Each pair is an independent async alignment ' +
-        'job, fanned out with a concurrency cap and per-pair partial success — a pair still computing when the ' +
-        'budget elapses returns status "computing" with its job UUID, and a failed pair degrades its row without ' +
-        "sinking the others. Re-call with a matching entry in resume[] to poll a computing pair's UUID instead " +
-        "of resubmitting. Returns TM-score, RMSD, and aligned-residue count per pair, plus each structure's " +
-        'modeled-residue count and alignment coverage. TM-score is ' +
-        'length-normalized and can shift sharply between structures that differ only by a terminal residue or ' +
-        'two — the greedy superposition can settle into a worse local optimum — so read tmScore alongside rmsd, ' +
-        'alignedResidues, modeledResidues and coverage, the columns that make such cases diagnosable.',
+    description: `Structurally align multiple structures (up to the configured batch cap) via the RCSB Structural Comparison service (TM-align / jFATCAT). reference:"first" aligns every structure to the first; reference:"all_pairs" computes the full pairwise matrix. Each pair is an independent async alignment job with per-pair partial success — a pair still computing when the budget elapses returns status "computing" with its job UUID, and a failed pair degrades its row without sinking the others. Re-call with a matching entry in resume[] to poll a computing pair's UUID instead of resubmitting; a resumed pair reports a and b in the order its job was submitted, and a resume under a different method is rejected. Returns TM-score, RMSD, and aligned-residue count per pair, plus each structure's modeled-residue count and alignment coverage. TM-score is length-normalized and can shift sharply between structures that differ only by a terminal residue or two — the greedy superposition can settle into a worse local optimum — so read tmScore alongside rmsd, alignedResidues, modeledResidues and coverage, the columns that make such cases diagnosable.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -123,13 +112,28 @@ export const compareStructures = tool('protein_compare_structures', {
             when: 'Every entry in structures[] denotes the same structure, leaving no pair to align.',
             recovery: 'Pass at least two different structures (entry ID, or entry ID + chain); a structure repeated in the list is compared once.',
         },
+        {
+            reason: 'resume_method_mismatch',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: "A resumed alignment job completed under a different method than this call's method input.",
+            recovery: 'Re-call with the method the job ran (named in the message), or drop that resume entry to submit a fresh alignment with the new method.',
+        },
+        {
+            reason: 'resume_job_mismatch',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: "A resume entry's uuid belongs to an alignment job for a different structure pair than its a/b labels.",
+            recovery: "Copy each resume entry's uuid from the same pairs[] row as its a and b, or drop the entry to submit a fresh alignment for that pair.",
+        },
     ],
     input: inputSchema,
     output: outputSchema,
     enrichment: {
         pairsTotal: z.number().describe('Number of pairs compared.'),
         computing: z.number().describe('Number of pairs still computing.'),
-        notice: z.string().optional().describe('Advisory note (pending pairs, failures).'),
+        notice: z
+            .string()
+            .optional()
+            .describe('Advisory note: pairs still computing or failed (with how to resume them), structures beyond the batch cap that were ignored, and repeated structures compared once.'),
     },
     async handler(input, ctx) {
         const cfg = getServerConfig();
@@ -164,12 +168,23 @@ export const compareStructures = tool('protein_compare_structures', {
             }
         }
         const alignment = getAlignmentService();
+        // A resumed job whose own record contradicts this call is a client error, but
+        // it only surfaces once that job completes. Record the first one and throw
+        // after the fanout settles, so no sibling pair is left polling in the background.
+        let rejection;
         const rows = await mapWithConcurrency(pairs, cfg.fanoutConcurrency, async ([a, b]) => {
             const resumeUuid = resumeByPair.get(pairKey(label(a), label(b)));
             const outcome = resumeUuid
                 ? await alignment.resumePair(resumeUuid, timeoutMs, ctx)
                 : await alignment.comparePair(toCompare(a), toCompare(b), method, timeoutMs, ctx);
-            const base = { a: label(a), b: label(b) };
+            let base = { a: label(a), b: label(b) };
+            if (outcome.status === 'complete' && resumeUuid && outcome.job) {
+                const oriented = orientResumedJob(outcome.job, base, method, resumeUuid);
+                if ('reason' in oriented)
+                    rejection ??= oriented;
+                else
+                    base = oriented;
+            }
             if (outcome.status === 'complete') {
                 return {
                     ...base,
@@ -193,12 +208,17 @@ export const compareStructures = tool('protein_compare_structures', {
             }
             return { ...base, status: 'failed', error: outcome.error };
         });
+        if (rejection) {
+            throw ctx.fail(rejection.reason, rejection.message, {
+                ...ctx.recoveryFor(rejection.reason),
+            });
+        }
         const computing = rows.filter((r) => r.status === 'computing').length;
         const failed = rows.filter((r) => r.status === 'failed').length;
         ctx.enrich({ pairsTotal: rows.length, computing });
         if (computing > 0 || failed > 0) {
             notices.push(`${computing} pair(s) still computing${failed > 0 ? `, ${failed} failed` : ''}. ` +
-                `Re-call with a resume entry per pair (copy a, b, uuid from the pairs above) to poll existing jobs — cold alignment jobs typically finish within 30–60 s.`);
+                `Re-call with a resume entry per pair (copy a, b, uuid from the pairs above) to poll existing jobs — cold alignment jobs typically finish within 30–60 s. The alignment service answers an expired job the same way as a running one, so a pair that stays computing across several resumes should be resubmitted without its resume entry.`);
         }
         if (notices.length > 0)
             ctx.enrich.notice(notices.join(' '));
@@ -234,9 +254,9 @@ export const compareStructures = tool('protein_compare_structures', {
  * keyed exactly as {@link pairKey} normalizes labels. Two entries for one
  * structure yield pairs that are indistinguishable under that key — `(A,B)` and
  * `(B,A)` collapse to one — so a single resume ticket would be applied to two
- * separate alignment jobs, silently discarding one. Case-folding the whole label
- * follows the same normalization: distinguishing chains `A` and `a` here would
- * hand the resume lookup two pairs it cannot tell apart.
+ * separate alignment jobs, silently discarding one. The entry ID is case-folded
+ * and the chain suffix kept as-is, matching that normalization: chains `A` and
+ * `a` are distinct chains and stay distinct here too.
  */
 function dedupeStructures(structures) {
     const seen = new Set();
@@ -279,7 +299,7 @@ function toCompare(s) {
     return { entryId: s.pdb_id, ...(s.chain ? { asymId: s.chain } : {}) };
 }
 function label(s) {
-    return s.chain ? `${s.pdb_id.toUpperCase()}.${s.chain}` : s.pdb_id.toUpperCase();
+    return compareLabel(toCompare(s));
 }
 /**
  * Canonical, order-insensitive key for a pair of structure labels, so a resume
@@ -296,4 +316,37 @@ function normalizeLabel(value) {
 function pairKey(a, b) {
     return [normalizeLabel(a), normalizeLabel(b)].sort().join('\u0000');
 }
+/**
+ * Orient a completed resumed pair by the job's own record rather than this
+ * call's `structures[]` order. Resume matching is order-insensitive, but every
+ * per-structure value (and the TM-score, normalized by the first structure) is
+ * ordered as the job was submitted — so the row's `a`/`b` follow the job. The
+ * method can't be remapped: a job that ran a different one is rejected, as is a
+ * ticket whose job aligned a different pair. A record missing either echo keeps
+ * the current order.
+ */
+function orientResumedJob(job, current, method, uuid) {
+    if (job.method && job.method !== method) {
+        return {
+            reason: 'resume_method_mismatch',
+            message: `Alignment job ${uuid} for ${current.a} ↔ ${current.b} ran ${job.method}, not the requested ${method}.`,
+        };
+    }
+    if (!job.structures)
+        return current;
+    const first = compareLabel(job.structures[0]);
+    const second = compareLabel(job.structures[1]);
+    if (pairKey(first, second) !== pairKey(current.a, current.b)) {
+        return {
+            reason: 'resume_job_mismatch',
+            message: `Alignment job ${uuid} aligned ${first} ↔ ${second}, not ${current.a} ↔ ${current.b}.`,
+        };
+    }
+    return normalizeLabel(first) === normalizeLabel(current.a)
+        ? current
+        : { a: current.b, b: current.a };
+}
+function compareLabel(s) {
+    return s.asymId ? `${s.entryId.toUpperCase()}.${s.asymId}` : s.entryId.toUpperCase();
+}
 //# sourceMappingURL=compare-structures.tool.js.map

package/dist/mcp-server/tools/definitions/compare-structures.tool.js.map CHANGED Viewed

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

@@ -56,27 +56,32 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
     readonly code: JsonRpcErrorCode.InvalidParams;
     readonly when: "None of sequence, pdb_id, or uniprot was provided.";
     readonly recovery: "Provide a raw sequence, a PDB entry ID, or a UniProt accession to search from.";
+    readonly thrownBy: "service";
 }, {
     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 thrownBy: "service";
 }, {
     readonly reason: "no_sequence";
     readonly code: JsonRpcErrorCode.NotFound;
     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: "search_failed";
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
     readonly when: "The Foldseek search service rejected or failed the structure job.";
     readonly retryable: true;
     readonly recovery: "Retry shortly; if it persists, verify the source structure has coordinates via protein_get_structure.";
+    readonly thrownBy: "service";
 }, {
     readonly reason: "ticket_not_found";
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "The supplied ticket_id was rejected by Foldseek as an invalid or expired ticket.";
     readonly recovery: "Tickets expire once results age out; drop ticket_id and re-run the by:structure search from pdb_id or uniprot to get a fresh one.";
+    readonly thrownBy: "service";
 }], {
     totalCount: z.ZodOptional<z.ZodNumber>;
     start: z.ZodOptional<z.ZodNumber>;

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

	@@ -1 +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~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgFtB~~,CAAC"}
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;AAmIjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsFtB,CAAC"}

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

@@ -107,30 +107,37 @@ 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, or a start past the end of the results.'),
 };
 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.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
+    // Every reason is thrown by a helper below the handler, hence thrownBy on each entry.
     errors: [
         {
             reason: 'missing_query',
             code: JsonRpcErrorCode.InvalidParams,
             when: 'None of sequence, pdb_id, or uniprot was provided.',
             recovery: 'Provide a raw sequence, a PDB entry ID, or a UniProt accession to search from.',
+            thrownBy: 'service',
         },
         {
             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".',
+            thrownBy: 'service',
         },
         {
             reason: 'no_sequence',
             code: JsonRpcErrorCode.NotFound,
             when: 'A sequence could not be resolved from the given PDB ID or UniProt accession.',
             recovery: 'Verify the identifier, or pass a raw one-letter sequence directly via the sequence parameter.',
+            thrownBy: 'service',
         },
         {
             reason: 'search_failed',
@@ -138,12 +145,14 @@ export const findSimilar = tool('protein_find_similar', {
             when: 'The Foldseek search service rejected or failed the structure job.',
             retryable: true,
             recovery: 'Retry shortly; if it persists, verify the source structure has coordinates via protein_get_structure.',
+            thrownBy: 'service',
         },
         {
             reason: 'ticket_not_found',
             code: JsonRpcErrorCode.NotFound,
             when: 'The supplied ticket_id was rejected by Foldseek as an invalid or expired ticket.',
             recovery: 'Tickets expire once results age out; drop ticket_id and re-run the by:structure search from pdb_id or uniprot to get a fresh one.',
+            thrownBy: 'service',
         },
     ],
     input: inputSchema,
@@ -203,8 +212,12 @@ 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 ${result.total} matches. Re-call with a lower start to read a populated page.`);
     return {
         by: 'sequence',
         engine: 'RCSB mmseqs2',
@@ -352,13 +365,14 @@ async function resolveSequence(input, ctx) {
         ...ctx.recoveryFor('missing_query'),
     });
 }
-/** Resolve a query coordinate file (PDB-format text) from a PDB ID or UniProt accession. */
+/** Resolve a query coordinate file (mmCIF or PDB-format text) from a PDB ID or UniProt accession. */
 async function resolveCoordinateFile(input, ctx) {
-    const rcsb = getRcsbService();
     if (input.pdb_id && isPdbId(input.pdb_id)) {
+        // mmCIF, not PDB format: every entry has an mmCIF file, while large entries
+        // are archived without a PDB-format one, and Foldseek reads either.
         const id = input.pdb_id.toUpperCase();
-        const content = await fetchCoordinateText(rcsb.coordinateFileUrl(id, 'pdb'), ctx);
-        return { content, fileName: `${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 CHANGED Viewed

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

	@@ -1 +1 @@
1	- {"version":3,"file":"get-annotations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-annotations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwEjE,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EA8SzB~~,CAAC"}
1	+ {"version":3,"file":"get-annotations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-annotations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwEjE,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAoSzB,CAAC"}

package/dist/mcp-server/tools/definitions/get-annotations.tool.js CHANGED Viewed

@@ -63,13 +63,7 @@ const ambiguitySchema = z
     .describe('Present only when a PDB ID mapped to more than one distinct UniProt accession and no chain was supplied. The returned accession is the deterministic lowest-chain pick — re-call with chain set to a specific author chain ID to select another.');
 export const getAnnotations = tool('protein_get_annotations', {
     title: 'protein-mcp-server: get annotations',
-    description: 'Sequence and functional annotation for a protein: UniProt features (domains, binding sites, PTMs), ' +
-        'natural variants, and InterPro domain/family memberships (Pfam, PROSITE, …) with GO terms. Provide a ' +
-        "UniProt accession directly, or a PDB ID — it is resolved to its UniProt accession via the structure's " +
-        'sequence cross-reference. A multi-chain PDB entry can map to several accessions; the default pick is ' +
-        'deterministic (lowest author chain ID) and the alternatives are listed in "ambiguity" — pass "chain" to ' +
-        'select a specific one. Use "include" to scope which annotation classes are fetched. Every response carries ' +
-        'an "attribution" block with the upstream data licenses and citations.',
+    description: `Sequence and functional annotation for a protein: UniProt features (domains, binding sites, PTMs), natural variants, and InterPro domain/family memberships (Pfam, PROSITE, …) with GO terms. Provide a UniProt accession directly, or a PDB ID — it is resolved to its UniProt accession via the structure's sequence cross-reference. A multi-chain PDB entry can map to several accessions; the default pick is deterministic (lowest author chain ID) and the alternatives are listed in "ambiguity" — pass "chain" to select a specific one. Use "include" to scope which annotation classes are fetched. Every response carries an "attribution" block with the upstream data licenses and citations.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -120,10 +114,7 @@ export const getAnnotations = tool('protein_get_annotations', {
             .min(1)
             .max(200)
             .default(50)
-            .describe('Per-class cap (1–200): features, natural variants, and InterPro domains are each independently ' +
-            'truncated to at most this many records. The default keeps a typical annotation set intact while ' +
-            'bounding a densely-annotated protein (a well-studied protein can carry 150+ natural variants); a ' +
-            'truncated class is disclosed in the response notice — raise it to retrieve more.'),
+            .describe('Per-class cap (1–200): features, natural variants, and InterPro domains are each independently truncated to at most this many records. The default keeps a typical annotation set intact while bounding a densely-annotated protein (a well-studied protein can carry 150+ natural variants); a truncated class is disclosed in the response notice — raise it to retrieve more.'),
     }),
     output: z.object({
         accession: z.string().describe('UniProt accession the annotations describe.'),

package/dist/mcp-server/tools/definitions/get-annotations.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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