@cyanheads/protein-mcp-server 0.6.0 → 0.8.0

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

@@ -3,6 +3,10 @@
  * proteins. by:sequence runs a synchronous RCSB mmseqs2 search; by:structure runs
  * an async Foldseek search against experimental + predicted databases (submit →
  * 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.
  * @module mcp-server/tools/definitions/find-similar.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
@@ -51,7 +55,7 @@ const inputSchema = z.object({
         .int()
         .min(0)
         .default(0)
-        .describe('Zero-based result offset (by:sequence only).'),
+        .describe('Zero-based result offset. Pages a by:sequence search, and a completed by:structure job when re-called with its ticket_id.'),
 });
 const outputSchema = z.object({
     by: z.enum(['sequence', 'structure']).describe('Echoed similarity axis.'),
@@ -62,7 +66,7 @@ const outputSchema = z.object({
     ticketId: z
         .string()
         .optional()
-        .describe('Async job ticket ID when status is computing (by:structure).'),
+        .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.'),
     hits: z
         .array(z
         .object({
@@ -97,25 +101,17 @@ const outputSchema = z.object({
         .describe('Similar proteins, best first.'),
 });
 const enrichmentShape = {
-    totalCount: z
-        .number()
-        .optional()
-        .describe('Total upstream matches before pagination (by:sequence).'),
-    start: z.number().optional().describe('Zero-based offset of the sequence-result page.'),
+    totalCount: z.number().optional().describe('Total upstream matches before pagination.'),
+    start: z.number().optional().describe('Zero-based offset of the returned result page.'),
     nextStart: z
         .number()
         .optional()
-        .describe('Offset for the next sequence-result page; absent on the final or past-end page.'),
+        .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).'),
 };
 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. 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. 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 },
     errors: [
         {
@@ -124,6 +120,12 @@ export const findSimilar = tool('protein_find_similar', {
             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.',
         },
+        {
+            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".',
+        },
         {
             reason: 'no_sequence',
             code: JsonRpcErrorCode.NotFound,
@@ -147,16 +149,20 @@ export const findSimilar = tool('protein_find_similar', {
     input: inputSchema,
     output: outputSchema,
     enrichment: enrichmentShape,
-    handler(input, ctx) {
+    // `async` so the pre-dispatch guard rejects rather than throwing synchronously
+    // out of the call itself — every failure on this tool reaches the caller the
+    // same way.
+    async handler(input, ctx) {
         const cfg = getServerConfig();
-        if (input.by === 'sequence')
-            return runSequence(input, ctx);
-        return runStructure(input, cfg.asyncPollTimeoutMs, ctx);
+        rejectModeMismatchedFields(input, ctx);
+        return input.by === 'sequence'
+            ? await runSequence(input, ctx)
+            : await runStructure(input, cfg.asyncPollTimeoutMs, ctx);
     },
     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.`);
+            lines.push(`**Ticket:** ${result.ticketId} — re-call with ticket_id to resume or re-page this job.`);
         for (const h of result.hits) {
             lines.push(`\n### ${h.id} _(${h.source})_`);
             if (h.title)
@@ -224,8 +230,10 @@ async function runStructure(input, timeoutMs, ctx) {
     const foldseek = getFoldseekService();
     let outcome;
     if (input.ticket_id) {
-        // Resume path: poll the existing ticket, skipping coordinate resolution + submit.
-        outcome = await foldseek.resume({ ticketId: input.ticket_id, limit: input.limit, timeoutMs }, ctx);
+        // 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);
     }
     else {
         const { content, fileName } = await resolveCoordinateFile(input, ctx);
@@ -235,6 +243,7 @@ async function runStructure(input, timeoutMs, ctx) {
             databases: input.databases && input.databases.length > 0 ? input.databases : DEFAULT_FOLDSEEK_DBS,
             mode: FOLDSEEK_MODE,
             limit: input.limit,
+            start: input.start,
             timeoutMs,
         }, ctx);
     }
@@ -258,12 +267,28 @@ async function runStructure(input, timeoutMs, ctx) {
             hits: [],
         };
     }
-    if (outcome.hits.length === 0)
-        ctx.enrich.notice('Foldseek returned no fold-similar hits in the selected databases.');
+    // Same paging contract the sequence branch emits: the completed job's full hit
+    // count plus the offsets needed to walk it, computed from the hit array the
+    // service already parsed — no extra upstream call.
+    ctx.enrich.total(outcome.total);
+    const nextStart = input.start + outcome.hits.length;
+    ctx.enrich({
+        start: input.start,
+        ...(nextStart < outcome.total ? { nextStart } : {}),
+    });
+    // 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.
+    if (outcome.hits.length === 0) {
+        ctx.enrich.notice(outcome.total === 0
+            ? 'Foldseek returned no fold-similar hits in the selected databases.'
+            : `start ${input.start} is past the end of this job's ${outcome.total} hits. Re-call with a lower start to read a populated page.`);
+    }
     return {
         by: 'structure',
         engine: 'Foldseek',
         status: 'complete',
+        ticketId: outcome.ticketId,
         hits: outcome.hits.map((h) => ({
             id: h.pdbId ?? h.uniprotAccession ?? h.target,
             source: h.targetType === 'alphafold' ? 'predicted' : 'experimental',
@@ -275,6 +300,38 @@ async function runStructure(input, timeoutMs, ctx) {
         })),
     };
 }
+/**
+ * Reject an input field the selected `by` mode cannot consume. Each branch reads
+ * only its own subset — `runSequence` alone reads sequence/max_evalue/
+ * min_identity, `runStructure` alone reads ticket_id/databases — so a field
+ * supplied for the other mode would be dropped silently, making an unfiltered
+ * search look filtered or an unscoped one look scoped. Guarded here rather than
+ * by a Zod refine so the rejection carries `data.reason` and a recovery hint
+ * naming the mode that accepts the field. `start` and `limit` are shared by both
+ * modes and are never read here; an empty `databases` array matches
+ * `runStructure`'s own fallback and is treated as omitted.
+ */
+function rejectModeMismatchedFields(input, ctx) {
+    const offenders = (input.by === 'structure'
+        ? [
+            input.sequence ? 'sequence' : null,
+            typeof input.max_evalue === 'number' ? 'max_evalue' : null,
+            typeof input.min_identity === 'number' ? 'min_identity' : null,
+        ]
+        : [
+            typeof input.ticket_id === 'string' ? 'ticket_id' : null,
+            input.databases && input.databases.length > 0 ? 'databases' : null,
+        ]).filter((field) => field !== null);
+    if (offenders.length === 0)
+        return;
+    const accepting = input.by === 'structure' ? 'sequence' : 'structure';
+    const plural = offenders.length > 1;
+    throw ctx.fail('mode_mismatched_field', `by:"${input.by}" does not consume ${offenders.join(', ')}.`, {
+        recovery: {
+            hint: `${offenders.join(', ')} ${plural ? 'are' : 'is'} only read under by:"${accepting}". Drop ${plural ? 'them' : 'it'}, or set by:"${accepting}" to apply ${plural ? 'them' : 'it'}.`,
+        },
+    });
+}
 /** Resolve a query sequence from a direct sequence, PDB ID, or UniProt accession. */
 async function resolveSequence(input, ctx) {
     if (input.sequence)
@@ -313,7 +370,14 @@ async function resolveCoordinateFile(input, ctx) {
             fileName: `${input.uniprot.toUpperCase()}.pdb`,
         };
     }
-    throw ctx.fail('missing_query', 'by:structure requires a pdb_id or uniprot accession to derive coordinates.', { ...ctx.recoveryFor('missing_query') });
+    // The declared recovery hint offers a raw sequence, which by:"structure"
+    // rejects outright — this branch names only the two identifiers that mode can
+    // actually derive coordinates from.
+    throw ctx.fail('missing_query', 'by:structure requires a pdb_id or uniprot accession to derive coordinates.', {
+        recovery: {
+            hint: 'Provide pdb_id (e.g. 1CRN) or uniprot (e.g. P69905); by:"structure" derives coordinates from an identifier, never from a raw sequence.',
+        },
+    });
 }
 function fetchCoordinateText(url, ctx) {
     return fetchText(url, ctx, {

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package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts

@@ -64,15 +64,25 @@ export declare const getAnnotations: import("@cyanheads/mcp-ts-core").ToolDefini
         homepage: z.ZodString;
     }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
+    readonly reason: "missing_identifier";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "Neither uniprot nor pdb_id was supplied, so there is no protein to look up.";
+    readonly recovery: "Provide uniprot (e.g. P69905) or pdb_id (e.g. 4HHB) — either one identifies the protein.";
+}, {
+    readonly reason: "invalid_accession";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "The supplied uniprot value is not a syntactically valid UniProt accession.";
+    readonly recovery: "Pass a UniProt accession in its 6- or 10-character form (e.g. P69905, A0A024R161), or supply pdb_id instead.";
+}, {
     readonly reason: "no_uniprot_mapping";
     readonly code: JsonRpcErrorCode.NotFound;
-    readonly when: "A PDB ID has no UniProt cross-reference (e.g. nucleic-acid-only entry), or neither uniprot nor pdb_id was provided.";
+    readonly when: "A supplied PDB ID resolved to no usable UniProt cross-reference (e.g. a nucleic-acid-only entry).";
     readonly recovery: "Pass a UniProt accession directly, or use protein_search_structures to find a structure with a modeled protein chain.";
 }, {
     readonly reason: "chain_not_found";
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "A supplied chain matches no UniProt-mapped polymer entity in the resolved PDB entry.";
-    readonly recovery: "Omit chain for the deterministic default mapping, or pass an author chain ID the entry exposes (see polymerEntities[].chains in the pdb://{entry_id} resource).";
+    readonly recovery: "Omit chain for the deterministic default mapping, or pass an author chain ID the entry exposes (see polymerEntities[].authAsymIds in the pdb://{entry_id} resource).";
 }], {
     readonly resolvedFrom: z.ZodOptional<z.ZodString>;
     readonly truncated: z.ZodOptional<z.ZodBoolean>;

package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts.map

@@ -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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6QzB,CAAC"}
+{"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"}

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

@@ -72,17 +72,29 @@ export const getAnnotations = tool('protein_get_annotations', {
         'an "attribution" block with the upstream data licenses and citations.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
+        {
+            reason: 'missing_identifier',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: 'Neither uniprot nor pdb_id was supplied, so there is no protein to look up.',
+            recovery: 'Provide uniprot (e.g. P69905) or pdb_id (e.g. 4HHB) — either one identifies the protein.',
+        },
+        {
+            reason: 'invalid_accession',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: 'The supplied uniprot value is not a syntactically valid UniProt accession.',
+            recovery: 'Pass a UniProt accession in its 6- or 10-character form (e.g. P69905, A0A024R161), or supply pdb_id instead.',
+        },
         {
             reason: 'no_uniprot_mapping',
             code: JsonRpcErrorCode.NotFound,
-            when: 'A PDB ID has no UniProt cross-reference (e.g. nucleic-acid-only entry), or neither uniprot nor pdb_id was provided.',
+            when: 'A supplied PDB ID resolved to no usable UniProt cross-reference (e.g. a nucleic-acid-only entry).',
             recovery: 'Pass a UniProt accession directly, or use protein_search_structures to find a structure with a modeled protein chain.',
         },
         {
             reason: 'chain_not_found',
             code: JsonRpcErrorCode.NotFound,
             when: 'A supplied chain matches no UniProt-mapped polymer entity in the resolved PDB entry.',
-            recovery: 'Omit chain for the deterministic default mapping, or pass an author chain ID the entry exposes (see polymerEntities[].chains in the pdb://{entry_id} resource).',
+            recovery: 'Omit chain for the deterministic default mapping, or pass an author chain ID the entry exposes (see polymerEntities[].authAsymIds in the pdb://{entry_id} resource).',
         },
     ],
     input: z.object({
@@ -97,7 +109,7 @@ export const getAnnotations = tool('protein_get_annotations', {
         chain: z
             .string()
             .optional()
-            .describe('Author chain ID (auth_asym_id, e.g. "A") that disambiguates a multi-chain PDB entry to a specific UniProt accession. Case-sensitive — must match the author chain ID exactly (large structures can carry distinct "A" and "a" chains). Only applies with pdb_id; ignored when uniprot is supplied directly. See polymerEntities[].chains in the pdb://{entry_id} resource for an entry\'s author chain IDs.'),
+            .describe('Author chain ID (auth_asym_id, e.g. "A") that disambiguates a multi-chain PDB entry to a specific UniProt accession. Case-sensitive — must match the author chain ID exactly (large structures can carry distinct "A" and "a" chains). Only applies with pdb_id; ignored when uniprot is supplied directly. See polymerEntities[].authAsymIds in the pdb://{entry_id} resource for an entry\'s author chain IDs.'),
         include: z
             .enum(['features', 'domains', 'variants', 'all'])
             .default('all')
@@ -147,6 +159,21 @@ export const getAnnotations = tool('protein_get_annotations', {
     async handler(input, ctx) {
         const uniprot = getUniProtService();
         const rcsb = getRcsbService();
+        // Reject unusable input up front, before any upstream call: a caller that
+        // omitted both parameters or mistyped an accession has an input problem, not a
+        // lookup that found nothing, and the two are different next moves. Guarded
+        // here rather than by a Zod refine so the rejection carries `data.reason` and
+        // the declared recovery hint.
+        if (!input.uniprot && !input.pdb_id) {
+            throw ctx.fail('missing_identifier', 'Provide uniprot (e.g. P69905) or pdb_id (e.g. 4HHB).', {
+                ...ctx.recoveryFor('missing_identifier'),
+            });
+        }
+        if (input.uniprot && !isUniProtAccession(input.uniprot)) {
+            throw ctx.fail('invalid_accession', `"${input.uniprot}" is not a valid UniProt accession.`, {
+                ...ctx.recoveryFor('invalid_accession'),
+            });
+        }
         let accession = input.uniprot?.toUpperCase();
         let resolvedFrom;
         let ambiguity;
@@ -181,8 +208,11 @@ export const getAnnotations = tool('protein_get_annotations', {
                 }
             }
         }
+        // Both checks below are upstream-resolution outcomes now: an absent or
+        // malformed `uniprot` input was rejected before any lookup ran, so reaching
+        // either means a supplied pdb_id resolved to nothing usable.
         if (!accession) {
-            throw ctx.fail('no_uniprot_mapping', 'Provide a UniProt accession, or a PDB ID with a modeled protein chain.', { ...ctx.recoveryFor('no_uniprot_mapping') });
+            throw ctx.fail('no_uniprot_mapping', 'The supplied PDB ID carries no UniProt-mapped protein chain.', { ...ctx.recoveryFor('no_uniprot_mapping') });
         }
         if (!isUniProtAccession(accession)) {
             throw ctx.fail('no_uniprot_mapping', `"${accession}" is not a valid UniProt accession.`, {

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

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

@@ -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 { z } from '@cyanheads/mcp-ts-core';
@@ -30,6 +33,21 @@ export declare const getStructure: import("@cyanheads/mcp-ts-core").ToolDefiniti
         method: z.ZodOptional<z.ZodString>;
         resolution: z.ZodOptional<z.ZodNumber>;
         organism: z.ZodOptional<z.ZodString>;
+        molecularWeight: z.ZodOptional<z.ZodNumber>;
+        releaseDate: z.ZodOptional<z.ZodString>;
+        polymerEntities: z.ZodOptional<z.ZodArray<z.ZodObject<{
+            entityId: z.ZodString;
+            description: z.ZodOptional<z.ZodString>;
+            organism: z.ZodOptional<z.ZodString>;
+            authAsymIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
+            labelAsymIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
+            sequenceLength: z.ZodOptional<z.ZodNumber>;
+        }, z.core.$strip>>>;
+        ligands: z.ZodOptional<z.ZodArray<z.ZodObject<{
+            compId: z.ZodString;
+            name: z.ZodOptional<z.ZodString>;
+            formula: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>>>;
         provider: z.ZodOptional<z.ZodString>;
         confidence: z.ZodOptional<z.ZodNumber>;
         confidenceType: z.ZodOptional<z.ZodString>;
@@ -82,6 +100,7 @@ export declare const getStructure: import("@cyanheads/mcp-ts-core").ToolDefiniti
     readonly recovery: "Verify ID formats (PDB IDs are 4 chars; UniProt accessions match the standard pattern) or locate IDs via protein_search_structures.";
 }], {
     readonly requested: z.ZodNumber;
+    readonly processed: z.ZodNumber;
     readonly resolved: z.ZodNumber;
     readonly notice: z.ZodOptional<z.ZodString>;
 }>;

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

@@ -1 +1 @@
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+{"version":3,"file":"get-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-structure.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8GjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkUvB,CAAC"}