@cyanheads/interpro-mcp-server 0.1.2 → 0.2.0

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

@@ -0,0 +1,171 @@
+/**
+ * @fileoverview PDB structure domain maps in budget-bounded segments of whole matches.
+ * @module mcp-server/tools/definitions/interpro-get-structure-domains.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+/** Map signatures onto one PDB entry's chains in budget-bounded segments of whole matches. */
+export declare const interproGetStructureDomains: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    pdbId: z.ZodString;
+    chain: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+    cursor: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
+}, z.core.$strip>, z.ZodObject<{
+    pdbId: z.ZodString;
+    chain: z.ZodOptional<z.ZodString>;
+    structure: z.ZodOptional<z.ZodObject<{
+        accession: z.ZodString;
+        source_database: z.ZodString;
+        chains: z.ZodArray<z.ZodString>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>;
+    matches: z.ZodArray<z.ZodObject<{
+        metadata: z.ZodObject<{
+            accession: z.ZodString;
+            source_database: z.ZodString;
+            name: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+            type: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+            integrated: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+            member_databases: z.ZodOptional<z.ZodNullable<z.ZodRecord<z.ZodString, z.ZodRecord<z.ZodString, z.ZodString>>>>;
+            go_terms: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodObject<{
+                identifier: z.ZodString;
+                name: z.ZodString;
+                category: z.ZodObject<{
+                    code: z.ZodString;
+                    name: z.ZodString;
+                }, z.core.$catchall<z.ZodJSONSchema>>;
+            }, z.core.$catchall<z.ZodJSONSchema>>>>>;
+        }, z.core.$catchall<z.ZodJSONSchema>>;
+        chainRecordCount: z.ZodNumber;
+        chainRecordLimitReached: z.ZodBoolean;
+    }, z.core.$catchall<z.ZodJSONSchema>>>;
+    structures: z.ZodArray<z.ZodObject<{
+        entry: z.ZodString;
+        record: z.ZodObject<{
+            accession: z.ZodString;
+            chain: z.ZodString;
+            protein: z.ZodNullable<z.ZodString>;
+            entry_structure_locations: z.ZodArray<z.ZodObject<{
+                fragments: z.ZodArray<z.ZodObject<{
+                    start: z.ZodNumber;
+                    end: z.ZodNumber;
+                    'dc-status': z.ZodOptional<z.ZodString>;
+                }, z.core.$catchall<z.ZodJSONSchema>>>;
+                representative: z.ZodOptional<z.ZodNullable<z.ZodBoolean>>;
+                model: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+                score: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
+            }, z.core.$catchall<z.ZodJSONSchema>>>;
+            entry_protein_locations: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodObject<{
+                fragments: z.ZodArray<z.ZodObject<{
+                    start: z.ZodNumber;
+                    end: z.ZodNumber;
+                    'dc-status': z.ZodOptional<z.ZodString>;
+                }, z.core.$catchall<z.ZodJSONSchema>>>;
+                representative: z.ZodOptional<z.ZodNullable<z.ZodBoolean>>;
+                model: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+                score: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
+            }, z.core.$catchall<z.ZodJSONSchema>>>>>;
+            structure_protein_locations: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodObject<{
+                fragments: z.ZodArray<z.ZodObject<{
+                    start: z.ZodNumber;
+                    end: z.ZodNumber;
+                    'dc-status': z.ZodOptional<z.ZodString>;
+                }, z.core.$catchall<z.ZodJSONSchema>>>;
+                representative: z.ZodOptional<z.ZodNullable<z.ZodBoolean>>;
+                model: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+                score: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
+            }, z.core.$catchall<z.ZodJSONSchema>>>>>;
+        }, z.core.$catchall<z.ZodJSONSchema>>;
+    }, z.core.$strip>>;
+    coverage: z.ZodObject<{
+        totalMatches: z.ZodNumber;
+        returnedMatches: z.ZodNumber;
+        complete: z.ZodBoolean;
+        hasMore: z.ZodBoolean;
+        nextCursor: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>;
+    url: z.ZodString;
+    sourceUrls: z.ZodArray<z.ZodString>;
+}, z.core.$strip>, readonly [{
+    readonly reason: "structure_not_found";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "InterPro has no current structure for the PDB ID: unassigned, obsolete, or not yet loaded.";
+    readonly retryable: false;
+    readonly recovery: "Check the PDB ID at rcsb.org; for a superseded entry retry interpro_get_structure_domains with its replacement ID.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "entry_withdrawn";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "InterPro reports the structure or its match list withdrawn with HTTP 410.";
+    readonly retryable: false;
+    readonly recovery: "Check the PDB ID at rcsb.org, then retry interpro_get_structure_domains with the ID that replaced it.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "chain_not_found";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "The chain is not one of the structure’s protein chains; IDs are case-sensitive and nucleic-acid chains are not listed.";
+    readonly retryable: false;
+    readonly recovery: "Retry interpro_get_structure_domains with a chain from availableChains, matching its case exactly, or omit chain.";
+}, {
+    readonly reason: "retry_deadline_exceeded";
+    readonly code: JsonRpcErrorCode.Timeout;
+    readonly when: "The shared fifty-second budget expires across the structure metadata and match pages.";
+    readonly retryable: true;
+    readonly recovery: "Retry interpro_get_structure_domains after waiting; set chain to read a smaller map.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "invalid_cursor";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "Cursor decoding or scope fails, the page it resumes inside changed, or upstream rejects continuation.";
+    readonly retryable: false;
+    readonly recovery: "Repeat the same tool without cursor to restart pagination, keeping the intended pdbId and chain.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: "upstream_shape_invalid";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "Upstream JSON, structure, or continuation is incompatible.";
+    readonly retryable: false;
+    readonly recovery: "Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.";
+    readonly thrownBy: "service";
+}, {
+    readonly reason: 'upstream_response_too_large';
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: 'An upstream response exceeds 4 MiB.';
+    readonly retryable: false;
+    readonly recovery: 'Retry list tools with a smaller limit, or retrieve individual members with interpro_get_entry instead of a large clan.';
+    readonly thrownBy: 'service';
+}, {
+    readonly reason: 'upstream_rejected';
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: 'InterPro returns an unhandled redirect or client rejection.';
+    readonly retryable: false;
+    readonly recovery: 'Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.';
+    readonly thrownBy: 'service';
+}, {
+    readonly reason: 'upstream_unavailable';
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: 'InterPro has a network or server failure; HTTP 501 is not retryable.';
+    readonly retryable: true;
+    readonly recovery: 'Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.';
+    readonly thrownBy: 'service';
+}, {
+    readonly reason: 'upstream_timeout';
+    readonly code: JsonRpcErrorCode.Timeout;
+    readonly when: 'InterPro returns HTTP 408/504 or an attempt exceeds its deadline.';
+    readonly retryable: true;
+    readonly recovery: 'Retry with a smaller limit where available, then repeat the same tool after waiting.';
+    readonly thrownBy: 'service';
+}, {
+    readonly reason: 'upstream_rate_limited';
+    readonly code: JsonRpcErrorCode.RateLimited;
+    readonly when: 'InterPro returns HTTP 429.';
+    readonly retryable: true;
+    readonly recovery: 'Wait for retryAfter when supplied, then repeat the same tool with fewer concurrent calls.';
+    readonly thrownBy: 'service';
+}], {
+    readonly notice: z.ZodOptional<z.ZodString>;
+    readonly totalCount: z.ZodOptional<z.ZodNumber>;
+    readonly truncated: z.ZodOptional<z.ZodBoolean>;
+    readonly shown: z.ZodOptional<z.ZodNumber>;
+    readonly cap: z.ZodOptional<z.ZodNumber>;
+    readonly effectiveQuery: z.ZodOptional<z.ZodString>;
+}>;
+//# sourceMappingURL=interpro-get-structure-domains.tool.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/definitions/interpro-get-structure-domains.tool.js

@@ -0,0 +1,290 @@
+/**
+ * @fileoverview PDB structure domain maps in budget-bounded segments of whole matches.
+ * @module mcp-server/tools/definitions/interpro-get-structure-domains.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { BUDGET_LABEL, fitWithinBudget, jsonByteLength, RESPONSE_BYTE_BUDGET, } from '../../../services/interpro/budget.js';
+import { continuation, decodePositionCursor, encodePositionCursor, } from '../../../services/interpro/cursors.js';
+import { formatInterpro } from '../../../services/interpro/format.js';
+import { getInterproService } from '../../../services/interpro/interpro-service.js';
+import { detailSchema, EntrySummarySchema, isAccession, JsonValueSchema, listSchema, optionalString, } from '../../../services/interpro/schemas.js';
+import { ChainSchema, isChain, PdbIdSchema, StructureMatchSchema, StructureMetadataSchema, StructureRecordSchema, } from '../../../services/interpro/structure-schemas.js';
+import { UPSTREAM_ERRORS } from '../../../services/interpro/upstream-errors.js';
+const OPERATION = 'interpro_get_structure_domains';
+/** Uncached 200-row structure pages can outlast an attempt, so pages stay at InterPro's default. */
+const PAGE_SIZE = 20;
+const MAX_PAGES = 3;
+/** InterPro nests at most this many chain records in one match, whatever the page size. */
+const NESTED_CHAIN_LIMIT = 20;
+/**
+ * Where a continuation resumes: `skip` records into the upstream page whose cursor is `page`
+ * (absent for the first page). `after` names the match before it, so a changed page is rejected.
+ */
+const PositionSchema = z
+    .object({
+    page: z.string().min(1).optional(),
+    skip: z.number().int().nonnegative(),
+    after: z.string().min(1).optional(),
+})
+    .strict()
+    .refine((point) => point.skip > 0 === (point.after !== undefined) &&
+    (point.page !== undefined || point.skip > 0));
+const CoverageSchema = z.object({
+    totalMatches: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Upstream total match count for the structure, or for the chain when one is set.'),
+    returnedMatches: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe("Whole matches in this segment; totalMatches is upstream's reported count, and a complete walk can return a different number."),
+    complete: z
+        .boolean()
+        .describe('True only when this call starts without a cursor and returns every match.'),
+    hasMore: z.boolean().describe('Whether another segment remains.'),
+    nextCursor: z
+        .string()
+        .optional()
+        .describe('Opaque cursor resuming at the next whole match for the same pdbId and chain.'),
+});
+/** Map signatures onto one PDB entry's chains in budget-bounded segments of whole matches. */
+export const interproGetStructureDomains = tool('interpro_get_structure_domains', {
+    title: 'Map structure domains',
+    description: "Retrieve InterPro and member-signature matches on one PDB entry's protein chains. Each chain record keeps match locations in chain numbering (1-based start/end beside author auth_start/auth_end, which can be null), in UniProt numbering, and the chain-to-UniProt residue map, with discontinuous fragments preserved; the UniProt protein is null for unmapped chains. InterPro nests at most 20 chain records per match; set chain to read one chain completely. Budgeted segments hold whole matches; the first carries structure metadata listing the protein chains. Continue coverage.nextCursor until hasMore is false.",
+    annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
+    auth: ['tool:interpro_get_structure_domains:read'],
+    input: z.object({
+        pdbId: PdbIdSchema,
+        chain: optionalString(ChainSchema).describe('Protein chain to map, case-sensitive and one of structure.chains, such as A; omit for every chain.'),
+        cursor: optionalString(z.string().trim().max(4096)).describe('Opaque coverage.nextCursor with unchanged pdbId and chain.'),
+    }),
+    inputAliases: { accession: 'pdbId' },
+    output: z.object({
+        pdbId: z.string().describe('Lowercase PDB ID.'),
+        chain: z.string().optional().describe('Chain the map is restricted to, when one was set.'),
+        structure: StructureMetadataSchema.optional().describe('Complete upstream structure metadata on the first segment, the call without cursor; continuation segments omit it.'),
+        matches: z
+            .array(z
+            .object({
+            metadata: EntrySummarySchema.describe('Entry metadata.'),
+            chainRecordCount: z
+                .number()
+                .int()
+                .nonnegative()
+                .describe('Chain records InterPro nested in this match, all returned in structures.'),
+            chainRecordLimitReached: z
+                .boolean()
+                .describe('True when the match carries InterPro’s 20-record nesting limit, so it may match chains not returned; set chain to read one chain.'),
+        })
+            .catchall(JsonValueSchema)
+            .describe('Whole entry match; its chain records are in structures under its accession.'))
+            .describe('Whole matches in this segment, in upstream order; never split across segments.'),
+        structures: z
+            .array(z
+            .object({
+            entry: z.string().describe('Accession of the match in matches this record belongs to.'),
+            record: StructureRecordSchema,
+        })
+            .describe('One upstream chain record of a match, unchanged.'))
+            .describe('Every chain record of this segment’s matches, grouped by match in matches order.'),
+        coverage: CoverageSchema.describe('Where this segment sits in the structure map.'),
+        url: z.string().describe('Canonical structure website URL.'),
+        sourceUrls: z.array(z.string()).describe('Official API URLs this call read.'),
+    }),
+    enrichment: {
+        notice: z.string().optional().describe('Interpretation, continuation, or recovery guidance.'),
+        totalCount: z.number().optional().describe('Upstream total matching records.'),
+        truncated: z.boolean().optional().describe('More segments remain.'),
+        shown: z.number().int().optional().describe('Whole matches in this segment.'),
+        cap: z
+            .number()
+            .int()
+            .optional()
+            .describe('Most matches one call reads; a segment can stop sooner at the response byte budget.'),
+        effectiveQuery: z.string().optional().describe('Applied pdbId and chain as JSON.'),
+    },
+    errors: [
+        {
+            reason: 'structure_not_found',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'InterPro has no current structure for the PDB ID: unassigned, obsolete, or not yet loaded.',
+            retryable: false,
+            recovery: 'Check the PDB ID at rcsb.org; for a superseded entry retry interpro_get_structure_domains with its replacement ID.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'entry_withdrawn',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'InterPro reports the structure or its match list withdrawn with HTTP 410.',
+            retryable: false,
+            recovery: 'Check the PDB ID at rcsb.org, then retry interpro_get_structure_domains with the ID that replaced it.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'chain_not_found',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'The chain is not one of the structure’s protein chains; IDs are case-sensitive and nucleic-acid chains are not listed.',
+            retryable: false,
+            recovery: 'Retry interpro_get_structure_domains with a chain from availableChains, matching its case exactly, or omit chain.',
+        },
+        {
+            reason: 'retry_deadline_exceeded',
+            code: JsonRpcErrorCode.Timeout,
+            when: 'The shared fifty-second budget expires across the structure metadata and match pages.',
+            retryable: true,
+            recovery: 'Retry interpro_get_structure_domains after waiting; set chain to read a smaller map.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'invalid_cursor',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'Cursor decoding or scope fails, the page it resumes inside changed, or upstream rejects continuation.',
+            retryable: false,
+            recovery: 'Repeat the same tool without cursor to restart pagination, keeping the intended pdbId and chain.',
+            thrownBy: 'service',
+        },
+        {
+            reason: 'upstream_shape_invalid',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'Upstream JSON, structure, or continuation is incompatible.',
+            retryable: false,
+            recovery: 'Retry the same tool later; call interpro_list_reference with topic release to check upstream availability.',
+            thrownBy: 'service',
+        },
+        ...UPSTREAM_ERRORS,
+    ],
+    async handler(input, ctx) {
+        const pdbId = input.pdbId.toLowerCase();
+        const { chain } = input;
+        const scope = { pdbId, ...(chain !== undefined ? { chain } : {}) };
+        const start = decodePositionCursor(input.cursor, OPERATION, scope, PositionSchema);
+        const stale = () => ctx.fail('invalid_cursor', 'Cursor no longer matches the InterPro page it resumes inside.');
+        const service = getInterproService();
+        const call = service.begin(ctx);
+        const missing = {
+            reason: 'structure_not_found',
+            accession: pdbId,
+            sourceDatabase: 'pdb',
+        };
+        const sourceUrls = [];
+        let structure;
+        if (!start) {
+            // A list 204 means no matches, so only the detail tells an unknown ID or chain apart.
+            const detail = await service.request(call, ['structure', 'pdb', pdbId], {}, detailSchema(StructureMetadataSchema), { missing });
+            if (!detail.data)
+                throw ctx.fail('upstream_shape_invalid', 'Structure metadata response is missing.');
+            structure = detail.data.metadata;
+            sourceUrls.push(detail.sourceUrl);
+            if (chain !== undefined && !structure.chains.includes(chain)) {
+                const named = structure.chains.filter(isChain);
+                throw ctx.fail('chain_not_found', named.length
+                    ? `Chain ${chain} is not a protein chain of ${pdbId}; chain IDs are case-sensitive. Available chains: ${named.join(', ')}.`
+                    : `${pdbId} has no protein chains, so InterPro maps no domains onto chain ${chain}.`, { pdbId, chain, availableChains: structure.chains });
+            }
+        }
+        const segments = ['entry', 'all', 'structure', 'pdb', pdbId, ...(chain ? [chain] : [])];
+        const items = [];
+        let totalMatches = 0;
+        /** Where the walk resumes after the last gathered match; undefined once the walk ends. */
+        let end;
+        const segment = (count) => {
+            const resume = items[count]?.at ?? end;
+            const matches = items.slice(0, count).map((item) => item.match);
+            return {
+                pdbId,
+                ...(chain !== undefined ? { chain } : {}),
+                ...(structure ? { structure } : {}),
+                matches: matches.map(({ metadata, structures, ...rest }) => ({
+                    ...rest,
+                    metadata,
+                    chainRecordCount: structures.length,
+                    chainRecordLimitReached: structures.length >= NESTED_CHAIN_LIMIT,
+                })),
+                structures: matches.flatMap(({ metadata, structures }) => structures.map((record) => ({ entry: metadata.accession, record }))),
+                coverage: {
+                    totalMatches,
+                    returnedMatches: matches.length,
+                    complete: !start && resume === undefined,
+                    hasMore: resume !== undefined,
+                    ...(resume ? { nextCursor: encodePositionCursor(OPERATION, scope, resume) } : {}),
+                },
+                url: `https://www.ebi.ac.uk/interpro/structure/PDB/${pdbId}/`,
+                sourceUrls,
+            };
+        };
+        let page = start?.page;
+        let skip = start?.skip ?? 0;
+        const seen = new Set(page ? [page] : []);
+        for (let read = 1;; read++) {
+            const response = await service.request(call, segments, { page_size: PAGE_SIZE, cursor: page }, listSchema(StructureMatchSchema), page ? { continuation: true } : { missing: { ...missing, list: true } });
+            sourceUrls.push(response.sourceUrl);
+            // A continuation page cannot be empty: the structure or its matches changed underneath it.
+            if (page && !response.data)
+                throw stale();
+            if (read === 1)
+                totalMatches = response.data?.count ?? 0;
+            const records = response.data?.results ?? [];
+            if (skip > 0 &&
+                (skip >= records.length || records[skip - 1]?.metadata.accession !== start?.after))
+                throw stale();
+            for (let index = skip; index < records.length; index++)
+                items.push({
+                    match: records[index],
+                    at: {
+                        ...(page ? { page } : {}),
+                        skip: index,
+                        ...(index ? { after: records[index - 1].metadata.accession } : {}),
+                    },
+                });
+            const next = continuation(response.data?.next ?? null, seen);
+            end = next ? { page: next, skip: 0 } : undefined;
+            if (!next)
+                break;
+            seen.add(next);
+            page = next;
+            skip = 0;
+            if (read === MAX_PAGES || jsonByteLength(segment(items.length)) > RESPONSE_BYTE_BUDGET)
+                break;
+        }
+        const { count, output, oversized } = fitWithinBudget(items.length, segment);
+        const { coverage } = output;
+        const notices = [];
+        if (oversized) {
+            const id = items[0]?.match.metadata.accession;
+            notices.push(`${isAccession(id) ? `Match ${id}` : 'This match'} cannot be split, so this segment holds it alone and exceeds the ${BUDGET_LABEL}.`);
+        }
+        const limited = output.matches.filter((match) => match.chainRecordLimitReached);
+        if (limited.length) {
+            const named = limited.map((match) => match.metadata.accession).filter(isAccession);
+            notices.push(`InterPro nests at most ${NESTED_CHAIN_LIMIT} chain records in one match, and ${limited.length === 1 ? 'one match carries' : `${limited.length} matches carry`} that many${named.length ? ` (${named.join(', ')})` : ''}, so ${limited.length === 1 ? 'it' : 'they'} may match chains not returned. Repeat interpro_get_structure_domains with chain set to one of structure.chains to read that chain's matches completely.`);
+        }
+        if (coverage.nextCursor) {
+            const reason = items[count]
+                ? ` and stopped at the ${BUDGET_LABEL} before the next whole match`
+                : ` and reached the ${MAX_PAGES}-page read limit`;
+            notices.push(`This segment covers part of the structure map${oversized ? '' : reason}. Continue with interpro_get_structure_domains ${JSON.stringify({ ...scope, cursor: coverage.nextCursor })} before concluding that a chain has no annotation.`);
+        }
+        else if (start)
+            notices.push('This is the final resumed segment. Only the combined segments cover the traversal; upstream pagination is not a snapshot.');
+        else if (!coverage.returnedMatches)
+            notices.push(structure && !structure.chains.length
+                ? `${pdbId} has no protein chains, so InterPro maps no domains onto it.`
+                : chain !== undefined
+                    ? `InterPro reports no match on chain ${chain} of ${pdbId}.`
+                    : `InterPro reports no match on the protein chains of ${pdbId}.`);
+        if (start)
+            notices.push('Continuation segments omit the structure metadata the first segment returned.');
+        ctx.enrich.total(totalMatches);
+        ctx.enrich.echo(JSON.stringify(scope));
+        if (coverage.nextCursor)
+            ctx.enrich.truncated({ shown: coverage.returnedMatches, cap: MAX_PAGES * PAGE_SIZE });
+        if (notices.length)
+            ctx.enrich.notice(notices.join(' '));
+        return output;
+    },
+    format: formatInterpro,
+});
+//# sourceMappingURL=interpro-get-structure-domains.tool.js.map

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

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/definitions/interpro-list-reference.tool.js

@@ -11,7 +11,7 @@ import { JsonObjectSchema } from '../../../services/interpro/schemas.js';
 /** Decode supported vocabulary or retrieve coherent current release counts. */
 export const interproListReference = tool('interpro_list_reference', {
     title: 'InterPro reference vocabulary',
-    description: 'List supported InterPro database slugs, entry types, accession routing patterns, common taxon IDs, or current release information.',
+    description: 'List supported InterPro database slugs, entry types, accession and PDB identifier patterns, common taxon IDs, or current release information.',
     annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
     auth: ['tool:interpro_list_reference:read'],
     input: z.object({ topic: ReferenceTopicSchema }),

package/dist/mcp-server/tools/definitions/interpro-list-reference.tool.js.map

@@ -1 +1 @@
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