@cyanheads/interpro-mcp-server 0.1.2 → 0.2.0

package/dist/mcp-server/tools/definitions/interpro-find-proteins-by-domain.tool.js

@@ -22,7 +22,20 @@ const QuerySchema = z.object({
         .boolean()
         .optional()
         .describe('Applied fragment annotation filter; omitted includes both groups.'),
+    architectureId: z
+        .string()
+        .optional()
+        .describe('Applied lowercase Pfam architecture grouping identifier.'),
+    proteomeId: z.string().optional().describe('Applied uppercase UniProt proteome accession.'),
 });
+const ProteomesSchema = z
+    .array(z
+    .object({
+    accession: z.string().describe('Proteome accession as upstream writes it, lowercase.'),
+})
+    .catchall(JsonValueSchema)
+    .describe('Complete proteome record.'))
+    .describe('Complete records of the selected proteome, preserved verbatim.');
 const ProteinResultSchema = z
     .object({
     metadata: ProteinMetadataSchema.describe('Complete sparse protein summary.'),
@@ -59,10 +72,27 @@ const ProteinResultSchema = z
 })
     .catchall(JsonValueSchema)
     .describe('Complete protein discovery record.');
+const ProteomeResultSchema = ProteinResultSchema.extend({ proteomes: ProteomesSchema }).describe('Complete proteome-filtered protein discovery record.');
+const ArchitectureResultSchema = ProteinResultSchema.extend({
+    entries: ProteinResultSchema.shape.entries.optional(),
+    taxa: ProteinResultSchema.shape.taxa.optional(),
+    proteomes: ProteomesSchema.optional(),
+});
+const Availability = z.enum(['available', 'unavailable']);
+const availability = (details) => details === undefined ? 'unavailable' : 'available';
+const ArchitectureOutputSchema = ArchitectureResultSchema.extend({
+    detailAvailability: z
+        .object({
+        entries: Availability.describe('Whether upstream supplied entry records.'),
+        taxa: Availability.describe('Whether upstream supplied taxon records.'),
+        proteomes: Availability.optional().describe('Whether upstream supplied proteome records; present only when proteomeId is set.'),
+    })
+        .describe('Absent details are unavailable, rather than biologically empty.'),
+}).describe('Complete architecture-filtered protein record with explicit detail availability.');
 /** Discover proteins without fetching per-protein metadata. */
 export const interproFindProteinsByDomain = tool('interpro_find_proteins_by_domain', {
     title: 'Find proteins by domain',
-    description: 'Find UniProt proteins carrying an InterPro or member signature. Defaults to reviewed human proteins; reviewedOnly=false includes reviewed and unreviewed proteins in the chosen taxon. Optional isFragment filters fragment annotations; false does not prove a complete canonical sequence.',
+    description: 'Find UniProt proteins carrying an InterPro or member signature. Defaults to reviewed human proteins; reviewedOnly=false includes all review statuses in the chosen taxon. Optional isFragment filters fragment annotations; false does not prove sequence completeness. architectureId intersects the provider Pfam grouping with these selections, without implying functional equivalence; metadata-only hits disclose unavailable entry and taxon details without per-protein requests. proteomeId intersects one UniProt proteome, such as protein.proteome from interpro_get_protein_domains, with every selection including taxonId.',
     annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
     auth: ['tool:interpro_find_proteins_by_domain:read'],
     input: z.object({
@@ -82,17 +112,32 @@ export const interproFindProteinsByDomain = tool('interpro_find_proteins_by_doma
             .boolean()
             .optional()
             .describe('Select fragment annotations: true for fragments, false for proteins not annotated as fragments; omit to include both. False does not establish sequence completeness.'),
+        architectureId: optionalString(z
+            .string()
+            .trim()
+            .regex(/^[a-fA-F0-9]{40}$/)
+            .toLowerCase()).describe('Optional 40-character hexadecimal Pfam architecture grouping ID from protein.ida_accession; grouping does not establish functional equivalence.'),
+        proteomeId: optionalString(z
+            .string()
+            .trim()
+            .max(11)
+            .regex(/^[Uu][Pp][0-9]{9}$/)
+            .toUpperCase()).describe('Optional UniProt proteome accession, UP followed by 9 digits, such as protein.proteome from interpro_get_protein_domains. taxonId still applies, including its 9606 default: set taxonId to the mapped protein.source_organism.taxId or an ancestor, or no proteins match.'),
         limit: z
             .number()
             .int()
             .min(1)
             .default(20)
             .describe('Positive integer page size; values above 50 are clamped to 50 with a notice; defaults to 20.'),
-        cursor: optionalString(z.string().trim().max(4096)).describe('Opaque nextCursor with unchanged target, taxonId, reviewedOnly, and isFragment selection; limit may change.'),
+        cursor: optionalString(z.string().trim().max(4096)).describe('Opaque nextCursor with unchanged target, taxonId, reviewedOnly, isFragment, architectureId, and proteomeId selection; limit may change.'),
     }),
     output: z.object({
         query: QuerySchema.describe('Applied canonical target and selection, including defaults.'),
-        proteins: z.array(ProteinResultSchema).describe('Complete upstream protein result records.'),
+        proteins: z
+            .array(z
+            .union([ProteinResultSchema, ProteomeResultSchema, ArchitectureOutputSchema])
+            .describe('Ordinary protein details, with proteome records when proteomeId is set, or an architecture-filtered record with detail availability.'))
+            .describe('Complete upstream protein records; architecture mode discloses unavailable details.'),
         page: PageSchema.describe('Page coverage and continuation.'),
         sourceUrl: z.string().describe('Official API source URL.'),
     }),
@@ -163,9 +208,32 @@ export const interproFindProteinsByDomain = tool('interpro_find_proteins_by_doma
             taxonId: input.taxonId,
             reviewedOnly: input.reviewedOnly,
             ...(input.isFragment !== undefined ? { isFragment: input.isFragment } : {}),
+            ...(input.architectureId !== undefined ? { architectureId: input.architectureId } : {}),
+            ...(input.proteomeId !== undefined ? { proteomeId: input.proteomeId } : {}),
         };
         const cursor = decodeCursor(input.cursor, 'interpro_find_proteins_by_domain', query);
         const service = getInterproService();
+        const rowSchema = input.architectureId
+            ? ArchitectureResultSchema.refine((row) => {
+                const fields = row.extra_fields;
+                return (!fields ||
+                    typeof fields !== 'object' ||
+                    Array.isArray(fields) ||
+                    fields.ida_id === undefined ||
+                    fields.ida_id === null ||
+                    fields.ida_id === input.architectureId);
+            }, 'A supplied architecture identifier must match the requested grouping.').transform((row) => Object.assign({}, row, {
+                detailAvailability: {
+                    entries: availability(row.entries),
+                    taxa: availability(row.taxa),
+                    ...(input.proteomeId !== undefined
+                        ? { proteomes: availability(row.proteomes) }
+                        : {}),
+                },
+            }))
+            : input.proteomeId
+                ? ProteomeResultSchema
+                : ProteinResultSchema;
         const response = await service.request(service.begin(ctx), [
             'protein',
             query.reviewedOnly ? 'reviewed' : 'uniprot',
@@ -175,7 +243,14 @@ export const interproFindProteinsByDomain = tool('interpro_find_proteins_by_doma
             'taxonomy',
             'uniprot',
             query.taxonId,
-        ], { page_size: limit, cursor, extra_fields: 'is_fragment', is_fragment: query.isFragment }, listSchema(ProteinResultSchema), {
+            ...(query.proteomeId ? ['proteome', 'uniprot', query.proteomeId] : []),
+        ], {
+            page_size: limit,
+            cursor,
+            extra_fields: input.architectureId ? 'is_fragment,ida_id' : 'is_fragment',
+            is_fragment: query.isFragment,
+            ida: input.architectureId,
+        }, listSchema(rowSchema), {
             continuation: cursor !== undefined,
             missing: {
                 reason: 'entry_not_found',
@@ -198,7 +273,7 @@ export const interproFindProteinsByDomain = tool('interpro_find_proteins_by_doma
         ctx.enrich.total(page.total);
         ctx.enrich.echo(JSON.stringify(query));
         if (!proteins.length)
-            notices.push(`No proteins matched the applied entry and selection. Retry interpro_find_proteins_by_domain with reviewedOnly=false or another taxonId${input.isFragment !== undefined ? ', or omit isFragment to include both fragment annotation groups' : ''}; use interpro_get_entry to verify the accession.`);
+            notices.push(`No proteins matched the applied entry and selection. Retry interpro_find_proteins_by_domain with reviewedOnly=false or another taxonId${input.isFragment !== undefined ? ', or omit isFragment to include both fragment annotation groups' : ''}; use interpro_get_entry to verify the accession.${query.proteomeId ? ` taxonId ${query.taxonId} still applies with proteomeId ${query.proteomeId}: set taxonId to protein.source_organism.taxId from interpro_get_protein_domains for a protein in that proteome, or an ancestor taxon, and confirm proteomeId against its protein.proteome.` : ''}`);
         if (next) {
             notices.push(pageGuidance('interpro_find_proteins_by_domain', 'proteins', limit, MAX_LIMIT));
             ctx.enrich.truncated({ shown: proteins.length, cap: limit, guidance: notices.join(' ') });

package/dist/mcp-server/tools/definitions/interpro-find-proteins-by-domain.tool.js.map

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

@@ -25,6 +25,19 @@ export declare const interproGetEntry: import("@cyanheads/mcp-ts-core").ToolDefi
         ssf: "ssf";
     }>>, unknown>;
     includeThumbnail: z.ZodDefault<z.ZodBoolean>;
+    sections: z.ZodOptional<z.ZodArray<z.ZodEnum<{
+        counters: "counters";
+        cross_references: "cross_references";
+        description: "description";
+        go_terms: "go_terms";
+        hierarchy: "hierarchy";
+        literature: "literature";
+        member_databases: "member_databases";
+        overlaps_with: "overlaps_with";
+        wikipedia: "wikipedia";
+    }>>>;
+    overlapLimit: z.ZodOptional<z.ZodNumber>;
+    overlapOffset: z.ZodOptional<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     accession: z.ZodString;
     sourceDatabase: z.ZodEnum<{
@@ -55,7 +68,52 @@ export declare const interproGetEntry: import("@cyanheads/mcp-ts-core").ToolDefi
     }, z.core.$catchall<z.ZodJSONSchema>>;
     url: z.ZodString;
     sourceUrl: z.ZodString;
+    sections: z.ZodOptional<z.ZodArray<z.ZodEnum<{
+        counters: "counters";
+        cross_references: "cross_references";
+        description: "description";
+        go_terms: "go_terms";
+        hierarchy: "hierarchy";
+        literature: "literature";
+        member_databases: "member_databases";
+        overlaps_with: "overlaps_with";
+        wikipedia: "wikipedia";
+    }>>>;
+    omittedSections: z.ZodOptional<z.ZodArray<z.ZodEnum<{
+        counters: "counters";
+        cross_references: "cross_references";
+        description: "description";
+        go_terms: "go_terms";
+        hierarchy: "hierarchy";
+        literature: "literature";
+        member_databases: "member_databases";
+        overlaps_with: "overlaps_with";
+        wikipedia: "wikipedia";
+    }>>>;
+    overlapsPage: z.ZodOptional<z.ZodDiscriminatedUnion<[z.ZodObject<{
+        available: z.ZodLiteral<true>;
+        total: z.ZodNumber;
+        offset: z.ZodNumber;
+        returned: z.ZodNumber;
+        hasMore: z.ZodBoolean;
+        nextOffset: z.ZodOptional<z.ZodNumber>;
+    }, z.core.$strip>, z.ZodObject<{
+        available: z.ZodLiteral<false>;
+        offset: z.ZodNumber;
+    }, z.core.$strip>], "available">>;
 }, z.core.$strip>, readonly [{
+    readonly reason: "overlap_limit_required";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "overlapOffset is supplied without overlapLimit.";
+    readonly retryable: false;
+    readonly recovery: "Supply overlapLimit to enable paging, or omit overlapOffset for full overlaps.";
+}, {
+    readonly reason: "overlaps_not_selected";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "Overlap paging is requested but sections excludes overlaps_with.";
+    readonly retryable: false;
+    readonly recovery: "Include overlaps_with in sections or omit sections, then retry with overlapLimit.";
+}, {
     readonly reason: "database_mismatch";
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "Explicit database conflicts with accession routing.";
@@ -126,6 +184,7 @@ export declare const interproGetEntry: import("@cyanheads/mcp-ts-core").ToolDefi
     readonly recovery: 'Wait for retryAfter when supplied, then repeat the same tool with fewer concurrent calls.';
     readonly thrownBy: 'service';
 }], {
+    readonly totalCount: z.ZodOptional<z.ZodNumber>;
     readonly notice: z.ZodOptional<z.ZodString>;
 }>;
 //# sourceMappingURL=interpro-get-entry.tool.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"interpro-get-entry.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/interpro-get-entry.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAuDjE,wEAAwE;AACxE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2O3B,CAAC"}

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

@@ -10,10 +10,45 @@ import { getInterproService } from '../../../services/interpro/interpro-service.
 import { resolveEntry } from '../../../services/interpro/routing.js';
 import { AccessionSchema, detailSchema, EntryDetailMetadataSchema, EntryMetadataSchema, optionalString, SourceDatabaseSchema, } from '../../../services/interpro/schemas.js';
 import { UPSTREAM_ERRORS } from '../../../services/interpro/upstream-errors.js';
+const SECTIONS = [
+    'description',
+    'hierarchy',
+    'member_databases',
+    'go_terms',
+    'literature',
+    'cross_references',
+    'wikipedia',
+    'counters',
+    'overlaps_with',
+];
+const SectionSchema = z.enum(SECTIONS);
+const OverlapsPageSchema = z.discriminatedUnion('available', [
+    z
+        .object({
+        available: z.literal(true).describe('Overlap array was supplied.'),
+        total: z.number().int().nonnegative().describe('Complete upstream overlap count.'),
+        offset: z.number().int().nonnegative().describe('Requested record offset.'),
+        returned: z.number().int().nonnegative().describe('Complete records returned.'),
+        hasMore: z.boolean().describe('More overlap records remain.'),
+        nextOffset: z
+            .number()
+            .int()
+            .nonnegative()
+            .optional()
+            .describe('Next offset when more records remain.'),
+    })
+        .describe('Page of complete upstream overlap records.'),
+    z
+        .object({
+        available: z.literal(false).describe('Overlap array was not supplied.'),
+        offset: z.number().int().nonnegative().describe('Requested record offset.'),
+    })
+        .describe('Overlap paging unavailable for a missing or null source section.'),
+]);
 /** Retrieve one complete entry with deterministic accession routing. */
 export const interproGetEntry = tool('interpro_get_entry', {
     title: 'InterPro entry metadata',
-    description: 'Retrieve one InterPro or member-database entry, including description, hierarchy, member signatures, GO terms, literature, cross-references, clan membership, and coverage counters.',
+    description: 'Retrieve one InterPro or member-database entry with full metadata by default. Select optional sections while retaining core and unknown metadata, or supply overlapLimit to page whole overlap records in upstream order; offsets are not a snapshot across calls.',
     annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
     auth: ['tool:interpro_get_entry:read'],
     input: z.object({
@@ -23,21 +58,68 @@ export const interproGetEntry = tool('interpro_get_entry', {
             .boolean()
             .default(false)
             .describe('Include each Wikipedia thumbnail image, base64 data often hundreds of KB; defaults to false.'),
+        sections: z
+            .array(SectionSchema.describe('Optional metadata section to retain.'))
+            .optional()
+            .describe('Retain these named sections and all core or unknown metadata; omitted means full detail, and an empty array retains core metadata only.'),
+        overlapLimit: z
+            .number()
+            .int()
+            .positive()
+            .max(Number.MAX_SAFE_INTEGER)
+            .optional()
+            .describe('Positive safe integer number of whole overlap records; supplying it enables overlap paging.'),
+        overlapOffset: z
+            .number()
+            .int()
+            .nonnegative()
+            .max(Number.MAX_SAFE_INTEGER)
+            .optional()
+            .describe('Nonnegative safe integer overlap offset; requires overlapLimit, defaults to zero.'),
     }),
     output: z.object({
         accession: z.string().describe('Canonical requested accession.'),
         sourceDatabase: SourceDatabaseSchema,
-        entry: EntryDetailMetadataSchema.describe('Complete upstream metadata with readable descriptionText, preserving raw description shapes and sparse annotations; Wikipedia thumbnails are omitted unless includeThumbnail is true.'),
+        entry: EntryDetailMetadataSchema.describe('Upstream metadata after explicit section selection and overlap paging, with readable descriptionText when description is retained; raw description shapes and sparse annotations survive. Wikipedia thumbnails are omitted unless includeThumbnail is true.'),
         url: z.string().describe('Canonical InterPro website URL.'),
         sourceUrl: z.string().describe('Official API source URL.'),
+        sections: z
+            .array(SectionSchema.describe('Retained optional section.'))
+            .optional()
+            .describe('Canonical selected sections, when explicitly selected.'),
+        omittedSections: z
+            .array(SectionSchema.describe('Omitted source section.'))
+            .optional()
+            .describe('Named sections actually removed from upstream metadata.'),
+        overlapsPage: OverlapsPageSchema.optional().describe('Explicit overlap paging state; unavailable arrays have no fabricated total.'),
     }),
     enrichment: {
+        totalCount: z
+            .number()
+            .int()
+            .nonnegative()
+            .optional()
+            .describe('Total upstream overlap records when explicit paging has an available array.'),
         notice: z
             .string()
             .optional()
-            .describe('Omitted Wikipedia thumbnail size and how to include it.'),
+            .describe('Section selection, overlap page continuation or availability, and omitted Wikipedia thumbnail guidance.'),
     },
     errors: [
+        {
+            reason: 'overlap_limit_required',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'overlapOffset is supplied without overlapLimit.',
+            retryable: false,
+            recovery: 'Supply overlapLimit to enable paging, or omit overlapOffset for full overlaps.',
+        },
+        {
+            reason: 'overlaps_not_selected',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'Overlap paging is requested but sections excludes overlaps_with.',
+            retryable: false,
+            recovery: 'Include overlaps_with in sections or omit sections, then retry with overlapLimit.',
+        },
         {
             reason: 'database_mismatch',
             code: JsonRpcErrorCode.ValidationError,
@@ -81,14 +163,64 @@ export const interproGetEntry = tool('interpro_get_entry', {
         ...UPSTREAM_ERRORS,
     ],
     async handler(input, ctx) {
+        if (input.overlapOffset !== undefined && input.overlapLimit === undefined)
+            throw ctx.fail('overlap_limit_required');
+        if (input.overlapLimit !== undefined &&
+            input.sections &&
+            !input.sections.includes('overlaps_with'))
+            throw ctx.fail('overlaps_not_selected');
         const target = resolveEntry(input.accession, input.sourceDatabase);
         const service = getInterproService();
         const response = await service.request(service.begin(ctx), ['entry', target.sourceDatabase, target.accession], {}, detailSchema(EntryMetadataSchema), { missing: { reason: 'entry_not_found', ...target } });
         if (!response.data)
             throw ctx.fail('upstream_shape_invalid', 'Entry metadata response is missing.');
-        const { metadata, notice } = projectWikipediaThumbnails(response.data.metadata, input.includeThumbnail, 'interpro_get_entry');
+        const sourceMetadata = response.data.metadata;
+        const selected = input.sections === undefined
+            ? undefined
+            : SECTIONS.filter((section) => input.sections?.includes(section));
+        const omittedSections = selected === undefined
+            ? undefined
+            : SECTIONS.filter((section) => !selected.includes(section) && Object.hasOwn(sourceMetadata, section));
+        const projected = { ...sourceMetadata };
+        for (const section of omittedSections ?? [])
+            delete projected[section];
+        const notices = [];
+        if (selected)
+            notices.push(`Selected sections: ${JSON.stringify(selected)}; omitted source sections: ${JSON.stringify(omittedSections)}. Core and unknown metadata are retained.`);
+        let overlapsPage;
+        if (input.overlapLimit !== undefined) {
+            const offset = input.overlapOffset ?? 0;
+            const overlaps = projected.overlaps_with;
+            if (overlaps === undefined || overlaps === null) {
+                overlapsPage = { available: false, offset };
+                notices.push('Overlap paging is unavailable because upstream overlaps_with is missing or null; no total is known.');
+            }
+            else {
+                if (!Array.isArray(overlaps))
+                    throw ctx.fail('upstream_shape_invalid', 'Entry overlaps_with is not an array.');
+                const slice = overlaps.slice(offset, offset + Math.min(input.overlapLimit, overlaps.length));
+                projected.overlaps_with = slice;
+                const nextOffset = offset + slice.length;
+                const hasMore = nextOffset < overlaps.length;
+                ctx.enrich.total(overlaps.length);
+                overlapsPage = {
+                    available: true,
+                    total: overlaps.length,
+                    offset,
+                    returned: slice.length,
+                    hasMore,
+                    ...(hasMore ? { nextOffset } : {}),
+                };
+                notices.push(`Overlap page returned ${slice.length} of ${overlaps.length} records at offset ${offset}.`);
+                if (hasMore)
+                    notices.push(`Continue with interpro_get_entry ${JSON.stringify({ ...target, includeThumbnail: input.includeThumbnail, ...(selected ? { sections: selected } : {}), overlapLimit: input.overlapLimit, overlapOffset: nextOffset })}.`);
+            }
+        }
+        const { metadata, notice } = projectWikipediaThumbnails(projected, input.includeThumbnail, 'interpro_get_entry');
         if (notice)
-            ctx.enrich.notice(notice);
+            notices.push(notice);
+        if (notices.length)
+            ctx.enrich.notice(notices.join(' '));
         const readable = descriptionText(metadata.description);
         const entry = normalizeImages(metadata);
         if (readable)
@@ -98,6 +230,8 @@ export const interproGetEntry = tool('interpro_get_entry', {
             entry,
             url: `https://www.ebi.ac.uk/interpro/entry/${target.sourceDatabase}/${encodeURIComponent(target.accession)}/`,
             sourceUrl: response.sourceUrl,
+            ...(selected ? { sections: selected, omittedSections } : {}),
+            ...(overlapsPage ? { overlapsPage } : {}),
         };
     },
     format: formatInterpro,

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

@@ -9,6 +9,7 @@ export declare const interproGetProteinDomains: import("@cyanheads/mcp-ts-core")
     accession: z.ZodString;
     residuePosition: z.ZodOptional<z.ZodNumber>;
     includeExtraFeatures: z.ZodDefault<z.ZodBoolean>;
+    includeResidueAnnotations: z.ZodDefault<z.ZodBoolean>;
     cursor: z.ZodPreprocess<z.ZodOptional<z.ZodString>, unknown>;
 }, z.core.$strip>, z.ZodObject<{
     accession: z.ZodString;
@@ -23,6 +24,7 @@ export declare const interproGetProteinDomains: import("@cyanheads/mcp-ts-core")
             scientificName: z.ZodString;
             fullName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
         }, z.core.$catchall<z.ZodJSONSchema>>>;
+        proteome: z.ZodOptional<z.ZodNullable<z.ZodString>>;
     }, z.core.$catchall<z.ZodJSONSchema>>>;
     matches: z.ZodArray<z.ZodObject<{
         metadata: z.ZodObject<{
@@ -69,9 +71,24 @@ export declare const interproGetProteinDomains: import("@cyanheads/mcp-ts-core")
             score: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
         }, z.core.$catchall<z.ZodJSONSchema>>>;
     }, z.core.$catchall<z.ZodJSONSchema>>>>;
+    residueAnnotations: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodObject<{
+        accession: z.ZodString;
+        source_database: z.ZodString;
+        locations: z.ZodArray<z.ZodObject<{
+            fragments: z.ZodArray<z.ZodObject<{
+                start: z.ZodNumber;
+                end: z.ZodNumber;
+                'dc-status': z.ZodOptional<z.ZodString>;
+            }, z.core.$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.$catchall<z.ZodJSONSchema>>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>>;
     selection: z.ZodObject<{
         residuePosition: z.ZodOptional<z.ZodNumber>;
         includeExtraFeatures: z.ZodBoolean;
+        includeResidueAnnotations: z.ZodOptional<z.ZodLiteral<true>>;
     }, z.core.$strip>;
     coverage: z.ZodObject<{
         totalMatches: z.ZodNumber;
@@ -79,6 +96,8 @@ export declare const interproGetProteinDomains: import("@cyanheads/mcp-ts-core")
         returnedMatches: z.ZodNumber;
         totalFeatures: z.ZodOptional<z.ZodNumber>;
         returnedFeatures: z.ZodOptional<z.ZodNumber>;
+        totalResidueAnnotations: z.ZodOptional<z.ZodNumber>;
+        returnedResidueAnnotations: z.ZodOptional<z.ZodNumber>;
         complete: z.ZodBoolean;
         hasMore: z.ZodBoolean;
         nextCursor: z.ZodOptional<z.ZodString>;
@@ -88,9 +107,9 @@ export declare const interproGetProteinDomains: import("@cyanheads/mcp-ts-core")
 }, z.core.$strip>, readonly [{
     readonly reason: "retry_deadline_exceeded";
     readonly code: JsonRpcErrorCode.Timeout;
-    readonly when: "The shared fifty-second budget expires across protein metadata, match pages, and extra features.";
+    readonly when: "The shared fifty-second budget expires across metadata, match pages, extra features, and residue rules.";
     readonly retryable: true;
-    readonly recovery: "Retry interpro_get_protein_domains after waiting; omit extra features when they are not needed.";
+    readonly recovery: "Retry interpro_get_protein_domains after waiting; omit optional annotations when they are not needed.";
     readonly thrownBy: "service";
 }, {
     readonly reason: "invalid_cursor";

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

@@ -1 +1 @@
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+{"version":3,"file":"interpro-get-protein-domains.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/interpro-get-protein-domains.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmLjE,gGAAgG;AAChG,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAoYpC,CAAC"}