@cyanheads/interpro-mcp-server 0.0.0-stage → 0.1.2

package/dist/services/interpro/reference.js

@@ -0,0 +1,122 @@
+/**
+ * @fileoverview Static API vocabulary and common taxonomy examples.
+ * @module services/interpro/reference
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { DOCUMENTATION_URL, ENTRY_ROUTES } from './routing.js';
+/** Available reference topics; only release performs network operations. */
+export const ReferenceTopicSchema = z
+    .enum(['databases', 'entry_types', 'accession_patterns', 'taxa', 'release'])
+    .describe('Reference topic; release retrieves current upstream metadata.');
+/** Applicable reference fields, without fabricated empty annotations. */
+export const ReferenceItemSchema = z
+    .object({
+    id: z.string().describe('Reference identifier.'),
+    label: z.string().describe('Human-readable label.'),
+    description: z.string().optional().describe('Meaning and coverage.'),
+    sourceDatabase: z.string().optional().describe('Entry API database slug.'),
+    accessionPattern: z.string().optional().describe('Case-insensitive accession routing pattern.'),
+    example: z
+        .string()
+        .optional()
+        .describe('Example accession spelling; assignment is not guaranteed.'),
+    taxonId: z.string().optional().describe('NCBI taxonomy identifier.'),
+})
+    .describe('One reference vocabulary item.');
+const databaseLabels = {
+    interpro: 'InterPro',
+    pfam: 'Pfam',
+    prosite: 'PROSITE patterns',
+    profile: 'PROSITE profiles',
+    smart: 'SMART',
+    cdd: 'CDD',
+    panther: 'PANTHER',
+    cathgene3d: 'CATH-Gene3D',
+    ssf: 'SUPERFAMILY',
+    ncbifam: 'NCBIFAM',
+    hamap: 'HAMAP',
+    prints: 'PRINTS',
+    pirsf: 'PIRSF',
+    sfld: 'SFLD',
+    antifam: 'AntiFam',
+};
+const types = [
+    ['domain', 'Domain', 'A distinct structural or functional protein unit.'],
+    ['family', 'Family', 'A group of evolutionarily related proteins.'],
+    ['repeat', 'Repeat', 'A repeated sequence or structural unit.'],
+    [
+        'homologous_superfamily',
+        'Homologous superfamily',
+        'Proteins or domains with a shared evolutionary origin.',
+    ],
+    ['active_site', 'Active site', 'Residues involved in catalysis.'],
+    ['binding_site', 'Binding site', 'Residues involved in binding.'],
+    ['conserved_site', 'Conserved site', 'A conserved functional sequence site.'],
+    ['ptm', 'Post-translational modification', 'A post-translational modification site.'],
+    [
+        'region',
+        'Region',
+        'A sequence region; AntiFam signatures of spurious protein predictions use this type.',
+    ],
+    [
+        'coiled_coil',
+        'Coiled coil',
+        'A coiled-coil region, where alpha-helices wind around each other.',
+    ],
+    [
+        'disordered',
+        'Disordered region',
+        'An intrinsically disordered region without a fixed three-dimensional structure.',
+    ],
+];
+const taxa = [
+    ['9606', 'Human'],
+    ['10090', 'Mouse'],
+    ['10116', 'Rat'],
+    ['7955', 'Zebrafish'],
+    ['7227', 'Fruit fly'],
+    ['6239', 'Nematode'],
+    ['559292', 'Budding yeast'],
+    ['3702', 'Arabidopsis'],
+    ['562', 'Escherichia coli'],
+];
+/** Return bounded local reference data without making upstream requests. */
+export function staticReference(topic) {
+    if (topic === 'entry_types')
+        return {
+            items: types.map(([id, label, description]) => ({ id, label, description })),
+            sourceUrls: [DOCUMENTATION_URL],
+        };
+    if (topic === 'taxa')
+        return {
+            items: taxa.map(([taxonId, label]) => ({
+                id: taxonId,
+                label,
+                taxonId,
+                description: 'Common taxonomy example; this is not an exhaustive taxonomy.',
+            })),
+            sourceUrls: [DOCUMENTATION_URL, 'https://www.ncbi.nlm.nih.gov/taxonomy'],
+        };
+    return {
+        items: ENTRY_ROUTES.map(({ source, pattern, example }) => ({
+            id: source,
+            label: databaseLabels[source],
+            sourceDatabase: source,
+            accessionPattern: pattern.source,
+            example,
+            description: topic === 'accession_patterns'
+                ? 'Routing syntax does not guarantee that an accession is assigned.'
+                : source === 'interpro'
+                    ? 'Integrating database combining member signatures.'
+                    : source === 'antifam'
+                        ? 'Additional API source for spurious protein predictions.'
+                        : source === 'prosite'
+                            ? 'PROSITE pattern signatures; profiles use the profile route.'
+                            : source === 'profile'
+                                ? 'PROSITE profile signatures; patterns use the prosite route.'
+                                : 'Member-database signatures exposed through the InterPro entry API.',
+        })),
+        sourceUrls: [DOCUMENTATION_URL],
+    };
+}
+//# sourceMappingURL=reference.js.map

package/dist/services/interpro/reference.js.map

@@ -0,0 +1 @@
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package/dist/services/interpro/relationships.d.ts

@@ -0,0 +1,38 @@
+/**
+ * @fileoverview Deterministic, whole-record slices of a clan relationship graph.
+ * @module services/interpro/relationships
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+/** The graph InterPro attaches to set metadata: node and link records plus any additional fields. */
+export declare const RelationshipGraphSchema: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+    nodes: z.ZodArray<z.ZodJSONSchema>;
+    links: z.ZodArray<z.ZodJSONSchema>;
+}, z.core.$catchall<z.ZodJSONSchema>>>>;
+/** A relationship graph as supplied, or null/absent when InterPro supplied none. */
+type RelationshipGraph = z.infer<typeof RelationshipGraphSchema>;
+/**
+ * Order nodes by accession and links by source, target, and method, so an offset addresses the
+ * same record on every call whatever order the upstream arrays arrive in.
+ */
+export declare function orderRelationships(graph: RelationshipGraph): RelationshipGraph;
+/**
+ * The `count` whole records starting at `offset` in the sequence of every node followed by every
+ * link, as a graph of the upstream shape, with the page block that locates it.
+ */
+export declare function sliceRelationships(graph: RelationshipGraph, offset: number, count: number): {
+    relationships: {
+        nodes: z.JSONType[];
+        links: z.JSONType[];
+    } | null | undefined;
+    page: {
+        totalNodes: number;
+        totalLinks: number;
+        offset: number;
+        returnedNodes: number;
+        returnedLinks: number;
+        hasMore: boolean;
+        nextOffset?: number;
+    };
+};
+export {};
+//# sourceMappingURL=relationships.d.ts.map

package/dist/services/interpro/relationships.d.ts.map

@@ -0,0 +1 @@
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package/dist/services/interpro/relationships.js

@@ -0,0 +1,70 @@
+/**
+ * @fileoverview Deterministic, whole-record slices of a clan relationship graph.
+ * @module services/interpro/relationships
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { compareText, cursorScope } from './cursors.js';
+import { JsonValueSchema } from './schemas.js';
+/** The graph InterPro attaches to set metadata: node and link records plus any additional fields. */
+export const RelationshipGraphSchema = z
+    .object({ nodes: z.array(JsonValueSchema), links: z.array(JsonValueSchema) })
+    .catchall(JsonValueSchema)
+    .nullable()
+    .optional();
+const field = (record, key) => {
+    if (!record || typeof record !== 'object' || Array.isArray(record))
+        return '';
+    const value = record[key];
+    return typeof value === 'string' ? value : '';
+};
+/** Sort by the named string fields in turn; canonical JSON breaks any remaining tie. */
+function ordered(records, keys) {
+    return records.toSorted((a, b) => {
+        for (const key of keys) {
+            const difference = compareText(field(a, key), field(b, key));
+            if (difference)
+                return difference;
+        }
+        return compareText(cursorScope(a), cursorScope(b));
+    });
+}
+/**
+ * Order nodes by accession and links by source, target, and method, so an offset addresses the
+ * same record on every call whatever order the upstream arrays arrive in.
+ */
+export function orderRelationships(graph) {
+    return (graph && {
+        ...graph,
+        nodes: ordered(graph.nodes, ['accession']),
+        links: ordered(graph.links, ['source', 'target', 'method']),
+    });
+}
+/**
+ * The `count` whole records starting at `offset` in the sequence of every node followed by every
+ * link, as a graph of the upstream shape, with the page block that locates it.
+ */
+export function sliceRelationships(graph, offset, count) {
+    const nodes = graph?.nodes ?? [];
+    const links = graph?.links ?? [];
+    const total = nodes.length + links.length;
+    const start = Math.min(offset, total);
+    const end = Math.min(start + count, total);
+    const slice = {
+        nodes: nodes.slice(Math.min(start, nodes.length), Math.min(end, nodes.length)),
+        links: links.slice(Math.max(0, start - nodes.length), Math.max(0, end - nodes.length)),
+    };
+    const hasMore = end < total;
+    return {
+        relationships: graph && { ...graph, ...slice },
+        page: {
+            totalNodes: nodes.length,
+            totalLinks: links.length,
+            offset,
+            returnedNodes: slice.nodes.length,
+            returnedLinks: slice.links.length,
+            hasMore,
+            ...(hasMore ? { nextOffset: end } : {}),
+        },
+    };
+}
+//# sourceMappingURL=relationships.js.map

package/dist/services/interpro/relationships.js.map

@@ -0,0 +1 @@
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package/dist/services/interpro/routing.d.ts

@@ -0,0 +1,24 @@
+import { type SourceDatabase } from './schemas.js';
+/** Canonical API origin; no upstream continuation URL is fetched directly. */
+export declare const API_BASE = "https://www.ebi.ac.uk/interpro/api/";
+/** Official reference documentation. */
+export declare const DOCUMENTATION_URL = "https://interpro-documentation.readthedocs.io/en/latest/api.html";
+/** Routing patterns and examples are shared with the reference vocabulary. */
+export declare const ENTRY_ROUTES: readonly {
+    source: SourceDatabase;
+    pattern: RegExp;
+    example: string;
+}[];
+/** Resolve one entry accession without guessing alternate databases after a miss. */
+export declare function resolveEntry(accession: string, sourceDatabase?: SourceDatabase): {
+    accession: string;
+    sourceDatabase: SourceDatabase;
+};
+/** Resolve case-sensitive CL clan prefixes, with explicit source disambiguation. */
+export declare function resolveClan(accession: string, sourceDatabase?: 'pfam' | 'cdd' | 'pirsf'): {
+    accession: string;
+    sourceDatabase: 'pfam' | 'cdd' | 'pirsf';
+};
+/** Build fixed-origin requests from independently validated, encoded path segments. */
+export declare function apiUrl(segments: readonly string[], query?: Readonly<Record<string, string | number | boolean | undefined>>): string;
+//# sourceMappingURL=routing.d.ts.map

package/dist/services/interpro/routing.d.ts.map

@@ -0,0 +1 @@
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package/dist/services/interpro/routing.js

@@ -0,0 +1,106 @@
+/**
+ * @fileoverview Validated accession routing and fixed-origin InterPro URLs.
+ * @module services/interpro/routing
+ */
+import { notFound, validationError } from '@cyanheads/mcp-ts-core/errors';
+import { AccessionSchema } from './schemas.js';
+/** Canonical API origin; no upstream continuation URL is fetched directly. */
+export const API_BASE = 'https://www.ebi.ac.uk/interpro/api/';
+/** Official reference documentation. */
+export const DOCUMENTATION_URL = 'https://interpro-documentation.readthedocs.io/en/latest/api.html';
+/** Routing patterns and examples are shared with the reference vocabulary. */
+export const ENTRY_ROUTES = [
+    { source: 'interpro', pattern: /^IPR\d{6}$/i, example: 'IPR011615' },
+    { source: 'pfam', pattern: /^PF\d{5}$/i, example: 'PF00870' },
+    { source: 'prosite', pattern: /^PS00\d{3}$/i, example: 'PS00107' },
+    { source: 'profile', pattern: /^PS5\d{4}$/i, example: 'PS50011' },
+    { source: 'smart', pattern: /^SM\d{5}$/i, example: 'SM00220' },
+    { source: 'cdd', pattern: /^cd\d+$/i, example: 'cd08367' },
+    { source: 'panther', pattern: /^PTHR\d+(?::SF\d+)?$/i, example: 'PTHR11447' },
+    { source: 'cathgene3d', pattern: /^G3DSA:\d+\.\d+\.\d+\.\d+$/i, example: 'G3DSA:3.30.200.20' },
+    { source: 'ssf', pattern: /^SSF\d+$/i, example: 'SSF56112' },
+    { source: 'ncbifam', pattern: /^(?:TIGR|NF)\d+$/i, example: 'TIGR00001' },
+    { source: 'hamap', pattern: /^MF_\d+$/i, example: 'MF_00001' },
+    { source: 'prints', pattern: /^PR\d+$/i, example: 'PR00386' },
+    { source: 'pirsf', pattern: /^PIRSF\d+$/i, example: 'PIRSF000047' },
+    { source: 'sfld', pattern: /^SFLD[A-Z]?\d+$/i, example: 'SFLDF00001' },
+    { source: 'antifam', pattern: /^ANF\d+$/i, example: 'ANF00001' },
+];
+/** Pfam clan (`CL`) and CDD superfamily (`cl`) accessions name sets, never entries. */
+const CLAN_PATTERN = /^cl\d+$/i;
+/** Resolve one entry accession without guessing alternate databases after a miss. */
+export function resolveEntry(accession, sourceDatabase) {
+    const safe = AccessionSchema.parse(accession);
+    if (CLAN_PATTERN.test(safe))
+        throw notFound(`${safe} is a set accession, not an entry accession.`, {
+            reason: 'entry_not_found',
+            retryable: false,
+            accession: safe,
+            recovery: {
+                hint: 'Call interpro_get_clan with this accession to read the set and its member entries.',
+            },
+        });
+    const inferred = ENTRY_ROUTES.find((route) => route.pattern.test(safe))?.source;
+    if (inferred && sourceDatabase && inferred !== sourceDatabase)
+        throw validationError(`Accession ${safe} routes to sourceDatabase ${inferred} by its prefix, not ${sourceDatabase}.`, {
+            reason: 'database_mismatch',
+            retryable: false,
+            accession: safe,
+            sourceDatabase,
+            inferredSourceDatabase: inferred,
+        });
+    const source = sourceDatabase ?? inferred;
+    if (!source)
+        throw validationError(`Accession ${safe} matches no standard prefix, and no sourceDatabase was supplied.`, { reason: 'accession_source_unknown', retryable: false, accession: safe });
+    return {
+        accession: inferred ? (source === 'cdd' ? safe.toLowerCase() : safe.toUpperCase()) : safe,
+        sourceDatabase: source,
+    };
+}
+/** Resolve case-sensitive CL clan prefixes, with explicit source disambiguation. */
+export function resolveClan(accession, sourceDatabase) {
+    const safe = AccessionSchema.parse(accession);
+    const isCl = CLAN_PATTERN.test(safe);
+    const isPirsf = /^PIRSF\d+$/i.test(safe);
+    const inferred = /^CL\d+$/.test(safe)
+        ? 'pfam'
+        : /^cl\d+$/.test(safe)
+            ? 'cdd'
+            : isPirsf
+                ? 'pirsf'
+                : undefined;
+    if ((isPirsf && sourceDatabase && sourceDatabase !== 'pirsf') ||
+        (isCl && sourceDatabase === 'pirsf'))
+        throw validationError(`Set accession ${safe} routes to sourceDatabase ${inferred ?? 'pfam or cdd'} by its prefix, not ${sourceDatabase}.`, {
+            reason: 'database_mismatch',
+            retryable: false,
+            accession: safe,
+            sourceDatabase,
+            ...(inferred ? { inferredSourceDatabase: inferred } : {}),
+        });
+    const source = sourceDatabase ?? inferred;
+    if (!source)
+        throw validationError(isCl
+            ? `Set accession ${safe} has a mixed-case CL prefix, which can name a Pfam or CDD set, and no sourceDatabase was supplied.`
+            : `Set accession ${safe} matches no set prefix, and no sourceDatabase was supplied.`, { reason: 'accession_source_unknown', retryable: false, accession: safe });
+    return {
+        accession: isCl
+            ? source === 'cdd'
+                ? safe.toLowerCase()
+                : safe.toUpperCase()
+            : inferred
+                ? safe.toUpperCase()
+                : safe,
+        sourceDatabase: source,
+    };
+}
+/** Build fixed-origin requests from independently validated, encoded path segments. */
+export function apiUrl(segments, query = {}) {
+    const path = segments.map((part) => encodeURIComponent(AccessionSchema.parse(part))).join('/');
+    const url = new URL(`${path}${path ? '/' : ''}`, API_BASE);
+    for (const [key, value] of Object.entries(query))
+        if (value !== undefined)
+            url.searchParams.set(key, String(value));
+    return url.href;
+}
+//# sourceMappingURL=routing.js.map

package/dist/services/interpro/routing.js.map

@@ -0,0 +1 @@
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package/dist/services/interpro/schemas.d.ts

@@ -0,0 +1,192 @@
+/**
+ * @fileoverview Lossless InterPro wire schemas and shared input vocabulary.
+ * @module services/interpro/schemas
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+/** JSON values retained verbatim from upstream records. */
+export declare const JsonValueSchema: z.ZodJSONSchema;
+/** An upstream object with every additional JSON field retained. */
+export declare const JsonObjectSchema: z.ZodRecord<z.ZodString, z.ZodJSONSchema>;
+/** Supported entry API routes, including separate PROSITE pattern and profile routes. */
+export declare const SourceDatabaseSchema: z.ZodEnum<{
+    antifam: "antifam";
+    cathgene3d: "cathgene3d";
+    cdd: "cdd";
+    hamap: "hamap";
+    interpro: "interpro";
+    ncbifam: "ncbifam";
+    panther: "panther";
+    pfam: "pfam";
+    pirsf: "pirsf";
+    prints: "prints";
+    profile: "profile";
+    prosite: "prosite";
+    sfld: "sfld";
+    smart: "smart";
+    ssf: "ssf";
+}>;
+/** Entry annotation categories. */
+export declare const EntryTypeSchema: z.ZodEnum<{
+    active_site: "active_site";
+    binding_site: "binding_site";
+    coiled_coil: "coiled_coil";
+    conserved_site: "conserved_site";
+    disordered: "disordered";
+    domain: "domain";
+    family: "family";
+    homologous_superfamily: "homologous_superfamily";
+    ptm: "ptm";
+    region: "region";
+    repeat: "repeat";
+}>;
+/** A validated database route. */
+export type SourceDatabase = z.infer<typeof SourceDatabaseSchema>;
+/** Form clients may submit blank optional strings. */
+export declare const optionalString: <T extends z.ZodType>(schema: T) => z.ZodPreprocess<z.ZodOptional<T>, unknown>;
+/** A blank string takes the `.default()` that `schema` declares, as an omitted one does. */
+export declare const defaultedString: <T extends z.ZodType>(schema: T) => z.ZodPreprocess<T, unknown>;
+/** Safe identifiers are encoded as a single path segment after validation. */
+export declare const AccessionSchema: z.ZodString;
+/**
+ * Whether an upstream value is exactly an accession, the only form server-written text may name
+ * it in. The schema trims, so a value padded with blank lines must not pass as one.
+ */
+export declare const isAccession: (value: unknown) => value is string;
+/** Canonical UniProt accessions exclude isoform suffixes. */
+export declare const ProteinAccessionSchema: z.ZodString;
+/** GO annotation returned by InterPro. */
+export declare const GoTermSchema: 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>>;
+/** Sparse list metadata; only routing fields are required. */
+export declare const EntrySummarySchema: 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.$catchall<z.ZodJSONSchema>>;
+/** Detail metadata differs from summary metadata: names are objects. */
+export declare const EntryMetadataSchema: z.ZodObject<{
+    accession: z.ZodString;
+    source_database: z.ZodString;
+    name: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+        name: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        short: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>>;
+}, z.core.$catchall<z.ZodJSONSchema>>;
+/** Detail-only output adds readable text without changing upstream description fields. */
+export declare const EntryDetailMetadataSchema: z.ZodObject<{
+    accession: z.ZodString;
+    source_database: z.ZodString;
+    name: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+        name: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        short: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>>;
+    descriptionText: z.ZodOptional<z.ZodString>;
+}, z.core.$catchall<z.ZodJSONSchema>>;
+/** Complete location fragments retain discontinuity and arbitrary annotations. */
+export declare const LocationSchema: z.ZodObject<{
+    fragments: z.ZodArray<z.ZodObject<{
+        start: z.ZodNumber;
+        end: z.ZodNumber;
+        'dc-status': z.ZodOptional<z.ZodString>;
+    }, z.core.$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.$catchall<z.ZodJSONSchema>>;
+/** Protein metadata preserves omitted annotations and additional source fields. */
+export declare const ProteinMetadataSchema: z.ZodObject<{
+    accession: z.ZodString;
+    length: z.ZodNumber;
+    source_database: z.ZodString;
+    name: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    gene: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    source_organism: z.ZodOptional<z.ZodObject<{
+        taxId: z.ZodUnion<readonly [z.ZodString, z.ZodNumber]>;
+        scientificName: z.ZodString;
+        fullName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>>;
+}, z.core.$catchall<z.ZodJSONSchema>>;
+/** Protein match rows retain complete nested source records. */
+export declare const MatchSchema: z.ZodObject<{
+    metadata: z.ZodObject<{
+        accession: z.ZodString;
+        source_database: z.ZodString;
+        name: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        type: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        integrated: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        member_databases: z.ZodOptional<z.ZodNullable<z.ZodRecord<z.ZodString, z.ZodRecord<z.ZodString, z.ZodString>>>>;
+        go_terms: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodObject<{
+            identifier: z.ZodString;
+            name: z.ZodString;
+            category: z.ZodObject<{
+                code: z.ZodString;
+                name: z.ZodString;
+            }, z.core.$catchall<z.ZodJSONSchema>>;
+        }, z.core.$catchall<z.ZodJSONSchema>>>>>;
+    }, z.core.$catchall<z.ZodJSONSchema>>;
+    proteins: z.ZodArray<z.ZodObject<{
+        accession: z.ZodString;
+        entry_protein_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.$catchall<z.ZodJSONSchema>>>;
+}, z.core.$catchall<z.ZodJSONSchema>>;
+/** Feature-keyed extra annotations, not a protein detail envelope. */
+export declare const ExtraFeaturesSchema: 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.$catchall<z.ZodJSONSchema>>>;
+/** Standard list envelope; callers select the operation-specific row schema. */
+export declare const listSchema: <T extends z.ZodType>(row: T) => z.ZodObject<{
+    count: z.ZodNumber;
+    next: z.ZodNullable<z.ZodString>;
+    previous: z.ZodNullable<z.ZodString>;
+    results: z.ZodArray<T>;
+}, z.core.$catchall<z.ZodJSONSchema>>;
+/** Detail response envelope. */
+export declare const detailSchema: <T extends z.ZodType>(metadata: T) => z.ZodObject<{
+    metadata: T;
+}, z.core.$catchall<z.ZodJSONSchema>>;
+/** Server-owned page metadata. */
+export declare const PageSchema: z.ZodObject<{
+    total: z.ZodNumber;
+    returned: z.ZodNumber;
+    limit: z.ZodNumber;
+    hasMore: z.ZodBoolean;
+    nextCursor: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>;
+//# sourceMappingURL=schemas.d.ts.map

package/dist/services/interpro/schemas.d.ts.map

@@ -0,0 +1 @@
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