@cyanheads/interpro-mcp-server 0.1.2 → 0.2.0

package/dist/services/interpro/http-adapter.js

@@ -1,17 +1,31 @@
 /**
- * @fileoverview Bounded HTTP/1.1 adapter for InterPro's malformed bodyless 204 responses.
+ * @fileoverview Bounded HTTP/1.1 adapter for InterPro's malformed bodyless 204 responses, also
+ * carrying the Matches API and Job Dispatcher requests on the same fixed origin.
  * @module services/interpro/http-adapter
  */
 import { request } from 'node:https';
-import { serviceUnavailable, timeout } from '@cyanheads/mcp-ts-core/errors';
+import { JsonRpcErrorCode, serviceUnavailable, timeout, } from '@cyanheads/mcp-ts-core/errors';
+import { httpErrorFromResponse } from '@cyanheads/mcp-ts-core/utils';
 import { API_BASE } from './routing.js';
 /** Maximum decoded response size, shared by native and injected transports. */
 export const MAX_RESPONSE_BYTES = 4 * 1024 * 1024;
-/** Collect one response without following redirects or retaining malformed connections. */
-export const interproHttpFetch = (url, init) => new Promise((resolve, reject) => {
+/**
+ * The documented path prefixes on the fixed origin: the InterPro API, the InterPro Matches API,
+ * and the Job Dispatcher's InterProScan 6 service. The URL parser resolves dot segments first.
+ */
+const ALLOWED_PATH_PREFIXES = [
+    '/interpro/api/',
+    '/interpro/matches/api/',
+    '/Tools/services/rest/iprscan6/',
+];
+/**
+ * Collect one response without following redirects or retaining malformed connections, failing
+ * as `upstream_timeout` when the whole response outlasts `attemptMs`.
+ */
+const collect = (url, init, attemptMs) => new Promise((resolve, reject) => {
     const target = new URL(url);
     if (target.origin !== new URL(API_BASE).origin ||
-        !target.pathname.startsWith('/interpro/api/')) {
+        !ALLOWED_PATH_PREFIXES.some((prefix) => target.pathname.startsWith(prefix))) {
         reject(serviceUnavailable('InterPro request left the fixed API origin.', {
             reason: 'upstream_rejected',
             retryable: false,
@@ -39,13 +53,26 @@ export const interproHttpFetch = (url, init) => new Promise((resolve, reject) =>
     const timer = setTimeout(() => fail(timeout('InterPro response exceeded its attempt deadline.', {
         reason: 'upstream_timeout',
         retryable: true,
-    })), 15_000);
+    })), attemptMs);
     const connectionOptions = { ALPNProtocols: ['http/1.1'] };
+    const body = typeof init.body === 'string' ? init.body : undefined;
+    const requestHeaders = new Headers(init.headers);
+    const accept = requestHeaders.get('accept') ?? 'application/json';
+    const contentType = requestHeaders.get('content-type');
     const req = request(target, {
         ...connectionOptions,
-        method: 'GET',
+        method: body === undefined ? 'GET' : 'POST',
         agent: false,
-        headers: { Accept: 'application/json', 'Accept-Encoding': 'identity' },
+        headers: {
+            Accept: accept,
+            'Accept-Encoding': 'identity',
+            ...(body === undefined
+                ? {}
+                : {
+                    'Content-Type': contentType ?? 'application/json',
+                    'Content-Length': String(Buffer.byteLength(body, 'utf8')),
+                }),
+        },
     });
     req.on('error', (cause) => fail(serviceUnavailable('InterPro connection failed.', { reason: 'upstream_unavailable', retryable: true }, { cause })));
     req.on('close', () => {
@@ -128,7 +155,38 @@ export const interproHttpFetch = (url, init) => new Promise((resolve, reject) =>
     signal?.addEventListener('abort', abort, { once: true });
     if (signal?.aborted)
         abort();
-    else
+    else if (body === undefined)
         req.end();
+    else
+        req.end(body);
 });
+/**
+ * Classify a non-OK upstream response: 5xx (except 501), 408, and 429 are retryable; any other
+ * client status is reported as a non-retryable service failure, not a caller error.
+ */
+export async function upstreamStatusError(response, service) {
+    const status = response.status;
+    const reason = status === 408 || status === 504
+        ? 'upstream_timeout'
+        : status === 429
+            ? 'upstream_rate_limited'
+            : status >= 500
+                ? 'upstream_unavailable'
+                : 'upstream_rejected';
+    return await httpErrorFromResponse(response, {
+        service,
+        captureBody: false,
+        codeOverride: (value) => value < 500 && value !== 408 && value !== 429
+            ? JsonRpcErrorCode.ServiceUnavailable
+            : undefined,
+        data: {
+            reason,
+            retryable: (status >= 500 && status !== 501) || status === 408 || status === 429,
+        },
+    });
+}
+/** A transport whose whole-response backstop is `attemptMs`; callers bound attempts more tightly. */
+export const createInterproHttpFetch = (attemptMs) => (url, init) => collect(url, init, attemptMs);
+/** The InterPro API transport: small JSON pages, so 15 seconds bounds each whole response. */
+export const interproHttpFetch = createInterproHttpFetch(15_000);
 //# sourceMappingURL=http-adapter.js.map

package/dist/services/interpro/http-adapter.js.map

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package/dist/services/interpro/interpro-service.d.ts

@@ -15,7 +15,7 @@ export interface MissingRecord {
     readonly accession: string;
     /** A list scoped to the record: 204 is a valid empty page, so only 404 reports it missing. */
     readonly list?: boolean;
-    readonly reason: 'entry_not_found' | 'protein_not_found' | 'clan_not_found';
+    readonly reason: 'entry_not_found' | 'protein_not_found' | 'clan_not_found' | 'structure_not_found';
     readonly sourceDatabase: string;
 }
 /** Domain status handling selected by the tool workflow. */

package/dist/services/interpro/interpro-service.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"interpro-service.d.ts","sourceRoot":"","sources":["../../../src/services/interpro/interpro-service.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAS3C,OAAO,EACL,KAAK,aAAa,EAInB,MAAM,mBAAmB,CAAC;AAU3B,4EAA4E;AAC5E,MAAM,WAAW,YAAY;IAC3B,QAAQ,CAAC,GAAG,EAAE,OAAO,CAAC;IACtB,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC;CAC3B;AACD,gGAAgG;AAChG,MAAM,WAAW,aAAa;IAC5B,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,8FAA8F;IAC9F,QAAQ,CAAC,IAAI,CAAC,EAAE,OAAO,CAAC;IACxB,QAAQ,CAAC,MAAM,EACX,iBAAiB,GACjB,mBAAmB,GACnB,gBAAgB,GAChB,qBAAqB,CAAC;IAC1B,QAAQ,CAAC,cAAc,EAAE,MAAM,CAAC;CACjC;AAwBD,4DAA4D;AAC5D,MAAM,WAAW,cAAc;IAC7B,QAAQ,CAAC,YAAY,CAAC,EAAE,OAAO,CAAC;IAChC,QAAQ,CAAC,OAAO,CAAC,EAAE,aAAa,CAAC;CAClC;AACD,sEAAsE;AACtE,MAAM,WAAW,gBAAgB,CAAC,CAAC;IACjC,QAAQ,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC;IACxB,QAAQ,CAAC,OAAO,EAAE,OAAO,CAAC;IAC1B,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;CAC5B;AAED,0FAA0F;AAC1F,qBAAa,eAAe;IACd,OAAO,CAAC,QAAQ,CAAC,KAAK;IAAlC,YAA6B,KAAK,GAAE,aAAiC,EAAI;IAEzE,kEAAkE;IAClE,KAAK,CAAC,GAAG,EAAE,OAAO,GAAG,YAAY,CAEhC;IAED,2FAA2F;IACrF,OAAO,CAAC,CAAC,SAAS,CAAC,CAAC,OAAO,EAC/B,IAAI,EAAE,YAAY,EAClB,QAAQ,EAAE,SAAS,MAAM,EAAE,EAC3B,KAAK,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,GAAG,OAAO,GAAG,SAAS,CAAC,CAAC,EACtE,MAAM,EAAE,CAAC,EACT,OAAO,GAAE,cAAmB,GAC3B,OAAO,CAAC,gBAAgB,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CA0JxC;IAED,kFAAkF;IAC5E,OAAO,CAAC,GAAG,EAAE,OAAO;;cA0CU,MAAM;;;;;;OAIzC;CACF;AAmCD,yDAAyD;AACzD,wBAAgB,mBAAmB,CAAC,KAAK,GAAE,aAAiC,GAAG,IAAI,CAElF;AACD,8CAA8C;AAC9C,wBAAgB,kBAAkB,IAAI,eAAe,CAGpD;AACD,8DAA8D;AAC9D,wBAAgB,sBAAsB,IAAI,IAAI,CAE7C"}

package/dist/services/interpro/interpro-service.js

@@ -1,7 +1,7 @@
 import { z } from '@cyanheads/mcp-ts-core';
-import { JsonRpcErrorCode, McpError, notFound, serviceUnavailable, timeout, validationError, } from '@cyanheads/mcp-ts-core/errors';
-import { createPacer, defaultIsTransient, httpErrorFromResponse, withRetry, } from '@cyanheads/mcp-ts-core/utils';
-import { interproHttpFetch, MAX_RESPONSE_BYTES } from './http-adapter.js';
+import { McpError, notFound, serviceUnavailable, timeout, validationError, } from '@cyanheads/mcp-ts-core/errors';
+import { createPacer, defaultIsTransient, withRetry } from '@cyanheads/mcp-ts-core/utils';
+import { interproHttpFetch, MAX_RESPONSE_BYTES, upstreamStatusError, } from './http-adapter.js';
 import { apiUrl } from './routing.js';
 import { isAccession, JsonObjectSchema, JsonValueSchema } from './schemas.js';
 const pacer = createPacer({
@@ -28,6 +28,7 @@ const RECORD_NOUNS = {
     entry_not_found: 'entry',
     clan_not_found: 'set',
     protein_not_found: 'protein',
+    structure_not_found: 'structure',
 };
 /** Name a record in a caller-facing message, e.g. `entry PF00870 in pfam`. */
 const describeRecord = ({ reason, accession, sourceDatabase }) => `${RECORD_NOUNS[reason]} ${accession} in ${sourceDatabase}`;
@@ -116,27 +117,8 @@ export class InterproService {
                         ...(missing ? { accession: missing.accession } : {}),
                     });
                 }
-                if (!response.ok) {
-                    const status = response.status;
-                    const reason = status === 408 || status === 504
-                        ? 'upstream_timeout'
-                        : status === 429
-                            ? 'upstream_rate_limited'
-                            : status >= 500
-                                ? 'upstream_unavailable'
-                                : 'upstream_rejected';
-                    throw await httpErrorFromResponse(response, {
-                        service: 'InterPro',
-                        captureBody: false,
-                        codeOverride: (value) => value < 500 && value !== 408 && value !== 429
-                            ? JsonRpcErrorCode.ServiceUnavailable
-                            : undefined,
-                        data: {
-                            reason,
-                            retryable: (status >= 500 && status !== 501) || status === 408 || status === 429,
-                        },
-                    });
-                }
+                if (!response.ok)
+                    throw await upstreamStatusError(response, 'InterPro');
                 const encoding = response.headers.get('content-encoding');
                 if (encoding && encoding.toLowerCase() !== 'identity')
                     throw serviceUnavailable('InterPro returned an unexpected content encoding.', {

package/dist/services/interpro/interpro-service.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"reference.d.ts","sourceRoot":"","sources":["../../../src/services/interpro/reference.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAK3C,4EAA4E;AAC5E,eAAO,MAAM,oBAAoB;;;;;;EAE2C,CAAC;AAC7E,yEAAyE;AACzE,eAAO,MAAM,mBAAmB;;;;;;;;iBAkBa,CAAC;AAC9C,kCAAkC;AAClC,MAAM,MAAM,aAAa,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC,CAAC;AA6EhE,4EAA4E;AAC5E,wBAAgB,eAAe,CAAC,KAAK,EAAE,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,EAAE,SAAS,CAAC,GAAG;IAChG,KAAK,EAAE,aAAa,EAAE,CAAC;IACvB,UAAU,EAAE,MAAM,EAAE,CAAC;CACtB,CAwCA"}

package/dist/services/interpro/reference.js

@@ -4,6 +4,7 @@
  */
 import { z } from '@cyanheads/mcp-ts-core';
 import { DOCUMENTATION_URL, ENTRY_ROUTES } from './routing.js';
+import { CHAIN_PATTERN, PDB_ID_PATTERN } from './structure-schemas.js';
 /** Available reference topics; only release performs network operations. */
 export const ReferenceTopicSchema = z
     .enum(['databases', 'entry_types', 'accession_patterns', 'taxa', 'release'])
@@ -15,7 +16,10 @@ export const ReferenceItemSchema = z
     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.'),
+    accessionPattern: z
+        .string()
+        .optional()
+        .describe('Accession routing pattern, case-insensitive except where the item description says otherwise.'),
     example: z
         .string()
         .optional()
@@ -80,6 +84,23 @@ const taxa = [
     ['3702', 'Arabidopsis'],
     ['562', 'Escherichia coli'],
 ];
+/** Structure identifiers, listed after the entry routes under accession_patterns. */
+const structureIdentifiers = [
+    {
+        id: 'pdb',
+        label: 'PDB entry',
+        accessionPattern: PDB_ID_PATTERN.source,
+        example: '1tsr',
+        description: 'Four-character structure ID for interpro_get_structure_domains, matched case-insensitively; extended pdb_0000… IDs are not supported.',
+    },
+    {
+        id: 'pdb_chain',
+        label: 'PDB chain',
+        accessionPattern: CHAIN_PATTERN.source,
+        example: 'A',
+        description: 'Case-sensitive chain ID within one PDB entry, one of its structure.chains; a and A are different chains.',
+    },
+];
 /** Return bounded local reference data without making upstream requests. */
 export function staticReference(topic) {
     if (topic === 'entry_types')
@@ -115,7 +136,7 @@ export function staticReference(topic) {
                             : source === 'profile'
                                 ? 'PROSITE profile signatures; patterns use the prosite route.'
                                 : 'Member-database signatures exposed through the InterPro entry API.',
-        })),
+        })).concat(topic === 'accession_patterns' ? structureIdentifiers : []),
         sourceUrls: [DOCUMENTATION_URL],
     };
 }

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

@@ -1 +1 @@
-{"version":3,"file":"reference.js","sourceRoot":"","sources":["../../../src/services/interpro/reference.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,EAAE,iBAAiB,EAAE,YAAY,EAAE,MAAM,cAAc,CAAC;AAG/D,4EAA4E;AAC5E,MAAM,CAAC,MAAM,oBAAoB,GAAG,CAAC;KAClC,IAAI,CAAC,CAAC,WAAW,EAAE,aAAa,EAAE,oBAAoB,EAAE,MAAM,EAAE,SAAS,CAAC,CAAC;KAC3E,QAAQ,CAAC,+DAA+D,CAAC,CAAC;AAC7E,yEAAyE;AACzE,MAAM,CAAC,MAAM,mBAAmB,GAAG,CAAC;KACjC,MAAM,CAAC;IACN,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;IAChD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;IACnD,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;IACpE,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;IAC1E,gBAAgB,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;IAC/F,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,2DAA2D,CAAC;IACxE,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;CACrE,CAAC;KACD,QAAQ,CAAC,gCAAgC,CAAC,CAAC;AAG9C,MAAM,cAAc,GAAmC;IACrD,QAAQ,EAAE,UAAU;IACpB,IAAI,EAAE,MAAM;IACZ,OAAO,EAAE,kBAAkB;IAC3B,OAAO,EAAE,kBAAkB;IAC3B,KAAK,EAAE,OAAO;IACd,GAAG,EAAE,KAAK;IACV,OAAO,EAAE,SAAS;IAClB,UAAU,EAAE,aAAa;IACzB,GAAG,EAAE,aAAa;IAClB,OAAO,EAAE,SAAS;IAClB,KAAK,EAAE,OAAO;IACd,MAAM,EAAE,QAAQ;IAChB,KAAK,EAAE,OAAO;IACd,IAAI,EAAE,MAAM;IACZ,OAAO,EAAE,SAAS;CACnB,CAAC;AACF,MAAM,KAAK,GAAG;IACZ,CAAC,QAAQ,EAAE,QAAQ,EAAE,mDAAmD,CAAC;IACzE,CAAC,QAAQ,EAAE,QAAQ,EAAE,6CAA6C,CAAC;IACnE,CAAC,QAAQ,EAAE,QAAQ,EAAE,yCAAyC,CAAC;IAC/D;QACE,wBAAwB;QACxB,wBAAwB;QACxB,wDAAwD;KACzD;IACD,CAAC,aAAa,EAAE,aAAa,EAAE,iCAAiC,CAAC;IACjE,CAAC,cAAc,EAAE,cAAc,EAAE,+BAA+B,CAAC;IACjE,CAAC,gBAAgB,EAAE,gBAAgB,EAAE,uCAAuC,CAAC;IAC7E,CAAC,KAAK,EAAE,iCAAiC,EAAE,yCAAyC,CAAC;IACrF;QACE,QAAQ;QACR,QAAQ;QACR,sFAAsF;KACvF;IACD;QACE,aAAa;QACb,aAAa;QACb,mEAAmE;KACpE;IACD;QACE,YAAY;QACZ,mBAAmB;QACnB,iFAAiF;KAClF;CACO,CAAC;AACX,MAAM,IAAI,GAAG;IACX,CAAC,MAAM,EAAE,OAAO,CAAC;IACjB,CAAC,OAAO,EAAE,OAAO,CAAC;IAClB,CAAC,OAAO,EAAE,KAAK,CAAC;IAChB,CAAC,MAAM,EAAE,WAAW,CAAC;IACrB,CAAC,MAAM,EAAE,WAAW,CAAC;IACrB,CAAC,MAAM,EAAE,UAAU,CAAC;IACpB,CAAC,QAAQ,EAAE,eAAe,CAAC;IAC3B,CAAC,MAAM,EAAE,aAAa,CAAC;IACvB,CAAC,KAAK,EAAE,kBAAkB,CAAC;CACnB,CAAC;AACX,4EAA4E;AAC5E,MAAM,UAAU,eAAe,CAAC,KAA+D;IAI7F,IAAI,KAAK,KAAK,aAAa;QACzB,OAAO;YACL,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,KAAK,EAAE,WAAW,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,KAAK,EAAE,WAAW,EAAE,CAAC,CAAC;YAC5E,UAAU,EAAE,CAAC,iBAAiB,CAAC;SAChC,CAAC;IACJ,IAAI,KAAK,KAAK,MAAM;QAClB,OAAO;YACL,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,OAAO,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CAAC;gBACrC,EAAE,EAAE,OAAO;gBACX,KAAK;gBACL,OAAO;gBACP,WAAW,EAAE,8DAA8D;aAC5E,CAAC,CAAC;YACH,UAAU,EAAE,CAAC,iBAAiB,EAAE,uCAAuC,CAAC;SACzE,CAAC;IACJ,OAAO;QACL,KAAK,EAAE,YAAY,CAAC,GAAG,CAAC,CAAC,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,EAAE,EAAE,CAAC,CAAC;YACzD,EAAE,EAAE,MAAM;YACV,KAAK,EAAE,cAAc,CAAC,MAAM,CAAC;YAC7B,cAAc,EAAE,MAAM;YACtB,gBAAgB,EAAE,OAAO,CAAC,MAAM;YAChC,OAAO;YACP,WAAW,EACT,KAAK,KAAK,oBAAoB;gBAC5B,CAAC,CAAC,kEAAkE;gBACpE,CAAC,CAAC,MAAM,KAAK,UAAU;oBACrB,CAAC,CAAC,mDAAmD;oBACrD,CAAC,CAAC,MAAM,KAAK,SAAS;wBACpB,CAAC,CAAC,yDAAyD;wBAC3D,CAAC,CAAC,MAAM,KAAK,SAAS;4BACpB,CAAC,CAAC,6DAA6D;4BAC/D,CAAC,CAAC,MAAM,KAAK,SAAS;gCACpB,CAAC,CAAC,6DAA6D;gCAC/D,CAAC,CAAC,oEAAoE;SACnF,CAAC,CAAC;QACH,UAAU,EAAE,CAAC,iBAAiB,CAAC;KAChC,CAAC;AACJ,CAAC"}
+{"version":3,"file":"reference.js","sourceRoot":"","sources":["../../../src/services/interpro/reference.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,EAAE,iBAAiB,EAAE,YAAY,EAAE,MAAM,cAAc,CAAC;AAE/D,OAAO,EAAE,aAAa,EAAE,cAAc,EAAE,MAAM,wBAAwB,CAAC;AAEvE,4EAA4E;AAC5E,MAAM,CAAC,MAAM,oBAAoB,GAAG,CAAC;KAClC,IAAI,CAAC,CAAC,WAAW,EAAE,aAAa,EAAE,oBAAoB,EAAE,MAAM,EAAE,SAAS,CAAC,CAAC;KAC3E,QAAQ,CAAC,+DAA+D,CAAC,CAAC;AAC7E,yEAAyE;AACzE,MAAM,CAAC,MAAM,mBAAmB,GAAG,CAAC;KACjC,MAAM,CAAC;IACN,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;IAChD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;IACnD,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;IACpE,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;IAC1E,gBAAgB,EAAE,CAAC;SAChB,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,+FAA+F,CAChG;IACH,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,2DAA2D,CAAC;IACxE,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;CACrE,CAAC;KACD,QAAQ,CAAC,gCAAgC,CAAC,CAAC;AAG9C,MAAM,cAAc,GAAmC;IACrD,QAAQ,EAAE,UAAU;IACpB,IAAI,EAAE,MAAM;IACZ,OAAO,EAAE,kBAAkB;IAC3B,OAAO,EAAE,kBAAkB;IAC3B,KAAK,EAAE,OAAO;IACd,GAAG,EAAE,KAAK;IACV,OAAO,EAAE,SAAS;IAClB,UAAU,EAAE,aAAa;IACzB,GAAG,EAAE,aAAa;IAClB,OAAO,EAAE,SAAS;IAClB,KAAK,EAAE,OAAO;IACd,MAAM,EAAE,QAAQ;IAChB,KAAK,EAAE,OAAO;IACd,IAAI,EAAE,MAAM;IACZ,OAAO,EAAE,SAAS;CACnB,CAAC;AACF,MAAM,KAAK,GAAG;IACZ,CAAC,QAAQ,EAAE,QAAQ,EAAE,mDAAmD,CAAC;IACzE,CAAC,QAAQ,EAAE,QAAQ,EAAE,6CAA6C,CAAC;IACnE,CAAC,QAAQ,EAAE,QAAQ,EAAE,yCAAyC,CAAC;IAC/D;QACE,wBAAwB;QACxB,wBAAwB;QACxB,wDAAwD;KACzD;IACD,CAAC,aAAa,EAAE,aAAa,EAAE,iCAAiC,CAAC;IACjE,CAAC,cAAc,EAAE,cAAc,EAAE,+BAA+B,CAAC;IACjE,CAAC,gBAAgB,EAAE,gBAAgB,EAAE,uCAAuC,CAAC;IAC7E,CAAC,KAAK,EAAE,iCAAiC,EAAE,yCAAyC,CAAC;IACrF;QACE,QAAQ;QACR,QAAQ;QACR,sFAAsF;KACvF;IACD;QACE,aAAa;QACb,aAAa;QACb,mEAAmE;KACpE;IACD;QACE,YAAY;QACZ,mBAAmB;QACnB,iFAAiF;KAClF;CACO,CAAC;AACX,MAAM,IAAI,GAAG;IACX,CAAC,MAAM,EAAE,OAAO,CAAC;IACjB,CAAC,OAAO,EAAE,OAAO,CAAC;IAClB,CAAC,OAAO,EAAE,KAAK,CAAC;IAChB,CAAC,MAAM,EAAE,WAAW,CAAC;IACrB,CAAC,MAAM,EAAE,WAAW,CAAC;IACrB,CAAC,MAAM,EAAE,UAAU,CAAC;IACpB,CAAC,QAAQ,EAAE,eAAe,CAAC;IAC3B,CAAC,MAAM,EAAE,aAAa,CAAC;IACvB,CAAC,KAAK,EAAE,kBAAkB,CAAC;CACnB,CAAC;AACX,qFAAqF;AACrF,MAAM,oBAAoB,GAAoB;IAC5C;QACE,EAAE,EAAE,KAAK;QACT,KAAK,EAAE,WAAW;QAClB,gBAAgB,EAAE,cAAc,CAAC,MAAM;QACvC,OAAO,EAAE,MAAM;QACf,WAAW,EACT,uIAAuI;KAC1I;IACD;QACE,EAAE,EAAE,WAAW;QACf,KAAK,EAAE,WAAW;QAClB,gBAAgB,EAAE,aAAa,CAAC,MAAM;QACtC,OAAO,EAAE,GAAG;QACZ,WAAW,EACT,0GAA0G;KAC7G;CACF,CAAC;AACF,4EAA4E;AAC5E,MAAM,UAAU,eAAe,CAAC,KAA+D;IAI7F,IAAI,KAAK,KAAK,aAAa;QACzB,OAAO;YACL,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,KAAK,EAAE,WAAW,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE,EAAE,KAAK,EAAE,WAAW,EAAE,CAAC,CAAC;YAC5E,UAAU,EAAE,CAAC,iBAAiB,CAAC;SAChC,CAAC;IACJ,IAAI,KAAK,KAAK,MAAM;QAClB,OAAO;YACL,KAAK,EAAE,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,OAAO,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CAAC;gBACrC,EAAE,EAAE,OAAO;gBACX,KAAK;gBACL,OAAO;gBACP,WAAW,EAAE,8DAA8D;aAC5E,CAAC,CAAC;YACH,UAAU,EAAE,CAAC,iBAAiB,EAAE,uCAAuC,CAAC;SACzE,CAAC;IACJ,OAAO;QACL,KAAK,EAAE,YAAY,CAAC,GAAG,CACrB,CAAC,EAAE,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,EAAiB,EAAE,CAAC,CAAC;YAChD,EAAE,EAAE,MAAM;YACV,KAAK,EAAE,cAAc,CAAC,MAAM,CAAC;YAC7B,cAAc,EAAE,MAAM;YACtB,gBAAgB,EAAE,OAAO,CAAC,MAAM;YAChC,OAAO;YACP,WAAW,EACT,KAAK,KAAK,oBAAoB;gBAC5B,CAAC,CAAC,kEAAkE;gBACpE,CAAC,CAAC,MAAM,KAAK,UAAU;oBACrB,CAAC,CAAC,mDAAmD;oBACrD,CAAC,CAAC,MAAM,KAAK,SAAS;wBACpB,CAAC,CAAC,yDAAyD;wBAC3D,CAAC,CAAC,MAAM,KAAK,SAAS;4BACpB,CAAC,CAAC,6DAA6D;4BAC/D,CAAC,CAAC,MAAM,KAAK,SAAS;gCACpB,CAAC,CAAC,6DAA6D;gCAC/D,CAAC,CAAC,oEAAoE;SACnF,CAAC,CACH,CAAC,MAAM,CAAC,KAAK,KAAK,oBAAoB,CAAC,CAAC,CAAC,oBAAoB,CAAC,CAAC,CAAC,EAAE,CAAC;QACpE,UAAU,EAAE,CAAC,iBAAiB,CAAC;KAChC,CAAC;AACJ,CAAC"}

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

@@ -122,6 +122,7 @@ export declare const ProteinMetadataSchema: z.ZodObject<{
         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>>;
 /** Protein match rows retain complete nested source records. */
 export declare const MatchSchema: z.ZodObject<{
@@ -170,6 +171,21 @@ export declare const ExtraFeaturesSchema: z.ZodRecord<z.ZodString, z.ZodObject<{
         score: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
     }, z.core.$catchall<z.ZodJSONSchema>>>;
 }, z.core.$catchall<z.ZodJSONSchema>>>;
+/** Separate residue-rule annotations retain complete provenance and location records. */
+export declare const ResidueAnnotationsSchema: 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;

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

@@ -1 +1 @@
-{"version":3,"file":"schemas.d.ts","sourceRoot":"","sources":["../../../src/services/interpro/schemas.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,2DAA2D;AAC3D,eAAO,MAAM,eAAe,iBAAiD,CAAC;AAC9E,oEAAoE;AACpE,eAAO,MAAM,gBAAgB,2CAEgB,CAAC;AAC9C,yFAAyF;AACzF,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;EAkBe,CAAC;AACjD,mCAAmC;AACnC,eAAO,MAAM,eAAe;;;;;;;;;;;;EAcS,CAAC;AACtC,kCAAkC;AAClC,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAIlE,sDAAsD;AACtD,eAAO,MAAM,cAAc,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,UAAU,CAAC,+CACjB,CAAC;AAC7C,4FAA4F;AAC5F,eAAO,MAAM,eAAe,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,UAAU,CAAC,gCAAoC,CAAC;AACnG,8EAA8E;AAC9E,eAAO,MAAM,eAAe,aAOyC,CAAC;AACtE;;;GAGG;AACH,eAAO,MAAM,WAAW,UAAW,OAAO,KAAG,KAAK,IAAI,MACwB,CAAC;AAC/E,6DAA6D;AAC7D,eAAO,MAAM,sBAAsB,aAIyD,CAAC;AAC7F,0CAA0C;AAC1C,eAAO,MAAM,YAAY;;;;;;;qCAaI,CAAC;AAC9B,8DAA8D;AAC9D,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;qCAcH,CAAC;AAC7B,wEAAwE;AACxE,eAAO,MAAM,mBAAmB;;;;;;;qCAcJ,CAAC;AAC7B,0FAA0F;AAC1F,eAAO,MAAM,yBAAyB;;;;;;;;qCAOpC,CAAC;AACH,kFAAkF;AAClF,eAAO,MAAM,cAAc;;;;;;;;;qCAqBqB,CAAC;AACjD,mFAAmF;AACnF,eAAO,MAAM,qBAAqB;;;;;;;;;;;qCAsBN,CAAC;AAC7B,gEAAgE;AAChE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qCAmBI,CAAC;AAC7B,sEAAsE;AACtE,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;sCAS/B,CAAC;AACF,gFAAgF;AAChF,eAAO,MAAM,UAAU,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,OAAO,CAAC;;;;;qCAQxB,CAAC;AAC/B,gCAAgC;AAChC,eAAO,MAAM,YAAY,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,YAAY,CAAC;;qCACqC,CAAC;AACnG,kCAAkC;AAClC,eAAO,MAAM,UAAU;;;;;;iBAarB,CAAC"}
+{"version":3,"file":"schemas.d.ts","sourceRoot":"","sources":["../../../src/services/interpro/schemas.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,2DAA2D;AAC3D,eAAO,MAAM,eAAe,iBAAiD,CAAC;AAC9E,oEAAoE;AACpE,eAAO,MAAM,gBAAgB,2CAEgB,CAAC;AAC9C,yFAAyF;AACzF,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;EAkBe,CAAC;AACjD,mCAAmC;AACnC,eAAO,MAAM,eAAe;;;;;;;;;;;;EAcS,CAAC;AACtC,kCAAkC;AAClC,MAAM,MAAM,cAAc,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAIlE,sDAAsD;AACtD,eAAO,MAAM,cAAc,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,UAAU,CAAC,+CACjB,CAAC;AAC7C,4FAA4F;AAC5F,eAAO,MAAM,eAAe,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,UAAU,CAAC,gCAAoC,CAAC;AACnG,8EAA8E;AAC9E,eAAO,MAAM,eAAe,aAOyC,CAAC;AACtE;;;GAGG;AACH,eAAO,MAAM,WAAW,UAAW,OAAO,KAAG,KAAK,IAAI,MACwB,CAAC;AAC/E,6DAA6D;AAC7D,eAAO,MAAM,sBAAsB,aAIyD,CAAC;AAC7F,0CAA0C;AAC1C,eAAO,MAAM,YAAY;;;;;;;qCAaI,CAAC;AAC9B,8DAA8D;AAC9D,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;qCAcH,CAAC;AAC7B,wEAAwE;AACxE,eAAO,MAAM,mBAAmB;;;;;;;qCAcJ,CAAC;AAC7B,0FAA0F;AAC1F,eAAO,MAAM,yBAAyB;;;;;;;;qCAOpC,CAAC;AACH,kFAAkF;AAClF,eAAO,MAAM,cAAc;;;;;;;;;qCAqBqB,CAAC;AACjD,mFAAmF;AACnF,eAAO,MAAM,qBAAqB;;;;;;;;;;;;qCA6BN,CAAC;AAC7B,gEAAgE;AAChE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qCAmBI,CAAC;AAC7B,sEAAsE;AACtE,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;sCAS/B,CAAC;AACF,yFAAyF;AACzF,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;sCASpC,CAAC;AACF,gFAAgF;AAChF,eAAO,MAAM,UAAU,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,OAAO,CAAC;;;;;qCAQxB,CAAC;AAC/B,gCAAgC;AAChC,eAAO,MAAM,YAAY,GAAI,CAAC,SAAS,CAAC,CAAC,OAAO,YAAY,CAAC;;qCACqC,CAAC;AACnG,kCAAkC;AAClC,eAAO,MAAM,UAAU;;;;;;iBAarB,CAAC"}

package/dist/services/interpro/schemas.js

@@ -168,6 +168,11 @@ export const ProteinMetadataSchema = z
         .catchall(JsonValueSchema)
         .optional()
         .describe('Source organism.'),
+    proteome: z
+        .string()
+        .nullable()
+        .optional()
+        .describe('UniProt proteome accession, such as UP000000625; pass it as interpro_find_proteins_by_domain proteomeId with taxonId set to source_organism.taxId or an ancestor. Null when the protein belongs to no proteome.'),
 })
     .catchall(JsonValueSchema);
 /** Protein match rows retain complete nested source records. */
@@ -197,6 +202,14 @@ export const ExtraFeaturesSchema = z.record(z.string(), z
     locations: z.array(LocationSchema).describe('Feature locations.'),
 })
     .catchall(JsonValueSchema));
+/** Separate residue-rule annotations retain complete provenance and location records. */
+export const ResidueAnnotationsSchema = z.record(z.string(), z
+    .object({
+    accession: z.string().describe('Residue rule accession.'),
+    source_database: z.string().describe('Rule source database.'),
+    locations: z.array(LocationSchema).describe('Complete rule locations and residue fragments.'),
+})
+    .catchall(JsonValueSchema));
 /** Standard list envelope; callers select the operation-specific row schema. */
 export const listSchema = (row) => z
     .object({

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

@@ -1 +1 @@
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+{"version":3,"file":"schemas.js","sourceRoot":"","sources":["../../../src/services/interpro/schemas.ts"],"names":[],"mappings":"AAAA;;;GAGG;AACH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,2DAA2D;AAC3D,MAAM,CAAC,MAAM,eAAe,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC,CAAC;AAC9E,oEAAoE;AACpE,MAAM,CAAC,MAAM,gBAAgB,GAAG,CAAC;KAC9B,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,eAAe,CAAC;KACnC,QAAQ,CAAC,gCAAgC,CAAC,CAAC;AAC9C,yFAAyF;AACzF,MAAM,CAAC,MAAM,oBAAoB,GAAG,CAAC;KAClC,IAAI,CAAC;IACJ,UAAU;IACV,MAAM;IACN,SAAS;IACT,SAAS;IACT,OAAO;IACP,KAAK;IACL,SAAS;IACT,YAAY;IACZ,KAAK;IACL,SAAS;IACT,OAAO;IACP,QAAQ;IACR,OAAO;IACP,MAAM;IACN,SAAS;CACV,CAAC;KACD,QAAQ,CAAC,mCAAmC,CAAC,CAAC;AACjD,mCAAmC;AACnC,MAAM,CAAC,MAAM,eAAe,GAAG,CAAC;KAC7B,IAAI,CAAC;IACJ,QAAQ;IACR,QAAQ;IACR,QAAQ;IACR,wBAAwB;IACxB,aAAa;IACb,cAAc;IACd,gBAAgB;IAChB,KAAK;IACL,QAAQ;IACR,aAAa;IACb,YAAY;CACb,CAAC;KACD,QAAQ,CAAC,wBAAwB,CAAC,CAAC;AAGtC,6EAA6E;AAC7E,MAAM,SAAS,GAAG,CAAC,KAAc,EAAE,EAAE,CACnC,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,CAAC,IAAI,EAAE,KAAK,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK,CAAC;AACvE,sDAAsD;AACtD,MAAM,CAAC,MAAM,cAAc,GAAG,CAAsB,MAAS,EAAE,EAAE,CAC/D,CAAC,CAAC,UAAU,CAAC,SAAS,EAAE,MAAM,CAAC,QAAQ,EAAE,CAAC,CAAC;AAC7C,4FAA4F;AAC5F,MAAM,CAAC,MAAM,eAAe,GAAG,CAAsB,MAAS,EAAE,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC,SAAS,EAAE,MAAM,CAAC,CAAC;AACnG,8EAA8E;AAC9E,MAAM,CAAC,MAAM,eAAe,GAAG,CAAC;KAC7B,MAAM,EAAE;KACR,IAAI,EAAE;KACN,GAAG,CAAC,CAAC,CAAC;KACN,GAAG,CAAC,GAAG,CAAC;KACR,KAAK,CAAC,oBAAoB,CAAC;KAC3B,MAAM,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,KAAK,GAAG,IAAI,KAAK,KAAK,IAAI,EAAE,kCAAkC,CAAC;KACtF,QAAQ,CAAC,wDAAwD,CAAC,CAAC;AACtE;;;GAGG;AACH,MAAM,CAAC,MAAM,WAAW,GAAG,CAAC,KAAc,EAAmB,EAAE,CAC7D,OAAO,KAAK,KAAK,QAAQ,IAAI,eAAe,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,IAAI,KAAK,KAAK,CAAC;AAC/E,6DAA6D;AAC7D,MAAM,CAAC,MAAM,sBAAsB,GAAG,CAAC;KACpC,MAAM,EAAE;KACR,IAAI,EAAE;KACN,KAAK,CAAC,+EAA+E,CAAC;KACtF,QAAQ,CAAC,+EAA+E,CAAC,CAAC;AAC7F,0CAA0C;AAC1C,MAAM,CAAC,MAAM,YAAY,GAAG,CAAC;KAC1B,MAAM,CAAC;IACN,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;IACjD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;IAC1C,QAAQ,EAAE,CAAC;SACR,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;QAC9C,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;KAC/C,CAAC;SACD,QAAQ,CAAC,eAAe,CAAC;SACzB,QAAQ,CAAC,cAAc,CAAC;CAC5B,CAAC;KACD,QAAQ,CAAC,eAAe,CAAC;KACzB,QAAQ,CAAC,gBAAgB,CAAC,CAAC;AAC9B,8DAA8D;AAC9D,MAAM,CAAC,MAAM,kBAAkB,GAAG,CAAC;KAChC,MAAM,CAAC;IACN,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;IAClD,eAAe,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;IACjE,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;IAC5E,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;IAC5E,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;IACvF,gBAAgB,EAAE,CAAC;SAChB,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;SACpD,QAAQ,EAAE;SACV,QAAQ,EAAE;SACV,QAAQ,CAAC,wCAAwC,CAAC;IACrD,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;CAChG,CAAC;KACD,QAAQ,CAAC,eAAe,CAAC,CAAC;AAC7B,wEAAwE;AACxE,MAAM,CAAC,MAAM,mBAAmB,GAAG,CAAC;KACjC,MAAM,CAAC;IACN,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;IAClD,eAAe,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;IAC1D,IAAI,EAAE,CAAC;SACJ,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC;QAC7D,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,aAAa,CAAC;KAChE,CAAC;SACD,QAAQ,CAAC,eAAe,CAAC;SACzB,QAAQ,EAAE;SACV,QAAQ,EAAE;SACV,QAAQ,CAAC,qBAAqB,CAAC;CACnC,CAAC;KACD,QAAQ,CAAC,eAAe,CAAC,CAAC;AAC7B,0FAA0F;AAC1F,MAAM,CAAC,MAAM,yBAAyB,GAAG,mBAAmB,CAAC,MAAM,CAAC;IAClE,eAAe,EAAE,CAAC;SACf,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,+FAA+F,CAChG;CACJ,CAAC,CAAC;AACH,kFAAkF;AAClF,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC;KAC5B,MAAM,CAAC;IACN,SAAS,EAAE,CAAC;SACT,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QAC/E,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;QAC3E,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;KACrE,CAAC;SACD,QAAQ,CAAC,eAAe,CAAC;SACzB,MAAM,CAAC,CAAC,QAAQ,EAAE,EAAE,CAAC,QAAQ,CAAC,KAAK,IAAI,QAAQ,CAAC,GAAG,EAAE,6BAA6B,CAAC;SACnF,QAAQ,CAAC,yDAAyD,CAAC,CACvE;SACA,GAAG,CAAC,CAAC,CAAC;SACN,QAAQ,CAAC,8BAA8B,CAAC;IAC3C,cAAc,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,4BAA4B,CAAC;IACxF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;IACjE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;CAC1E,CAAC;KACD,QAAQ,CAAC,eAAe,CAAC;KACzB,QAAQ,CAAC,mCAAmC,CAAC,CAAC;AACjD,mFAAmF;AACnF,MAAM,CAAC,MAAM,qBAAqB,GAAG,CAAC;KACnC,MAAM,CAAC;IACN,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;IACpD,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CA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package/dist/services/interpro/structure-schemas.d.ts

@@ -0,0 +1,116 @@
+/**
+ * @fileoverview PDB identifier grammar and lossless structure match schemas.
+ * @module services/interpro/structure-schemas
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+/** Classic four-character PDB IDs; InterPro answers extended `pdb_0000…` IDs with 404. */
+export declare const PDB_ID_PATTERN: RegExp;
+/** Chain IDs as InterPro lists them: case-sensitive, one to four letters or digits. */
+export declare const CHAIN_PATTERN: RegExp;
+/** Caller-supplied PDB ID, matched case-insensitively and sent lowercase. */
+export declare const PdbIdSchema: z.ZodString;
+/** Caller-supplied chain ID, compared exactly against the structure's protein chains. */
+export declare const ChainSchema: z.ZodString;
+/** Whether an upstream value is exactly a chain ID, the only form server-written text names it in. */
+export declare const isChain: (value: unknown) => value is string;
+/** Structure detail metadata: `chains` lists protein chains only; other fields are retained. */
+export declare const StructureMetadataSchema: z.ZodObject<{
+    accession: z.ZodString;
+    source_database: z.ZodString;
+    chains: z.ZodArray<z.ZodString>;
+}, z.core.$catchall<z.ZodJSONSchema>>;
+/**
+ * One upstream chain record of a structure match. `entry_structure_locations` fragments carry
+ * 1-based chain `start`/`end` beside author `auth_start`/`auth_end`, which may be null; the
+ * UniProt `protein`, its residue maps, and both protein-side location arrays may be null or empty.
+ */
+export declare const StructureRecordSchema: z.ZodObject<{
+    accession: z.ZodString;
+    chain: z.ZodString;
+    protein: z.ZodNullable<z.ZodString>;
+    entry_structure_locations: z.ZodArray<z.ZodObject<{
+        fragments: z.ZodArray<z.ZodObject<{
+            start: z.ZodNumber;
+            end: z.ZodNumber;
+            'dc-status': z.ZodOptional<z.ZodString>;
+        }, z.core.$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>>;
+/** Upstream structure match row: entry metadata plus at most 20 nested chain records. */
+export declare const StructureMatchSchema: 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.$catchall<z.ZodJSONSchema>>;
+    structures: z.ZodArray<z.ZodObject<{
+        accession: z.ZodString;
+        chain: z.ZodString;
+        protein: z.ZodNullable<z.ZodString>;
+        entry_structure_locations: z.ZodArray<z.ZodObject<{
+            fragments: z.ZodArray<z.ZodObject<{
+                start: z.ZodNumber;
+                end: z.ZodNumber;
+                'dc-status': z.ZodOptional<z.ZodString>;
+            }, z.core.$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.$catchall<z.ZodJSONSchema>>;
+//# sourceMappingURL=structure-schemas.d.ts.map

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

@@ -0,0 +1 @@
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