@cyanheads/protein-mcp-server 0.1.0

package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts

@@ -0,0 +1,61 @@
+/**
+ * @fileoverview protein_analyze_collection — profile the PDB into distributions
+ * and trends (counts by method / organism / polymer type, resolution histograms,
+ * release-year timelines, and multidimensional cross-tabs) over an optional
+ * scoping query. Backed by RCSB's server-side facet engine: one call, compact
+ * buckets, no row pull, no SQL canvas. Fully portable.
+ * @module mcp-server/tools/definitions/analyze-collection.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+export declare const analyzeCollection: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    group_by: z.ZodArray<z.ZodEnum<{
+        method: "method";
+        organism: "organism";
+        resolution: "resolution";
+        molecular_weight: "molecular_weight";
+        polymer_type: "polymer_type";
+        release_year: "release_year";
+    }>>;
+    query: z.ZodOptional<z.ZodString>;
+    organism: z.ZodOptional<z.ZodString>;
+    method: z.ZodOptional<z.ZodString>;
+    max_resolution: z.ZodOptional<z.ZodNumber>;
+    content_type: z.ZodDefault<z.ZodEnum<{
+        experimental: "experimental";
+        predicted: "predicted";
+        all: "all";
+    }>>;
+    interval: z.ZodOptional<z.ZodUnion<readonly [z.ZodNumber, z.ZodEnum<{
+        year: "year";
+        month: "month";
+        quarter: "quarter";
+    }>]>>;
+    bucket_limit: z.ZodOptional<z.ZodNumber>;
+}, z.core.$strip>, z.ZodObject<{
+    total: z.ZodNumber;
+    facets: z.ZodArray<z.ZodObject<{
+        dimension: z.ZodString;
+        buckets: z.ZodArray<z.ZodObject<{
+            label: z.ZodString;
+            count: z.ZodNumber;
+            children: z.ZodOptional<z.ZodArray<z.ZodObject<{
+                dimension: z.ZodString;
+                buckets: z.ZodArray<z.ZodObject<{
+                    label: z.ZodString;
+                    count: z.ZodNumber;
+                }, z.core.$strip>>;
+            }, z.core.$strip>>>;
+        }, z.core.$strip>>;
+        truncated: z.ZodOptional<z.ZodBoolean>;
+    }, z.core.$strip>>;
+}, z.core.$strip>, readonly [{
+    readonly reason: "unknown_dimension";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "A group_by value is outside the supported dimension set.";
+    readonly recovery: "Use a supported dimension: method, organism, polymer_type, resolution, release_year, or molecular_weight.";
+}], {
+    readonly scope: z.ZodOptional<z.ZodString>;
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
+//# sourceMappingURL=analyze-collection.tool.d.ts.map

package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"analyze-collection.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAOjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsH5B,CAAC"}

package/dist/mcp-server/tools/definitions/analyze-collection.tool.js

@@ -0,0 +1,115 @@
+/**
+ * @fileoverview protein_analyze_collection — profile the PDB into distributions
+ * and trends (counts by method / organism / polymer type, resolution histograms,
+ * release-year timelines, and multidimensional cross-tabs) over an optional
+ * scoping query. Backed by RCSB's server-side facet engine: one call, compact
+ * buckets, no row pull, no SQL canvas. Fully portable.
+ * @module mcp-server/tools/definitions/analyze-collection.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { getServerConfig } from '../../../config/server-config.js';
+import { buildFacetSpec, FACET_DIMENSION_NAMES } from '../../../services/rcsb/facets.js';
+import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
+import { facetDimensionSchema, renderFacets, toFacetOutput } from './_schemas.js';
+export const analyzeCollection = tool('protein_analyze_collection', {
+    title: 'protein-mcp-server: analyze collection',
+    description: 'Profile the PDB into distributions and trends over an optional scoping query: counts by method, ' +
+        'organism, or polymer composition; resolution and molecular-weight histograms; release-year timelines; ' +
+        'and multidimensional cross-tabs (e.g. method × release_year). Aggregation runs server-side at RCSB — ' +
+        'one call returns compact buckets, no row pull. Pass one group_by dimension for a single breakdown, or ' +
+        'two for a cross-tab (the first nests the second).',
+    annotations: { readOnlyHint: true, openWorldHint: true },
+    errors: [
+        {
+            reason: 'unknown_dimension',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: 'A group_by value is outside the supported dimension set.',
+            recovery: 'Use a supported dimension: method, organism, polymer_type, resolution, release_year, or molecular_weight.',
+        },
+    ],
+    input: z.object({
+        group_by: z
+            .array(z.enum(FACET_DIMENSION_NAMES))
+            .min(1)
+            .max(2)
+            .describe('1 dimension for a breakdown, or 2 for a cross-tab (the first nests the second).'),
+        query: z
+            .string()
+            .optional()
+            .describe('Optional free-text scope (e.g. "kinase"); omit to profile the whole PDB.'),
+        organism: z.string().optional().describe('Optional source-organism scope.'),
+        method: z.string().optional().describe('Optional experimental-method scope.'),
+        max_resolution: z
+            .number()
+            .positive()
+            .optional()
+            .describe('Optional maximum-resolution scope (Å).'),
+        content_type: z
+            .enum(['experimental', 'predicted', 'all'])
+            .default('experimental')
+            .describe('Which structure universe to profile. Default experimental.'),
+        interval: z
+            .union([
+            z
+                .number()
+                .positive()
+                .describe('Numeric bin width for a value histogram (e.g. resolution Å).'),
+            z.enum(['year', 'month', 'quarter']).describe('Period granularity for a date histogram.'),
+        ])
+            .optional()
+            .describe('Bin width for a histogram dimension (number) or period for a date histogram (year/month/quarter).'),
+        bucket_limit: z
+            .number()
+            .int()
+            .min(1)
+            .max(500)
+            .optional()
+            .describe('Max buckets per dimension. Defaults to the server PROTEIN_FACET_BUCKET_CAP.'),
+    }),
+    output: z.object({
+        total: z.number().describe('Total entries in the scoped collection.'),
+        facets: z.array(facetDimensionSchema).describe('The requested breakdown(s).'),
+    }),
+    enrichment: {
+        scope: z.string().optional().describe('Echoed scope description for follow-up calls.'),
+        notice: z.string().optional().describe('Advisory note (e.g. bucket truncation, empty scope).'),
+    },
+    async handler(input, ctx) {
+        const cfg = getServerConfig();
+        const rcsb = getRcsbService();
+        const cap = input.bucket_limit ?? cfg.facetBucketCap;
+        const contentType = input.content_type === 'all'
+            ? undefined
+            : input.content_type === 'predicted'
+                ? 'computational'
+                : 'experimental';
+        const [primary, secondary] = input.group_by;
+        if (!primary)
+            throw ctx.fail('unknown_dimension', 'group_by requires at least one dimension.');
+        const spec = buildFacetSpec(primary, input.interval, secondary);
+        const { total, facets } = await rcsb.analyzeFacets({
+            ...(input.query ? { text: input.query } : {}),
+            ...(input.organism ? { organism: input.organism } : {}),
+            ...(input.method ? { method: input.method } : {}),
+            ...(typeof input.max_resolution === 'number'
+                ? { maxResolution: input.max_resolution }
+                : {}),
+            ...(contentType ? { contentType } : {}),
+        }, [spec], ctx);
+        const out = facets.map((f) => toFacetOutput(f, cap));
+        if (out.some((f) => f.truncated)) {
+            ctx.enrich.notice(`One or more dimensions exceeded ${cap} buckets and were capped; scope the query tighter for the long tail.`);
+        }
+        const scopeBits = [input.query, input.organism, input.method].filter(Boolean);
+        if (scopeBits.length > 0)
+            ctx.enrich({ scope: scopeBits.join(' · ') });
+        return { total, facets: out };
+    },
+    format: (result) => {
+        const lines = [`## Collection profile — ${result.total} entries`];
+        lines.push(...renderFacets(result.facets));
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+//# sourceMappingURL=analyze-collection.tool.js.map

package/dist/mcp-server/tools/definitions/analyze-collection.tool.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"analyze-collection.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,qBAAqB,EAAE,MAAM,2BAA2B,CAAC;AAClF,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,OAAO,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE,MAAM,eAAe,CAAC;AAElF,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IAClE,KAAK,EAAE,wCAAwC;IAC/C,WAAW,EACT,kGAAkG;QAClG,wGAAwG;QACxG,uGAAuG;QACvG,wGAAwG;QACxG,mDAAmD;IACrD,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,mBAAmB;YAC3B,IAAI,EAAE,gBAAgB,CAAC,aAAa;YACpC,IAAI,EAAE,0DAA0D;YAChE,QAAQ,EACN,2GAA2G;SAC9G;KACF;IAED,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC;aACpC,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,iFAAiF,CAAC;QAC9F,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,0EAA0E,CAAC;QACvF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QAC3E,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QAC7E,cAAc,EAAE,CAAC;aACd,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,EAAE;aACV,QAAQ,CAAC,wCAAwC,CAAC;QACrD,YAAY,EAAE,CAAC;aACZ,IAAI,CAAC,CAAC,cAAc,EAAE,WAAW,EAAE,KAAK,CAAC,CAAC;aAC1C,OAAO,CAAC,cAAc,CAAC;aACvB,QAAQ,CAAC,4DAA4D,CAAC;QACzE,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC;YACL,CAAC;iBACE,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,8DAA8D,CAAC;YAC3E,CAAC,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,OAAO,EAAE,SAAS,CAAC,CAAC,CAAC,QAAQ,CAAC,0CAA0C,CAAC;SAC1F,CAAC;aACD,QAAQ,EAAE;aACV,QAAQ,CACP,mGAAmG,CACpG;QACH,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,6EAA6E,CAAC;KAC3F,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;QACrE,MAAM,EAAE,CAAC,CAAC,KAAK,CAAC,oBAAoB,CAAC,CAAC,QAAQ,CAAC,6BAA6B,CAAC;KAC9E,CAAC;IAEF,UAAU,EAAE;QACV,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+CAA+C,CAAC;QACtF,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;KAC/F;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,GAAG,GAAG,eAAe,EAAE,CAAC;QAC9B,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,IAAI,GAAG,CAAC,cAAc,CAAC;QACrD,MAAM,WAAW,GACf,KAAK,CAAC,YAAY,KAAK,KAAK;YAC1B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,KAAK,CAAC,YAAY,KAAK,WAAW;gBAClC,CAAC,CAAC,eAAe;gBACjB,CAAC,CAAC,cAAc,CAAC;QAEvB,MAAM,CAAC,OAAO,EAAE,SAAS,CAAC,GAAG,KAAK,CAAC,QAAQ,CAAC;QAC5C,IAAI,CAAC,OAAO;YAAE,MAAM,GAAG,CAAC,IAAI,CAAC,mBAAmB,EAAE,2CAA2C,CAAC,CAAC;QAC/F,MAAM,IAAI,GAAG,cAAc,CAAC,OAAO,EAAE,KAAK,CAAC,QAAQ,EAAE,SAAS,CAAC,CAAC;QAEhE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,CAChD;YACE,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC7C,GAAG,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,KAAK,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACvD,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACjD,GAAG,CAAC,OAAO,KAAK,CAAC,cAAc,KAAK,QAAQ;gBAC1C,CAAC,CAAC,EAAE,aAAa,EAAE,KAAK,CAAC,cAAc,EAAE;gBACzC,CAAC,CAAC,EAAE,CAAC;YACP,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;SACxC,EACD,CAAC,IAAI,CAAC,EACN,GAAG,CACJ,CAAC;QAEF,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,aAAa,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC;QACrD,IAAI,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,EAAE,CAAC;YACjC,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,mCAAmC,GAAG,sEAAsE,CAC7G,CAAC;QACJ,CAAC;QACD,MAAM,SAAS,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;QAC9E,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC;YAAE,GAAG,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAEvE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC;IAChC,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,CAAC,2BAA2B,MAAM,CAAC,KAAK,UAAU,CAAC,CAAC;QAC5E,KAAK,CAAC,IAAI,CAAC,GAAG,YAAY,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;QAC3C,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts

@@ -0,0 +1,49 @@
+/**
+ * @fileoverview protein_compare_structures — structural alignment of 2–10
+ * structures via the RCSB Structural Comparison service. Aligns each structure to
+ * a reference (default the first) or computes the full all-pairs matrix, fanning
+ * out pairwise async jobs with a concurrency cap and per-pair partial success.
+ * @module mcp-server/tools/definitions/compare-structures.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const compareStructures: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    structures: z.ZodArray<z.ZodObject<{
+        pdb_id: z.ZodString;
+        chain: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>>;
+    reference: z.ZodDefault<z.ZodEnum<{
+        first: "first";
+        all_pairs: "all_pairs";
+    }>>;
+    method: z.ZodDefault<z.ZodEnum<{
+        "tm-align": "tm-align";
+        "fatcat-rigid": "fatcat-rigid";
+        "fatcat-flexible": "fatcat-flexible";
+    }>>;
+    timeout_s: z.ZodOptional<z.ZodNumber>;
+}, z.core.$strip>, z.ZodObject<{
+    method: z.ZodString;
+    reference: z.ZodEnum<{
+        first: "first";
+        all_pairs: "all_pairs";
+    }>;
+    pairs: z.ZodArray<z.ZodObject<{
+        a: z.ZodString;
+        b: z.ZodString;
+        status: z.ZodEnum<{
+            complete: "complete";
+            computing: "computing";
+            failed: "failed";
+        }>;
+        tmScore: z.ZodOptional<z.ZodNumber>;
+        rmsd: z.ZodOptional<z.ZodNumber>;
+        alignedResidues: z.ZodOptional<z.ZodNumber>;
+        uuid: z.ZodOptional<z.ZodString>;
+        error: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>>;
+}, z.core.$strip>, undefined, {
+    readonly pairsTotal: z.ZodNumber;
+    readonly computing: z.ZodNumber;
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
+//# sourceMappingURL=compare-structures.tool.d.ts.map

package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"compare-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/compare-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAmEjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6F5B,CAAC"}

package/dist/mcp-server/tools/definitions/compare-structures.tool.js

@@ -0,0 +1,168 @@
+/**
+ * @fileoverview protein_compare_structures — structural alignment of 2–10
+ * structures via the RCSB Structural Comparison service. Aligns each structure to
+ * a reference (default the first) or computes the full all-pairs matrix, fanning
+ * out pairwise async jobs with a concurrency cap and per-pair partial success.
+ * @module mcp-server/tools/definitions/compare-structures.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { getServerConfig } from '../../../config/server-config.js';
+import { getAlignmentService } from '../../../services/alignment/alignment-service.js';
+import { mapWithConcurrency } from '../../../services/shared/async.js';
+const inputSchema = z.object({
+    structures: z
+        .array(z
+        .object({
+        pdb_id: z.string().min(1).describe('PDB entry ID.'),
+        chain: z
+            .string()
+            .optional()
+            .describe('Chain (label_asym_id) to restrict the alignment to a single chain.'),
+    })
+        .describe('A structure to align, by PDB entry ID with optional chain.'))
+        .min(2)
+        .max(10)
+        .describe('The 2–10 structures to compare.'),
+    reference: z
+        .enum(['first', 'all_pairs'])
+        .default('first')
+        .describe('Align all to the first structure, or compute the full pairwise matrix.'),
+    method: z
+        .enum(['tm-align', 'fatcat-rigid', 'fatcat-flexible'])
+        .default('tm-align')
+        .describe('Alignment algorithm: tm-align, fatcat-rigid, or fatcat-flexible.'),
+    timeout_s: z
+        .number()
+        .int()
+        .min(5)
+        .max(120)
+        .optional()
+        .describe('Poll budget per pair in seconds before returning "computing". Defaults to the server setting.'),
+});
+const outputSchema = z.object({
+    method: z.string().describe('Alignment method used.'),
+    reference: z.enum(['first', 'all_pairs']).describe('Comparison mode used.'),
+    pairs: z
+        .array(z
+        .object({
+        a: z.string().describe('First structure of the pair (entry[.chain]).'),
+        b: z.string().describe('Second structure of the pair (entry[.chain]).'),
+        status: z.enum(['complete', 'computing', 'failed']).describe('Outcome for this pair.'),
+        tmScore: z.number().optional().describe('TM-score (0–1; higher is more similar).'),
+        rmsd: z.number().optional().describe('RMSD in Å over aligned residues.'),
+        alignedResidues: z.number().optional().describe('Number of aligned residue pairs.'),
+        uuid: z
+            .string()
+            .optional()
+            .describe('Alignment job UUID (present for computing/complete pairs).'),
+        error: z.string().optional().describe('Failure detail (failed pairs).'),
+    })
+        .describe('Alignment outcome for one structure pair.'))
+        .describe('One row per aligned pair.'),
+});
+export const compareStructures = tool('protein_compare_structures', {
+    title: 'protein-mcp-server: compare structures',
+    description: 'Structurally align 2–10 structures via the RCSB Structural Comparison service (TM-align / jFATCAT). ' +
+        'reference:"first" aligns every structure to the first; reference:"all_pairs" computes the full pairwise ' +
+        'matrix. Each pair is an independent async alignment job, fanned out with a concurrency cap and per-pair ' +
+        'partial success — a pair still computing when the budget elapses returns status "computing" with its ' +
+        'job UUID (re-call to resume), and a failed pair degrades its row without sinking the others. Returns ' +
+        'TM-score, RMSD, and aligned-residue count per pair.',
+    annotations: { readOnlyHint: true, openWorldHint: true },
+    input: inputSchema,
+    output: outputSchema,
+    enrichment: {
+        pairsTotal: z.number().describe('Number of pairs compared.'),
+        computing: z.number().describe('Number of pairs still computing.'),
+        notice: z.string().optional().describe('Advisory note (pending pairs, failures).'),
+    },
+    async handler(input, ctx) {
+        const cfg = getServerConfig();
+        const structures = input.structures.slice(0, cfg.maxCompareStructures);
+        const timeoutMs = input.timeout_s ? input.timeout_s * 1000 : cfg.asyncPollTimeoutMs;
+        const method = input.method;
+        const pairs = buildPairs(structures, input.reference);
+        const alignment = getAlignmentService();
+        const rows = await mapWithConcurrency(pairs, cfg.fanoutConcurrency, async ([a, b]) => {
+            const outcome = await alignment.comparePair(toCompare(a), toCompare(b), method, timeoutMs, ctx);
+            const base = { a: label(a), b: label(b) };
+            if (outcome.status === 'complete') {
+                return {
+                    ...base,
+                    status: 'complete',
+                    uuid: outcome.uuid,
+                    ...(typeof outcome.scores.tmScore === 'number'
+                        ? { tmScore: outcome.scores.tmScore }
+                        : {}),
+                    ...(typeof outcome.scores.rmsd === 'number' ? { rmsd: outcome.scores.rmsd } : {}),
+                    ...(typeof outcome.scores.alignedResidues === 'number'
+                        ? { alignedResidues: outcome.scores.alignedResidues }
+                        : {}),
+                };
+            }
+            if (outcome.status === 'computing') {
+                return { ...base, status: 'computing', uuid: outcome.uuid };
+            }
+            return { ...base, status: 'failed', error: outcome.error };
+        });
+        const computing = rows.filter((r) => r.status === 'computing').length;
+        const failed = rows.filter((r) => r.status === 'failed').length;
+        ctx.enrich({ pairsTotal: rows.length, computing });
+        if (computing > 0 || failed > 0) {
+            ctx.enrich.notice(`${computing} pair(s) still computing${failed > 0 ? `, ${failed} failed` : ''}. ` +
+                `Re-call to resume computing pairs (cold alignment jobs typically finish within 30–60 s).`);
+        }
+        return { method, reference: input.reference, pairs: rows };
+    },
+    format: (result) => {
+        const lines = [`## Structure comparison (${result.method}, ${result.reference})`];
+        lines.push('\n| Pair | Status | TM-score | RMSD (Å) | Aligned |');
+        lines.push('|---|---|---|---|---|');
+        for (const p of result.pairs) {
+            const tm = typeof p.tmScore === 'number' ? p.tmScore.toFixed(3) : '—';
+            const rmsd = typeof p.rmsd === 'number' ? p.rmsd.toFixed(2) : '—';
+            const aligned = typeof p.alignedResidues === 'number' ? String(p.alignedResidues) : '—';
+            lines.push(`| ${p.a} ↔ ${p.b} | ${p.status} | ${tm} | ${rmsd} | ${aligned} |`);
+        }
+        const notes = result.pairs.filter((p) => p.error || p.uuid);
+        if (notes.length > 0) {
+            lines.push('');
+            for (const p of notes) {
+                if (p.error)
+                    lines.push(`- ${p.a} ↔ ${p.b}: ${p.error}`);
+                if (p.uuid)
+                    lines.push(`- ${p.a} ↔ ${p.b}: job ${p.uuid}${p.status === 'computing' ? ' (computing)' : ''}`);
+            }
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+function buildPairs(structures, reference) {
+    const pairs = [];
+    if (reference === 'first') {
+        const [ref, ...rest] = structures;
+        if (ref)
+            for (const s of rest)
+                pairs.push([ref, s]);
+    }
+    else {
+        for (let i = 0; i < structures.length; i++) {
+            const a = structures[i];
+            if (!a)
+                continue;
+            for (let j = i + 1; j < structures.length; j++) {
+                const b = structures[j];
+                if (b)
+                    pairs.push([a, b]);
+            }
+        }
+    }
+    return pairs;
+}
+function toCompare(s) {
+    return { entryId: s.pdb_id, ...(s.chain ? { asymId: s.chain } : {}) };
+}
+function label(s) {
+    return s.chain ? `${s.pdb_id.toUpperCase()}.${s.chain}` : s.pdb_id.toUpperCase();
+}
+//# sourceMappingURL=compare-structures.tool.js.map

package/dist/mcp-server/tools/definitions/compare-structures.tool.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"compare-structures.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/compare-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAE5D,OAAO,EAAE,mBAAmB,EAAE,MAAM,2CAA2C,CAAC;AAChF,OAAO,EAAE,kBAAkB,EAAE,MAAM,4BAA4B,CAAC;AAEhE,MAAM,WAAW,GAAG,CAAC,CAAC,MAAM,CAAC;IAC3B,UAAU,EAAE,CAAC;SACV,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,eAAe,CAAC;QACnD,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,oEAAoE,CAAC;KAClF,CAAC;SACD,QAAQ,CAAC,4DAA4D,CAAC,CAC1E;SACA,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,EAAE,CAAC;SACP,QAAQ,CAAC,iCAAiC,CAAC;IAC9C,SAAS,EAAE,CAAC;SACT,IAAI,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC;SAC5B,OAAO,CAAC,OAAO,CAAC;SAChB,QAAQ,CAAC,wEAAwE,CAAC;IACrF,MAAM,EAAE,CAAC;SACN,IAAI,CAAC,CAAC,UAAU,EAAE,cAAc,EAAE,iBAAiB,CAAC,CAAC;SACrD,OAAO,CAAC,UAAU,CAAC;SACnB,QAAQ,CAAC,kEAAkE,CAAC;IAC/E,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,GAAG,EAAE;SACL,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,GAAG,CAAC;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,+FAA+F,CAChG;CACJ,CAAC,CAAC;AAEH,MAAM,YAAY,GAAG,CAAC,CAAC,MAAM,CAAC;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;IACrD,SAAS,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAC,QAAQ,CAAC,uBAAuB,CAAC;IAC3E,KAAK,EAAE,CAAC;SACL,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,CAAC,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,8CAA8C,CAAC;QACtE,CAAC,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+CAA+C,CAAC;QACvE,MAAM,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,UAAU,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QACtF,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;QAClF,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QACxE,eAAe,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QACnF,IAAI,EAAE,CAAC;aACJ,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,4DAA4D,CAAC;QACzE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;KACxE,CAAC;SACD,QAAQ,CAAC,2CAA2C,CAAC,CACzD;SACA,QAAQ,CAAC,2BAA2B,CAAC;CACzC,CAAC,CAAC;AAIH,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IAClE,KAAK,EAAE,wCAAwC;IAC/C,WAAW,EACT,sGAAsG;QACtG,0GAA0G;QAC1G,0GAA0G;QAC1G,uGAAuG;QACvG,uGAAuG;QACvG,qDAAqD;IACvD,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,WAAW;IAClB,MAAM,EAAE,YAAY;IAEpB,UAAU,EAAE;QACV,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;QAC5D,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QAClE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0CAA0C,CAAC;KACnF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,GAAG,GAAG,eAAe,EAAE,CAAC;QAC9B,MAAM,UAAU,GAAG,KAAK,CAAC,UAAU,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,oBAAoB,CAAC,CAAC;QACvE,MAAM,SAAS,GAAG,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,KAAK,CAAC,SAAS,GAAG,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,kBAAkB,CAAC;QACpF,MAAM,MAAM,GAAG,KAAK,CAAC,MAAyB,CAAC;QAE/C,MAAM,KAAK,GAAG,UAAU,CAAC,UAAU,EAAE,KAAK,CAAC,SAAS,CAAC,CAAC;QACtD,MAAM,SAAS,GAAG,mBAAmB,EAAE,CAAC;QACxC,MAAM,IAAI,GAAG,MAAM,kBAAkB,CAAC,KAAK,EAAE,GAAG,CAAC,iBAAiB,EAAE,KAAK,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE;YACnF,MAAM,OAAO,GAAG,MAAM,SAAS,CAAC,WAAW,CACzC,SAAS,CAAC,CAAC,CAAC,EACZ,SAAS,CAAC,CAAC,CAAC,EACZ,MAAM,EACN,SAAS,EACT,GAAG,CACJ,CAAC;YACF,MAAM,IAAI,GAAG,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC;YAC1C,IAAI,OAAO,CAAC,MAAM,KAAK,UAAU,EAAE,CAAC;gBAClC,OAAO;oBACL,GAAG,IAAI;oBACP,MAAM,EAAE,UAAmB;oBAC3B,IAAI,EAAE,OAAO,CAAC,IAAI;oBAClB,GAAG,CAAC,OAAO,OAAO,CAAC,MAAM,CAAC,OAAO,KAAK,QAAQ;wBAC5C,CAAC,CAAC,EAAE,OAAO,EAAE,OAAO,CAAC,MAAM,CAAC,OAAO,EAAE;wBACrC,CAAC,CAAC,EAAE,CAAC;oBACP,GAAG,CAAC,OAAO,OAAO,CAAC,MAAM,CAAC,IAAI,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,OAAO,CAAC,MAAM,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;oBACjF,GAAG,CAAC,OAAO,OAAO,CAAC,MAAM,CAAC,eAAe,KAAK,QAAQ;wBACpD,CAAC,CAAC,EAAE,eAAe,EAAE,OAAO,CAAC,MAAM,CAAC,eAAe,EAAE;wBACrD,CAAC,CAAC,EAAE,CAAC;iBACR,CAAC;YACJ,CAAC;YACD,IAAI,OAAO,CAAC,MAAM,KAAK,WAAW,EAAE,CAAC;gBACnC,OAAO,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,WAAoB,EAAE,IAAI,EAAE,OAAO,CAAC,IAAI,EAAE,CAAC;YACvE,CAAC;YACD,OAAO,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,QAAiB,EAAE,KAAK,EAAE,OAAO,CAAC,KAAK,EAAE,CAAC;QACtE,CAAC,CAAC,CAAC;QAEH,MAAM,SAAS,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,WAAW,CAAC,CAAC,MAAM,CAAC;QACtE,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,KAAK,QAAQ,CAAC,CAAC,MAAM,CAAC;QAChE,GAAG,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,IAAI,CAAC,MAAM,EAAE,SAAS,EAAE,CAAC,CAAC;QACnD,IAAI,SAAS,GAAG,CAAC,IAAI,MAAM,GAAG,CAAC,EAAE,CAAC;YAChC,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,GAAG,SAAS,2BAA2B,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,MAAM,SAAS,CAAC,CAAC,CAAC,EAAE,IAAI;gBAC/E,0FAA0F,CAC7F,CAAC;QACJ,CAAC;QAED,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,KAAK,CAAC,SAAS,EAAE,KAAK,EAAE,IAAI,EAAE,CAAC;IAC7D,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,CAAC,4BAA4B,MAAM,CAAC,MAAM,KAAK,MAAM,CAAC,SAAS,GAAG,CAAC,CAAC;QAC5F,KAAK,CAAC,IAAI,CAAC,qDAAqD,CAAC,CAAC;QAClE,KAAK,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC;QACpC,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;YAC7B,MAAM,EAAE,GAAG,OAAO,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC;YACtE,MAAM,IAAI,GAAG,OAAO,CAAC,CAAC,IAAI,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC;YAClE,MAAM,OAAO,GAAG,OAAO,CAAC,CAAC,eAAe,KAAK,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC;YACxF,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,MAAM,MAAM,EAAE,MAAM,IAAI,MAAM,OAAO,IAAI,CAAC,CAAC;QACjF,CAAC;QACD,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC;QAC5D,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACrB,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACf,KAAK,MAAM,CAAC,IAAI,KAAK,EAAE,CAAC;gBACtB,IAAI,CAAC,CAAC,KAAK;oBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;gBACzD,IAAI,CAAC,CAAC,IAAI;oBACR,KAAK,CAAC,IAAI,CACR,KAAK,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,MAAM,KAAK,WAAW,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,EAAE,CACpF,CAAC;YACN,CAAC;QACH,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC;AAEH,SAAS,UAAU,CACjB,UAAyB,EACzB,SAAgC;IAEhC,MAAM,KAAK,GAAsC,EAAE,CAAC;IACpD,IAAI,SAAS,KAAK,OAAO,EAAE,CAAC;QAC1B,MAAM,CAAC,GAAG,EAAE,GAAG,IAAI,CAAC,GAAG,UAAU,CAAC;QAClC,IAAI,GAAG;YAAE,KAAK,MAAM,CAAC,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC;IACtD,CAAC;SAAM,CAAC;QACN,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3C,MAAM,CAAC,GAAG,UAAU,CAAC,CAAC,CAAC,CAAC;YACxB,IAAI,CAAC,CAAC;gBAAE,SAAS;YACjB,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC/C,MAAM,CAAC,GAAG,UAAU,CAAC,CAAC,CAAC,CAAC;gBACxB,IAAI,CAAC;oBAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;YAC5B,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED,SAAS,SAAS,CAAC,CAAc;IAC/B,OAAO,EAAE,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC;AACxE,CAAC;AAED,SAAS,KAAK,CAAC,CAAc;IAC3B,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,MAAM,CAAC,WAAW,EAAE,IAAI,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC;AACnF,CAAC"}

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

@@ -0,0 +1,67 @@
+/**
+ * @fileoverview protein_find_similar — find structurally or evolutionarily related
+ * proteins. by:sequence runs a synchronous RCSB mmseqs2 search; by:structure runs
+ * an async Foldseek search against experimental + predicted databases (submit →
+ * poll → bounded timeout, returning "still computing" rather than blocking).
+ * @module mcp-server/tools/definitions/find-similar.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    by: z.ZodEnum<{
+        sequence: "sequence";
+        structure: "structure";
+    }>;
+    sequence: z.ZodOptional<z.ZodString>;
+    pdb_id: z.ZodOptional<z.ZodString>;
+    uniprot: z.ZodOptional<z.ZodString>;
+    databases: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    max_evalue: z.ZodOptional<z.ZodNumber>;
+    min_identity: z.ZodOptional<z.ZodNumber>;
+    limit: z.ZodDefault<z.ZodNumber>;
+}, z.core.$strip>, z.ZodObject<{
+    by: z.ZodEnum<{
+        sequence: "sequence";
+        structure: "structure";
+    }>;
+    engine: z.ZodString;
+    status: z.ZodEnum<{
+        complete: "complete";
+        computing: "computing";
+    }>;
+    ticketId: z.ZodOptional<z.ZodString>;
+    hits: z.ZodArray<z.ZodObject<{
+        id: z.ZodString;
+        source: z.ZodEnum<{
+            experimental: "experimental";
+            predicted: "predicted";
+        }>;
+        score: z.ZodOptional<z.ZodNumber>;
+        evalue: z.ZodOptional<z.ZodNumber>;
+        identity: z.ZodOptional<z.ZodNumber>;
+        database: z.ZodOptional<z.ZodString>;
+        title: z.ZodOptional<z.ZodString>;
+        organism: z.ZodOptional<z.ZodString>;
+        uniprotAccession: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>>;
+}, z.core.$strip>, readonly [{
+    readonly reason: "missing_query";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "None of sequence, pdb_id, or uniprot was provided.";
+    readonly recovery: "Provide a raw sequence, a PDB entry ID, or a UniProt accession to search from.";
+}, {
+    readonly reason: "no_sequence";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "A sequence could not be resolved from the given PDB ID or UniProt accession.";
+    readonly recovery: "Verify the identifier, or pass a raw one-letter sequence directly via the sequence parameter.";
+}, {
+    readonly reason: "search_failed";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "The Foldseek search service rejected or failed the structure job.";
+    readonly retryable: true;
+    readonly recovery: "Retry shortly; if it persists, verify the source structure has coordinates via protein_get_structure.";
+}], {
+    totalCount: z.ZodOptional<z.ZodNumber>;
+    notice: z.ZodOptional<z.ZodString>;
+}>;
+//# sourceMappingURL=find-similar.tool.d.ts.map

package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"find-similar.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-similar.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAA6B,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkGjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA+DtB,CAAC"}