npm - @cyanheads/protein-mcp-server - Versions diffs - 0.4.2 → 0.5.1 - Mend

@cyanheads/protein-mcp-server 0.4.2 → 0.5.1

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Files changed (31) hide show

package/AGENTS.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** protein-mcp-server
-**Version:** 0.4.2
+**Version:** 0.5.1
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.11.5`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/sdk` ^1.30.0

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** protein-mcp-server
-**Version:** 0.4.2
+**Version:** 0.5.1
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.11.5`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/sdk` ^1.30.0

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![Version](https://img.shields.io/badge/Version-0.4.2-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/protein-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.30.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/protein-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.14-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-0.5.1-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/protein-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.30.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/protein-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.14-blueviolet.svg?style=flat-square)](https://bun.sh/)
 </div>
@@ -48,7 +48,7 @@ Federated search across experimental (PDB) and predicted (computed-model) struct
 - Free-text, protein-sequence (triggers an mmseqs2 similarity search), and organism / method / resolution filters
 - `content_type` scopes the search to `experimental`, `predicted`, or `all` — the default `all` is a genuine union of both universes, so computed models appear alongside PDB entries
 - Every hit names its `source`; experimental hits are enriched with title, method, resolution, and organism, while computed models carry the UniProt accession parsed from their ID
-- Optional `facets` return a method / organism / release-year breakdown alongside the hits at no extra call, each reporting how many matches carry no value for that dimension
+- Optional `facets` return a method / organism / release-year breakdown alongside the hits at no extra call, each reporting how many matches carry no value for that dimension; each dimension may be listed once
 - Chain hit IDs straight into `protein_get_structure`
 ---
@@ -96,6 +96,7 @@ Structural alignment of multiple structures (up to the configured `PROTEIN_MAX_C
 - Methods: `tm-align`, `fatcat-rigid`, `fatcat-flexible`
 - `reference: first` aligns every structure to the first; `reference: all_pairs` computes the full pairwise matrix
 - Optional per-structure `chain` restricts the alignment to a single chain
+- A structure repeated in `structures[]` is compared once — the repeat would only add a self-alignment and a mirrored pair, which the resume mechanism cannot tell apart from the original
 - Each pair is an independent async 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`, and a failed pair degrades its row without sinking the others
 - Re-call with a matching `{ a, b, uuid }` entry in `resume[]` (copied from a prior response's `pairs[]`) to poll a computing pair's job instead of resubmitting
 - Returns TM-score, RMSD, and aligned-residue count per pair, plus `modeledResidues` and `coverage` — each a `[a, b]` tuple, with coverage a 0–100 percentage of that structure's own modeled-residue count
@@ -107,10 +108,10 @@ Structural alignment of multiple structures (up to the configured `PROTEIN_MAX_C
 Profile the PDB into distributions and trends over an optional scoping query — backed by RCSB's server-side facet engine (one call, compact buckets, no row pull).
 - Group by `method`, `organism`, `polymer_type`, `resolution`, `release_year`, or `molecular_weight`
-- One `group_by` dimension for a breakdown, or two for a cross-tab (the first nests the second)
+- One `group_by` dimension for a breakdown, or two distinct dimensions for a cross-tab (the first nests the second); a repeated dimension is rejected
 - `interval` sets the bin width for value histograms or the period for date histograms (`year` / `month` / `quarter`)
 - Scope with a free-text `query`, `organism`, `method`, or `max_resolution`; `content_type` selects the structure universe
-- `bucket_limit` caps buckets per dimension; truncation is flagged in the response
+- `bucket_limit` caps buckets per dimension level, not per response — a cross-tab applies it separately to the parent dimension and to the nested child inside each parent bucket, so up to `bucket_limit × (1 + bucket_limit)` buckets come back. Each level flags its own truncation, and `bucketsReturned` gives the realized total
 - Every dimension reports `missingValueCount` — matches in scope carrying no value for that attribute, which therefore fall in no bucket (a `resolution` breakdown does not cover NMR entries, and neither `method` nor `resolution` covers computed models)
 ---

package/changelog/0.5.x/0.5.0.md ADDED Viewed

@@ -0,0 +1,19 @@
+---
+summary: "protein_analyze_collection's nested facet child is now a single optional field instead of an array, and all three collection/comparison tools reject duplicate or ambiguous inputs with typed errors."
+breaking: true
+---
+# 0.5.0 — 2026-08-16
+## Changed
+- **`protein_analyze_collection` facet output**: a bucket's nested cross-tab is now a single optional `child` object, replacing the `children[]` array that was always at most one element ([#28](https://github.com/cyanheads/protein-mcp-server/issues/28)). Breaking change to the tool's output schema.
+- **`child` projection**: an empty `child` (empty `buckets[]`) is now emitted when the requested cross-tab dimension carries no upstream facet, so `child` present means a cross-tab was requested and `buckets: []` means it aggregated to nothing — previously both cases omitted `child` ([#31](https://github.com/cyanheads/protein-mcp-server/issues/31)).
+- **`protein_search_structures` facet output**: switched to a flat facet schema, dropping the nested-child field the tool could never populate ([#34](https://github.com/cyanheads/protein-mcp-server/issues/34)). Breaking change to the tool's output schema.
+## Fixed
+- **`protein_analyze_collection`**: `group_by` now rejects a repeated dimension with a new `duplicate_dimension` error instead of silently deduping the cross-tab request ([#30](https://github.com/cyanheads/protein-mcp-server/issues/30)).
+- **`protein_search_structures`**: `facets` now rejects a repeated dimension with the same `duplicate_dimension` error instead of returning the breakdown twice ([#35](https://github.com/cyanheads/protein-mcp-server/issues/35)).
+- **`protein_compare_structures`**: repeated structures in `structures[]` are now de-duplicated before pairing, with a new `no_distinct_pair` error when fewer than two distinct structures remain — previously two pairs generated from a duplicate collapsed onto one resume key and one job's UUID was applied to both ([#33](https://github.com/cyanheads/protein-mcp-server/issues/33)).
+- **`protein_compare_structures` `pairKey`**: now case-folds only the entry-ID portion of a structure label and preserves the chain suffix's case, since mmCIF `label_asym_id` is case-sensitive and chains `A` and `a` are different chains.

package/changelog/0.5.x/0.5.1.md ADDED Viewed

@@ -0,0 +1,14 @@
+---
+summary: "protein_analyze_collection reports the realized bucket total, and bucket_limit's per-dimension-level semantics are now stated explicitly everywhere it's described."
+breaking: false
+---
+# 0.5.1 — 2026-08-16
+## Added
+- **`protein_analyze_collection` `bucketsReturned`**: new required enrichment field reporting the realized bucket total summed across every dimension level — the size a cross-tab returns isn't legible from `bucket_limit` alone ([#36](https://github.com/cyanheads/protein-mcp-server/issues/36)).
+## Changed
+- **`bucket_limit` semantics**: the input description, the tool description, `PROTEIN_FACET_BUCKET_CAP`'s config description, and the README now state that the cap applies per dimension level, not per response — a cross-tab can return up to `bucket_limit × (1 + bucket_limit)` buckets ([#36](https://github.com/cyanheads/protein-mcp-server/issues/36)).

package/dist/config/server-config.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/config/server-config.js CHANGED Viewed

@@ -78,7 +78,7 @@ const ServerConfigSchema = z.object({
         .min(1)
         .max(500)
         .default(50)
-        .describe('Default cap on buckets returned per protein_analyze_collection dimension.'),
+        .describe('Default cap on buckets returned per protein_analyze_collection dimension level — applied separately to a cross-tab parent dimension and to the nested child inside each of its buckets.'),
     fanoutConcurrency: z.coerce
         .number()
         .int()

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package/dist/mcp-server/tools/definitions/_schemas.d.ts CHANGED Viewed

@@ -3,8 +3,10 @@
  * breakdown and a `content_type` scope — `protein_analyze_collection` and
  * `protein_search_structures`. Facet nesting is bounded to two levels (a
  * dimension's buckets may each carry one child dimension), matching the deepest
- * cross-tab the facet engine produces. Every dimension position also reports its
- * coverage gap, so buckets that sum to less than the stated total say so.
+ * cross-tab the facet engine produces; the flat variant drops the child position
+ * for the tool that requests single-dimension breakdowns only. Every dimension
+ * position also reports its coverage gap, so buckets that sum to less than the
+ * stated total say so.
  * @module mcp-server/tools/definitions/_schemas
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -20,15 +22,32 @@ export declare const CONTENT_TYPE_SCOPES: {
     predicted: "computational"[];
     all: ("computational" | "experimental")[];
 };
-/** A facet dimension and its buckets. */
+/**
+ * A facet dimension whose buckets are flat — the shape for a tool that requests
+ * single-dimension breakdowns only, so no bucket can ever carry a cross-tab.
+ */
+export declare const flatFacetDimensionSchema: z.ZodObject<{
+    dimension: z.ZodString;
+    buckets: z.ZodArray<z.ZodObject<{
+        label: z.ZodString;
+        count: z.ZodNumber;
+        rangeFrom: z.ZodOptional<z.ZodNumber>;
+        rangeTo: z.ZodOptional<z.ZodNumber>;
+    }, z.core.$strip>>;
+    truncated: z.ZodOptional<z.ZodBoolean>;
+    missingValueCount: z.ZodNumber;
+}, z.core.$strip>;
+/** A facet dimension whose buckets may each carry one nested cross-tab dimension. */
 export declare const facetDimensionSchema: z.ZodObject<{
     dimension: z.ZodString;
+    truncated: z.ZodOptional<z.ZodBoolean>;
+    missingValueCount: z.ZodNumber;
     buckets: z.ZodArray<z.ZodObject<{
         label: z.ZodString;
         count: z.ZodNumber;
         rangeFrom: z.ZodOptional<z.ZodNumber>;
         rangeTo: z.ZodOptional<z.ZodNumber>;
-        children: z.ZodOptional<z.ZodArray<z.ZodObject<{
+        child: z.ZodOptional<z.ZodObject<{
             dimension: z.ZodString;
             buckets: z.ZodArray<z.ZodObject<{
                 label: z.ZodString;
@@ -38,18 +57,29 @@ export declare const facetDimensionSchema: z.ZodObject<{
             }, z.core.$strip>>;
             truncated: z.ZodOptional<z.ZodBoolean>;
             missingValueCount: z.ZodNumber;
-        }, z.core.$strip>>>;
+        }, z.core.$strip>>;
     }, z.core.$strip>>;
-    truncated: z.ZodOptional<z.ZodBoolean>;
-    missingValueCount: z.ZodNumber;
 }, z.core.$strip>;
 export type FacetDimensionOutput = z.infer<typeof facetDimensionSchema>;
+export type FlatFacetDimensionOutput = z.infer<typeof flatFacetDimensionSchema>;
 /**
  * Project a domain {@link FacetDimension} to the output shape, capping buckets.
  * `total` is the population the buckets describe — the response total for a
  * top-level dimension, and the parent bucket's count for a nested one.
  */
 export declare function toFacetOutput(facet: FacetDimension, cap: number, total: number): FacetDimensionOutput;
+/**
+ * Buckets the response actually carries, summed over every dimension position:
+ * each dimension's own bucket list plus the nested cross-tab list under each of
+ * its buckets.
+ *
+ * Counted after {@link toFacetOutput} has sliced each position to the cap, so it
+ * is the realized size rather than what upstream aggregated. The cap bounds each
+ * position independently — a cross-tab reaches `cap × (1 + cap)` buckets — and
+ * the per-position `truncated` flags do not compose into that size, so a caller
+ * cannot derive it from the levels.
+ */
+export declare function countBuckets(facets: FacetDimensionOutput[]): number;
 /** Render a list of facet dimensions to markdown lines for `format()` parity. */
 export declare function renderFacets(facets: FacetDimensionOutput[]): string[];
 /**

package/dist/mcp-server/tools/definitions/_schemas.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/_schemas.js CHANGED Viewed

@@ -3,8 +3,10 @@
  * breakdown and a `content_type` scope — `protein_analyze_collection` and
  * `protein_search_structures`. Facet nesting is bounded to two levels (a
  * dimension's buckets may each carry one child dimension), matching the deepest
- * cross-tab the facet engine produces. Every dimension position also reports its
- * coverage gap, so buckets that sum to less than the stated total say so.
+ * cross-tab the facet engine produces; the flat variant drops the child position
+ * for the tool that requests single-dimension breakdowns only. Every dimension
+ * position also reports its coverage gap, so buckets that sum to less than the
+ * stated total say so.
  * @module mcp-server/tools/definitions/_schemas
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -49,31 +51,23 @@ const childDimensionSchema = z
 })
     .describe('A nested cross-tab dimension within a parent bucket.');
 /** A top-level facet bucket, optionally carrying a nested cross-tab dimension. */
-const bucketSchema = z
-    .object({
-    label: z.string().describe('Bucket value — category, numeric bin start, or period.'),
-    count: z.number().describe('Number of entries in the bucket.'),
-    rangeFrom: z
-        .number()
-        .optional()
-        .describe('Inclusive lower bound of a numeric histogram bin (= label). Present only for numeric facets (resolution, molecular_weight); absent for term/period facets.'),
-    rangeTo: z
-        .number()
-        .optional()
-        .describe('Exclusive upper bound of a numeric histogram bin (rangeFrom + bin interval), so the bin covers [rangeFrom, rangeTo). Present only for numeric facets.'),
-    children: z
-        .array(childDimensionSchema)
+const bucketSchema = leafBucketSchema
+    .extend({
+    child: childDimensionSchema
         .optional()
-        .describe('Nested dimension breakdown for cross-tabs (present only for multidimensional facets).'),
+        .describe('Nested dimension breakdown for a cross-tab. Present whenever a second dimension was requested — with an empty bucket list when nothing in this bucket carries a value for it — so its absence means no cross-tab was asked for. At most one: a bucket is never cross-tabbed by more than one dimension.'),
 })
     .describe('A top-level aggregation bucket, optionally cross-tabbed by a nested dimension.');
-/** A facet dimension and its buckets. */
-export const facetDimensionSchema = z
+/**
+ * A facet dimension whose buckets are flat — the shape for a tool that requests
+ * single-dimension breakdowns only, so no bucket can ever carry a cross-tab.
+ */
+export const flatFacetDimensionSchema = z
     .object({
     dimension: z
         .string()
         .describe('Friendly dimension name (e.g. method, organism, release_year).'),
-    buckets: z.array(bucketSchema).describe('Aggregation buckets, count-descending for terms.'),
+    buckets: z.array(leafBucketSchema).describe('Aggregation buckets, count-descending for terms.'),
     truncated: z
         .boolean()
         .optional()
@@ -83,6 +77,12 @@ export const facetDimensionSchema = z
         .describe('Matches in scope that carry no value for this attribute, so they count toward the response total but fall in no bucket (e.g. computed models have no experimental method; solution-NMR entries have no diffraction resolution). Independent of truncation — measured before the bucket cap is applied. 0 means no shortfall was detectable: a multi-valued attribute such as organism can place one match in several buckets, which offsets the shortfall rather than adding to it.'),
 })
     .describe('A facet dimension and its aggregation buckets.');
+/** A facet dimension whose buckets may each carry one nested cross-tab dimension. */
+export const facetDimensionSchema = flatFacetDimensionSchema
+    .extend({
+    buckets: z.array(bucketSchema).describe('Aggregation buckets, count-descending for terms.'),
+})
+    .describe('A facet dimension and its aggregation buckets, each optionally cross-tabbed.');
 /** Copy the numeric-histogram range onto an output bucket when present. */
 function withRange(b) {
     return b.rangeFrom !== undefined && b.rangeTo !== undefined
@@ -122,16 +122,16 @@ export function toFacetOutput(facet, cap, total) {
             label: b.label,
             count: b.count,
             ...withRange(b),
-            ...(b.children
+            ...(b.child
                 ? {
-                    children: b.children.map((c) => ({
-                        dimension: c.dimension,
-                        buckets: c.buckets
+                    child: {
+                        dimension: b.child.dimension,
+                        buckets: b.child.buckets
                             .slice(0, cap)
                             .map((cb) => ({ label: cb.label, count: cb.count, ...withRange(cb) })),
-                        ...(c.buckets.length > cap ? { truncated: true } : {}),
-                        missingValueCount: missingValueCount(c.buckets, b.count),
-                    })),
+                        ...(b.child.buckets.length > cap ? { truncated: true } : {}),
+                        missingValueCount: missingValueCount(b.child.buckets, b.count),
+                    },
                 }
                 : {}),
         })),
@@ -139,6 +139,26 @@ export function toFacetOutput(facet, cap, total) {
         missingValueCount: missingValueCount(facet.buckets, total),
     };
 }
+/**
+ * Buckets the response actually carries, summed over every dimension position:
+ * each dimension's own bucket list plus the nested cross-tab list under each of
+ * its buckets.
+ *
+ * Counted after {@link toFacetOutput} has sliced each position to the cap, so it
+ * is the realized size rather than what upstream aggregated. The cap bounds each
+ * position independently — a cross-tab reaches `cap × (1 + cap)` buckets — and
+ * the per-position `truncated` flags do not compose into that size, so a caller
+ * cannot derive it from the levels.
+ */
+export function countBuckets(facets) {
+    let count = 0;
+    for (const f of facets) {
+        count += f.buckets.length;
+        for (const b of f.buckets)
+            count += b.child?.buckets.length ?? 0;
+    }
+    return count;
+}
 /**
  * Render one bucket's `label: count` line, annotating numeric histogram buckets
  * with their explicit half-open `[rangeFrom, rangeTo)` bin so the bare boundary
@@ -180,12 +200,13 @@ export function renderFacets(facets) {
         }
         for (const b of f.buckets) {
             lines.push(`- ${renderBucket(b)}`);
-            for (const c of b.children ?? []) {
-                const inner = c.buckets.length === 0
-                    ? EMPTY_CHILD_DIMENSION_TEXT
-                    : c.buckets.map(renderBucket).join(', ');
-                lines.push(`  - ${c.dimension} → ${inner}${dimensionFlags(c)}`);
-            }
+            const c = b.child;
+            if (!c)
+                continue;
+            const inner = c.buckets.length === 0
+                ? EMPTY_CHILD_DIMENSION_TEXT
+                : c.buckets.map(renderBucket).join(', ');
+            lines.push(`  - ${c.dimension} → ${inner}${dimensionFlags(c)}`);
         }
     }
     return lines;
@@ -221,13 +242,14 @@ function coveragePositions(facets, total) {
         });
         const children = new Map();
         for (const b of f.buckets) {
-            for (const c of b.children ?? []) {
-                const acc = children.get(c.dimension) ?? { missing: 0, scope: 0, bucketCount: 0 };
-                acc.missing += c.missingValueCount;
-                acc.scope += b.count;
-                acc.bucketCount += c.buckets.length;
-                children.set(c.dimension, acc);
-            }
+            const c = b.child;
+            if (!c)
+                continue;
+            const acc = children.get(c.dimension) ?? { missing: 0, scope: 0, bucketCount: 0 };
+            acc.missing += c.missingValueCount;
+            acc.scope += b.count;
+            acc.bucketCount += c.buckets.length;
+            children.set(c.dimension, acc);
         }
         for (const [dimension, acc] of children)
             positions.push({ dimension, ...acc });

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1	+ 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package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts CHANGED Viewed

@@ -36,12 +36,14 @@ export declare const analyzeCollection: import("@cyanheads/mcp-ts-core").ToolDef
     total: z.ZodNumber;
     facets: z.ZodArray<z.ZodObject<{
         dimension: z.ZodString;
+        truncated: z.ZodOptional<z.ZodBoolean>;
+        missingValueCount: z.ZodNumber;
         buckets: z.ZodArray<z.ZodObject<{
             label: z.ZodString;
             count: z.ZodNumber;
             rangeFrom: z.ZodOptional<z.ZodNumber>;
             rangeTo: z.ZodOptional<z.ZodNumber>;
-            children: z.ZodOptional<z.ZodArray<z.ZodObject<{
+            child: z.ZodOptional<z.ZodObject<{
                 dimension: z.ZodString;
                 buckets: z.ZodArray<z.ZodObject<{
                     label: z.ZodString;
@@ -51,21 +53,25 @@ export declare const analyzeCollection: import("@cyanheads/mcp-ts-core").ToolDef
                 }, z.core.$strip>>;
                 truncated: z.ZodOptional<z.ZodBoolean>;
                 missingValueCount: z.ZodNumber;
-            }, z.core.$strip>>>;
+            }, z.core.$strip>>;
         }, z.core.$strip>>;
-        truncated: z.ZodOptional<z.ZodBoolean>;
-        missingValueCount: z.ZodNumber;
     }, 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 reason: "duplicate_dimension";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "group_by lists the same dimension twice, which would cross a dimension with itself.";
+    readonly recovery: "List each dimension at most once: one dimension for a breakdown, or two distinct dimensions for a cross-tab.";
 }], {
     readonly scope: z.ZodOptional<z.ZodString>;
     readonly notice: z.ZodOptional<z.ZodString>;
     readonly truncated: z.ZodOptional<z.ZodBoolean>;
     readonly shown: z.ZodOptional<z.ZodNumber>;
     readonly cap: z.ZodOptional<z.ZodNumber>;
+    readonly bucketsReturned: z.ZodNumber;
 }>;
 //# sourceMappingURL=analyze-collection.tool.d.ts.map

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

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/analyze-collection.tool.js CHANGED Viewed

@@ -11,7 +11,7 @@ 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 { CONTENT_TYPE_SCOPES, coverageNotices, facetDimensionSchema, renderFacets, toFacetOutput, } from './_schemas.js';
+import { CONTENT_TYPE_SCOPES, countBuckets, coverageNotices, facetDimensionSchema, renderFacets, toFacetOutput, } from './_schemas.js';
 /**
  * Dimensions RCSB cannot aggregate over computed models: an AlphaFold /
  * ModelArchive record carries no experimental method or resolution, so the
@@ -25,7 +25,9 @@ export const analyzeCollection = tool('protein_analyze_collection', {
         '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).',
+        'two distinct dimensions for a cross-tab (the first nests the second). bucket_limit caps each dimension ' +
+        'level separately rather than the response, so a cross-tab returns up to that many nested buckets under ' +
+        'each of its capped parent buckets; bucketsReturned reports the realized total.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -34,13 +36,19 @@ export const analyzeCollection = tool('protein_analyze_collection', {
             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.',
         },
+        {
+            reason: 'duplicate_dimension',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: 'group_by lists the same dimension twice, which would cross a dimension with itself.',
+            recovery: 'List each dimension at most once: one dimension for a breakdown, or two distinct dimensions for a cross-tab.',
+        },
     ],
     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).'),
+            .describe('1 dimension for a breakdown, or 2 distinct dimensions for a cross-tab (the first nests the second). Repeating a dimension is rejected.'),
         query: z
             .string()
             .optional()
@@ -76,7 +84,10 @@ export const analyzeCollection = tool('protein_analyze_collection', {
             .min(1)
             .max(500)
             .optional()
-            .describe('Max buckets per dimension. Defaults to the server PROTEIN_FACET_BUCKET_CAP.'),
+            .describe('Max buckets per dimension level, not per response. A cross-tab applies the cap separately to the ' +
+            'parent dimension and to the nested child inside each parent bucket, so up to ' +
+            'bucket_limit × (1 + bucket_limit) buckets can come back — 2550 at the default 50. The realized ' +
+            'count comes back as bucketsReturned. Defaults to the server PROTEIN_FACET_BUCKET_CAP.'),
     }),
     output: z.object({
         total: z.number().describe('Total entries in the scoped collection.'),
@@ -94,6 +105,11 @@ export const analyzeCollection = tool('protein_analyze_collection', {
             .describe('True when a dimension had more buckets than the applied cap.'),
         shown: z.number().optional().describe('Buckets returned for the capped dimension.'),
         cap: z.number().optional().describe('Per-dimension bucket cap that was applied.'),
+        bucketsReturned: z
+            .number()
+            .describe('Buckets in this response, summed over every dimension level: the top-level buckets plus, for a ' +
+            'cross-tab, the nested child buckets under each of them. Since bucket_limit caps each level ' +
+            'separately, this is the size those caps actually produced — always present, cross-tab or not.'),
     },
     async handler(input, ctx) {
         const cfg = getServerConfig();
@@ -104,6 +120,12 @@ export const analyzeCollection = tool('protein_analyze_collection', {
             throw ctx.fail('unknown_dimension', 'group_by requires at least one dimension.', {
                 ...ctx.recoveryFor('unknown_dimension'),
             });
+        // A repeated dimension would nest a facet inside itself upstream. RCSB answers
+        // that with same-attribute overlap, not a cross-tab between two dimensions —
+        // an undocumented shape no caller can read, so reject before the call.
+        const duplicate = input.group_by.find((d, i, all) => all.indexOf(d) !== i);
+        if (duplicate)
+            throw ctx.fail('duplicate_dimension', `group_by lists "${duplicate}" twice; a cross-tab needs two distinct dimensions.`, { ...ctx.recoveryFor('duplicate_dimension') });
         const spec = buildFacetSpec(primary, input.interval, secondary);
         const { total, facets } = await rcsb.analyzeFacets({
             ...(input.query ? { text: input.query } : {}),
@@ -115,6 +137,9 @@ export const analyzeCollection = tool('protein_analyze_collection', {
             contentType: CONTENT_TYPE_SCOPES[input.content_type],
         }, [spec], ctx);
         const out = facets.map((f) => toFacetOutput(f, cap, total));
+        // The cap bounds each dimension level, so a cross-tab's size is the product of
+        // two capped lists rather than one. Report what the response actually holds.
+        ctx.enrich({ bucketsReturned: countBuckets(out) });
         // Every advisory writes the same `notice` field (ctx.enrich.truncated routes
         // through it and is last-wins), and a cross-tab under predicted content can
         // trip several at once — collect the fragments and emit them as ONE notice.
@@ -125,9 +150,7 @@ export const analyzeCollection = tool('protein_analyze_collection', {
             notices.push(`One or more dimensions exceeded ${cap} buckets and were capped; scope the query tighter for the long tail.`);
         }
         if (input.content_type === 'predicted') {
-            // Deduped: group_by permits the same dimension twice, and "method and
-            // method" would read as two findings.
-            const blind = [...new Set(input.group_by.filter((d) => EXPERIMENTAL_ONLY_DIMENSIONS.has(d)))];
+            const blind = input.group_by.filter((d) => EXPERIMENTAL_ONLY_DIMENSIONS.has(d));
             if (blind.length > 0) {
                 notices.push(`${blind.join(' and ')} ${blind.length > 1 ? 'are' : 'is'} empty under content_type "predicted": computed models carry no experimental method or resolution metadata. Use content_type "experimental" or "all", or group by organism, polymer_type, release_year, or molecular_weight.`);
             }

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

@@ -54,6 +54,11 @@ export declare const compareStructures: import("@cyanheads/mcp-ts-core").ToolDef
     readonly code: JsonRpcErrorCode.InvalidParams;
     readonly when: "A resume entry's a/b labels don't match any pair generated from structures + reference.";
     readonly recovery: "Copy each resume entry's a, b, and uuid verbatim from a prior response's pairs[], and keep structures and reference unchanged between calls.";
+}, {
+    readonly reason: "no_distinct_pair";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "Every entry in structures[] denotes the same structure, leaving no pair to align.";
+    readonly recovery: "Pass at least two different structures (entry ID, or entry ID + chain); a structure repeated in the list is compared once.";
 }], {
     readonly pairsTotal: z.ZodNumber;
     readonly computing: z.ZodNumber;

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

	@@ -1 +1 @@
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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;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAsHjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmK5B,CAAC"}

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

@@ -23,7 +23,7 @@ const inputSchema = z.object({
         .describe('A structure to align, by PDB entry ID with optional chain.'))
         .min(2)
         .max(25)
-        .describe('The structures to compare, up to the configured batch cap (excess is dropped with a notice).'),
+        .describe('The structures to compare, up to the configured batch cap (excess is dropped with a notice). A structure repeated here is compared once.'),
     reference: z
         .enum(['first', 'all_pairs'])
         .default('first')
@@ -117,6 +117,12 @@ export const compareStructures = tool('protein_compare_structures', {
             when: "A resume entry's a/b labels don't match any pair generated from structures + reference.",
             recovery: "Copy each resume entry's a, b, and uuid verbatim from a prior response's pairs[], and keep structures and reference unchanged between calls.",
         },
+        {
+            reason: 'no_distinct_pair',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: 'Every entry in structures[] denotes the same structure, leaving no pair to align.',
+            recovery: 'Pass at least two different structures (entry ID, or entry ID + chain); a structure repeated in the list is compared once.',
+        },
     ],
     input: inputSchema,
     output: outputSchema,
@@ -127,10 +133,18 @@ export const compareStructures = tool('protein_compare_structures', {
     },
     async handler(input, ctx) {
         const cfg = getServerConfig();
-        const structures = input.structures.slice(0, cfg.maxCompareStructures);
         const notices = [];
-        if (input.structures.length > cfg.maxCompareStructures) {
-            notices.push(`Capped at ${cfg.maxCompareStructures} structures; ${input.structures.length - cfg.maxCompareStructures} ignored.`);
+        const { unique, repeated } = dedupeStructures(input.structures);
+        if (repeated.length > 0) {
+            notices.push(`Compared ${[...new Set(repeated)].join(', ')} once: a structure repeated in structures[] adds a self-alignment and a mirrored pair, not a new comparison.`);
+        }
+        if (unique.length < 2) {
+            const [only] = unique;
+            throw ctx.fail('no_distinct_pair', `Every entry in structures[] denotes ${only ? label(only) : 'one structure'}; there is no second structure to align it against.`, { ...ctx.recoveryFor('no_distinct_pair') });
+        }
+        const structures = unique.slice(0, cfg.maxCompareStructures);
+        if (unique.length > cfg.maxCompareStructures) {
+            notices.push(`Capped at ${cfg.maxCompareStructures} structures; ${unique.length - cfg.maxCompareStructures} ignored.`);
         }
         const timeoutMs = input.timeout_s ? input.timeout_s * 1000 : cfg.asyncPollTimeoutMs;
         const method = input.method;
@@ -215,6 +229,30 @@ export const compareStructures = tool('protein_compare_structures', {
         return [{ type: 'text', text: lines.join('\n') }];
     },
 });
+/**
+ * Collapse entries that denote the same structure to their first occurrence,
+ * keyed exactly as {@link pairKey} normalizes labels. Two entries for one
+ * structure yield pairs that are indistinguishable under that key — `(A,B)` and
+ * `(B,A)` collapse to one — so a single resume ticket would be applied to two
+ * separate alignment jobs, silently discarding one. Case-folding the whole label
+ * follows the same normalization: distinguishing chains `A` and `a` here would
+ * hand the resume lookup two pairs it cannot tell apart.
+ */
+function dedupeStructures(structures) {
+    const seen = new Set();
+    const unique = [];
+    const repeated = [];
+    for (const s of structures) {
+        const key = label(s);
+        if (seen.has(key)) {
+            repeated.push(label(s));
+            continue;
+        }
+        seen.add(key);
+        unique.push(s);
+    }
+    return { unique, repeated };
+}
 function buildPairs(structures, reference) {
     const pairs = [];
     if (reference === 'first') {
@@ -244,10 +282,18 @@ function label(s) {
     return s.chain ? `${s.pdb_id.toUpperCase()}.${s.chain}` : s.pdb_id.toUpperCase();
 }
 /**
- * Canonical, order- and case-insensitive key for a pair of structure labels, so a
- * resume entry matches its pair regardless of which side the client copied first.
+ * Canonical, order-insensitive key for a pair of structure labels, so a resume
+ * entry matches its pair regardless of which side the client copied first. The
+ * entry ID is case-folded; the chain suffix is NOT — mmCIF `label_asym_id` is
+ * case-sensitive, so chains `A` and `a` are different chains and must key apart.
  */
+function normalizeLabel(value) {
+    const dot = value.indexOf('.');
+    return dot === -1
+        ? value.toUpperCase()
+        : `${value.slice(0, dot).toUpperCase()}.${value.slice(dot + 1)}`;
+}
 function pairKey(a, b) {
-    return [a.toUpperCase(), b.toUpperCase()].sort().join('\u0000');
+    return [normalizeLabel(a), normalizeLabel(b)].sort().join('\u0000');
 }
 //# sourceMappingURL=compare-structures.tool.js.map

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

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts CHANGED Viewed

@@ -50,17 +50,6 @@ export declare const searchStructures: import("@cyanheads/mcp-ts-core").ToolDefi
             count: z.ZodNumber;
             rangeFrom: z.ZodOptional<z.ZodNumber>;
             rangeTo: z.ZodOptional<z.ZodNumber>;
-            children: z.ZodOptional<z.ZodArray<z.ZodObject<{
-                dimension: z.ZodString;
-                buckets: z.ZodArray<z.ZodObject<{
-                    label: z.ZodString;
-                    count: z.ZodNumber;
-                    rangeFrom: z.ZodOptional<z.ZodNumber>;
-                    rangeTo: z.ZodOptional<z.ZodNumber>;
-                }, z.core.$strip>>;
-                truncated: z.ZodOptional<z.ZodBoolean>;
-                missingValueCount: z.ZodNumber;
-            }, z.core.$strip>>>;
         }, z.core.$strip>>;
         truncated: z.ZodOptional<z.ZodBoolean>;
         missingValueCount: z.ZodNumber;
@@ -70,6 +59,11 @@ export declare const searchStructures: import("@cyanheads/mcp-ts-core").ToolDefi
     readonly code: JsonRpcErrorCode.InvalidParams;
     readonly when: "No query, sequence, or organism was provided — nothing to search on.";
     readonly recovery: "Provide a free-text query, a protein sequence, or an organism name (filters alone are not enough).";
+}, {
+    readonly reason: "duplicate_dimension";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "facets lists the same dimension twice, which would return that breakdown twice.";
+    readonly recovery: "List each facet dimension at most once; drop the repeated value and re-call.";
 }], {
     readonly totalCount: z.ZodNumber;
     readonly effectiveQuery: z.ZodOptional<z.ZodString>;

package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"search-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqCjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAoN3B,CAAC"}

package/dist/mcp-server/tools/definitions/search-structures.tool.js CHANGED Viewed

@@ -11,7 +11,7 @@ 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 { entryIdOf } from '../../../services/shared/identifiers.js';
-import { CONTENT_TYPE_SCOPES, coverageNotices, facetDimensionSchema, renderFacets, toFacetOutput, } from './_schemas.js';
+import { CONTENT_TYPE_SCOPES, coverageNotices, flatFacetDimensionSchema, renderFacets, toFacetOutput, } from './_schemas.js';
 /**
  * Zero-hit advice, per scope. Only the two single-universe scopes have a wider
  * one to switch to; under `all` both universes were already searched, so telling
@@ -49,6 +49,12 @@ export const searchStructures = tool('protein_search_structures', {
             when: 'No query, sequence, or organism was provided — nothing to search on.',
             recovery: 'Provide a free-text query, a protein sequence, or an organism name (filters alone are not enough).',
         },
+        {
+            reason: 'duplicate_dimension',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: 'facets lists the same dimension twice, which would return that breakdown twice.',
+            recovery: 'List each facet dimension at most once; drop the repeated value and re-call.',
+        },
     ],
     input: z.object({
         query: z
@@ -90,7 +96,7 @@ export const searchStructures = tool('protein_search_structures', {
         facets: z
             .array(z.enum(FACET_DIMENSION_NAMES))
             .optional()
-            .describe('Optional dimensions to summarize as a facet breakdown alongside the hits.'),
+            .describe('Optional dimensions to summarize as a facet breakdown alongside the hits. Each dimension at most once; repeating one is rejected.'),
         limit: z.number().int().min(1).max(100).default(25).describe('Maximum hits to return (1–100).'),
     }),
     output: z.object({
@@ -123,9 +129,9 @@ export const searchStructures = tool('protein_search_structures', {
             .describe('A ranked structure hit with optional enrichment metadata.'))
             .describe('Ranked structure hits.'),
         facets: z
-            .array(facetDimensionSchema)
+            .array(flatFacetDimensionSchema)
             .optional()
-            .describe('Optional facet breakdown when requested.'),
+            .describe('Optional facet breakdown when requested — one flat dimension per requested facet. Cross-tabs (a dimension nested inside another) are protein_analyze_collection territory.'),
     }),
     enrichment: {
         totalCount: z.number().describe('Total matches upstream before pagination.'),
@@ -141,6 +147,12 @@ export const searchStructures = tool('protein_search_structures', {
                 ...ctx.recoveryFor('no_criteria'),
             });
         }
+        // RCSB collapses two identically-named facet requests into one raw facet, and
+        // the attribute-keyed lookup maps both specs back onto it — a repeated
+        // dimension would return the same breakdown twice and double-count on any sum.
+        const duplicate = input.facets?.find((d, i, all) => all.indexOf(d) !== i);
+        if (duplicate)
+            throw ctx.fail('duplicate_dimension', `facets lists "${duplicate}" more than once; each dimension is summarized once.`, { ...ctx.recoveryFor('duplicate_dimension') });
         const cfg = getServerConfig();
         const rcsb = getRcsbService();
         const facetSpecs = input.facets?.map((d) => buildFacetSpec(d));

package/dist/mcp-server/tools/definitions/search-structures.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/rcsb/rcsb-service.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/rcsb/rcsb-service.js CHANGED Viewed

@@ -386,14 +386,18 @@ function normalizeBuckets(raw, spec) {
                 bucket.rangeTo = from + interval;
             }
         }
-        if (child && b.facets) {
-            bucket.children = [
-                {
-                    dimension: child.dimension,
-                    attribute: child.attribute,
-                    buckets: normalizeBuckets(b.facets[0]?.buckets, child),
-                },
-            ];
+        // Keyed on the SPEC, not the response: RCSB omits the nested facet key
+        // outright when nothing in the parent bucket carries a value for the child
+        // attribute (computed models have no experimental method). Emitting the child
+        // with an empty bucket list keeps a two-dimension request two-dimensional, so
+        // a present child means "a cross-tab was requested" and empty buckets mean
+        // "it aggregated to nothing" — conditions an absent child conflated.
+        if (child) {
+            bucket.child = {
+                dimension: child.dimension,
+                attribute: child.attribute,
+                buckets: normalizeBuckets(b.facets?.[0]?.buckets, child),
+            };
         }
         return bucket;
     });

package/dist/services/rcsb/rcsb-service.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/services/rcsb/types.d.ts CHANGED Viewed

@@ -11,10 +11,17 @@ export interface SearchHit {
     /** RCSB relevance score. */
     score: number;
 }
-/** One facet bucket; `children` present only for multidimensional (nested) facets. */
+/** One facet bucket; `child` present only for multidimensional (nested) facets. */
 export interface FacetBucket {
-    /** Nested sub-facets for multidimensional cross-tabs. */
-    children?: FacetDimension[];
+    /**
+     * The single nested sub-facet for a multidimensional cross-tab. A facet spec
+     * carries at most one child and the request builder sends exactly one nested
+     * facet, so a bucket is never cross-tabbed by more than one dimension. Present
+     * whenever a child dimension was requested — with an empty bucket list when the
+     * scope carries no value for it (computed models have no experimental method),
+     * so the shape reflects what was asked for rather than dropping the dimension.
+     */
+    child?: FacetDimension;
     /** Count of entries in the bucket. */
     count: number;
     /** Bucket label (category value, numeric bin start, or period). */

package/dist/services/rcsb/types.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/protein-mcp-server",
-  "version": "0.4.2",
+  "version": "0.5.1",
   "mcpName": "io.github.cyanheads/protein-mcp-server",
   "description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
   "type": "module",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/protein-mcp-server",
     "source": "github"
   },
-  "version": "0.4.2",
+  "version": "0.5.1",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.4.2",
+      "version": "0.5.1",
       "packageArguments": [
         {
           "type": "positional",
@@ -48,7 +48,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.4.2",
+      "version": "0.5.1",
       "packageArguments": [
         {
           "type": "positional",