npm - @cyanheads/protein-mcp-server - Versions diffs - 0.6.0 → 0.8.0 - Mend

@cyanheads/protein-mcp-server 0.6.0 → 0.8.0

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Files changed (40) hide show

package/AGENTS.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** protein-mcp-server
-**Version:** 0.6.0
+**Version:** 0.8.0
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.7`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0
@@ -63,7 +63,7 @@ export const getAnnotations = tool('protein_get_annotations', {
     {
       reason: 'no_uniprot_mapping',
       code: JsonRpcErrorCode.NotFound,
-      when: 'A PDB ID has no UniProt cross-reference, or neither uniprot nor pdb_id was provided.',
+      when: 'A supplied PDB ID resolved to no usable UniProt cross-reference.',
       recovery: 'Pass a UniProt accession directly, or use protein_search_structures to find a modeled protein chain.',
     },
   ],

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** protein-mcp-server
-**Version:** 0.6.0
+**Version:** 0.8.0
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.7`
 **Engines:** Bun ≥1.3.0, Node ≥24.0.0
 **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0
@@ -63,7 +63,7 @@ export const getAnnotations = tool('protein_get_annotations', {
     {
       reason: 'no_uniprot_mapping',
       code: JsonRpcErrorCode.NotFound,
-      when: 'A PDB ID has no UniProt cross-reference, or neither uniprot nor pdb_id was provided.',
+      when: 'A supplied PDB ID resolved to no usable UniProt cross-reference.',
       recovery: 'Pass a UniProt accession directly, or use protein_search_structures to find a modeled protein chain.',
     },
   ],

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![Version](https://img.shields.io/badge/Version-0.6.0-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-^2.0.0-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-v1.4.0-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-0.8.0-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-^2.0.0-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-v1.4.0-blueviolet.svg?style=flat-square)](https://bun.sh/)
 </div>
@@ -62,7 +62,9 @@ Fetch structures with metadata and coordinate-file URLs, resolving across provid
 - `source: predicted` takes UniProt accessions and returns the AlphaFold model with pLDDT/PAE confidence
 - `source: best_available` takes UniProt accessions and returns the top federated model (experimental if one exists, else the best prediction)
 - Per-ID partial success — unresolved IDs are listed in `failed[]`, not a batch-level error
-- `include_coords` inlines coordinate content; when a batch overflows the response budget it returns a per-structure size outline, so you can re-call with `sections: [ids]` for specific structures
+- Batch cap disclosure — `requested` is the original request length and `processed` the count after the cap, so IDs dropped beyond the cap are visible rather than silently discarded; every advisory (cap, partial failure, coordinate overflow, failed inlining) is joined into one `notice`
+- Records served by the RCSB entry endpoint also carry `polymerEntities` (with both `authAsymIds` and `labelAsymIds`), `ligands`, `molecularWeight`, and `releaseDate`
+- `include_coords` inlines coordinate content, subject to the response budget: a batch over budget returns a per-structure size outline you can re-call with `sections: [ids]`, and a single file over budget is withheld with a pointer to its `coordinateUrls` (a `sections` re-call would return the same bytes). A `sections` re-call is not re-gated — `structuredContent` carries the named payload whole at any size, while the token-bounded text surface withholds anything over the budget and points at `coordinateUrls` instead of truncating it
 - Every response carries an `attribution` block naming the upstream data licenses and citations (see [Upstream data licensing](#upstream-data-licensing))
 ---
@@ -73,9 +75,10 @@ Find structurally or evolutionarily related proteins, by sequence or by fold.
 - `by: sequence` runs a synchronous RCSB mmseqs2 search; `by: structure` runs an asynchronous Foldseek search against experimental and predicted databases
 - Query from a raw one-letter sequence, a PDB ID, or a UniProt accession
-- Sequence searches accept `start` with `limit` and return `nextStart` while another page remains
+- Both modes accept `start` with `limit` and report `totalCount`, echoing `start` and returning `nextStart` while another page remains
 - Foldseek targets default to `pdb100` + `afdb50`; override via `databases` (e.g. `afdb-swissprot`, `BFVD`)
-- Async jobs that exceed the poll budget return `status: computing` with a `ticketId` — re-call with `ticket_id` set to that value to poll the same job instead of resubmitting
+- Async jobs that exceed the poll budget return `status: computing` with a `ticketId` — re-call with `ticket_id` set to that value to poll the same job instead of resubmitting. A completed structure search returns the same ticket, so a new `start` pages the finished job without resubmitting the structure
+- Each mode reads only its own controls — `sequence`, `max_evalue` and `min_identity` under `by: sequence`; `ticket_id` and `databases` under `by: structure`; `pdb_id`, `uniprot`, `start` and `limit` shared — and a field the selected mode cannot consume is rejected rather than ignored
 - Each hit names the engine and source database it came from
 ---
@@ -85,6 +88,7 @@ Find structurally or evolutionarily related proteins, by sequence or by fold.
 Ligand discovery and binding-site analysis across the PDB.
 - `mode: find_ligand` resolves a name or formula to chemical component IDs with formula, weight, SMILES, and InChIKey
+- A formula-shaped `query` matches on exact composition — spaced (`C29 H31 N7 O`) or unspaced (`C29H31N7O`), either resolves the same component; anything else, a component ID included, matches on name and synonyms and is ranked by deposition frequency
 - `mode: structures_with_ligand` returns PDB entries containing a ligand by exact component ID
 - `mode: structures_with_ligand` accepts `start` with `limit` and returns `nextStart` while another page remains
 - `mode: binding_site` returns the protein residues lining a ligand's pocket in a structure, with contact distances
@@ -136,7 +140,7 @@ Sequence and functional annotation for a protein.
 | Type | Name | Description |
 |:---|:---|:---|
-| Resource | `pdb://{entry_id}` | Experimental structure summary for a PDB entry — title, method, resolution, organism, chains, and bound ligands. |
+| Resource | `pdb://{entry_id}` | Experimental structure summary for a PDB entry — title, method, resolution, organism, bound ligands, and per-entity chain IDs in both the author (`authAsymIds`) and mmCIF label (`labelAsymIds`) namespaces. |
 | Resource | `af://{uniprot}` | Predicted-structure summary for a UniProt accession from AlphaFold DB — mean pLDDT, confidence-band fractions, model URLs, and version. |
 All resource data is also reachable via tools — `pdb://{entry_id}` mirrors `protein_get_structure` for `source: experimental`, and `af://{uniprot}` mirrors it for `source: predicted`. Many MCP clients are tool-only and don't surface resources; the summaries remain reachable through the tools.

package/changelog/0.7.x/0.7.0.md ADDED Viewed

@@ -0,0 +1,25 @@
+---
+summary: "protein_get_structure exposes per-entity authAsymIds/labelAsymIds chain namespaces plus entry detail (ligands, molecular weight, release date), accumulates every advisory instead of overwriting, and gates the coordinate overflow budget on a single oversized file too; pdb://{entry_id}'s polymerEntities[].chains is renamed to authAsymIds."
+breaking: true
+security: false
+---
+# 0.7.0 — 2026-09-08
+## Added
+- **`protein_get_structure`** and **`pdb://{entry_id}`** expose per-polymer-entity `authAsymIds` (`auth_asym_id`) and `labelAsymIds` (`label_asym_id`) — the two chain namespaces are unrelated by any transformation and each feeds a different tool parameter ([#45](https://github.com/cyanheads/protein-mcp-server/issues/45)).
+- **`protein_get_structure`** experimental records now also carry `polymerEntities`, `ligands`, `molecularWeight`, and `releaseDate`, matching `pdb://{entry_id}` for the same entry ([#45](https://github.com/cyanheads/protein-mcp-server/issues/45)).
+- **`protein_get_structure`** enrichment gains a `processed` field — the ID count after the batch cap — alongside `requested` ([#43](https://github.com/cyanheads/protein-mcp-server/issues/43)).
+## Changed
+- **`pdb://{entry_id}`'s `polymerEntities[].chains`** is renamed to `authAsymIds`; `protein_get_annotations`' `chain` description and its `chain_not_found` recovery hint now point at `authAsymIds` ([#45](https://github.com/cyanheads/protein-mcp-server/issues/45)).
+- **`protein_get_structure`'s `requested`** now reports the original `input.ids.length`, not the post-cap count — a call over the batch cap previously reported `requested` equal to the capped `processed` value ([#43](https://github.com/cyanheads/protein-mcp-server/issues/43)).
+- **`protein_compare_structures`'** `chain` description now names `label_asym_id` and points at `polymerEntities[].labelAsymIds`, distinguishing it from the author-chain namespace `protein_get_annotations.chain` takes ([#45](https://github.com/cyanheads/protein-mcp-server/issues/45)).
+## Fixed
+- **`protein_get_structure`** no longer loses the batch-cap advisory when a partial failure or coordinate overflow follows it — every applicable advisory (cap, partial failure, overflow, failed inlining) now accumulates into one `notice` instead of the last write winning ([#43](https://github.com/cyanheads/protein-mcp-server/issues/43)).
+- **`protein_get_structure`'s coordinate-inlining budget** now also gates a single requested file — previously only a batch of 2+ triggered the overflow guard, so one oversized file (e.g. `4HHB.cif` at 772 KB) inlined whole on `structuredContent` while `format()` silently truncated it to a 2,000-byte prefix ([#42](https://github.com/cyanheads/protein-mcp-server/issues/42)).
+- **`protein_get_structure`** now names the structure ID when its coordinate fetch fails, instead of returning a response indistinguishable from one where coordinates were never requested ([#42](https://github.com/cyanheads/protein-mcp-server/issues/42)).

package/changelog/0.8.x/0.8.0.md ADDED Viewed

@@ -0,0 +1,22 @@
+---
+summary: "protein_find_similar rejects fields the selected by mode can't consume and paginates completed structure searches with a re-usable ticket; protein_get_annotations reclassifies a missing or malformed identifier as InvalidParams; plus RCSB GraphQL, ligand-formula, and get_structure text-surface fixes."
+breaking: true
+security: false
+---
+# 0.8.0 — 2026-09-09
+## Added
+- **`protein_find_similar`** (`by: "structure"`) reports `totalCount`/`start`/`nextStart` on a completed Foldseek search, and a complete response now carries `ticketId` so a finished job can be re-paged with a new `start` instead of resubmitted ([#53](https://github.com/cyanheads/protein-mcp-server/issues/53)).
+## Changed
+- **`protein_find_similar`** rejects an input field the selected `by` mode can't consume — `sequence`/`max_evalue`/`min_identity` under `by: "structure"`, `ticket_id`/a non-empty `databases` under `by: "sequence"` — under a new `mode_mismatched_field` reason, instead of silently dropping it ([#57](https://github.com/cyanheads/protein-mcp-server/issues/57)).
+- **`protein_get_annotations`** rejects a missing identifier or a malformed `uniprot` accession as `InvalidParams` (`missing_identifier`/`invalid_accession`), instead of `NotFound`/`no_uniprot_mapping` ([#46](https://github.com/cyanheads/protein-mcp-server/issues/46)).
+## Fixed
+- **`RcsbService.graphql()`** throws on a non-empty `errors` array even when `data` is also present, instead of returning the partial payload as an ordinary sparse record ([#48](https://github.com/cyanheads/protein-mcp-server/issues/48)).
+- **`protein_track_ligands`** (`mode: find_ligand`) routes a formula-shaped `query` (spaced or unspaced Hill notation) through RCSB's `chemical`/`formula` terminal instead of the name/synonym search, falling back to the name search when the formula terminal matches nothing ([#50](https://github.com/cyanheads/protein-mcp-server/issues/50)).
+- **`protein_get_structure`**'s text surface no longer truncates inlined coordinates to a 2,000-character prefix — a structure under the response budget renders whole, one over it gets the same withheld marker the batch-overflow gate already renders ([#59](https://github.com/cyanheads/protein-mcp-server/issues/59)).

package/dist/mcp-server/resources/definitions/pdb-summary.resource.d.ts CHANGED Viewed

@@ -1,7 +1,8 @@
 /**
  * @fileoverview pdb://{entry_id} — experimental structure summary (title, method,
- * resolution, organism, ligands, chains). The injectable-context twin of
- * protein_get_structure for source: experimental.
+ * resolution, organism, ligands, and per-entity chain IDs in both the author and
+ * mmCIF label namespaces). The injectable-context twin of protein_get_structure
+ * for source: experimental.
  * @module mcp-server/resources/definitions/pdb-summary.resource
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -19,7 +20,8 @@ export declare const pdbSummaryResource: import("@cyanheads/mcp-ts-core").Resour
         entityId: z.ZodString;
         description: z.ZodOptional<z.ZodString>;
         organism: z.ZodOptional<z.ZodString>;
-        chains: z.ZodOptional<z.ZodArray<z.ZodString>>;
+        authAsymIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
+        labelAsymIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
         sequenceLength: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
     ligands: z.ZodArray<z.ZodObject<{

package/dist/mcp-server/resources/definitions/pdb-summary.resource.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"pdb-summary.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/pdb-summary.resource.ts"],"names":[],"mappings":"AAAA~~;;;;;GAKG~~;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAIrD~~,eAAO,MAAM,kBAAkB~~;;;;;;;;;;;;;;;;;;;;;;6BA+D7B~~,CAAC"}
1	+ {"version":3,"file":"pdb-summary.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/pdb-summary.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAKrD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;6BA6C7B,CAAC"}

package/dist/mcp-server/resources/definitions/pdb-summary.resource.js CHANGED Viewed

@@ -1,16 +1,18 @@
 /**
  * @fileoverview pdb://{entry_id} — experimental structure summary (title, method,
- * resolution, organism, ligands, chains). The injectable-context twin of
- * protein_get_structure for source: experimental.
+ * resolution, organism, ligands, and per-entity chain IDs in both the author and
+ * mmCIF label namespaces). The injectable-context twin of protein_get_structure
+ * for source: experimental.
  * @module mcp-server/resources/definitions/pdb-summary.resource
  */
 import { resource, z } from '@cyanheads/mcp-ts-core';
 import { notFound } from '@cyanheads/mcp-ts-core/errors';
+import { ligandSchema, polymerEntitySchema } from '../../tools/definitions/_schemas.js';
 import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
 export const pdbSummaryResource = resource('pdb://{entry_id}', {
     name: 'pdb-structure-summary',
     title: 'PDB structure summary',
-    description: 'Experimental structure summary for a PDB entry: title, method, resolution, organism, chains, and bound ligands.',
+    description: 'Experimental structure summary for a PDB entry: title, method, resolution, organism, bound ligands, and per-entity chain IDs in both the author (auth_asym_id) and mmCIF label (label_asym_id) namespaces.',
     mimeType: 'application/json',
     params: z.object({
         entry_id: z.string().describe('PDB entry ID (e.g. 4HHB).'),
@@ -24,25 +26,9 @@ export const pdbSummaryResource = resource('pdb://{entry_id}', {
         releaseDate: z.string().optional().describe('Initial release date (ISO 8601).'),
         organisms: z.array(z.string()).describe('Source organisms.'),
         polymerEntities: z
-            .array(z
-            .object({
-            entityId: z.string().describe('Polymer entity ID.'),
-            description: z.string().optional().describe('Entity description.'),
-            organism: z.string().optional().describe('Source organism.'),
-            chains: z.array(z.string()).optional().describe('Author chain IDs.'),
-            sequenceLength: z.number().optional().describe('Residue count.'),
-        })
-            .describe('A modeled polymer entity (chain group).'))
-            .describe('Modeled polymer entities.'),
-        ligands: z
-            .array(z
-            .object({
-            compId: z.string().describe('Chemical component ID.'),
-            name: z.string().optional().describe('Chemical name.'),
-            formula: z.string().optional().describe('Molecular formula.'),
-        })
-            .describe('A bound ligand (non-polymer chemical component).'))
-            .describe('Bound ligands.'),
+            .array(polymerEntitySchema)
+            .describe('Modeled polymer entities, each carrying both chain namespaces — authAsymIds for protein_get_annotations, labelAsymIds for protein_compare_structures.'),
+        ligands: z.array(ligandSchema).describe('Bound ligands.'),
     }),
     async handler(params, ctx) {
         const [meta] = await getRcsbService().getEntries([params.entry_id], ctx);

package/dist/mcp-server/resources/definitions/pdb-summary.resource.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"pdb-summary.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/pdb-summary.resource.ts"],"names":[],"mappings":"AAAA~~;;;;;GAKG~~;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AACzD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,MAAM,CAAC,MAAM,kBAAkB,GAAG,QAAQ,CAAC,kBAAkB,EAAE;IAC7D,IAAI,EAAE,uBAAuB;IAC7B,KAAK,EAAE,uBAAuB;IAC9B,WAAW,EACT,~~iHAAiH~~;~~IACnH~~,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;KAC3D,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;QACxC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QACzD,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;QAC3E,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QAC9D,eAAe,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;QACpF,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QAC/E,SAAS,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,mBAAmB,CAAC;QAC5D,eAAe,EAAE,CAAC;aACf,KAAK,~~CACJ,~~CAAC~~;aACE~~,MAAM,CAAC;YACN,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;YACnD,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qBAAqB,CAAC;YAClE,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;YAC5D,MAAM,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;~~YACpE~~,~~cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,~~QAAQ,~~EAAE~~,~~CAAC~~,~~QAAQ,CAAC,gBAAgB,CAAC~~;~~SACjE~~,~~CAAC;aACD,QAAQ,CAAC,yCAAyC,CAAC,CACvD;aACA,QAAQ,CAAC,2BAA2B,CAAC;QACxC,~~OAAO,EAAE,CAAC~~;aACP~~,~~KAAK,CACJ,~~CAAC~~;aACE~~,~~MAAM~~,CAAC~~;YACN~~,~~MAAM~~,~~EAAE,~~CAAC,CAAC,~~MAAM,EAAE,CAAC,~~QAAQ,CAAC,~~wBAAwB,CAAC;YACrD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,~~gBAAgB,CAAC;~~YACtD~~,~~OAAO,EAAE,~~CAAC~~,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC~~;~~SAC9D,CAAC;aACD,QAAQ,CAAC,kDAAkD,CAAC,CAChE;aACA,QAAQ,CAAC,gBAAgB,CAAC;KAC9B,CAAC;~~IAEF,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,MAAM,CAAC,IAAI,CAAC,GAAG,MAAM,cAAc,EAAE,CAAC,UAAU,CAAC,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,GAAG,CAAC,CAAC;QACzE,IAAI,CAAC,IAAI;YACP,MAAM,QAAQ,CAAC,0BAA0B,MAAM,CAAC,QAAQ,CAAC,WAAW,EAAE,EAAE,EAAE;gBACxE,OAAO,EAAE,MAAM,CAAC,QAAQ;aACzB,CAAC,CAAC;QACL,OAAO;YACL,EAAE,EAAE,IAAI,CAAC,EAAE;YACX,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,IAAI,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC5C,GAAG,CAAC,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,OAAO,EAAE,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC7E,GAAG,CAAC,OAAO,IAAI,CAAC,UAAU,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,IAAI,CAAC,UAAU,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC/E,GAAG,CAAC,OAAO,IAAI,CAAC,eAAe,KAAK,QAAQ;gBAC1C,CAAC,CAAC,EAAE,eAAe,EAAE,IAAI,CAAC,eAAe,EAAE;gBAC3C,CAAC,CAAC,EAAE,CAAC;YACP,GAAG,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,IAAI,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC9D,SAAS,EAAE,IAAI,CAAC,SAAS;YACzB,eAAe,EAAE,IAAI,CAAC,eAAe;YACrC,OAAO,EAAE,IAAI,CAAC,OAAO;SACtB,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}
1	+ {"version":3,"file":"pdb-summary.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/pdb-summary.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AACzD,OAAO,EAAE,YAAY,EAAE,mBAAmB,EAAE,MAAM,4CAA4C,CAAC;AAC/F,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,MAAM,CAAC,MAAM,kBAAkB,GAAG,QAAQ,CAAC,kBAAkB,EAAE;IAC7D,IAAI,EAAE,uBAAuB;IAC7B,KAAK,EAAE,uBAAuB;IAC9B,WAAW,EACT,4MAA4M;IAC9M,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;KAC3D,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;QACxC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QACzD,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;QAC3E,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QAC9D,eAAe,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;QACpF,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QAC/E,SAAS,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,mBAAmB,CAAC;QAC5D,eAAe,EAAE,CAAC;aACf,KAAK,CAAC,mBAAmB,CAAC;aAC1B,QAAQ,CACP,uJAAuJ,CACxJ;QACH,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,QAAQ,CAAC,gBAAgB,CAAC;KAC1D,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,MAAM,CAAC,IAAI,CAAC,GAAG,MAAM,cAAc,EAAE,CAAC,UAAU,CAAC,CAAC,MAAM,CAAC,QAAQ,CAAC,EAAE,GAAG,CAAC,CAAC;QACzE,IAAI,CAAC,IAAI;YACP,MAAM,QAAQ,CAAC,0BAA0B,MAAM,CAAC,QAAQ,CAAC,WAAW,EAAE,EAAE,EAAE;gBACxE,OAAO,EAAE,MAAM,CAAC,QAAQ;aACzB,CAAC,CAAC;QACL,OAAO;YACL,EAAE,EAAE,IAAI,CAAC,EAAE;YACX,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,IAAI,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC5C,GAAG,CAAC,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,OAAO,EAAE,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC7E,GAAG,CAAC,OAAO,IAAI,CAAC,UAAU,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,IAAI,CAAC,UAAU,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC/E,GAAG,CAAC,OAAO,IAAI,CAAC,eAAe,KAAK,QAAQ;gBAC1C,CAAC,CAAC,EAAE,eAAe,EAAE,IAAI,CAAC,eAAe,EAAE;gBAC3C,CAAC,CAAC,EAAE,CAAC;YACP,GAAG,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,IAAI,CAAC,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC9D,SAAS,EAAE,IAAI,CAAC,SAAS;YACzB,eAAe,EAAE,IAAI,CAAC,eAAe;YACrC,OAAO,EAAE,IAAI,CAAC,OAAO;SACtB,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}

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

@@ -6,7 +6,9 @@
  * 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.
+ * stated total say so. Also holds the entry-level polymer-entity and ligand
+ * schemas shared by `protein_get_structure` and the `pdb://{entry_id}` resource,
+ * so tool and resource representations of the same record stay identical.
  * @module mcp-server/tools/definitions/_schemas
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -116,4 +118,26 @@ export declare const attributionSchema: z.ZodObject<{
 export type AttributionOutput = z.infer<typeof attributionSchema>;
 /** Render an attribution list to one compact markdown line per source for `format()` parity. */
 export declare function renderAttribution(attributions: AttributionOutput[]): string[];
+/**
+ * One modeled polymer entity (chain group) of a PDB entry. Shared by
+ * `protein_get_structure` and the `pdb://{entry_id}` resource so the tool and its
+ * resource twin cannot drift on how the two chain namespaces are named or
+ * described. The `label_asym_id` / `auth_asym_id` split is load-bearing: the two
+ * are unrelated by any transformation, and each is consumed by a different tool
+ * parameter, so a caller that substitutes one for the other gets no alignment.
+ */
+export declare const polymerEntitySchema: z.ZodObject<{
+    entityId: z.ZodString;
+    description: z.ZodOptional<z.ZodString>;
+    organism: z.ZodOptional<z.ZodString>;
+    authAsymIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    labelAsymIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    sequenceLength: z.ZodOptional<z.ZodNumber>;
+}, z.core.$strip>;
+/** One bound non-polymer component (ligand) of a PDB entry. */
+export declare const ligandSchema: z.ZodObject<{
+    compId: z.ZodString;
+    name: z.ZodOptional<z.ZodString>;
+    formula: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>;
 //# sourceMappingURL=_schemas.d.ts.map

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

	@@ -1 +1 @@
1	- {"version":3,"file":"_schemas.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA~~;;;;;;;;;;GAUG~~;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,KAAK,EAAe,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAE5E;;;;;GAKG;AACH,eAAO,MAAM,mBAAmB;;;;CAIuC,CAAC;AAkDxE;;;GAGG;AACH,eAAO,MAAM,wBAAwB;;;;;;;;;;iBAgBwB,CAAC;AAE9D,qFAAqF;AACrF,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;iBAI0D,CAAC;AAE5F,MAAM,MAAM,oBAAoB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAExE,MAAM,MAAM,wBAAwB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,wBAAwB,CAAC,CAAC;AAgChF;;;;GAIG;AACH,wBAAgB,aAAa,CAC3B,KAAK,EAAE,cAAc,EACrB,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,MAAM,GACZ,oBAAoB,CAwBtB;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,YAAY,CAAC,MAAM,EAAE,oBAAoB,EAAE,GAAG,MAAM,CAOnE;AA0CD,iFAAiF;AACjF,wBAAgB,YAAY,CAAC,MAAM,EAAE,oBAAoB,EAAE,GAAG,MAAM,EAAE,CAoBrE;AAuDD;;;;;;;GAOG;AACH,wBAAgB,eAAe,CAAC,MAAM,EAAE,oBAAoB,EAAE,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,EAAE,CAcvF;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,oBAAoB,EAAE,EAAE,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,CA8BvF;AAED,sFAAsF;AACtF,eAAO,MAAM,iBAAiB;;;;;iBAWmD,CAAC;AAElF,MAAM,MAAM,iBAAiB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC;AAElE,gGAAgG;AAChG,wBAAgB,iBAAiB,CAAC,YAAY,EAAE,iBAAiB,EAAE,GAAG,MAAM,EAAE,CAM7E"}
1	+ {"version":3,"file":"_schemas.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,KAAK,EAAe,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAE5E;;;;;GAKG;AACH,eAAO,MAAM,mBAAmB;;;;CAIuC,CAAC;AAkDxE;;;GAGG;AACH,eAAO,MAAM,wBAAwB;;;;;;;;;;iBAgBwB,CAAC;AAE9D,qFAAqF;AACrF,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;iBAI0D,CAAC;AAE5F,MAAM,MAAM,oBAAoB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAExE,MAAM,MAAM,wBAAwB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,wBAAwB,CAAC,CAAC;AAgChF;;;;GAIG;AACH,wBAAgB,aAAa,CAC3B,KAAK,EAAE,cAAc,EACrB,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,MAAM,GACZ,oBAAoB,CAwBtB;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,YAAY,CAAC,MAAM,EAAE,oBAAoB,EAAE,GAAG,MAAM,CAOnE;AA0CD,iFAAiF;AACjF,wBAAgB,YAAY,CAAC,MAAM,EAAE,oBAAoB,EAAE,GAAG,MAAM,EAAE,CAoBrE;AAuDD;;;;;;;GAOG;AACH,wBAAgB,eAAe,CAAC,MAAM,EAAE,oBAAoB,EAAE,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,EAAE,CAcvF;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,oBAAoB,EAAE,EAAE,GAAG,EAAE,MAAM,GAAG,MAAM,EAAE,CA8BvF;AAED,sFAAsF;AACtF,eAAO,MAAM,iBAAiB;;;;;iBAWmD,CAAC;AAElF,MAAM,MAAM,iBAAiB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC;AAElE,gGAAgG;AAChG,wBAAgB,iBAAiB,CAAC,YAAY,EAAE,iBAAiB,EAAE,GAAG,MAAM,EAAE,CAM7E;AAED;;;;;;;GAOG;AACH,eAAO,MAAM,mBAAmB;;;;;;;iBAmBkD,CAAC;AAEnF,+DAA+D;AAC/D,eAAO,MAAM,YAAY;;;;iBAMsC,CAAC"}

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

@@ -6,7 +6,9 @@
  * 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.
+ * stated total say so. Also holds the entry-level polymer-entity and ligand
+ * schemas shared by `protein_get_structure` and the `pdb://{entry_id}` resource,
+ * so tool and resource representations of the same record stay identical.
  * @module mcp-server/tools/definitions/_schemas
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -343,4 +345,36 @@ export function renderAttribution(attributions) {
     }
     return lines;
 }
+/**
+ * One modeled polymer entity (chain group) of a PDB entry. Shared by
+ * `protein_get_structure` and the `pdb://{entry_id}` resource so the tool and its
+ * resource twin cannot drift on how the two chain namespaces are named or
+ * described. The `label_asym_id` / `auth_asym_id` split is load-bearing: the two
+ * are unrelated by any transformation, and each is consumed by a different tool
+ * parameter, so a caller that substitutes one for the other gets no alignment.
+ */
+export const polymerEntitySchema = z
+    .object({
+    entityId: z.string().describe('Polymer entity ID (e.g. 4HHB_1).'),
+    description: z.string().optional().describe('Entity description.'),
+    organism: z.string().optional().describe('Source organism.'),
+    authAsymIds: z
+        .array(z.string())
+        .optional()
+        .describe('Author-assigned chain IDs (auth_asym_id, e.g. ["A","C"]) — the namespace protein_get_annotations.chain takes. Omitted when upstream does not report them.'),
+    labelAsymIds: z
+        .array(z.string())
+        .optional()
+        .describe('mmCIF label_asym_id chain IDs (e.g. ["I","OB"]) — the namespace protein_compare_structures.chain takes. Not derivable from authAsymIds: for 6QNR_9 the label chains are I/OB against author chains 82/8E. Omitted when upstream does not report them.'),
+    sequenceLength: z.number().optional().describe('Residue count of the sample sequence.'),
+})
+    .describe('A modeled polymer entity (chain group), with both chain namespaces.');
+/** One bound non-polymer component (ligand) of a PDB entry. */
+export const ligandSchema = z
+    .object({
+    compId: z.string().describe('Chemical component ID (e.g. HEM).'),
+    name: z.string().optional().describe('Chemical name.'),
+    formula: z.string().optional().describe('Molecular formula.'),
+})
+    .describe('A bound ligand (non-polymer chemical component).');
 //# sourceMappingURL=_schemas.js.map

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

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

	@@ -1 +1 @@
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"}
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;AAwHjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmK5B,CAAC"}

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

@@ -18,7 +18,7 @@ const inputSchema = z.object({
         chain: z
             .string()
             .optional()
-            .describe('Chain (label_asym_id) to restrict the alignment to a single chain.'),
+            .describe(`mmCIF label_asym_id restricting the alignment to a single chain. Read it from polymerEntities[].labelAsymIds on protein_get_structure (source experimental) or the pdb://{entry_id} resource. Author chain IDs are a different namespace — polymerEntities[].authAsymIds, what protein_get_annotations.chain takes — and are not interchangeable with this one. Case-sensitive.`),
     })
         .describe('A structure to align, by PDB entry ID with optional chain.'))
         .min(2)

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/find-similar.tool.d.ts CHANGED Viewed

@@ -3,6 +3,10 @@
  * 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).
+ * Both modes page their results the same way (totalCount / start / nextStart),
+ * and a completed structure job returns its ticket so it can be re-paged instead
+ * of resubmitted. Fields the selected mode cannot consume are rejected, not
+ * ignored.
  * @module mcp-server/tools/definitions/find-similar.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -52,6 +56,11 @@ export declare const findSimilar: import("@cyanheads/mcp-ts-core").ToolDefinitio
     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: "mode_mismatched_field";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "An input field only the other by mode consumes was supplied: sequence, max_evalue or min_identity under by:\"structure\"; ticket_id or a non-empty databases list under by:\"sequence\".";
+    readonly recovery: "Drop the field, or switch by to the mode that reads it — sequence, max_evalue and min_identity apply to by:\"sequence\"; ticket_id and databases apply to by:\"structure\".";
 }, {
     readonly reason: "no_sequence";
     readonly code: JsonRpcErrorCode.NotFound;

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

	@@ -1 +1 @@
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