npm - @cyanheads/protein-mcp-server - Versions diffs - 0.4.1 → 0.4.2 - Mend

@cyanheads/protein-mcp-server 0.4.1 → 0.4.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (27) hide show

package/AGENTS.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Developer Protocol
 **Server:** protein-mcp-server
-**Version:** 0.4.1
+**Version:** 0.4.2
 **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:** 0.4.1
+**Version:** 0.4.2
 **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-0.4.1-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/)
+[![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/)
 </div>
@@ -98,7 +98,7 @@ Structural alignment of multiple structures (up to the configured `PROTEIN_MAX_C
 - Optional per-structure `chain` restricts the alignment to a single chain
 - 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
+- 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
 ---

package/changelog/0.4.x/0.4.2.md ADDED Viewed

@@ -0,0 +1,16 @@
+---
+summary: "protein_find_similar's Foldseek identity score now returns a 0–1 fraction as declared, protein_get_structure and af:// no longer lose a whole predicted-source batch to one malformed ID, and protein_compare_structures reports per-structure modeled-residue count and coverage."
+breaking: false
+security: false
+---
+# 0.4.2 — 2026-08-16
+## Added
+- **`protein_compare_structures`** — each pair now reports `modeledResidues` and `coverage` tuples (`[a, b]`), coverage as a 0–100% of each structure's own modeled-residue count, both already present in the upstream alignment response. ([#23](https://github.com/cyanheads/protein-mcp-server/issues/23))
+## Fixed
+- **`protein_find_similar`** — Foldseek `identity` was passed through on Foldseek's 0–100 percentage scale despite the tool's declared 0–1 contract; normalized once at the service boundary. ([#24](https://github.com/cyanheads/protein-mcp-server/issues/24))
+- **`protein_get_structure` / `af://`** — a `source: "predicted"` ID that was neither PDB- nor UniProt-shaped reached AlphaFold, came back 400, and sank the whole batch. Both now shape-check per ID so a malformed entry degrades only its own row; AlphaFold DB entry IDs (`AF-P69905-F1`) are accepted alongside bare accessions. ([#25](https://github.com/cyanheads/protein-mcp-server/issues/25))

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

	@@ -1 +1 @@
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package/dist/mcp-server/resources/definitions/af-summary.resource.js CHANGED Viewed

@@ -6,8 +6,9 @@
  * @module mcp-server/resources/definitions/af-summary.resource
  */
 import { resource, z } from '@cyanheads/mcp-ts-core';
-import { notFound } from '@cyanheads/mcp-ts-core/errors';
+import { invalidParams, notFound } from '@cyanheads/mcp-ts-core/errors';
 import { getAlphaFoldService } from '../../../services/alphafold/alphafold-service.js';
+import { isAlphaFoldEntryId, isUniProtAccession } from '../../../services/shared/identifiers.js';
 export const afSummaryResource = resource('af://{uniprot}', {
     name: 'alphafold-structure-summary',
     title: 'AlphaFold structure summary',
@@ -38,6 +39,12 @@ export const afSummaryResource = resource('af://{uniprot}', {
         paeDocUrl: z.string().optional().describe('Predicted Aligned Error documentation URL.'),
     }),
     async handler(params, ctx) {
+        // AlphaFold answers a non-accession-shaped identifier with a 400 whose raw
+        // response body would otherwise surface verbatim; reject the shape locally.
+        // An AlphaFold DB entry ID resolves upstream too, and this resource emits one
+        // as `entryId`, so accept the form it hands back.
+        if (!isUniProtAccession(params.uniprot) && !isAlphaFoldEntryId(params.uniprot))
+            throw invalidParams(`"${params.uniprot}" is not a UniProt accession — af:// is keyed by UniProt accession (e.g. af://P69905) or an AlphaFold DB entry ID (e.g. af://AF-P69905-F1).`, { uniprot: params.uniprot });
         const model = await getAlphaFoldService().getPrediction(params.uniprot, ctx);
         if (!model)
             throw notFound(`No AlphaFold model found for ${params.uniprot.toUpperCase()}`, {

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

@@ -44,6 +44,8 @@ export declare const compareStructures: import("@cyanheads/mcp-ts-core").ToolDef
         tmScore: z.ZodOptional<z.ZodNumber>;
         rmsd: z.ZodOptional<z.ZodNumber>;
         alignedResidues: z.ZodOptional<z.ZodNumber>;
+        modeledResidues: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+        coverage: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
         uuid: z.ZodOptional<z.ZodString>;
         error: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;

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

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

@@ -77,6 +77,16 @@ const outputSchema = z.object({
             'rmsd and alignedResidues to spot such cases.'),
         rmsd: z.number().optional().describe('RMSD in Å over aligned residues.'),
         alignedResidues: z.number().optional().describe('Number of aligned residue pairs.'),
+        modeledResidues: z
+            .array(z.number())
+            .length(2)
+            .optional()
+            .describe('Modeled residue count per structure, ordered [a, b] to match this pair. A large gap between the two is the terminal-length asymmetry that can depress tmScore.'),
+        coverage: z
+            .array(z.number())
+            .length(2)
+            .optional()
+            .describe("Alignment coverage per structure as a 0–100 percentage of that structure's own modeled-residue count — not of the full sequence and not of the shorter structure — ordered [a, b] to match this pair. Read alongside modeledResidues: equal aligned counts give the shorter structure the higher coverage."),
         uuid: z
             .string()
             .optional()
@@ -94,10 +104,11 @@ export const compareStructures = tool('protein_compare_structures', {
         '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 entry in resume[] to poll a computing pair's UUID instead " +
-        'of resubmitting. Returns TM-score, RMSD, and aligned-residue count per pair. TM-score is ' +
+        "of resubmitting. Returns TM-score, RMSD, and aligned-residue count per pair, plus each structure's " +
+        'modeled-residue count and alignment coverage. TM-score is ' +
         'length-normalized and can shift sharply between structures that differ only by a terminal residue or ' +
-        'two — the greedy superposition can settle into a worse local optimum — so read tmScore alongside rmsd ' +
-        'and alignedResidues, the columns that make such cases diagnosable.',
+        'two — the greedy superposition can settle into a worse local optimum — so read tmScore alongside rmsd, ' +
+        'alignedResidues, modeledResidues and coverage, the columns that make such cases diagnosable.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -157,6 +168,10 @@ export const compareStructures = tool('protein_compare_structures', {
                     ...(typeof outcome.scores.alignedResidues === 'number'
                         ? { alignedResidues: outcome.scores.alignedResidues }
                         : {}),
+                    ...(outcome.scores.modeledResidues
+                        ? { modeledResidues: outcome.scores.modeledResidues }
+                        : {}),
+                    ...(outcome.scores.coverage ? { coverage: outcome.scores.coverage } : {}),
                 };
             }
             if (outcome.status === 'computing') {
@@ -177,13 +192,15 @@ export const compareStructures = tool('protein_compare_structures', {
     },
     format: (result) => {
         const lines = [`## Structure comparison (${result.method}, ${result.reference})`];
-        lines.push('\n| Pair | Status | TM-score | RMSD (Å) | Aligned |');
-        lines.push('|---|---|---|---|---|');
+        lines.push('\n| Pair | Status | TM-score | RMSD (Å) | Aligned | Modeled a / b | Coverage % a / b |');
+        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 modeled = p.modeledResidues ? p.modeledResidues.join(' / ') : '—';
+            const coverage = p.coverage ? p.coverage.join(' / ') : '—';
+            lines.push(`| ${p.a} ↔ ${p.b} | ${p.status} | ${tm} | ${rmsd} | ${aligned} | ${modeled} | ${coverage} |`);
         }
         const notes = result.pairs.filter((p) => p.error || p.uuid);
         if (notes.length > 0) {
@@ -231,6 +248,6 @@ function label(s) {
  * resume entry matches its pair regardless of which side the client copied first.
  */
 function pairKey(a, b) {
-    return [a.toUpperCase(), b.toUpperCase()].sort().join('');
+    return [a.toUpperCase(), b.toUpperCase()].sort().join('\u0000');
 }
 //# sourceMappingURL=compare-structures.tool.js.map

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

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

@@ -17,7 +17,7 @@ import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
 import { mapWithConcurrency } from '../../../services/shared/async.js';
 import { attributionsFor } from '../../../services/shared/attribution.js';
 import { fetchText } from '../../../services/shared/http.js';
-import { isPdbId, isUniProtAccession } from '../../../services/shared/identifiers.js';
+import { isAlphaFoldEntryId, isPdbId, isUniProtAccession } from '../../../services/shared/identifiers.js';
 import { attributionSchema, renderAttribution } from './_schemas.js';
 const confidenceBucketsSchema = z.object({
     veryLow: z.number().describe('Fraction of residues with pLDDT < 50.'),
@@ -325,16 +325,31 @@ async function fetchExperimental(ids, ctx) {
     }
     return { structures, failed };
 }
+/**
+ * Per-ID failure reason for an identifier that is not accession-shaped. Kept
+ * distinct from the upstream-miss reason so a caller can tell a typo from an
+ * accession the model providers simply do not cover.
+ */
+const MALFORMED_ACCESSION = 'Not a UniProt accession — predicted and best_available are keyed by UniProt accession (e.g. P69905) or an AlphaFold DB entry ID (e.g. AF-P69905-F1).';
 async function fetchPredictedOrBest(ids, source, concurrency, ctx) {
     const results = await mapWithConcurrency(ids, concurrency, async (id) => {
+        // The handler's source guard only catches ID-*type* confusion (a PDB ID under
+        // predicted). An ID that is neither PDB- nor UniProt-shaped passes it, and a
+        // shape both upstreams reject answers with a 400, whose throw inside this
+        // worker sinks every other ID in the batch. Shape-check per ID so a malformed
+        // entry degrades only its own row, which is the "handle your own failures"
+        // contract mapWithConcurrency states. AlphaFold and 3D-Beacons both resolve an
+        // AlphaFold DB entry ID as well as a bare accession, so accept either.
+        if (!isUniProtAccession(id) && !isAlphaFoldEntryId(id))
+            return { failedId: id, reason: MALFORMED_ACCESSION };
         const record = source === 'predicted' ? await fetchPrediction(id, ctx) : await fetchBest(id, ctx);
-        return record ?? { failedId: id };
+        return record ?? { failedId: id, reason: 'No predicted model found for this accession.' };
     });
     const structures = [];
     const failed = [];
     for (const r of results) {
         if ('failedId' in r)
-            failed.push({ id: r.failedId, reason: 'No predicted model found for this accession.' });
+            failed.push({ id: r.failedId, reason: r.reason });
         else
             structures.push(r);
     }

package/dist/mcp-server/tools/definitions/get-structure.tool.js.map CHANGED Viewed

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

@@ -20,6 +20,13 @@ export interface CompareStructure {
 /** Scores for one aligned pair. */
 export interface PairScores {
     alignedResidues?: number;
+    /**
+     * Alignment coverage as a 0–100 percentage of each structure's *own* modeled
+     * length, ordered `[a, b]` to match the submitted structures.
+     */
+    coverage?: [number, number];
+    /** Modeled residue count per structure, ordered `[a, b]` as submitted. */
+    modeledResidues?: [number, number];
     rmsd?: number;
     sequenceIdentity?: number;
     tmScore?: number;

package/dist/services/alignment/alignment-service.d.ts.map CHANGED Viewed

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

@@ -115,9 +115,10 @@ function toQueryStructure(s) {
     };
 }
 /**
- * Extract TM-score / RMSD / aligned-residue count from a result row. The summary
- * carries a heterogeneous `scores` array (`{ type, value }`); match by type name
- * so a field rename upstream degrades a single metric rather than the whole row.
+ * Extract TM-score / RMSD / aligned-residue count and the per-structure
+ * modeled-length and coverage tuples from a result row. The summary carries a
+ * heterogeneous `scores` array (`{ type, value }`); match by type name so a field
+ * rename upstream degrades a single metric rather than the whole row.
  */
 function normalizeScores(result) {
     const summary = result.summary ?? {};
@@ -131,6 +132,8 @@ function normalizeScores(result) {
         summary.aligned_residues ??
         summary.n_aligned_residues ??
         byType(/aligned/i);
+    const modeled = numberPair(summary.n_modeled_residues);
+    const coverage = numberPair(summary.aln_coverage);
     if (typeof tm === 'number')
         out.tmScore = tm;
     if (typeof rmsd === 'number')
@@ -139,8 +142,24 @@ function normalizeScores(result) {
         out.sequenceIdentity = seqId;
     if (typeof aligned === 'number')
         out.alignedResidues = aligned;
+    if (modeled)
+        out.modeledResidues = modeled;
+    if (coverage)
+        out.coverage = coverage;
     return out;
 }
+/**
+ * Accept a summary field only as exactly two numbers — one per submitted
+ * structure. Anything else is upstream drift and degrades to an absent field.
+ */
+function numberPair(value) {
+    if (!Array.isArray(value) || value.length !== 2)
+        return;
+    const [a, b] = value;
+    if (typeof a !== 'number' || typeof b !== 'number')
+        return;
+    return [a, b];
+}
 let _service;
 export function initAlignmentService(config, storage, serverConfig) {
     _service = new AlignmentService(config, storage, serverConfig);

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

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1	+ 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package/dist/services/foldseek/foldseek-service.d.ts CHANGED Viewed

@@ -26,7 +26,7 @@ export interface FoldseekHit {
     probability?: number;
     /** Alignment bit score. */
     score?: number;
-    /** Sequence identity (0–1) over the alignment. */
+    /** Sequence identity (0–1) over the alignment, normalized from upstream's 0–100 `seqId`. */
     sequenceIdentity?: number;
     /** Raw target identifier as returned by Foldseek. */
     target: string;

package/dist/services/foldseek/foldseek-service.d.ts.map CHANGED Viewed

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

@@ -127,8 +127,12 @@ export class FoldseekService {
 function normalizeHit(aln, database) {
     const target = aln.target;
     const hit = { target, database, ...parseTarget(target) };
+    // Upstream (MMseqs2-App, which serves search.foldseek.com) emits `seqId` on a
+    // 0–100 percentage scale for structure search, while this server declares
+    // sequence identity as a 0–1 fraction (matching the `min_identity` inputs on
+    // the RCSB paths), so convert once at the service boundary.
     if (typeof aln.seqId === 'number')
-        hit.sequenceIdentity = aln.seqId;
+        hit.sequenceIdentity = aln.seqId / 100;
     if (typeof aln.alnLength === 'number')
         hit.alignmentLength = aln.alnLength;
     if (typeof aln.prob === 'number')

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1	+ 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package/dist/services/shared/identifiers.d.ts CHANGED Viewed

@@ -5,6 +5,13 @@
  */
 /** True when `value` is a syntactically valid UniProt accession. */
 export declare function isUniProtAccession(value: string): boolean;
+/**
+ * True when `value` is an AlphaFold DB entry ID (`AF-P69905-F1`). Both AlphaFold's
+ * prediction endpoint and 3D-Beacons accept this form alongside the bare accession,
+ * and the `af://` resource emits it as `entryId`, so a caller can hand it straight
+ * back to a predicted-source lookup.
+ */
+export declare function isAlphaFoldEntryId(value: string): boolean;
 /** True when `value` is a syntactically valid PDB entry ID. */
 export declare function isPdbId(value: string): boolean;
 /** Extract the PDB entry ID from a polymer-entity ID (`4HHB_1` → `4HHB`). */

package/dist/services/shared/identifiers.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"identifiers.d.ts","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;~~AAQH~~,oEAAoE;AACpE,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED,+DAA+D;AAC/D,wBAAgB,OAAO,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAE9C;AAED,6EAA6E;AAC7E,wBAAgB,SAAS,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAGpD"}
1	+ {"version":3,"file":"identifiers.d.ts","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAcH,oEAAoE;AACpE,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAEzD;AAED,+DAA+D;AAC/D,wBAAgB,OAAO,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAE9C;AAED,6EAA6E;AAC7E,wBAAgB,SAAS,CAAC,UAAU,EAAE,MAAM,GAAG,MAAM,CAGpD"}

package/dist/services/shared/identifiers.js CHANGED Viewed

@@ -3,14 +3,27 @@
  * (PDB) and predicted (UniProt-keyed) halves of the federation. Pure, no I/O.
  * @module services/shared/identifiers
  */
+/** UniProt accession body (6- or 10-character forms), unanchored. */
+const UNIPROT_BODY = '(?:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2})';
 /** UniProt accession pattern (6- or 10-character forms). */
-const UNIPROT_RE = /^(?:[OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2})$/i;
+const UNIPROT_RE = new RegExp(`^${UNIPROT_BODY}$`, 'i');
+/** AlphaFold DB entry ID pattern: `AF-<accession>-F<fragment>` (e.g. AF-P69905-F1). */
+const AF_ENTRY_RE = new RegExp(`^AF-${UNIPROT_BODY}-F\\d+$`, 'i');
 /** PDB entry ID pattern: 4 alphanumerics, first character a digit (e.g. 4HHB, 1IEP). */
 const PDB_RE = /^[0-9][A-Za-z0-9]{3}$/;
 /** True when `value` is a syntactically valid UniProt accession. */
 export function isUniProtAccession(value) {
     return UNIPROT_RE.test(value.trim());
 }
+/**
+ * True when `value` is an AlphaFold DB entry ID (`AF-P69905-F1`). Both AlphaFold's
+ * prediction endpoint and 3D-Beacons accept this form alongside the bare accession,
+ * and the `af://` resource emits it as `entryId`, so a caller can hand it straight
+ * back to a predicted-source lookup.
+ */
+export function isAlphaFoldEntryId(value) {
+    return AF_ENTRY_RE.test(value.trim());
+}
 /** True when `value` is a syntactically valid PDB entry ID. */
 export function isPdbId(value) {
     return PDB_RE.test(value.trim());

package/dist/services/shared/identifiers.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"identifiers.js","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,4DAA4D;AAC5D,MAAM,UAAU,GAAG~~,+EAA+E~~,CAAC;~~AAEnG~~,wFAAwF;AACxF,MAAM,MAAM,GAAG,uBAAuB,CAAC;AAEvC,oEAAoE;AACpE,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACvC,CAAC;AAED,+DAA+D;AAC/D,MAAM,UAAU,OAAO,CAAC,KAAa;IACnC,OAAO,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACnC,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,SAAS,CAAC,UAAkB;IAC1C,MAAM,IAAI,GAAG,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC;IACvD,OAAO,IAAI,CAAC,WAAW,EAAE,CAAC;AAC5B,CAAC"}
1	+ {"version":3,"file":"identifiers.js","sourceRoot":"","sources":["../../../src/services/shared/identifiers.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,qEAAqE;AACrE,MAAM,YAAY,GAAG,4EAA4E,CAAC;AAElG,4DAA4D;AAC5D,MAAM,UAAU,GAAG,IAAI,MAAM,CAAC,IAAI,YAAY,GAAG,EAAE,GAAG,CAAC,CAAC;AAExD,uFAAuF;AACvF,MAAM,WAAW,GAAG,IAAI,MAAM,CAAC,OAAO,YAAY,SAAS,EAAE,GAAG,CAAC,CAAC;AAElE,wFAAwF;AACxF,MAAM,MAAM,GAAG,uBAAuB,CAAC;AAEvC,oEAAoE;AACpE,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACvC,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,kBAAkB,CAAC,KAAa;IAC9C,OAAO,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACxC,CAAC;AAED,+DAA+D;AAC/D,MAAM,UAAU,OAAO,CAAC,KAAa;IACnC,OAAO,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;AACnC,CAAC;AAED,6EAA6E;AAC7E,MAAM,UAAU,SAAS,CAAC,UAAkB;IAC1C,MAAM,IAAI,GAAG,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC;IACvD,OAAO,IAAI,CAAC,WAAW,EAAE,CAAC;AAC5B,CAAC"}

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/protein-mcp-server",
-  "version": "0.4.1",
+  "version": "0.4.2",
   "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": "0.4.1",
+  "version": "0.4.2",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.4.1",
+      "version": "0.4.2",
       "packageArguments": [
         {
           "type": "positional",
@@ -48,7 +48,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.4.1",
+      "version": "0.4.2",
       "packageArguments": [
         {
           "type": "positional",