npm - @cyanheads/protein-mcp-server - Versions diffs - 0.4.0 → 0.4.2 - Mend

@cyanheads/protein-mcp-server 0.4.0 → 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 (70) hide show

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

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package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts CHANGED Viewed

@@ -14,8 +14,8 @@ export declare const getAnnotations: import("@cyanheads/mcp-ts-core").ToolDefini
     chain: z.ZodOptional<z.ZodString>;
     include: z.ZodDefault<z.ZodEnum<{
         all: "all";
-        features: "features";
         domains: "domains";
+        features: "features";
         variants: "variants";
     }>>;
     limit: z.ZodDefault<z.ZodNumber>;

package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts CHANGED Viewed

@@ -12,9 +12,9 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const getStructure: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     ids: z.ZodArray<z.ZodString>;
     source: z.ZodDefault<z.ZodEnum<{
+        best_available: "best_available";
         experimental: "experimental";
         predicted: "predicted";
-        best_available: "best_available";
     }>>;
     include_coords: z.ZodDefault<z.ZodBoolean>;
     sections: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -47,9 +47,9 @@ export declare const getStructure: import("@cyanheads/mcp-ts-core").ToolDefiniti
             bcif: z.ZodOptional<z.ZodString>;
         }, z.core.$strip>;
         coordinateFormat: z.ZodOptional<z.ZodEnum<{
+            bcif: "bcif";
             cif: "cif";
             pdb: "pdb";
-            bcif: "bcif";
         }>>;
         coordinates: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;

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

	@@ -1 +1 @@
1	- {"version":3,"file":"get-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-structure.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiFjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EAsQvB~~,CAAC"}
1	+ {"version":3,"file":"get-structure.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-structure.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiFjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwQvB,CAAC"}

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.'),
@@ -79,7 +79,9 @@ const structureRecordSchema = z
 export const getStructure = tool('protein_get_structure', {
     title: 'protein-mcp-server: get structure',
     description: 'Fetch structures with metadata and coordinate-file URLs. source "experimental" takes PDB entry IDs ' +
-        '(batched in one call); "predicted" takes UniProt accessions (AlphaFold, with pLDDT/PAE confidence); ' +
+        '(batched in one call), and also resolves the computed-model IDs protein_search_structures returns ' +
+        '(AF_*/MA_*), which come back marked source "predicted" with their modelling provider; ' +
+        '"predicted" takes UniProt accessions (AlphaFold, with pLDDT/PAE confidence); ' +
         '"best_available" takes UniProt accessions and returns the top federated model — the highest-resolution ' +
         'experimental structure if one exists (optimizing resolution, not biological representativeness, so it can ' +
         'return an engineered mutant over the wild-type entry), else the best prediction. Resolves up to the ' +
@@ -105,7 +107,7 @@ export const getStructure = tool('protein_get_structure', {
         ids: z
             .array(z.string().min(1))
             .min(1)
-            .describe('PDB entry IDs (source experimental) or UniProt accessions (predicted / best_available).'),
+            .describe('PDB entry IDs or computed-model IDs such as AF_AFP69905F1 (source experimental), or UniProt accessions (predicted / best_available).'),
         source: z
             .enum(['experimental', 'predicted', 'best_available'])
             .default('experimental')
@@ -133,7 +135,7 @@ export const getStructure = tool('protein_get_structure', {
             .describe('IDs that could not be resolved (partial success).'),
         attribution: z
             .array(attributionSchema)
-            .describe('Upstream data-source licenses and citations for every source present in structures[] — RCSB PDB for experimental records, AlphaFold DB for predicted. Always present — the attribution obligation travels with the data.'),
+            .describe('Upstream data-source licenses and citations for every source present in structures[] — RCSB PDB for experimental records, the modelling provider (AlphaFold DB, ModelArchive, SWISS-MODEL, …) for predicted ones. Always present — the attribution obligation travels with the data.'),
         overflow: z
             .object({
             sections: z
@@ -301,9 +303,15 @@ async function fetchExperimental(ids, ctx) {
             failed.push({ id, reason: 'No PDB entry found for this ID.' });
             continue;
         }
+        // RCSB serves computed structure models (AF_* / MA_*) from the same entry
+        // endpoint as experimental entries, and protein_search_structures surfaces
+        // their IDs under the default content_type. Read the provenance rather than
+        // stamping every resolved ID experimental — that would both contradict the
+        // record and credit an AlphaFold/ModelArchive model to the PDB's CC0.
         structures.push({
             id: meta.id,
-            source: 'experimental',
+            source: meta.computedModelProvider ? 'predicted' : 'experimental',
+            ...(meta.computedModelProvider ? { provider: meta.computedModelProvider } : {}),
             ...(meta.title ? { title: meta.title } : {}),
             ...(meta.methods && meta.methods.length > 0 ? { method: meta.methods.join(', ') } : {}),
             ...(typeof meta.resolution === 'number' ? { resolution: meta.resolution } : {}),
@@ -317,16 +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 @@
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package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts CHANGED Viewed

@@ -16,17 +16,17 @@ export declare const searchStructures: import("@cyanheads/mcp-ts-core").ToolDefi
     min_identity: z.ZodOptional<z.ZodNumber>;
     max_evalue: z.ZodOptional<z.ZodNumber>;
     content_type: z.ZodDefault<z.ZodEnum<{
+        all: "all";
         experimental: "experimental";
         predicted: "predicted";
-        all: "all";
     }>>;
     facets: z.ZodOptional<z.ZodArray<z.ZodEnum<{
         method: "method";
-        organism: "organism";
-        resolution: "resolution";
         molecular_weight: "molecular_weight";
+        organism: "organism";
         polymer_type: "polymer_type";
         release_year: "release_year";
+        resolution: "resolution";
     }>>>;
     limit: z.ZodDefault<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
@@ -59,9 +59,11 @@ export declare const searchStructures: import("@cyanheads/mcp-ts-core").ToolDefi
                     rangeTo: z.ZodOptional<z.ZodNumber>;
                 }, z.core.$strip>>;
                 truncated: z.ZodOptional<z.ZodBoolean>;
+                missingValueCount: z.ZodNumber;
             }, z.core.$strip>>>;
         }, z.core.$strip>>;
         truncated: z.ZodOptional<z.ZodBoolean>;
+        missingValueCount: z.ZodNumber;
     }, z.core.$strip>>>;
 }, z.core.$strip>, readonly [{
     readonly reason: "no_criteria";

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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgM3B,CAAC"}

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

@@ -11,11 +11,16 @@ 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 { facetDimensionSchema, renderFacets, toFacetOutput } from './_schemas.js';
-const CONTENT_TYPE_MAP = {
-    experimental: ['experimental'],
-    predicted: ['computational'],
-    all: ['experimental', 'computational'],
+import { CONTENT_TYPE_SCOPES, coverageNotices, facetDimensionSchema, 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
+ * the caller to change content_type would send them nowhere.
+ */
+const ZERO_HIT_NOTICE = {
+    experimental: 'No experimental structures matched. Broaden the query, drop filters, or widen content_type to "all" to include computed models.',
+    predicted: 'No predicted models matched. Predicted search covers computed models indexed by RCSB; widen content_type to "all" to include experimental structures.',
+    all: 'No structures matched in either the experimental or computed-model universe — content_type "all" is already the widest scope. Broaden the query or drop filters.',
 };
 /** A computed-model identifier (AlphaFold / ModelArchive) vs an experimental PDB entry. */
 function isPredictedId(id) {
@@ -128,7 +133,7 @@ export const searchStructures = tool('protein_search_structures', {
         notice: z
             .string()
             .optional()
-            .describe('Advisory note (empty results, predicted-search caveats, truncation).'),
+            .describe('Advisory note (empty results, predicted-search caveats, truncation, facet dimensions whose buckets cover materially less than totalCount). Carries every applicable advisory in one string.'),
     },
     async handler(input, ctx) {
         if (!input.query && !input.sequence && !input.organism) {
@@ -138,7 +143,6 @@ export const searchStructures = tool('protein_search_structures', {
         }
         const cfg = getServerConfig();
         const rcsb = getRcsbService();
-        const contentTypes = CONTENT_TYPE_MAP[input.content_type];
         const facetSpecs = input.facets?.map((d) => buildFacetSpec(d));
         const result = await rcsb.search({
             ...(input.query ? { text: input.query } : {}),
@@ -150,8 +154,7 @@ export const searchStructures = tool('protein_search_structures', {
                 : {}),
             ...(typeof input.min_identity === 'number' ? { minIdentity: input.min_identity } : {}),
             ...(typeof input.max_evalue === 'number' ? { maxEvalue: input.max_evalue } : {}),
-            // RCSB scopes by content type; multi-content searches just union both halves.
-            ...(contentTypes.length === 1 ? { contentType: contentTypes[0] } : {}),
+            contentType: CONTENT_TYPE_SCOPES[input.content_type],
             limit: input.limit,
         }, ctx, facetSpecs);
         const experimentalIds = [
@@ -163,15 +166,19 @@ export const searchStructures = tool('protein_search_structures', {
                 metaById.set(meta.id, meta);
         }
         const hits = result.hits.map((h) => toHit(h, metaById));
-        const facets = result.facets?.map((f) => toFacetOutput(f, cfg.facetBucketCap));
+        const facets = result.facets?.map((f) => toFacetOutput(f, cfg.facetBucketCap, result.total));
         ctx.enrich.total(result.total);
         if (input.query)
             ctx.enrich.echo(input.query);
-        if (hits.length === 0) {
-            ctx.enrich.notice(input.content_type === 'predicted'
-                ? 'No predicted models matched. Predicted search covers computed models indexed by RCSB; try content_type "all".'
-                : 'No structures matched. Broaden the query, drop filters, or switch content_type.');
-        }
+        // `notice` is a single last-wins field, so the zero-hit advice and one
+        // fragment per under-covered facet dimension compose into ONE string.
+        const notices = [];
+        if (hits.length === 0)
+            notices.push(ZERO_HIT_NOTICE[input.content_type]);
+        if (facets)
+            notices.push(...coverageNotices(facets, result.total));
+        if (notices.length > 0)
+            ctx.enrich.notice(notices.join(' '));
         return { hits, ...(facets ? { facets } : {}) };
     },
     format: (result) => {

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

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

@@ -9,9 +9,9 @@ import { z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const trackLigands: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     mode: z.ZodEnum<{
+        binding_site: "binding_site";
         find_ligand: "find_ligand";
         structures_with_ligand: "structures_with_ligand";
-        binding_site: "binding_site";
     }>;
     query: z.ZodOptional<z.ZodString>;
     comp_id: z.ZodOptional<z.ZodString>;
@@ -19,9 +19,9 @@ export declare const trackLigands: import("@cyanheads/mcp-ts-core").ToolDefiniti
     limit: z.ZodDefault<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     mode: z.ZodEnum<{
+        binding_site: "binding_site";
         find_ligand: "find_ligand";
         structures_with_ligand: "structures_with_ligand";
-        binding_site: "binding_site";
     }>;
     ligands: z.ZodOptional<z.ZodArray<z.ZodObject<{
         compId: z.ZodString;

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/alphafold/alphafold-service.d.ts.map CHANGED Viewed

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

@@ -26,6 +26,7 @@ export class AlphaFoldService {
                 operation: 'AlphaFoldService.getPrediction',
                 label: 'AlphaFold DB',
                 baseDelayMs: 300,
+                expectedStatuses: [404],
             });
         }
         catch (err) {

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

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

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