npm - @cyanheads/protein-mcp-server - Versions diffs - 0.3.3 → 0.4.1 - Mend

@cyanheads/protein-mcp-server 0.3.3 → 0.4.1

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 (60) hide show

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

@@ -102,6 +102,16 @@ export const getAnnotations = tool('protein_get_annotations', {
             .enum(['features', 'domains', 'variants', 'all'])
             .default('all')
             .describe('Which annotation classes to fetch: features, domains (InterPro), variants, or all.'),
+        limit: z
+            .number()
+            .int()
+            .min(1)
+            .max(200)
+            .default(50)
+            .describe('Per-class cap (1–200): features, natural variants, and InterPro domains are each independently ' +
+            'truncated to at most this many records. The default keeps a typical annotation set intact while ' +
+            'bounding a densely-annotated protein (a well-studied protein can carry 150+ natural variants); a ' +
+            'truncated class is disclosed in the response notice — raise it to retrieve more.'),
     }),
     output: z.object({
         accession: z.string().describe('UniProt accession the annotations describe.'),
@@ -125,7 +135,14 @@ export const getAnnotations = tool('protein_get_annotations', {
             .string()
             .optional()
             .describe('PDB ID the accession was resolved from, when applicable.'),
-        notice: z.string().optional().describe('Advisory note (e.g. no variants present).'),
+        truncated: z
+            .boolean()
+            .optional()
+            .describe('True when at least one annotation class hit the per-class limit and was capped; the notice names each capped class with its pre-cap count.'),
+        notice: z
+            .string()
+            .optional()
+            .describe('Advisory note: a per-class "showing N of M" line for each capped class and a no-data note for any requested-but-empty class.'),
     },
     async handler(input, ctx) {
         const uniprot = getUniProtService();
@@ -182,6 +199,30 @@ export const getAnnotations = tool('protein_get_annotations', {
         const variants = entry.features.filter((f) => f.category === 'variant');
         const wantFeatures = include === 'features' || include === 'all';
         const wantVariants = include === 'variants' || include === 'all';
+        // Cap each annotation class independently to the per-class limit, so one dense
+        // class (e.g. a protein's 150+ natural variants) can't dominate the payload.
+        // Collect every advisory fragment — a "showing N of M" line per truncated class
+        // plus a "no <class> present" note per requested-but-empty class — and emit them
+        // as ONE notice: ctx.enrich.notice is last-wins, so a second call would silently
+        // drop the first fragment.
+        const { limit } = input;
+        const notices = [];
+        let truncated = false;
+        for (const cls of [
+            { want: wantFeatures, count: features.length, label: 'features' },
+            { want: wantVariants, count: variants.length, label: 'variants' },
+            { want: wantInterPro, count: interpro.length, label: 'domains' },
+        ]) {
+            if (!cls.want)
+                continue;
+            if (cls.count > limit) {
+                truncated = true;
+                notices.push(`Showing ${limit} of ${cls.count} ${cls.label}; raise limit to see more.`);
+            }
+            else if (cls.count === 0) {
+                notices.push(`No ${cls.label} present.`);
+            }
+        }
         // Attribution rides with the data. UniProt always contributes on success;
         // InterPro only when it returned entries; GO only when a returned entry carries
         // GO terms. InterPro (CC0) and GO (CC BY 4.0) are gated independently — an
@@ -193,6 +234,10 @@ export const getAnnotations = tool('protein_get_annotations', {
             sources.add('GO');
         if (resolvedFrom)
             ctx.enrich({ resolvedFrom });
+        if (truncated)
+            ctx.enrich({ truncated: true });
+        if (notices.length > 0)
+            ctx.enrich.notice(notices.join(' '));
         return {
             accession: entry.accession,
             ...(entry.proteinName ? { proteinName: entry.proteinName } : {}),
@@ -200,9 +245,9 @@ export const getAnnotations = tool('protein_get_annotations', {
             ...(entry.organism ? { organism: entry.organism } : {}),
             ...(entry.function ? { function: entry.function } : {}),
             ...(typeof entry.sequenceLength === 'number' ? { sequenceLength: entry.sequenceLength } : {}),
-            ...(wantFeatures ? { features: toFeatureOutput(features) } : {}),
-            ...(wantVariants ? { variants: toFeatureOutput(variants) } : {}),
-            ...(wantInterPro ? { domains: interpro } : {}),
+            ...(wantFeatures ? { features: toFeatureOutput(features.slice(0, limit)) } : {}),
+            ...(wantVariants ? { variants: toFeatureOutput(variants.slice(0, limit)) } : {}),
+            ...(wantInterPro ? { domains: interpro.slice(0, limit) } : {}),
             ...(ambiguity ? { ambiguity } : {}),
             attribution: attributionsFor(sources),
         };

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

	@@ -1 +1 @@
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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

@@ -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 } : {}),

package/dist/mcp-server/tools/definitions/get-structure.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

@@ -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.map CHANGED Viewed

	@@ -1 +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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