npm - @cyanheads/protein-mcp-server - Versions diffs - 0.4.1 → 0.5.0 - Mend

@cyanheads/protein-mcp-server 0.4.1 → 0.5.0

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 (45) hide show

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

@@ -23,7 +23,7 @@ const inputSchema = z.object({
         .describe('A structure to align, by PDB entry ID with optional chain.'))
         .min(2)
         .max(25)
-        .describe('The structures to compare, up to the configured batch cap (excess is dropped with a notice).'),
+        .describe('The structures to compare, up to the configured batch cap (excess is dropped with a notice). A structure repeated here is compared once.'),
     reference: z
         .enum(['first', 'all_pairs'])
         .default('first')
@@ -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: [
         {
@@ -106,6 +117,12 @@ export const compareStructures = tool('protein_compare_structures', {
             when: "A resume entry's a/b labels don't match any pair generated from structures + reference.",
             recovery: "Copy each resume entry's a, b, and uuid verbatim from a prior response's pairs[], and keep structures and reference unchanged between calls.",
         },
+        {
+            reason: 'no_distinct_pair',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: 'Every entry in structures[] denotes the same structure, leaving no pair to align.',
+            recovery: 'Pass at least two different structures (entry ID, or entry ID + chain); a structure repeated in the list is compared once.',
+        },
     ],
     input: inputSchema,
     output: outputSchema,
@@ -116,10 +133,18 @@ export const compareStructures = tool('protein_compare_structures', {
     },
     async handler(input, ctx) {
         const cfg = getServerConfig();
-        const structures = input.structures.slice(0, cfg.maxCompareStructures);
         const notices = [];
-        if (input.structures.length > cfg.maxCompareStructures) {
-            notices.push(`Capped at ${cfg.maxCompareStructures} structures; ${input.structures.length - cfg.maxCompareStructures} ignored.`);
+        const { unique, repeated } = dedupeStructures(input.structures);
+        if (repeated.length > 0) {
+            notices.push(`Compared ${[...new Set(repeated)].join(', ')} once: a structure repeated in structures[] adds a self-alignment and a mirrored pair, not a new comparison.`);
+        }
+        if (unique.length < 2) {
+            const [only] = unique;
+            throw ctx.fail('no_distinct_pair', `Every entry in structures[] denotes ${only ? label(only) : 'one structure'}; there is no second structure to align it against.`, { ...ctx.recoveryFor('no_distinct_pair') });
+        }
+        const structures = unique.slice(0, cfg.maxCompareStructures);
+        if (unique.length > cfg.maxCompareStructures) {
+            notices.push(`Capped at ${cfg.maxCompareStructures} structures; ${unique.length - cfg.maxCompareStructures} ignored.`);
         }
         const timeoutMs = input.timeout_s ? input.timeout_s * 1000 : cfg.asyncPollTimeoutMs;
         const method = input.method;
@@ -157,6 +182,10 @@ export const compareStructures = tool('protein_compare_structures', {
                     ...(typeof outcome.scores.alignedResidues === 'number'
                         ? { alignedResidues: outcome.scores.alignedResidues }
                         : {}),
+                    ...(outcome.scores.modeledResidues
+                        ? { modeledResidues: outcome.scores.modeledResidues }
+                        : {}),
+                    ...(outcome.scores.coverage ? { coverage: outcome.scores.coverage } : {}),
                 };
             }
             if (outcome.status === 'computing') {
@@ -177,13 +206,15 @@ export const compareStructures = tool('protein_compare_structures', {
     },
     format: (result) => {
         const lines = [`## Structure comparison (${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} | ${coverage} |`);
         }
         const notes = result.pairs.filter((p) => p.error || p.uuid);
         if (notes.length > 0) {
@@ -198,6 +229,30 @@ export const compareStructures = tool('protein_compare_structures', {
         return [{ type: 'text', text: lines.join('\n') }];
     },
 });
+/**
+ * Collapse entries that denote the same structure to their first occurrence,
+ * keyed exactly as {@link pairKey} normalizes labels. Two entries for one
+ * structure yield pairs that are indistinguishable under that key — `(A,B)` and
+ * `(B,A)` collapse to one — so a single resume ticket would be applied to two
+ * separate alignment jobs, silently discarding one. Case-folding the whole label
+ * follows the same normalization: distinguishing chains `A` and `a` here would
+ * hand the resume lookup two pairs it cannot tell apart.
+ */
+function dedupeStructures(structures) {
+    const seen = new Set();
+    const unique = [];
+    const repeated = [];
+    for (const s of structures) {
+        const key = label(s);
+        if (seen.has(key)) {
+            repeated.push(label(s));
+            continue;
+        }
+        seen.add(key);
+        unique.push(s);
+    }
+    return { unique, repeated };
+}
 function buildPairs(structures, reference) {
     const pairs = [];
     if (reference === 'first') {
@@ -227,10 +282,18 @@ function label(s) {
     return s.chain ? `${s.pdb_id.toUpperCase()}.${s.chain}` : s.pdb_id.toUpperCase();
 }
 /**
- * Canonical, order- and case-insensitive key for a pair of structure labels, so a
- * resume entry matches its pair regardless of which side the client copied first.
+ * Canonical, order-insensitive key for a pair of structure labels, so a resume
+ * entry matches its pair regardless of which side the client copied first. The
+ * entry ID is case-folded; the chain suffix is NOT — mmCIF `label_asym_id` is
+ * case-sensitive, so chains `A` and `a` are different chains and must key apart.
  */
+function normalizeLabel(value) {
+    const dot = value.indexOf('.');
+    return dot === -1
+        ? value.toUpperCase()
+        : `${value.slice(0, dot).toUpperCase()}.${value.slice(dot + 1)}`;
+}
 function pairKey(a, b) {
-    return [a.toUpperCase(), b.toUpperCase()].sort().join('');
+    return [normalizeLabel(a), normalizeLabel(b)].sort().join('\u0000');
 }
 //# sourceMappingURL=compare-structures.tool.js.map

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

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

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

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

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

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

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

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

	@@ -1 +1 @@
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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