@cyanheads/protein-mcp-server 0.1.0

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

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+/**
+ * @fileoverview protein_get_structure — fetch experimental, predicted, or
+ * best-available structures by ID. Batches up to N experimental IDs in one RCSB
+ * GraphQL call with per-ID partial success (`failed[]`). Optionally inlines
+ * coordinate-file content; when that overflows a byte budget it returns a
+ * per-structure section outline for targeted re-call instead of truncating.
+ * @module mcp-server/tools/definitions/get-structure.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { DEFAULT_OUTLINE_BUDGET_BYTES } from '@cyanheads/mcp-ts-core/utils';
+import { getServerConfig } from '../../../config/server-config.js';
+import { getAlphaFoldService } from '../../../services/alphafold/alphafold-service.js';
+import { getBeaconsService } from '../../../services/beacons/beacons-service.js';
+import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
+import { mapWithConcurrency } from '../../../services/shared/async.js';
+import { fetchText } from '../../../services/shared/http.js';
+import { isPdbId, isUniProtAccession } from '../../../services/shared/identifiers.js';
+const confidenceBucketsSchema = z.object({
+    veryLow: z.number().describe('Fraction of residues with pLDDT < 50.'),
+    low: z.number().describe('Fraction with pLDDT 50–70.'),
+    confident: z.number().describe('Fraction with pLDDT 70–90.'),
+    veryHigh: z.number().describe('Fraction with pLDDT > 90.'),
+});
+const structureRecordSchema = z
+    .object({
+    id: z.string().describe('Structure identifier (PDB entry ID or UniProt accession).'),
+    source: z
+        .enum(['experimental', 'predicted'])
+        .describe('Whether the structure is experimental or predicted.'),
+    title: z.string().optional().describe('Structure / protein title.'),
+    method: z.string().optional().describe('Experimental method(s).'),
+    resolution: z.number().optional().describe('Resolution in Å (experimental).'),
+    organism: z.string().optional().describe('Source organism.'),
+    provider: z.string().optional().describe('Model provider (predicted / best_available).'),
+    meanPlddt: z.number().optional().describe('Mean pLDDT confidence 0–100 (predicted).'),
+    confidenceBuckets: confidenceBucketsSchema
+        .optional()
+        .describe('pLDDT confidence-band fractions (predicted).'),
+    paeDocUrl: z
+        .string()
+        .optional()
+        .describe('Predicted Aligned Error documentation URL (predicted).'),
+    coordinateUrls: z
+        .object({
+        cif: z.string().optional().describe('mmCIF coordinate file URL.'),
+        pdb: z.string().optional().describe('PDB-format coordinate file URL.'),
+        bcif: z.string().optional().describe('Binary CIF coordinate file URL.'),
+    })
+        .describe('Coordinate file download URLs.'),
+    coordinateFormat: z
+        .enum(['cif', 'pdb', 'bcif'])
+        .optional()
+        .describe('Format of inlined coordinates, when present.'),
+    coordinates: z
+        .string()
+        .optional()
+        .describe('Inlined coordinate-file content (only when include_coords).'),
+})
+    .describe('A resolved structure with metadata and coordinate-file URLs.');
+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); ' +
+        '"best_available" takes UniProt accessions and returns the top federated model (experimental if one ' +
+        'exists, else the best prediction). Resolves up to the configured batch cap per call with per-ID partial ' +
+        'success — missed IDs are listed in failed[]. Set include_coords to inline coordinate content; if that ' +
+        'overflows, a section outline is returned — re-call with sections:[ids] to inline specific structures.',
+    annotations: { readOnlyHint: true, openWorldHint: true },
+    errors: [
+        {
+            reason: 'mixed_id_types',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: 'The batch mixes PDB IDs and UniProt accessions under a single source that cannot serve both.',
+            recovery: 'Split the call by source: PDB IDs with source experimental, UniProt accessions with source predicted or best_available.',
+        },
+        {
+            reason: 'all_failed',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'No requested ID resolved to a structure.',
+            recovery: 'Verify ID formats (PDB IDs are 4 chars; UniProt accessions match the standard pattern) or locate IDs via protein_search_structures.',
+        },
+    ],
+    input: z.object({
+        ids: z
+            .array(z.string().min(1))
+            .min(1)
+            .describe('PDB entry IDs (source experimental) or UniProt accessions (predicted / best_available).'),
+        source: z
+            .enum(['experimental', 'predicted', 'best_available'])
+            .default('experimental')
+            .describe('Where to fetch: experimental (PDB), predicted (AlphaFold), or best_available (federated pick).'),
+        include_coords: z
+            .boolean()
+            .default(false)
+            .describe('Inline coordinate-file content (cif). Off by default — URLs are always returned.'),
+        sections: z
+            .array(z.string())
+            .optional()
+            .describe('Structure IDs to inline coordinates for, from a prior overflow outline.'),
+    }),
+    output: z.object({
+        structures: z
+            .array(structureRecordSchema)
+            .describe('Resolved structures (metadata always present).'),
+        failed: z
+            .array(z
+            .object({
+            id: z.string().describe('Requested ID that failed.'),
+            reason: z.string().describe('Why it failed.'),
+        })
+            .describe('A requested ID that did not resolve, with the reason.'))
+            .describe('IDs that could not be resolved (partial success).'),
+        overflow: z
+            .object({
+            sections: z
+                .array(z
+                .object({
+                id: z.string().describe('Structure ID whose coordinates were withheld.'),
+                bytes: z.number().describe('Serialized size of the withheld coordinate content.'),
+            })
+                .describe('A withheld structure and its coordinate byte size.'))
+                .describe('Per-structure coordinate sizes available for targeted re-call.'),
+            notice: z
+                .string()
+                .describe('How to retrieve specific coordinates via the sections parameter.'),
+        })
+            .optional()
+            .describe('Present only when inlined coordinates across the batch exceeded the response budget.'),
+    }),
+    enrichment: {
+        requested: z.number().describe('Number of IDs requested.'),
+        resolved: z.number().describe('Number of IDs resolved.'),
+        notice: z.string().optional().describe('Advisory note (partial failures, overflow guidance).'),
+    },
+    async handler(input, ctx) {
+        const cfg = getServerConfig();
+        const ids = input.ids.slice(0, cfg.maxBatchIds).map((s) => s.trim());
+        if (input.ids.length > cfg.maxBatchIds) {
+            ctx.enrich.notice(`Batch capped at ${cfg.maxBatchIds} IDs; ${input.ids.length - cfg.maxBatchIds} ignored.`);
+        }
+        if (input.source === 'experimental') {
+            if (ids.some((id) => isUniProtAccession(id) && !isPdbId(id))) {
+                throw ctx.fail('mixed_id_types', 'source experimental expects PDB entry IDs, but UniProt accessions were present.');
+            }
+        }
+        else if (ids.some((id) => isPdbId(id) && !isUniProtAccession(id))) {
+            throw ctx.fail('mixed_id_types', `source ${input.source} expects UniProt accessions, but PDB IDs were present.`);
+        }
+        const { structures, failed } = input.source === 'experimental'
+            ? await fetchExperimental(ids, ctx)
+            : await fetchPredictedOrBest(ids, input.source, cfg.fanoutConcurrency, ctx);
+        if (structures.length === 0) {
+            throw ctx.fail('all_failed', `None of the ${ids.length} requested IDs resolved to a structure.`);
+        }
+        // Inline coordinates when requested (all, or only the re-called sections).
+        const inlineSet = input.sections?.length
+            ? new Set(input.sections.map((s) => s.toUpperCase()))
+            : input.include_coords
+                ? 'all'
+                : null;
+        if (inlineSet) {
+            await inlineCoordinates(structures, inlineSet, cfg.fanoutConcurrency, ctx);
+        }
+        // Overflow guard: inlining several coordinate files at once can blow the
+        // response budget. A single structure always inlines (re-calling for the lone
+        // section would return the same bytes); 2+ over budget collapse to a size index.
+        let overflow;
+        if (inlineSet === 'all') {
+            const withCoords = structures.filter((s) => s.coordinates);
+            const total = withCoords.reduce((n, s) => n + (s.coordinates?.length ?? 0), 0);
+            if (withCoords.length > 1 && total > DEFAULT_OUTLINE_BUDGET_BYTES) {
+                const sections = withCoords.map((s) => ({ id: s.id, bytes: s.coordinates?.length ?? 0 }));
+                for (const s of structures) {
+                    delete s.coordinates;
+                    delete s.coordinateFormat;
+                }
+                overflow = {
+                    sections,
+                    notice: `Inlined coordinates (${total} bytes across ${sections.length} structures) exceeded the ` +
+                        `${DEFAULT_OUTLINE_BUDGET_BYTES}-byte budget. Re-call with sections:["${sections[0]?.id}"] ` +
+                        `(add more IDs as needed) to inline specific structures.`,
+                };
+                ctx.enrich.notice('Coordinates exceeded the inline budget; re-call with sections for specific structures.');
+            }
+        }
+        ctx.enrich({ requested: ids.length, resolved: structures.length });
+        if (failed.length > 0) {
+            ctx.enrich.notice(`${failed.length} of ${ids.length} IDs did not resolve: ${failed.map((f) => f.id).join(', ')}.`);
+        }
+        return { structures, failed, ...(overflow ? { overflow } : {}) };
+    },
+    format: (result) => {
+        const lines = [`## Structures (${result.structures.length})`];
+        for (const s of result.structures) {
+            lines.push(`\n### ${s.id} _(${s.source})_`);
+            if (s.title)
+                lines.push(s.title);
+            const meta = [
+                s.method ? `**Method:** ${s.method}` : null,
+                typeof s.resolution === 'number' ? `**Resolution:** ${s.resolution} Å` : null,
+                s.organism ? `**Organism:** ${s.organism}` : null,
+                s.provider ? `**Provider:** ${s.provider}` : null,
+                typeof s.meanPlddt === 'number' ? `**Mean pLDDT:** ${s.meanPlddt.toFixed(1)}` : null,
+            ].filter(Boolean);
+            if (meta.length > 0)
+                lines.push(meta.join(' | '));
+            if (s.confidenceBuckets) {
+                const b = s.confidenceBuckets;
+                lines.push(`**Confidence:** veryHigh ${pct(b.veryHigh)} · confident ${pct(b.confident)} · low ${pct(b.low)} · veryLow ${pct(b.veryLow)}`);
+            }
+            const urls = [
+                s.coordinateUrls.cif ? `[cif](${s.coordinateUrls.cif})` : null,
+                s.coordinateUrls.pdb ? `[pdb](${s.coordinateUrls.pdb})` : null,
+                s.coordinateUrls.bcif ? `[bcif](${s.coordinateUrls.bcif})` : null,
+            ].filter(Boolean);
+            if (urls.length > 0)
+                lines.push(`**Coordinates:** ${urls.join(' · ')}`);
+            if (s.paeDocUrl)
+                lines.push(`**PAE:** ${s.paeDocUrl}`);
+            if (s.coordinates) {
+                lines.push(`**Inlined ${s.coordinateFormat ?? 'coordinates'} (${s.coordinates.length} bytes):**`);
+                lines.push('```', s.coordinates.slice(0, 2000), s.coordinates.length > 2000 ? '… (truncated in text view)' : '', '```');
+            }
+        }
+        if (result.failed.length > 0) {
+            lines.push(`\n### Failed (${result.failed.length})`);
+            for (const f of result.failed)
+                lines.push(`- ${f.id}: ${f.reason}`);
+        }
+        if (result.overflow) {
+            lines.push(`\n### Coordinates withheld (over budget)`);
+            lines.push(result.overflow.notice);
+            for (const s of result.overflow.sections)
+                lines.push(`- ${s.id}: ${s.bytes} bytes`);
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+function pct(fraction) {
+    return `${Math.round(fraction * 100)}%`;
+}
+async function fetchExperimental(ids, ctx) {
+    const rcsb = getRcsbService();
+    const entries = await rcsb.getEntries(ids, ctx);
+    const byId = new Map(entries.map((e) => [e.id.toUpperCase(), e]));
+    const structures = [];
+    const failed = [];
+    for (const id of ids) {
+        const meta = byId.get(id.toUpperCase());
+        if (!meta) {
+            failed.push({ id, reason: 'No PDB entry found for this ID.' });
+            continue;
+        }
+        structures.push({
+            id: meta.id,
+            source: 'experimental',
+            ...(meta.title ? { title: meta.title } : {}),
+            ...(meta.methods && meta.methods.length > 0 ? { method: meta.methods.join(', ') } : {}),
+            ...(typeof meta.resolution === 'number' ? { resolution: meta.resolution } : {}),
+            ...(meta.organisms.length > 0 ? { organism: meta.organisms[0] } : {}),
+            coordinateUrls: {
+                cif: rcsb.coordinateFileUrl(meta.id, 'cif'),
+                pdb: rcsb.coordinateFileUrl(meta.id, 'pdb'),
+                bcif: rcsb.coordinateFileUrl(meta.id, 'bcif'),
+            },
+        });
+    }
+    return { structures, failed };
+}
+async function fetchPredictedOrBest(ids, source, concurrency, ctx) {
+    const results = await mapWithConcurrency(ids, concurrency, async (id) => {
+        const record = source === 'predicted' ? await fetchPrediction(id, ctx) : await fetchBest(id, ctx);
+        return record ?? { failedId: id };
+    });
+    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.' });
+        else
+            structures.push(r);
+    }
+    return { structures, failed };
+}
+async function fetchPrediction(accession, ctx) {
+    const model = await getAlphaFoldService().getPrediction(accession, ctx);
+    if (!model)
+        return null;
+    return {
+        id: model.uniprotAccession,
+        source: 'predicted',
+        ...(model.uniprotDescription ? { title: model.uniprotDescription } : {}),
+        ...(model.organism ? { organism: model.organism } : {}),
+        provider: 'AlphaFold DB',
+        ...(typeof model.meanPlddt === 'number' ? { meanPlddt: model.meanPlddt } : {}),
+        ...(model.confidenceBuckets ? { confidenceBuckets: model.confidenceBuckets } : {}),
+        ...(model.paeDocUrl ? { paeDocUrl: model.paeDocUrl } : {}),
+        coordinateUrls: {
+            ...(model.cifUrl ? { cif: model.cifUrl } : {}),
+            ...(model.pdbUrl ? { pdb: model.pdbUrl } : {}),
+            ...(model.bcifUrl ? { bcif: model.bcifUrl } : {}),
+        },
+    };
+}
+async function fetchBest(accession, ctx) {
+    const summary = await getBeaconsService().getSummary(accession, ctx);
+    if (!summary.found || summary.models.length === 0)
+        return null;
+    // Prefer an experimental model; otherwise the highest-confidence prediction.
+    const experimental = summary.models.find((m) => /experimentally/i.test(m.modelCategory ?? ''));
+    const best = experimental ??
+        [...summary.models].sort((a, b) => (b.confidenceAvgLocalScore ?? 0) - (a.confidenceAvgLocalScore ?? 0))[0];
+    if (!best)
+        return null;
+    const isExperimental = /experimentally/i.test(best.modelCategory ?? '');
+    return {
+        id: summary.accession,
+        source: isExperimental ? 'experimental' : 'predicted',
+        ...(best.provider ? { provider: best.provider } : {}),
+        ...(typeof best.resolution === 'number' ? { resolution: best.resolution } : {}),
+        ...(best.experimentalMethod ? { method: best.experimentalMethod } : {}),
+        ...(typeof best.confidenceAvgLocalScore === 'number'
+            ? { meanPlddt: best.confidenceAvgLocalScore }
+            : {}),
+        coordinateUrls: best.modelUrl ? coordinateUrlFor(best.modelUrl) : {},
+    };
+}
+/** Slot a single federated model URL into the right format key. */
+function coordinateUrlFor(url) {
+    if (/\.bcif/i.test(url))
+        return { bcif: url };
+    if (/\.pdb/i.test(url))
+        return { pdb: url };
+    return { cif: url };
+}
+/** Fetch and inline coordinate content for the requested structures. */
+async function inlineCoordinates(structures, inline, concurrency, ctx) {
+    const targets = structures.filter((s) => inline === 'all' || inline.has(s.id.toUpperCase()));
+    await mapWithConcurrency(targets, concurrency, async (s) => {
+        const pick = s.coordinateUrls.cif
+            ? ['cif', s.coordinateUrls.cif]
+            : s.coordinateUrls.pdb
+                ? ['pdb', s.coordinateUrls.pdb]
+                : null;
+        if (!pick)
+            return;
+        try {
+            s.coordinates = await fetchText(pick[1], ctx, {
+                operation: 'getStructure.inlineCoordinates',
+                label: 'Coordinate file',
+                baseDelayMs: 400,
+                maxRetries: 1,
+            });
+            s.coordinateFormat = pick[0];
+        }
+        catch (err) {
+            ctx.log.warning('Failed to inline coordinates', {
+                id: s.id,
+                error: err instanceof Error ? err.message : err,
+            });
+        }
+    });
+}
+//# sourceMappingURL=get-structure.tool.js.map

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

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package/dist/mcp-server/tools/definitions/index.d.ts

@@ -0,0 +1,12 @@
+/**
+ * @fileoverview Barrel export for all protein-mcp-server tool definitions.
+ * @module mcp-server/tools/definitions/index
+ */
+export { analyzeCollection } from './analyze-collection.tool.js';
+export { compareStructures } from './compare-structures.tool.js';
+export { findSimilar } from './find-similar.tool.js';
+export { getAnnotations } from './get-annotations.tool.js';
+export { getStructure } from './get-structure.tool.js';
+export { searchStructures } from './search-structures.tool.js';
+export { trackLigands } from './track-ligands.tool.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/mcp-server/tools/definitions/index.d.ts.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/definitions/index.js

@@ -0,0 +1,12 @@
+/**
+ * @fileoverview Barrel export for all protein-mcp-server tool definitions.
+ * @module mcp-server/tools/definitions/index
+ */
+export { analyzeCollection } from './analyze-collection.tool.js';
+export { compareStructures } from './compare-structures.tool.js';
+export { findSimilar } from './find-similar.tool.js';
+export { getAnnotations } from './get-annotations.tool.js';
+export { getStructure } from './get-structure.tool.js';
+export { searchStructures } from './search-structures.tool.js';
+export { trackLigands } from './track-ligands.tool.js';
+//# sourceMappingURL=index.js.map

package/dist/mcp-server/tools/definitions/index.js.map

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

@@ -0,0 +1,71 @@
+/**
+ * @fileoverview protein_search_structures — federated search across experimental
+ * (PDB) and predicted (computed model) structures via RCSB Search v2, with
+ * optional metadata enrichment of the experimental page and an optional facet
+ * breakdown for instant corpus orientation.
+ * @module mcp-server/tools/definitions/search-structures.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+export declare const searchStructures: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    query: z.ZodOptional<z.ZodString>;
+    sequence: z.ZodOptional<z.ZodString>;
+    organism: z.ZodOptional<z.ZodString>;
+    method: z.ZodOptional<z.ZodString>;
+    max_resolution: z.ZodOptional<z.ZodNumber>;
+    min_identity: z.ZodOptional<z.ZodNumber>;
+    max_evalue: z.ZodOptional<z.ZodNumber>;
+    content_type: z.ZodDefault<z.ZodEnum<{
+        experimental: "experimental";
+        predicted: "predicted";
+        all: "all";
+    }>>;
+    facets: z.ZodOptional<z.ZodArray<z.ZodEnum<{
+        method: "method";
+        organism: "organism";
+        resolution: "resolution";
+        molecular_weight: "molecular_weight";
+        polymer_type: "polymer_type";
+        release_year: "release_year";
+    }>>>;
+    limit: z.ZodDefault<z.ZodNumber>;
+}, z.core.$strip>, z.ZodObject<{
+    hits: z.ZodArray<z.ZodObject<{
+        id: z.ZodString;
+        source: z.ZodEnum<{
+            experimental: "experimental";
+            predicted: "predicted";
+        }>;
+        score: z.ZodOptional<z.ZodNumber>;
+        uniprotAccession: z.ZodOptional<z.ZodString>;
+        title: z.ZodOptional<z.ZodString>;
+        method: z.ZodOptional<z.ZodString>;
+        resolution: z.ZodOptional<z.ZodNumber>;
+        organism: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>>;
+    facets: z.ZodOptional<z.ZodArray<z.ZodObject<{
+        dimension: z.ZodString;
+        buckets: z.ZodArray<z.ZodObject<{
+            label: z.ZodString;
+            count: z.ZodNumber;
+            children: z.ZodOptional<z.ZodArray<z.ZodObject<{
+                dimension: z.ZodString;
+                buckets: z.ZodArray<z.ZodObject<{
+                    label: z.ZodString;
+                    count: z.ZodNumber;
+                }, z.core.$strip>>;
+            }, z.core.$strip>>>;
+        }, z.core.$strip>>;
+        truncated: z.ZodOptional<z.ZodBoolean>;
+    }, z.core.$strip>>>;
+}, z.core.$strip>, readonly [{
+    readonly reason: "no_criteria";
+    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 totalCount: z.ZodNumber;
+    readonly effectiveQuery: z.ZodOptional<z.ZodString>;
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
+//# sourceMappingURL=search-structures.tool.d.ts.map

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