@cyanheads/protein-mcp-server 0.1.0

package/dist/mcp-server/tools/definitions/find-similar.tool.js

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+/**
+ * @fileoverview protein_find_similar — find structurally or evolutionarily related
+ * proteins. by:sequence runs a synchronous RCSB mmseqs2 search; by:structure runs
+ * an async Foldseek search against experimental + predicted databases (submit →
+ * poll → bounded timeout, returning "still computing" rather than blocking).
+ * @module mcp-server/tools/definitions/find-similar.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { getServerConfig } from '../../../config/server-config.js';
+import { getAlphaFoldService } from '../../../services/alphafold/alphafold-service.js';
+import { getFoldseekService } from '../../../services/foldseek/foldseek-service.js';
+import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
+import { fetchText } from '../../../services/shared/http.js';
+import { entryIdOf, isPdbId, isUniProtAccession } from '../../../services/shared/identifiers.js';
+import { getUniProtService } from '../../../services/uniprot/uniprot-service.js';
+const DEFAULT_FOLDSEEK_DBS = ['pdb100', 'afdb50'];
+const FOLDSEEK_MODE = '3diaa';
+const inputSchema = z.object({
+    by: z
+        .enum(['sequence', 'structure'])
+        .describe('Similarity axis: sequence (mmseqs2) or structure (Foldseek).'),
+    sequence: z
+        .string()
+        .optional()
+        .describe('One-letter amino-acid sequence to search from (by:sequence).'),
+    pdb_id: z.string().optional().describe('PDB entry ID to derive the query from.'),
+    uniprot: z.string().optional().describe('UniProt accession to derive the query from.'),
+    databases: z
+        .array(z.string())
+        .optional()
+        .describe('Foldseek target databases (by:structure). Default pdb100 + afdb50. e.g. afdb-swissprot, BFVD.'),
+    max_evalue: z
+        .number()
+        .positive()
+        .optional()
+        .describe('Maximum E-value (by:sequence). Default 1.'),
+    min_identity: z
+        .number()
+        .min(0)
+        .max(1)
+        .optional()
+        .describe('Minimum sequence identity 0–1 (by:sequence). Default 0.'),
+    limit: z.number().int().min(1).max(100).default(25).describe('Maximum hits to return (1–100).'),
+});
+const outputSchema = z.object({
+    by: z.enum(['sequence', 'structure']).describe('Echoed similarity axis.'),
+    engine: z.string().describe('The engine that answered (e.g. "RCSB mmseqs2", "Foldseek").'),
+    status: z
+        .enum(['complete', 'computing'])
+        .describe('complete with hits, or computing (async, re-call to resume).'),
+    ticketId: z
+        .string()
+        .optional()
+        .describe('Async job ticket ID when status is computing (by:structure).'),
+    hits: z
+        .array(z
+        .object({
+        id: z.string().describe('Hit identifier (PDB entry/entity ID or UniProt accession).'),
+        source: z
+            .enum(['experimental', 'predicted'])
+            .describe('Whether the hit is an experimental or predicted structure.'),
+        score: z.number().optional().describe('Relevance / alignment score.'),
+        evalue: z.number().optional().describe('Alignment E-value (structure hits).'),
+        identity: z
+            .number()
+            .optional()
+            .describe('Sequence identity 0–1 over the alignment (structure hits).'),
+        database: z
+            .string()
+            .optional()
+            .describe('Source database the hit came from (structure hits).'),
+        title: z.string().optional().describe('Structure title (enriched sequence hits).'),
+        organism: z.string().optional().describe('Source organism (enriched sequence hits).'),
+        uniprotAccession: z
+            .string()
+            .optional()
+            .describe('UniProt accession (predicted structure hits).'),
+    })
+        .describe('A similar protein, with alignment scores when available.'))
+        .describe('Similar proteins, best first.'),
+});
+const enrichmentShape = {
+    totalCount: z
+        .number()
+        .optional()
+        .describe('Total upstream matches before pagination (by:sequence).'),
+    notice: z.string().optional().describe('Advisory note (still computing, empty results).'),
+};
+export const findSimilar = tool('protein_find_similar', {
+    title: 'protein-mcp-server: find similar',
+    description: 'Find structurally or evolutionarily related proteins. by:"sequence" runs an RCSB mmseqs2 ' +
+        'sequence-similarity search (synchronous) over a sequence — supplied directly, or pulled from a PDB ID ' +
+        'or UniProt accession. by:"structure" runs a Foldseek fold-similarity search (asynchronous) against ' +
+        'experimental and predicted databases; if the job is still computing when the poll budget elapses, the ' +
+        'response reports status "computing" with a ticket — re-call to resume. Output names the engine and ' +
+        'database each hit came from.',
+    annotations: { readOnlyHint: true, openWorldHint: true },
+    errors: [
+        {
+            reason: 'missing_query',
+            code: JsonRpcErrorCode.InvalidParams,
+            when: 'None of sequence, pdb_id, or uniprot was provided.',
+            recovery: 'Provide a raw sequence, a PDB entry ID, or a UniProt accession to search from.',
+        },
+        {
+            reason: 'no_sequence',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'A sequence could not be resolved from the given PDB ID or UniProt accession.',
+            recovery: 'Verify the identifier, or pass a raw one-letter sequence directly via the sequence parameter.',
+        },
+        {
+            reason: 'search_failed',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'The Foldseek search service rejected or failed the structure job.',
+            retryable: true,
+            recovery: 'Retry shortly; if it persists, verify the source structure has coordinates via protein_get_structure.',
+        },
+    ],
+    input: inputSchema,
+    output: outputSchema,
+    enrichment: enrichmentShape,
+    handler(input, ctx) {
+        const cfg = getServerConfig();
+        if (input.by === 'sequence')
+            return runSequence(input, cfg.facetBucketCap, ctx);
+        return runStructure(input, cfg.asyncPollTimeoutMs, ctx);
+    },
+    format: (result) => {
+        const lines = [`## ${result.engine} (by:${result.by}) — ${result.status}`];
+        if (result.ticketId)
+            lines.push(`**Ticket:** ${result.ticketId} — re-call to resume.`);
+        for (const h of result.hits) {
+            lines.push(`\n### ${h.id} _(${h.source})_`);
+            if (h.title)
+                lines.push(h.title);
+            const parts = [
+                typeof h.score === 'number' ? `**Score:** ${h.score}` : null,
+                typeof h.evalue === 'number' ? `**E-value:** ${h.evalue}` : null,
+                typeof h.identity === 'number' ? `**Identity:** ${h.identity}` : null,
+                h.database ? `**DB:** ${h.database}` : null,
+                h.organism ? `**Organism:** ${h.organism}` : null,
+                h.uniprotAccession ? `**UniProt:** ${h.uniprotAccession}` : null,
+            ].filter(Boolean);
+            if (parts.length > 0)
+                lines.push(parts.join(' | '));
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+async function runSequence(input, enrichLimit, ctx) {
+    const rcsb = getRcsbService();
+    const sequence = await resolveSequence(input, ctx);
+    const result = await rcsb.searchSequence(sequence, {
+        ...(typeof input.max_evalue === 'number' ? { maxEvalue: input.max_evalue } : {}),
+        ...(typeof input.min_identity === 'number' ? { minIdentity: input.min_identity } : {}),
+        limit: input.limit,
+    }, ctx);
+    const entryIds = [...new Set(result.hits.map((h) => entryIdOf(h.id)))].slice(0, enrichLimit);
+    const metaById = new Map();
+    if (entryIds.length > 0) {
+        for (const meta of await rcsb.getEntries(entryIds, ctx))
+            metaById.set(meta.id, meta);
+    }
+    ctx.enrich.total(result.total);
+    if (result.hits.length === 0)
+        ctx.enrich.notice('No sequence-similar entries found. Lower min_identity or raise max_evalue.');
+    return {
+        by: 'sequence',
+        engine: 'RCSB mmseqs2',
+        status: 'complete',
+        hits: result.hits.map((h) => {
+            const meta = metaById.get(entryIdOf(h.id));
+            return {
+                id: h.id,
+                source: 'experimental',
+                score: h.score,
+                ...(meta?.title ? { title: meta.title } : {}),
+                ...(meta?.organisms[0] ? { organism: meta.organisms[0] } : {}),
+            };
+        }),
+    };
+}
+async function runStructure(input, timeoutMs, ctx) {
+    const { content, fileName } = await resolveCoordinateFile(input, ctx);
+    const outcome = await getFoldseekService().search({
+        fileContent: content,
+        fileName,
+        databases: input.databases && input.databases.length > 0 ? input.databases : DEFAULT_FOLDSEEK_DBS,
+        mode: FOLDSEEK_MODE,
+        limit: input.limit,
+        timeoutMs,
+    }, ctx);
+    if (outcome.status === 'failed') {
+        throw ctx.fail('search_failed', `Foldseek search failed: ${outcome.error}`, {
+            recovery: {
+                hint: 'Retry shortly; if it persists, confirm the source structure has coordinates.',
+            },
+        });
+    }
+    if (outcome.status === 'computing') {
+        ctx.enrich.notice(`Foldseek job still computing (ticket ${outcome.ticketId}). Re-call protein_find_similar to resume.`);
+        return {
+            by: 'structure',
+            engine: 'Foldseek',
+            status: 'computing',
+            ticketId: outcome.ticketId,
+            hits: [],
+        };
+    }
+    if (outcome.hits.length === 0)
+        ctx.enrich.notice('Foldseek returned no fold-similar hits in the selected databases.');
+    return {
+        by: 'structure',
+        engine: 'Foldseek',
+        status: 'complete',
+        hits: outcome.hits.map((h) => ({
+            id: h.pdbId ?? h.uniprotAccession ?? h.target,
+            source: h.targetType === 'alphafold' ? 'predicted' : 'experimental',
+            ...(typeof h.score === 'number' ? { score: h.score } : {}),
+            ...(typeof h.evalue === 'number' ? { evalue: h.evalue } : {}),
+            ...(typeof h.sequenceIdentity === 'number' ? { identity: h.sequenceIdentity } : {}),
+            database: h.database,
+            ...(h.uniprotAccession ? { uniprotAccession: h.uniprotAccession } : {}),
+        })),
+    };
+}
+/** Resolve a query sequence from a direct sequence, PDB ID, or UniProt accession. */
+async function resolveSequence(input, ctx) {
+    if (input.sequence)
+        return input.sequence.replace(/\s+/g, '');
+    if (input.pdb_id) {
+        const seq = await getRcsbService().getSequence(input.pdb_id, ctx);
+        if (!seq)
+            throw ctx.fail('no_sequence', `No protein sequence found for PDB entry ${input.pdb_id.toUpperCase()}.`);
+        return seq.sequence;
+    }
+    if (input.uniprot) {
+        const seq = await getUniProtService().getSequence(input.uniprot, ctx);
+        if (!seq)
+            throw ctx.fail('no_sequence', `No sequence found for UniProt accession ${input.uniprot.toUpperCase()}.`);
+        return seq;
+    }
+    throw ctx.fail('missing_query', 'Provide a sequence, pdb_id, or uniprot to search from.');
+}
+/** Resolve a query coordinate file (PDB-format text) from a PDB ID or UniProt accession. */
+async function resolveCoordinateFile(input, ctx) {
+    const rcsb = getRcsbService();
+    if (input.pdb_id && isPdbId(input.pdb_id)) {
+        const id = input.pdb_id.toUpperCase();
+        const content = await fetchCoordinateText(rcsb.coordinateFileUrl(id, 'pdb'), ctx);
+        return { content, fileName: `${id}.pdb` };
+    }
+    if (input.uniprot && isUniProtAccession(input.uniprot)) {
+        const model = await getAlphaFoldService().getPrediction(input.uniprot, ctx);
+        if (!model?.pdbUrl) {
+            throw ctx.fail('no_sequence', `No predicted model with coordinates found for ${input.uniprot.toUpperCase()}.`);
+        }
+        return {
+            content: await fetchCoordinateText(model.pdbUrl, ctx),
+            fileName: `${input.uniprot.toUpperCase()}.pdb`,
+        };
+    }
+    throw ctx.fail('missing_query', 'by:structure requires a pdb_id or uniprot accession to derive coordinates.');
+}
+function fetchCoordinateText(url, ctx) {
+    return fetchText(url, ctx, {
+        operation: 'findSimilar.fetchCoordinates',
+        label: 'Coordinate file',
+        baseDelayMs: 400,
+        maxRetries: 1,
+    });
+}
+//# sourceMappingURL=find-similar.tool.js.map

package/dist/mcp-server/tools/definitions/find-similar.tool.js.map

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

@@ -0,0 +1,58 @@
+/**
+ * @fileoverview protein_get_annotations — sequence & functional annotation for a
+ * protein: UniProt features (domains, binding sites, PTMs, variants) and InterPro
+ * domain/family memberships with GO terms. Keyed by UniProt accession; resolves a
+ * PDB ID to its accession when needed.
+ * @module mcp-server/tools/definitions/get-annotations.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+export declare const getAnnotations: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    uniprot: z.ZodOptional<z.ZodString>;
+    pdb_id: z.ZodOptional<z.ZodString>;
+    include: z.ZodDefault<z.ZodEnum<{
+        all: "all";
+        features: "features";
+        domains: "domains";
+        variants: "variants";
+    }>>;
+}, z.core.$strip>, z.ZodObject<{
+    accession: z.ZodString;
+    proteinName: z.ZodOptional<z.ZodString>;
+    geneNames: z.ZodArray<z.ZodString>;
+    organism: z.ZodOptional<z.ZodString>;
+    function: z.ZodOptional<z.ZodString>;
+    sequenceLength: z.ZodOptional<z.ZodNumber>;
+    features: z.ZodOptional<z.ZodArray<z.ZodObject<{
+        type: z.ZodString;
+        description: z.ZodOptional<z.ZodString>;
+        start: z.ZodOptional<z.ZodNumber>;
+        end: z.ZodOptional<z.ZodNumber>;
+    }, z.core.$strip>>>;
+    variants: z.ZodOptional<z.ZodArray<z.ZodObject<{
+        type: z.ZodString;
+        description: z.ZodOptional<z.ZodString>;
+        start: z.ZodOptional<z.ZodNumber>;
+        end: z.ZodOptional<z.ZodNumber>;
+    }, z.core.$strip>>>;
+    domains: z.ZodOptional<z.ZodArray<z.ZodObject<{
+        accession: z.ZodString;
+        name: z.ZodString;
+        type: z.ZodString;
+        memberDatabases: z.ZodArray<z.ZodString>;
+        goTerms: z.ZodArray<z.ZodObject<{
+            id: z.ZodString;
+            name: z.ZodString;
+            category: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>>;
+    }, z.core.$strip>>>;
+}, z.core.$strip>, readonly [{
+    readonly reason: "no_uniprot_mapping";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "A PDB ID has no UniProt cross-reference (e.g. nucleic-acid-only entry), or neither uniprot nor pdb_id was provided.";
+    readonly recovery: "Pass a UniProt accession directly, or use protein_search_structures to find a structure with a modeled protein chain.";
+}], {
+    readonly resolvedFrom: z.ZodOptional<z.ZodString>;
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
+//# sourceMappingURL=get-annotations.tool.d.ts.map

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

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

@@ -0,0 +1,180 @@
+/**
+ * @fileoverview protein_get_annotations — sequence & functional annotation for a
+ * protein: UniProt features (domains, binding sites, PTMs, variants) and InterPro
+ * domain/family memberships with GO terms. Keyed by UniProt accession; resolves a
+ * PDB ID to its accession when needed.
+ * @module mcp-server/tools/definitions/get-annotations.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
+import { isUniProtAccession } from '../../../services/shared/identifiers.js';
+import { getUniProtService } from '../../../services/uniprot/uniprot-service.js';
+const featureSchema = z
+    .object({
+    type: z.string().describe('Feature type (e.g. Domain, Binding site, Modified residue).'),
+    description: z.string().optional().describe('Feature description.'),
+    start: z.number().optional().describe('Start residue (1-based).'),
+    end: z.number().optional().describe('End residue (1-based).'),
+})
+    .describe('A sequence feature or natural variant over a residue range.');
+const domainSchema = z
+    .object({
+    accession: z.string().describe('InterPro accession (e.g. IPR000001).'),
+    name: z.string().describe('Domain/family name.'),
+    type: z.string().describe('Entry type (e.g. domain, family, homologous_superfamily).'),
+    memberDatabases: z
+        .array(z.string())
+        .describe('Contributing member databases (e.g. pfam, profile).'),
+    goTerms: z
+        .array(z
+        .object({
+        id: z.string().describe('GO term ID (e.g. GO:0005515).'),
+        name: z.string().describe('GO term name.'),
+        category: z
+            .string()
+            .optional()
+            .describe('GO aspect (molecular_function, biological_process, …).'),
+    })
+        .describe('An associated Gene Ontology term.'))
+        .describe('Associated GO terms.'),
+})
+    .describe('An InterPro domain/family membership with GO terms.');
+export const getAnnotations = tool('protein_get_annotations', {
+    title: 'protein-mcp-server: get annotations',
+    description: 'Sequence and functional annotation for a protein: UniProt features (domains, binding sites, PTMs), ' +
+        'natural variants, and InterPro domain/family memberships (Pfam, PROSITE, …) with GO terms. Provide a ' +
+        "UniProt accession directly, or a PDB ID — it is resolved to its UniProt accession via the structure's " +
+        'sequence cross-reference. Use the "include" parameter to scope which annotation classes are fetched.',
+    annotations: { readOnlyHint: true, openWorldHint: true },
+    errors: [
+        {
+            reason: 'no_uniprot_mapping',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'A PDB ID has no UniProt cross-reference (e.g. nucleic-acid-only entry), or neither uniprot nor pdb_id was provided.',
+            recovery: 'Pass a UniProt accession directly, or use protein_search_structures to find a structure with a modeled protein chain.',
+        },
+    ],
+    input: z.object({
+        uniprot: z
+            .string()
+            .optional()
+            .describe('UniProt accession (e.g. P69905). Takes precedence over pdb_id.'),
+        pdb_id: z
+            .string()
+            .optional()
+            .describe('PDB entry ID; resolved to a UniProt accession via cross-reference.'),
+        include: z
+            .enum(['features', 'domains', 'variants', 'all'])
+            .default('all')
+            .describe('Which annotation classes to fetch: features, domains (InterPro), variants, or all.'),
+    }),
+    output: z.object({
+        accession: z.string().describe('UniProt accession the annotations describe.'),
+        proteinName: z.string().optional().describe('Recommended protein name.'),
+        geneNames: z.array(z.string()).describe('Gene names.'),
+        organism: z.string().optional().describe('Source organism scientific name.'),
+        function: z.string().optional().describe('UniProt function summary.'),
+        sequenceLength: z.number().optional().describe('Sequence length in residues.'),
+        features: z.array(featureSchema).optional().describe('Structural/functional features.'),
+        variants: z.array(featureSchema).optional().describe('Natural sequence variants.'),
+        domains: z.array(domainSchema).optional().describe('InterPro domain/family memberships.'),
+    }),
+    enrichment: {
+        resolvedFrom: z
+            .string()
+            .optional()
+            .describe('PDB ID the accession was resolved from, when applicable.'),
+        notice: z.string().optional().describe('Advisory note (e.g. no variants present).'),
+    },
+    async handler(input, ctx) {
+        const uniprot = getUniProtService();
+        const rcsb = getRcsbService();
+        let accession = input.uniprot?.toUpperCase();
+        let resolvedFrom;
+        if (!accession && input.pdb_id) {
+            const accessions = await rcsb.resolveUniprot(input.pdb_id, ctx);
+            accession = accessions[0];
+            resolvedFrom = input.pdb_id.toUpperCase();
+        }
+        if (!accession) {
+            throw ctx.fail('no_uniprot_mapping', 'Provide a UniProt accession, or a PDB ID with a modeled protein chain.');
+        }
+        if (!isUniProtAccession(accession)) {
+            throw ctx.fail('no_uniprot_mapping', `"${accession}" is not a valid UniProt accession.`);
+        }
+        const include = input.include;
+        const wantInterPro = include === 'domains' || include === 'all';
+        const [entry, interpro] = await Promise.all([
+            uniprot.getEntry(accession, include, ctx),
+            wantInterPro ? uniprot.getInterPro(accession, ctx) : Promise.resolve([]),
+        ]);
+        const features = entry.features.filter((f) => f.category === 'feature');
+        const variants = entry.features.filter((f) => f.category === 'variant');
+        const wantFeatures = include === 'features' || include === 'all';
+        const wantVariants = include === 'variants' || include === 'all';
+        if (resolvedFrom)
+            ctx.enrich({ resolvedFrom });
+        return {
+            accession: entry.accession,
+            ...(entry.proteinName ? { proteinName: entry.proteinName } : {}),
+            geneNames: entry.geneNames,
+            ...(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 } : {}),
+        };
+    },
+    format: (result) => {
+        const lines = [
+            `## ${result.accession}${result.proteinName ? ` — ${result.proteinName}` : ''}`,
+        ];
+        const head = [
+            result.geneNames.length > 0 ? `**Genes:** ${result.geneNames.join(', ')}` : null,
+            result.organism ? `**Organism:** ${result.organism}` : null,
+            typeof result.sequenceLength === 'number' ? `**Length:** ${result.sequenceLength} aa` : null,
+        ].filter(Boolean);
+        if (head.length > 0)
+            lines.push(head.join(' | '));
+        if (result.function)
+            lines.push(`\n**Function:** ${result.function}`);
+        if (result.features && result.features.length > 0) {
+            lines.push(`\n### Features (${result.features.length})`);
+            for (const f of result.features)
+                lines.push(`- ${renderFeature(f)}`);
+        }
+        if (result.variants && result.variants.length > 0) {
+            lines.push(`\n### Variants (${result.variants.length})`);
+            for (const v of result.variants)
+                lines.push(`- ${renderFeature(v)}`);
+        }
+        if (result.domains && result.domains.length > 0) {
+            lines.push(`\n### InterPro domains (${result.domains.length})`);
+            for (const d of result.domains) {
+                lines.push(`- **${d.accession}** ${d.name} _(${d.type})_ — ${d.memberDatabases.join(', ') || 'no member DBs'}`);
+                for (const g of d.goTerms)
+                    lines.push(`  - ${g.id} ${g.name}${g.category ? ` [${g.category}]` : ''}`);
+            }
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+function toFeatureOutput(features) {
+    return features.map((f) => ({
+        type: f.type,
+        ...(f.description ? { description: f.description } : {}),
+        ...(typeof f.start === 'number' ? { start: f.start } : {}),
+        ...(typeof f.end === 'number' ? { end: f.end } : {}),
+    }));
+}
+function renderFeature(f) {
+    const range = f.start != null
+        ? f.end != null && f.end !== f.start
+            ? `${f.start}–${f.end}`
+            : `${f.start}`
+        : '';
+    return `**${f.type}**${range ? ` [${range}]` : ''}${f.description ? `: ${f.description}` : ''}`;
+}
+//# sourceMappingURL=get-annotations.tool.js.map

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

@@ -0,0 +1,78 @@
+/**
+ * @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 { z } from '@cyanheads/mcp-ts-core';
+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<{
+        experimental: "experimental";
+        predicted: "predicted";
+        best_available: "best_available";
+    }>>;
+    include_coords: z.ZodDefault<z.ZodBoolean>;
+    sections: z.ZodOptional<z.ZodArray<z.ZodString>>;
+}, z.core.$strip>, z.ZodObject<{
+    structures: z.ZodArray<z.ZodObject<{
+        id: z.ZodString;
+        source: z.ZodEnum<{
+            experimental: "experimental";
+            predicted: "predicted";
+        }>;
+        title: z.ZodOptional<z.ZodString>;
+        method: z.ZodOptional<z.ZodString>;
+        resolution: z.ZodOptional<z.ZodNumber>;
+        organism: z.ZodOptional<z.ZodString>;
+        provider: z.ZodOptional<z.ZodString>;
+        meanPlddt: z.ZodOptional<z.ZodNumber>;
+        confidenceBuckets: z.ZodOptional<z.ZodObject<{
+            veryLow: z.ZodNumber;
+            low: z.ZodNumber;
+            confident: z.ZodNumber;
+            veryHigh: z.ZodNumber;
+        }, z.core.$strip>>;
+        paeDocUrl: z.ZodOptional<z.ZodString>;
+        coordinateUrls: z.ZodObject<{
+            cif: z.ZodOptional<z.ZodString>;
+            pdb: z.ZodOptional<z.ZodString>;
+            bcif: z.ZodOptional<z.ZodString>;
+        }, z.core.$strip>;
+        coordinateFormat: z.ZodOptional<z.ZodEnum<{
+            cif: "cif";
+            pdb: "pdb";
+            bcif: "bcif";
+        }>>;
+        coordinates: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>>;
+    failed: z.ZodArray<z.ZodObject<{
+        id: z.ZodString;
+        reason: z.ZodString;
+    }, z.core.$strip>>;
+    overflow: z.ZodOptional<z.ZodObject<{
+        sections: z.ZodArray<z.ZodObject<{
+            id: z.ZodString;
+            bytes: z.ZodNumber;
+        }, z.core.$strip>>;
+        notice: z.ZodString;
+    }, z.core.$strip>>;
+}, z.core.$strip>, readonly [{
+    readonly reason: "mixed_id_types";
+    readonly code: JsonRpcErrorCode.InvalidParams;
+    readonly when: "The batch mixes PDB IDs and UniProt accessions under a single source that cannot serve both.";
+    readonly recovery: "Split the call by source: PDB IDs with source experimental, UniProt accessions with source predicted or best_available.";
+}, {
+    readonly reason: "all_failed";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "No requested ID resolved to a structure.";
+    readonly recovery: "Verify ID formats (PDB IDs are 4 chars; UniProt accessions match the standard pattern) or locate IDs via protein_search_structures.";
+}], {
+    readonly requested: z.ZodNumber;
+    readonly resolved: z.ZodNumber;
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
+//# sourceMappingURL=get-structure.tool.d.ts.map

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

@@ -0,0 +1 @@
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