@cyanheads/pubchem-mcp-server 0.1.1

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

@@ -0,0 +1,143 @@
+/**
+ * @fileoverview Get descriptive summaries for PubChem entities: assays, genes,
+ * proteins, pathways, taxonomy, cell lines, or substances.
+ * @module mcp-server/tools/definitions/get-summary
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
+const entityTypeEnum = z.enum(['assay', 'gene', 'protein', 'taxonomy']);
+export const getSummary = tool('pubchem_get_summary', {
+    title: 'Get Entity Summary',
+    description: 'Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), ' +
+        'proteins (UniProt accession), and taxonomy (Tax ID). Up to 10 per call.',
+    annotations: {
+        readOnlyHint: true,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: true,
+    },
+    input: z.object({
+        entityType: entityTypeEnum.describe('Entity type. Determines ID format and returned fields.'),
+        identifiers: z
+            .array(z.union([z.string(), z.number()]))
+            .min(1)
+            .max(10)
+            .describe('Entity identifiers (1-10). Type depends on entityType:\n' +
+            '- assay: AID (number), e.g. [1000]\n' +
+            '- gene: Gene ID (number), e.g. [1956]\n' +
+            '- protein: UniProt accession (string), e.g. ["P00533"]\n' +
+            '- taxonomy: Tax ID (number), e.g. [9606]'),
+    }),
+    output: z.object({
+        entityType: z.string().describe('Entity type queried.'),
+        summaries: z
+            .array(z.object({
+            identifier: z.union([z.string(), z.number()]).describe('Queried identifier.'),
+            found: z.boolean().describe('Whether the entity was found.'),
+            data: z
+                .record(z.string(), z.unknown())
+                .optional()
+                .describe('Entity summary data (shape varies by type).'),
+        }))
+            .describe('Summary results.'),
+    }),
+    async handler(input, ctx) {
+        const client = getPubChemClient();
+        const summaries = await Promise.all(input.identifiers.map(async (id) => {
+            const raw = await client.getEntitySummary(input.entityType, id);
+            if (!raw)
+                return { identifier: id, found: false };
+            const data = extractSummary(input.entityType, raw);
+            return { identifier: id, found: true, data };
+        }));
+        ctx.log.info('Summaries fetched', {
+            entityType: input.entityType,
+            requested: input.identifiers.length,
+            found: summaries.filter((s) => s.found).length,
+        });
+        return { entityType: input.entityType, summaries };
+    },
+    format(result) {
+        const lines = [`## ${capitalize(result.entityType)} Summaries`, ''];
+        for (const s of result.summaries) {
+            if (!s.found || !s.data) {
+                lines.push(`**${s.identifier}** — not found`);
+                lines.push('');
+                continue;
+            }
+            const d = s.data;
+            lines.push(`**${d.name ?? d.symbol ?? s.identifier}**`);
+            for (const [key, value] of Object.entries(d)) {
+                if (value == null || key === 'name' || key === 'symbol')
+                    continue;
+                if (Array.isArray(value)) {
+                    if (value.length === 0)
+                        continue;
+                    const display = value.length > 10
+                        ? `${value.slice(0, 10).join(', ')} (+${value.length - 10} more)`
+                        : value.join(', ');
+                    lines.push(`  ${formatKey(key)}: ${display}`);
+                }
+                else {
+                    lines.push(`  ${formatKey(key)}: ${value}`);
+                }
+            }
+            lines.push('');
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+// ── Summary extraction per entity type ──────────────────────────────
+function extractSummary(entityType, raw) {
+    switch (entityType) {
+        case 'assay':
+            return {
+                aid: raw.AID,
+                name: raw.Name ?? raw.AssayName,
+                description: Array.isArray(raw.Description)
+                    ? raw.Description.join('\n')
+                    : raw.Description,
+                sourceName: raw.SourceName,
+                numSubstances: raw.NumberOfSubstances ?? raw.TotalSIDCount,
+                numActive: raw.ActiveSidCount ?? raw.ActiveCount,
+            };
+        case 'gene':
+            return {
+                geneId: raw.GeneID,
+                symbol: raw.Symbol,
+                name: raw.Name,
+                taxonomyId: raw.TaxID ?? raw.TaxonomyID,
+                taxonomy: raw.Taxonomy ?? raw.ScientificName,
+                description: raw.Description ?? raw.Summary,
+                synonyms: raw.Synonym ?? raw.OtherNames,
+            };
+        case 'protein':
+            return {
+                proteinAccession: raw.ProteinAccession ?? raw.Accession,
+                name: raw.Name ?? raw.Title,
+                taxonomyId: raw.TaxID ?? raw.TaxonomyID,
+                taxonomy: raw.Taxonomy ?? raw.ScientificName,
+                synonyms: raw.Synonym ?? raw.OtherNames,
+            };
+        case 'taxonomy':
+            return {
+                taxonomyId: raw.TaxonomyID ?? raw.TaxID,
+                scientificName: raw.ScientificName,
+                commonName: raw.CommonName,
+                rank: raw.Rank,
+                lineage: raw.Lineage ?? raw.ParentTaxList,
+            };
+        default:
+            return raw;
+    }
+}
+function capitalize(s) {
+    return s.charAt(0).toUpperCase() + s.slice(1);
+}
+function formatKey(key) {
+    return key
+        .replace(/([A-Z])/g, ' $1')
+        .replace(/^./, (s) => s.toUpperCase())
+        .trim();
+}
+//# sourceMappingURL=get-summary.tool.js.map

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

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

@@ -0,0 +1,152 @@
+/**
+ * @fileoverview Tool definition barrel — all PubChem MCP tools.
+ * @module mcp-server/tools/definitions
+ */
+export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+    cid: import("zod").ZodNumber;
+    outcomeFilter: import("zod").ZodDefault<import("zod").ZodEnum<{
+        active: "active";
+        inactive: "inactive";
+        all: "all";
+    }>>;
+    maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
+}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
+    cid: import("zod").ZodNumber;
+    totalAssays: import("zod").ZodNumber;
+    activeCount: import("zod").ZodNumber;
+    inactiveCount: import("zod").ZodNumber;
+    results: import("zod").ZodArray<import("zod").ZodObject<{
+        aid: import("zod").ZodNumber;
+        assayName: import("zod").ZodString;
+        outcome: import("zod").ZodString;
+        targetAccession: import("zod").ZodOptional<import("zod").ZodString>;
+        targetGeneId: import("zod").ZodOptional<import("zod").ZodNumber>;
+        activityValues: import("zod").ZodArray<import("zod").ZodObject<{
+            name: import("zod").ZodString;
+            value: import("zod").ZodNumber;
+            unit: import("zod").ZodString;
+        }, import("zod/v4/core").$strip>>;
+    }, import("zod/v4/core").$strip>>;
+}, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+    cids: import("zod").ZodArray<import("zod").ZodNumber>;
+    properties: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodEnum<{
+        [x: string]: string;
+    }>>>;
+    includeDescription: import("zod").ZodDefault<import("zod").ZodBoolean>;
+    includeSynonyms: import("zod").ZodDefault<import("zod").ZodBoolean>;
+}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
+    compounds: import("zod").ZodArray<import("zod").ZodObject<{
+        cid: import("zod").ZodNumber;
+        properties: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
+        description: import("zod").ZodOptional<import("zod").ZodString>;
+        synonyms: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
+    }, import("zod/v4/core").$strip>>;
+}, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+    cid: import("zod").ZodNumber;
+    size: import("zod").ZodDefault<import("zod").ZodEnum<{
+        small: "small";
+        large: "large";
+    }>>;
+}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
+    cid: import("zod").ZodNumber;
+    imageBase64: import("zod").ZodString;
+    mimeType: import("zod").ZodString;
+    width: import("zod").ZodNumber;
+    height: import("zod").ZodNumber;
+}, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+    cid: import("zod").ZodNumber;
+}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
+    cid: import("zod").ZodNumber;
+    hasData: import("zod").ZodBoolean;
+    ghs: import("zod").ZodOptional<import("zod").ZodObject<{
+        signalWord: import("zod").ZodOptional<import("zod").ZodString>;
+        pictograms: import("zod").ZodArray<import("zod").ZodString>;
+        hazardStatements: import("zod").ZodArray<import("zod").ZodObject<{
+            code: import("zod").ZodString;
+            statement: import("zod").ZodString;
+        }, import("zod/v4/core").$strip>>;
+        precautionaryStatements: import("zod").ZodArray<import("zod").ZodObject<{
+            code: import("zod").ZodString;
+            statement: import("zod").ZodString;
+        }, import("zod/v4/core").$strip>>;
+    }, import("zod/v4/core").$strip>>;
+    source: import("zod").ZodOptional<import("zod").ZodString>;
+}, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+    cid: import("zod").ZodNumber;
+    xrefTypes: import("zod").ZodArray<import("zod").ZodEnum<{
+        [x: string]: string;
+    }>>;
+    maxPerType: import("zod").ZodDefault<import("zod").ZodNumber>;
+}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
+    cid: import("zod").ZodNumber;
+    xrefs: import("zod").ZodArray<import("zod").ZodObject<{
+        type: import("zod").ZodString;
+        ids: import("zod").ZodArray<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber]>>;
+        totalAvailable: import("zod").ZodNumber;
+        truncated: import("zod").ZodBoolean;
+    }, import("zod/v4/core").$strip>>;
+}, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+    entityType: import("zod").ZodEnum<{
+        assay: "assay";
+        gene: "gene";
+        protein: "protein";
+        taxonomy: "taxonomy";
+    }>;
+    identifiers: import("zod").ZodArray<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber]>>;
+}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
+    entityType: import("zod").ZodString;
+    summaries: import("zod").ZodArray<import("zod").ZodObject<{
+        identifier: import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber]>;
+        found: import("zod").ZodBoolean;
+        data: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>>;
+    }, import("zod/v4/core").$strip>>;
+}, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+    targetType: import("zod").ZodEnum<{
+        proteinaccession: "proteinaccession";
+        genesymbol: "genesymbol";
+        proteinname: "proteinname";
+        geneid: "geneid";
+    }>;
+    targetQuery: import("zod").ZodString;
+    maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
+}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
+    targetType: import("zod").ZodString;
+    targetQuery: import("zod").ZodString;
+    totalFound: import("zod").ZodNumber;
+    aids: import("zod").ZodArray<import("zod").ZodNumber>;
+}, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+    searchType: import("zod").ZodEnum<{
+        substructure: "substructure";
+        superstructure: "superstructure";
+        similarity: "similarity";
+        identifier: "identifier";
+        formula: "formula";
+    }>;
+    identifierType: import("zod").ZodOptional<import("zod").ZodEnum<{
+        smiles: "smiles";
+        name: "name";
+        inchikey: "inchikey";
+    }>>;
+    identifiers: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
+    formula: import("zod").ZodOptional<import("zod").ZodString>;
+    allowOtherElements: import("zod").ZodDefault<import("zod").ZodBoolean>;
+    query: import("zod").ZodOptional<import("zod").ZodString>;
+    queryType: import("zod").ZodOptional<import("zod").ZodEnum<{
+        smiles: "smiles";
+        cid: "cid";
+    }>>;
+    threshold: import("zod").ZodDefault<import("zod").ZodNumber>;
+    maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
+    properties: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodEnum<{
+        [x: string]: string;
+    }>>>;
+}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
+    searchType: import("zod").ZodString;
+    totalFound: import("zod").ZodNumber;
+    results: import("zod").ZodArray<import("zod").ZodObject<{
+        cid: import("zod").ZodNumber;
+        identifier: import("zod").ZodOptional<import("zod").ZodString>;
+        properties: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>>;
+    }, import("zod/v4/core").$strip>>;
+}, import("zod/v4/core").$strip>>)[];
+//# sourceMappingURL=index.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAWH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;oCAS9B,CAAC"}

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

@@ -0,0 +1,23 @@
+/**
+ * @fileoverview Tool definition barrel — all PubChem MCP tools.
+ * @module mcp-server/tools/definitions
+ */
+import { getBioactivity } from './get-bioactivity.tool.js';
+import { getCompoundDetails } from './get-compound-details.tool.js';
+import { getCompoundImage } from './get-compound-image.tool.js';
+import { getCompoundSafety } from './get-compound-safety.tool.js';
+import { getCompoundXrefs } from './get-compound-xrefs.tool.js';
+import { getSummary } from './get-summary.tool.js';
+import { searchAssays } from './search-assays.tool.js';
+import { searchCompounds } from './search-compounds.tool.js';
+export const allToolDefinitions = [
+    searchCompounds,
+    getCompoundDetails,
+    getCompoundImage,
+    getCompoundXrefs,
+    getCompoundSafety,
+    getBioactivity,
+    searchAssays,
+    getSummary,
+];
+//# sourceMappingURL=index.js.map

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

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts

@@ -0,0 +1,22 @@
+/**
+ * @fileoverview Find PubChem bioassays by biological target (gene symbol,
+ * protein name, Gene ID, or UniProt accession).
+ * @module mcp-server/tools/definitions/search-assays
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const searchAssays: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    targetType: z.ZodEnum<{
+        proteinaccession: "proteinaccession";
+        genesymbol: "genesymbol";
+        proteinname: "proteinname";
+        geneid: "geneid";
+    }>;
+    targetQuery: z.ZodString;
+    maxResults: z.ZodDefault<z.ZodNumber>;
+}, z.core.$strip>, z.ZodObject<{
+    targetType: z.ZodString;
+    targetQuery: z.ZodString;
+    totalFound: z.ZodNumber;
+    aids: z.ZodArray<z.ZodNumber>;
+}, z.core.$strip>>;
+//# sourceMappingURL=search-assays.tool.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/definitions/search-assays.tool.js

@@ -0,0 +1,76 @@
+/**
+ * @fileoverview Find PubChem bioassays by biological target (gene symbol,
+ * protein name, Gene ID, or UniProt accession).
+ * @module mcp-server/tools/definitions/search-assays
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
+export const searchAssays = tool('pubchem_search_assays', {
+    title: 'Search Assays',
+    description: 'Find PubChem bioassays associated with a biological target. Search by gene symbol ' +
+        '(e.g. "EGFR"), protein name, NCBI Gene ID, or UniProt accession. Returns assay IDs (AIDs) ' +
+        'which can be explored further with pubchem_get_summary.',
+    annotations: {
+        readOnlyHint: true,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: true,
+    },
+    input: z.object({
+        targetType: z
+            .enum(['genesymbol', 'proteinname', 'geneid', 'proteinaccession'])
+            .describe('Target identifier type. "genesymbol" and "proteinname" accept text names. ' +
+            '"geneid" accepts NCBI Gene IDs. "proteinaccession" accepts UniProt accessions.'),
+        targetQuery: z
+            .string()
+            .describe('Target identifier. Examples: "EGFR" (genesymbol), "Epidermal growth factor receptor" ' +
+            '(proteinname), "1956" (geneid), "P00533" (proteinaccession).'),
+        maxResults: z
+            .number()
+            .min(1)
+            .max(200)
+            .default(50)
+            .describe('Max AIDs to return (1-200). Popular targets may have thousands of assays. Default: 50.'),
+    }),
+    output: z.object({
+        targetType: z.string().describe('Target identifier type used.'),
+        targetQuery: z.string().describe('Target identifier searched.'),
+        totalFound: z.number().describe('Total AIDs found.'),
+        aids: z.array(z.number()).describe('PubChem Assay IDs.'),
+    }),
+    async handler(input, ctx) {
+        const client = getPubChemClient();
+        const allAids = await client.searchAssaysByTarget(input.targetType, input.targetQuery);
+        const totalFound = allAids.length;
+        const aids = allAids.slice(0, input.maxResults);
+        ctx.log.info('Assay search completed', {
+            targetType: input.targetType,
+            targetQuery: input.targetQuery,
+            totalFound,
+            returned: aids.length,
+        });
+        return {
+            targetType: input.targetType,
+            targetQuery: input.targetQuery,
+            totalFound,
+            aids,
+        };
+    },
+    format(result) {
+        const truncated = result.totalFound > result.aids.length
+            ? ` (showing ${result.aids.length} of ${result.totalFound})`
+            : '';
+        const lines = [
+            `Found ${result.totalFound} assay${result.totalFound !== 1 ? 's' : ''} for "${result.targetQuery}" (${result.targetType})${truncated}`,
+            '',
+        ];
+        if (result.aids.length > 0) {
+            lines.push(`AIDs: ${result.aids.join(', ')}`);
+        }
+        else {
+            lines.push('No assays found.');
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+//# sourceMappingURL=search-assays.tool.js.map

package/dist/mcp-server/tools/definitions/search-assays.tool.js.map

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

@@ -0,0 +1,42 @@
+/**
+ * @fileoverview Search PubChem for chemical compounds by name, SMILES, InChIKey,
+ * formula, substructure, superstructure, or 2D similarity.
+ * @module mcp-server/tools/definitions/search-compounds
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    searchType: z.ZodEnum<{
+        substructure: "substructure";
+        superstructure: "superstructure";
+        similarity: "similarity";
+        identifier: "identifier";
+        formula: "formula";
+    }>;
+    identifierType: z.ZodOptional<z.ZodEnum<{
+        smiles: "smiles";
+        name: "name";
+        inchikey: "inchikey";
+    }>>;
+    identifiers: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    formula: z.ZodOptional<z.ZodString>;
+    allowOtherElements: z.ZodDefault<z.ZodBoolean>;
+    query: z.ZodOptional<z.ZodString>;
+    queryType: z.ZodOptional<z.ZodEnum<{
+        smiles: "smiles";
+        cid: "cid";
+    }>>;
+    threshold: z.ZodDefault<z.ZodNumber>;
+    maxResults: z.ZodDefault<z.ZodNumber>;
+    properties: z.ZodOptional<z.ZodArray<z.ZodEnum<{
+        [x: string]: string;
+    }>>>;
+}, z.core.$strip>, z.ZodObject<{
+    searchType: z.ZodString;
+    totalFound: z.ZodNumber;
+    results: z.ZodArray<z.ZodObject<{
+        cid: z.ZodNumber;
+        identifier: z.ZodOptional<z.ZodString>;
+        properties: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+    }, z.core.$strip>>;
+}, z.core.$strip>>;
+//# sourceMappingURL=search-compounds.tool.d.ts.map

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

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