@cyanheads/pubchem-mcp-server 0.1.1

package/LICENSE

@@ -0,0 +1,190 @@
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package/README.md

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+<div align="center">
+  <h1>pubchem-mcp-server</h1>
+  <p><b>MCP server for the PubChem chemical database. Search compounds, fetch properties, safety data, bioactivity, cross-references, and entity summaries. Runs over stdio or HTTP.</b></p>
+</div>
+
+<div align="center">
+
+[![Version](https://img.shields.io/badge/Version-0.1.1-blue.svg?style=flat-square)](./CHANGELOG.md) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^5.9.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-^1.2.0-f472b6.svg?style=flat-square)](https://bun.sh/)
+
+</div>
+
+---
+
+## Tools
+
+Eight tools for querying PubChem's chemical information database:
+
+| Tool Name | Description |
+|:----------|:------------|
+| `pubchem_search_compounds` | Search for compounds by name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity. |
+| `pubchem_get_compound_details` | Get physicochemical properties, descriptions, and synonyms for compounds by CID. |
+| `pubchem_get_compound_image` | Fetch a 2D structure diagram (PNG) for a compound by CID. |
+| `pubchem_get_compound_safety` | Get GHS hazard classification and safety data for a compound. |
+| `pubchem_get_compound_xrefs` | Get external database cross-references (PubMed, patents, genes, proteins, etc.). |
+| `pubchem_get_bioactivity` | Get a compound's bioactivity profile: assay results, targets, and activity values. |
+| `pubchem_search_assays` | Find bioassays by biological target (gene symbol, protein, Gene ID, UniProt accession). |
+| `pubchem_get_summary` | Get summaries for PubChem entities: assays, genes, proteins, taxonomy. |
+
+### `pubchem_search_compounds`
+
+Search PubChem for chemical compounds across five search modes.
+
+- **Identifier lookup** — resolve compound names, SMILES, or InChIKeys to CIDs (batch up to 25)
+- **Formula search** — find compounds by molecular formula in Hill notation
+- **Substructure/superstructure** — find compounds containing or contained within a query structure
+- **2D similarity** — find structurally similar compounds by Tanimoto similarity (configurable threshold)
+- Optionally hydrate results with properties to avoid a follow-up details call
+
+---
+
+### `pubchem_get_compound_details`
+
+Get detailed compound information by CID.
+
+- Batches up to 100 CIDs in a single request
+- 24 available properties: molecular weight, SMILES, InChIKey, XLogP, TPSA, complexity, stereo counts, and more
+- Optionally includes textual descriptions (pharmacology, mechanism, therapeutic use) from PUG View
+- Optionally includes all known synonyms (trade names, systematic names, registry numbers)
+
+---
+
+### `pubchem_get_bioactivity`
+
+Get a compound's bioactivity profile from PubChem BioAssay.
+
+- Returns assay outcomes (Active/Inactive/Inconclusive), target info (protein accessions, NCBI Gene IDs), and quantitative values (IC50, EC50, Ki)
+- Filter by outcome to focus on active results
+- Caps at 100 results per request (well-studied compounds may have thousands)
+
+---
+
+### `pubchem_get_summary`
+
+Get descriptive summaries for four PubChem entity types.
+
+- Assays (AID), genes (Gene ID), proteins (UniProt accession), taxonomy (Tax ID)
+- Up to 10 entities per call
+- Type-specific field extraction for clean, structured output
+
+## Features
+
+Built on [`@cyanheads/mcp-ts-core`](https://github.com/cyanheads/mcp-ts-core):
+
+- Declarative tool definitions — single file per tool, framework handles registration and validation
+- Unified error handling across all tools
+- Pluggable auth (`none`, `jwt`, `oauth`)
+- Swappable storage backends: `in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`
+- Structured logging with optional OpenTelemetry tracing
+- Runs locally (stdio/HTTP) or containerized via Docker
+
+PubChem-specific:
+
+- Rate-limited client for PUG REST and PUG View APIs (5 req/s with automatic queuing)
+- Retry with exponential backoff on 5xx errors and network failures
+- All tools are read-only and idempotent — no API keys required
+
+## Getting Started
+
+### MCP Client Configuration
+
+Add to your MCP client config (e.g., `claude_desktop_config.json`):
+
+```json
+{
+  "mcpServers": {
+    "pubchem": {
+      "type": "stdio",
+      "command": "bunx",
+      "args": ["@cyanheads/pubchem-mcp-server@latest"],
+      "env": {
+        "MCP_TRANSPORT_TYPE": "stdio"
+      }
+    }
+  }
+}
+```
+
+### Prerequisites
+
+- [Bun v1.2.0](https://bun.sh/) or higher (or Node.js v22+)
+
+### Installation
+
+1. **Clone the repository:**
+```sh
+git clone https://github.com/cyanheads/pubchem-mcp-server.git
+```
+
+2. **Navigate into the directory:**
+```sh
+cd pubchem-mcp-server
+```
+
+3. **Install dependencies:**
+```sh
+bun install
+```
+
+## Configuration
+
+No API keys are required — PubChem's API is freely accessible.
+
+| Variable | Description | Default |
+|:---------|:------------|:--------|
+| `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http`. | `stdio` |
+| `MCP_HTTP_PORT` | Port for HTTP server. | `3010` |
+| `MCP_HTTP_HOST` | Host for HTTP server. | `localhost` |
+| `MCP_AUTH_MODE` | Auth mode: `none`, `jwt`, or `oauth`. | `none` |
+| `MCP_LOG_LEVEL` | Log level (RFC 5424). | `info` |
+| `STORAGE_PROVIDER_TYPE` | Storage backend. | `in-memory` |
+| `OTEL_ENABLED` | Enable OpenTelemetry. | `false` |
+
+## Running the Server
+
+### Local Development
+
+- **Build and run the production version:**
+  ```sh
+  bun run build
+  bun run start:http   # or start:stdio
+  ```
+
+- **Run in dev mode (auto-reload):**
+  ```sh
+  bun run dev:stdio    # or dev:http
+  ```
+
+- **Run checks and tests:**
+  ```sh
+  bun run devcheck     # Lints, formats, type-checks
+  bun run test         # Runs test suite
+  ```
+
+### Docker
+
+```sh
+docker build -t pubchem-mcp-server .
+docker run -p 3010:3010 pubchem-mcp-server
+```
+
+## Project Structure
+
+| Directory | Purpose |
+|:----------|:--------|
+| `src/mcp-server/tools/definitions/` | Tool definitions (`*.tool.ts`). |
+| `src/services/pubchem/` | PubChem API client with rate limiting and response parsing. |
+| `scripts/` | Build, clean, devcheck, and tree generation scripts. |
+
+## Development Guide
+
+See [`CLAUDE.md`](./CLAUDE.md) for development guidelines and architectural rules. The short version:
+
+- Handlers throw, framework catches — no `try/catch` in tool logic
+- Use `ctx.log` for domain-specific logging
+- Register new tools in the `index.ts` barrel file
+
+## Contributing
+
+Issues and pull requests are welcome. Run checks before submitting:
+
+```sh
+bun run devcheck
+bun run test
+```
+
+## License
+
+Apache-2.0 — see [LICENSE](LICENSE) for details.

package/dist/index.d.ts

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+#!/usr/bin/env node
+/**
+ * @fileoverview PubChem MCP server entry point. Provides read-only access to
+ * PubChem's chemical information database via PUG REST and PUG View APIs.
+ * @module index
+ */
+export {};
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;GAIG"}

package/dist/index.js

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+#!/usr/bin/env node
+/**
+ * @fileoverview PubChem MCP server entry point. Provides read-only access to
+ * PubChem's chemical information database via PUG REST and PUG View APIs.
+ * @module index
+ */
+import { createApp } from '@cyanheads/mcp-ts-core';
+import { allToolDefinitions } from './mcp-server/tools/definitions/index.js';
+import { initPubChemClient } from './services/pubchem/pubchem-client.js';
+await createApp({
+    tools: allToolDefinitions,
+    setup() {
+        initPubChemClient();
+    },
+});
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;GAIG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,kBAAkB,EAAE,MAAM,yCAAyC,CAAC;AAC7E,OAAO,EAAE,iBAAiB,EAAE,MAAM,sCAAsC,CAAC;AAEzE,MAAM,SAAS,CAAC;IACd,KAAK,EAAE,kBAAkB;IACzB,KAAK;QACH,iBAAiB,EAAE,CAAC;IACtB,CAAC;CACF,CAAC,CAAC"}

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

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+/**
+ * @fileoverview Get a compound's bioactivity profile — which assays tested it,
+ * activity outcomes, target information, and quantitative values.
+ * @module mcp-server/tools/definitions/get-bioactivity
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const getBioactivity: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    cid: z.ZodNumber;
+    outcomeFilter: z.ZodDefault<z.ZodEnum<{
+        active: "active";
+        inactive: "inactive";
+        all: "all";
+    }>>;
+    maxResults: z.ZodDefault<z.ZodNumber>;
+}, z.core.$strip>, z.ZodObject<{
+    cid: z.ZodNumber;
+    totalAssays: z.ZodNumber;
+    activeCount: z.ZodNumber;
+    inactiveCount: z.ZodNumber;
+    results: z.ZodArray<z.ZodObject<{
+        aid: z.ZodNumber;
+        assayName: z.ZodString;
+        outcome: z.ZodString;
+        targetAccession: z.ZodOptional<z.ZodString>;
+        targetGeneId: z.ZodOptional<z.ZodNumber>;
+        activityValues: z.ZodArray<z.ZodObject<{
+            name: z.ZodString;
+            value: z.ZodNumber;
+            unit: z.ZodString;
+        }, z.core.$strip>>;
+    }, z.core.$strip>>;
+}, z.core.$strip>>;
+//# sourceMappingURL=get-bioactivity.tool.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"get-bioactivity.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;kBA2HzB,CAAC"}

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

@@ -0,0 +1,115 @@
+/**
+ * @fileoverview Get a compound's bioactivity profile — which assays tested it,
+ * activity outcomes, target information, and quantitative values.
+ * @module mcp-server/tools/definitions/get-bioactivity
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
+export const getBioactivity = tool('pubchem_get_bioactivity', {
+    title: 'Get Bioactivity',
+    description: "Get a compound's bioactivity profile: which assays tested it, activity outcomes " +
+        '(Active/Inactive/Inconclusive), target information (gene symbols, protein names), ' +
+        'and quantitative values (IC50, EC50, Ki, etc.). Filter by outcome to focus on active results.',
+    annotations: {
+        readOnlyHint: true,
+        destructiveHint: false,
+        idempotentHint: true,
+        openWorldHint: true,
+    },
+    input: z.object({
+        cid: z.number().int().positive().describe('PubChem Compound ID.'),
+        outcomeFilter: z
+            .enum(['active', 'inactive', 'all'])
+            .default('all')
+            .describe('Filter by activity outcome. "active" shows only assays where the compound showed activity — ' +
+            'most useful for understanding biological profile. Default: "all".'),
+        maxResults: z
+            .number()
+            .min(1)
+            .max(100)
+            .default(20)
+            .describe('Max assay results to return (1-100). Well-studied compounds have thousands of records. Default: 20.'),
+    }),
+    output: z.object({
+        cid: z.number().describe('PubChem Compound ID.'),
+        totalAssays: z.number().describe('Total unique assays for this compound.'),
+        activeCount: z.number().describe('Assays with "Active" outcome.'),
+        inactiveCount: z.number().describe('Assays with "Inactive" outcome.'),
+        results: z
+            .array(z.object({
+            aid: z.number().describe('PubChem Assay ID.'),
+            assayName: z.string().describe('Assay name/title.'),
+            outcome: z
+                .string()
+                .describe('Activity outcome: Active, Inactive, Inconclusive, Unspecified.'),
+            targetAccession: z
+                .string()
+                .optional()
+                .describe('Target protein accession (UniProt/GenBank).'),
+            targetGeneId: z.number().optional().describe('Target NCBI Gene ID.'),
+            activityValues: z
+                .array(z.object({
+                name: z.string().describe('Measurement name (e.g. IC50, EC50, Ki).'),
+                value: z.number().describe('Measured value.'),
+                unit: z.string().describe('Unit of measurement (e.g. uM, nM).'),
+            }))
+                .describe('Quantitative activity measurements.'),
+        }))
+            .describe('Assay results matching the filter.'),
+    }),
+    async handler(input, ctx) {
+        const client = getPubChemClient();
+        const allRows = await client.getAssaySummary(input.cid);
+        const activeCount = allRows.filter((r) => r.outcome === 'Active').length;
+        const inactiveCount = allRows.filter((r) => r.outcome === 'Inactive').length;
+        // Filter by outcome
+        let filtered = allRows;
+        if (input.outcomeFilter === 'active') {
+            filtered = allRows.filter((r) => r.outcome === 'Active');
+        }
+        else if (input.outcomeFilter === 'inactive') {
+            filtered = allRows.filter((r) => r.outcome === 'Inactive');
+        }
+        const results = filtered.slice(0, input.maxResults);
+        ctx.log.info('Bioactivity fetched', {
+            cid: input.cid,
+            total: allRows.length,
+            active: activeCount,
+            returned: results.length,
+        });
+        return {
+            cid: input.cid,
+            totalAssays: allRows.length,
+            activeCount,
+            inactiveCount,
+            results,
+        };
+    },
+    format(result) {
+        const lines = [
+            `## Bioactivity — CID ${result.cid}`,
+            `Total assays: ${result.totalAssays} | Active: ${result.activeCount} | Inactive: ${result.inactiveCount}`,
+            '',
+        ];
+        if (result.results.length === 0) {
+            lines.push('No matching assay results.');
+            return [{ type: 'text', text: lines.join('\n') }];
+        }
+        for (const r of result.results) {
+            const target = [r.targetGeneId ? `GeneID:${r.targetGeneId}` : undefined, r.targetAccession]
+                .filter(Boolean)
+                .join(' — ');
+            lines.push(`**AID ${r.aid}** — ${r.assayName} (${r.outcome})`);
+            if (target)
+                lines.push(`  Target: ${target}`);
+            if (r.activityValues.length > 0) {
+                for (const av of r.activityValues) {
+                    lines.push(`  ${av.name}: ${av.value} ${av.unit}`);
+                }
+            }
+            lines.push('');
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+//# sourceMappingURL=get-bioactivity.tool.js.map

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

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

@@ -0,0 +1,22 @@
+/**
+ * @fileoverview Get detailed compound information: physicochemical properties,
+ * textual descriptions, and/or synonyms for one or more CIDs.
+ * @module mcp-server/tools/definitions/get-compound-details
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const getCompoundDetails: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    cids: z.ZodArray<z.ZodNumber>;
+    properties: z.ZodOptional<z.ZodArray<z.ZodEnum<{
+        [x: string]: string;
+    }>>>;
+    includeDescription: z.ZodDefault<z.ZodBoolean>;
+    includeSynonyms: z.ZodDefault<z.ZodBoolean>;
+}, z.core.$strip>, z.ZodObject<{
+    compounds: z.ZodArray<z.ZodObject<{
+        cid: z.ZodNumber;
+        properties: z.ZodRecord<z.ZodString, z.ZodUnknown>;
+        description: z.ZodOptional<z.ZodString>;
+        synonyms: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    }, z.core.$strip>>;
+}, z.core.$strip>>;
+//# sourceMappingURL=get-compound-details.tool.d.ts.map

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

@@ -0,0 +1 @@
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