@cyanheads/pubchem-mcp-server 0.1.1 → 0.1.2

package/Dockerfile

@@ -0,0 +1,85 @@
+# ==============================================================================
+# Build Stage
+#
+# This stage installs all dependencies (including dev), builds the TypeScript
+# source code into JavaScript, and prepares the production assets.
+# ==============================================================================
+FROM oven/bun:1 AS build
+
+WORKDIR /usr/src/app
+
+# Copy dependency manifests for optimized layer caching
+COPY package.json bun.lock ./
+
+# Install all dependencies (including dev dependencies for building)
+RUN bun install --frozen-lockfile
+
+# Copy the rest of the source code
+COPY . .
+
+# Build the application
+RUN bun run build
+
+
+# ==============================================================================
+# Production Stage
+#
+# This stage creates a minimal, optimized, and secure image for running the
+# application. It uses a slim base image and only includes production
+# dependencies and build artifacts.
+# ==============================================================================
+FROM oven/bun:1-slim AS production
+
+WORKDIR /usr/src/app
+
+# Set the environment to production for performance and to ensure only
+# production dependencies are installed.
+ENV NODE_ENV=production
+
+# OCI image metadata (https://github.com/opencontainers/image-spec/blob/main/annotations.md)
+LABEL org.opencontainers.image.title="pubchem-mcp-server"
+LABEL org.opencontainers.image.description="MCP server for the PubChem chemical database."
+LABEL org.opencontainers.image.source="https://github.com/cyanheads/pubchem-mcp-server"
+LABEL org.opencontainers.image.licenses="Apache-2.0"
+
+# Copy dependency manifests
+COPY package.json bun.lock ./
+
+# Install only production dependencies, ignoring any lifecycle scripts (like 'prepare')
+# that are not needed in the final production image.
+# Remove platform-specific bun/rollup binaries pulled as optionalDependencies
+# by @modelcontextprotocol/ext-apps — only needed for its build toolchain, not runtime.
+RUN bun install --production --frozen-lockfile --ignore-scripts \
+    && rm -rf node_modules/@oven node_modules/@rollup
+
+# Copy the compiled application code from the build stage
+COPY --from=build /usr/src/app/dist ./dist
+
+# The 'oven/bun' image already provides a non-root user named 'bun'.
+# We will use this existing user for enhanced security.
+
+# Create and set permissions for the log directory, assigning ownership to the 'bun' user.
+RUN mkdir -p /var/log/pubchem-mcp-server && chown -R bun:bun /var/log/pubchem-mcp-server
+
+# Switch to the non-root user
+USER bun
+
+# Define an argument for the port, allowing it to be overridden at build time.
+# The `PORT` variable is often injected by cloud environments at runtime.
+ARG PORT
+
+# Set runtime environment variables
+# Note: PORT is an automatic variable in many cloud environments (e.g., Cloud Run)
+ENV MCP_HTTP_PORT=${PORT:-3010}
+ENV MCP_HTTP_HOST="0.0.0.0"
+ENV MCP_TRANSPORT_TYPE="http"
+ENV MCP_SESSION_MODE="stateless"
+ENV MCP_LOG_LEVEL="info"
+ENV LOGS_DIR="/var/log/pubchem-mcp-server"
+ENV MCP_FORCE_CONSOLE_LOGGING="true"
+
+# Expose the port the server listens on
+EXPOSE ${MCP_HTTP_PORT}
+
+# The command to start the server
+CMD ["bun", "run", "dist/index.js"]

package/README.md

@@ -18,7 +18,7 @@ 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_details` | Get physicochemical properties, descriptions, synonyms, drug-likeness, and classification 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.). |
@@ -43,9 +43,11 @@ Search PubChem for chemical compounds across five search modes.
 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
+- 27 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)
+- Optionally computes drug-likeness assessment (Lipinski Rule of Five + Veber rules) from fetched properties
+- Optionally fetches pharmacological classification (FDA classes, mechanisms of action, MeSH classes, ATC codes)
 
 ---
 

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

@@ -1 +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"}
+{"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;;;;;;;;;;;;;;;;;;;;;;;;;kBA0HzB,CAAC"}

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

@@ -102,10 +102,9 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
             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}`);
-                }
+            const meaningful = r.activityValues.filter((av) => av.name);
+            for (const av of meaningful) {
+                lines.push(`  ${av.name}: ${av.value} ${av.unit}`);
             }
             lines.push('');
         }

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

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts

@@ -1,9 +1,10 @@
 /**
  * @fileoverview Get detailed compound information: physicochemical properties,
- * textual descriptions, and/or synonyms for one or more CIDs.
+ * textual descriptions, synonyms, drug-likeness assessment, and pharmacological classification.
  * @module mcp-server/tools/definitions/get-compound-details
  */
 import { z } from '@cyanheads/mcp-ts-core';
+import type { CompoundClassification, DrugLikenessAssessment } from '../../../services/pubchem/types.js';
 export declare const getCompoundDetails: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     cids: z.ZodArray<z.ZodNumber>;
     properties: z.ZodOptional<z.ZodArray<z.ZodEnum<{
@@ -11,12 +12,16 @@ export declare const getCompoundDetails: import("@cyanheads/mcp-ts-core").ToolDe
     }>>>;
     includeDescription: z.ZodDefault<z.ZodBoolean>;
     includeSynonyms: z.ZodDefault<z.ZodBoolean>;
+    includeDrugLikeness: z.ZodDefault<z.ZodBoolean>;
+    includeClassification: z.ZodDefault<z.ZodBoolean>;
 }, z.core.$strip>, z.ZodObject<{
     compounds: z.ZodArray<z.ZodObject<{
         cid: z.ZodNumber;
         properties: z.ZodRecord<z.ZodString, z.ZodUnknown>;
         description: z.ZodOptional<z.ZodString>;
         synonyms: z.ZodOptional<z.ZodArray<z.ZodString>>;
+        drugLikeness: z.ZodOptional<z.ZodCustom<DrugLikenessAssessment, DrugLikenessAssessment>>;
+        classification: z.ZodOptional<z.ZodCustom<CompoundClassification, CompoundClassification>>;
     }, z.core.$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

@@ -1 +1 @@
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+{"version":3,"file":"get-compound-details.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-details.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAEjD,OAAO,KAAK,EACV,sBAAsB,EACtB,sBAAsB,EAEvB,MAAM,6BAA6B,CAAC;AA4CrC,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;kBA8S7B,CAAC"}

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

@@ -1,18 +1,52 @@
 /**
  * @fileoverview Get detailed compound information: physicochemical properties,
- * textual descriptions, and/or synonyms for one or more CIDs.
+ * textual descriptions, synonyms, drug-likeness assessment, and pharmacological classification.
  * @module mcp-server/tools/definitions/get-compound-details
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
 import { COMPOUND_PROPERTIES, DEFAULT_PROPERTIES } from '../../../services/pubchem/types.js';
 const propertyEnum = z.enum(COMPOUND_PROPERTIES);
+// ── Drug-likeness computation ──────────────────────────────────────────
+/** Properties needed for drug-likeness — all included in DEFAULT_PROPERTIES */
+const DRUG_LIKENESS_PROPS = [
+    'MolecularWeight',
+    'XLogP',
+    'HBondDonorCount',
+    'HBondAcceptorCount',
+    'TPSA',
+    'RotatableBondCount',
+];
+function evaluateRule(value, limit) {
+    if (value == null || typeof value !== 'number')
+        return { limit, pass: null, value: null };
+    return { limit, pass: value <= limit, value };
+}
+function computeDrugLikeness(properties) {
+    const mw = evaluateRule(properties.MolecularWeight, 500);
+    const xLogP = evaluateRule(properties.XLogP, 5);
+    const hbd = evaluateRule(properties.HBondDonorCount, 5);
+    const hba = evaluateRule(properties.HBondAcceptorCount, 10);
+    const tpsa = evaluateRule(properties.TPSA, 140);
+    const rotatableBonds = evaluateRule(properties.RotatableBondCount, 10);
+    const lipinskiRules = [mw, xLogP, hbd, hba];
+    const veberRules = [tpsa, rotatableBonds];
+    const lipinskiViolations = lipinskiRules.filter((r) => r.pass === false).length;
+    const veberViolations = veberRules.filter((r) => r.pass === false).length;
+    return {
+        lipinski: { hba, hbd, mw, violations: lipinskiViolations, xLogP },
+        pass: lipinskiViolations <= 1 && veberViolations === 0,
+        veber: { rotatableBonds, tpsa, violations: veberViolations },
+    };
+}
+// ── Tool definition ────────────────────────────────────────────────────
 export const getCompoundDetails = tool('pubchem_get_compound_details', {
     title: 'Get Compound Details',
     description: 'Get detailed compound information by CID. Returns physicochemical properties ' +
         '(molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual ' +
-        'description (pharmacology, mechanism, therapeutic use) and/or all known synonyms. ' +
-        'Efficiently batches up to 100 CIDs in a single request.',
+        'description (pharmacology, mechanism, therapeutic use), all known synonyms, ' +
+        'drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification ' +
+        '(FDA classes, MeSH classes, ATC codes). Efficiently batches up to 100 CIDs.',
     annotations: {
         readOnlyHint: true,
         destructiveHint: false,
@@ -40,6 +74,17 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
             .boolean()
             .default(false)
             .describe('Fetch all known names and synonyms (trade names, systematic names, registry numbers).'),
+        includeDrugLikeness: z
+            .boolean()
+            .default(false)
+            .describe('Compute drug-likeness assessment: Lipinski Rule of Five (MW, XLogP, HBD, HBA) and ' +
+            'Veber rules (TPSA, rotatable bonds). No extra API calls — computed from properties.'),
+        includeClassification: z
+            .boolean()
+            .default(false)
+            .describe('Fetch pharmacological classification from PUG View: FDA Established Pharmacologic ' +
+            'Classes, mechanisms of action, MeSH classes, and ATC codes. ' +
+            'Adds one API call per CID — consider limiting CID count when enabled.'),
     }),
     output: z.object({
         compounds: z
@@ -50,44 +95,64 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 .describe('Requested physicochemical properties.'),
             description: z.string().optional().describe('Textual description from PUG View.'),
             synonyms: z.array(z.string()).optional().describe('Known names and synonyms.'),
+            drugLikeness: z
+                .custom()
+                .optional()
+                .describe('Drug-likeness assessment. lipinski.violations ≤ 1 and veber.violations = 0 → pass.'),
+            classification: z
+                .custom()
+                .optional()
+                .describe('Pharmacological classification (FDA, MeSH, ATC).'),
         }))
             .describe('Compound detail records.'),
     }),
     async handler(input, ctx) {
         const client = getPubChemClient();
-        const props = input.properties ?? [...DEFAULT_PROPERTIES];
+        const requestedProps = input.properties ?? [...DEFAULT_PROPERTIES];
+        // Ensure drug-likeness properties are fetched when needed
+        let props = requestedProps;
+        if (input.includeDrugLikeness) {
+            const propsSet = new Set(requestedProps);
+            const missing = DRUG_LIKENESS_PROPS.filter((p) => !propsSet.has(p));
+            if (missing.length > 0)
+                props = [...requestedProps, ...missing];
+        }
         // Batch property fetch
         const propertyRows = await client.getProperties(input.cids, props);
         const propsMap = new Map(propertyRows.map((r) => [r.CID, r]));
-        // Optional: descriptions (per-CID, parallelized with concurrency limit)
+        // PUG View calls (per-CID, capped at 10)
+        const viewCids = input.cids.slice(0, 10);
+        if ((input.includeDescription || input.includeClassification) &&
+            viewCids.length < input.cids.length) {
+            ctx.log.info('PUG View fetch capped at 10 CIDs', {
+                requested: input.cids.length,
+                fetching: viewCids.length,
+            });
+        }
+        // Optional: descriptions
         let descMap;
         if (input.includeDescription) {
-            const descCids = input.cids.slice(0, 10); // Cap at 10 to limit API calls
-            if (descCids.length < input.cids.length) {
-                ctx.log.info('Description fetch capped at 10 CIDs', {
-                    requested: input.cids.length,
-                    fetching: descCids.length,
-                });
-            }
-            const entries = await Promise.all(descCids.map(async (cid) => {
-                const desc = await client.getDescription(cid);
-                return [cid, desc];
-            }));
+            const entries = await Promise.all(viewCids.map(async (cid) => [cid, await client.getDescription(cid)]));
             descMap = new Map(entries.filter((e) => e[1] !== null));
         }
         // Optional: synonyms (per-CID)
         let synMap;
         if (input.includeSynonyms) {
-            const entries = await Promise.all(input.cids.map(async (cid) => {
-                const syns = await client.getSynonyms(cid);
-                return [cid, syns];
-            }));
+            const entries = await Promise.all(input.cids.map(async (cid) => [cid, await client.getSynonyms(cid)]));
             synMap = new Map(entries.filter((e) => e[1].length > 0));
         }
+        // Optional: classification
+        let classMap;
+        if (input.includeClassification) {
+            const entries = await Promise.all(viewCids.map(async (cid) => [cid, await client.getClassification(cid)]));
+            classMap = new Map(entries.filter((e) => e[1] !== null));
+        }
         ctx.log.info('Details fetched', {
             cids: input.cids.length,
             withDescription: input.includeDescription,
             withSynonyms: input.includeSynonyms,
+            withDrugLikeness: input.includeDrugLikeness,
+            withClassification: input.includeClassification,
         });
         const compounds = input.cids.map((cid) => {
             const rawProps = propsMap.get(cid) ?? {};
@@ -100,6 +165,11 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
             const syns = synMap?.get(cid);
             if (syns)
                 compound.synonyms = syns;
+            if (input.includeDrugLikeness)
+                compound.drugLikeness = computeDrugLikeness(properties);
+            const cls = classMap?.get(cid);
+            if (cls)
+                compound.classification = cls;
             return compound;
         });
         return { compounds };
@@ -172,19 +242,72 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 lines.push(extra.map(([k, v]) => `**${k}:** ${v}`).join(' | '));
             }
             blocks.push(lines.join('\n'));
+            // Drug-likeness assessment
+            if (c.drugLikeness) {
+                const dl = c.drugLikeness;
+                const status = dl.pass ? 'PASS' : 'FAIL';
+                lines.length = 0;
+                lines.push(`\n**Drug-likeness:** ${status}`);
+                lines.push(`  Lipinski (${dl.lipinski.violations}/4 violations): ` +
+                    formatRules([
+                        ['MW', dl.lipinski.mw],
+                        ['XLogP', dl.lipinski.xLogP],
+                        ['HBD', dl.lipinski.hbd],
+                        ['HBA', dl.lipinski.hba],
+                    ]));
+                lines.push(`  Veber (${dl.veber.violations}/2 violations): ` +
+                    formatRules([
+                        ['TPSA', dl.veber.tpsa],
+                        ['RotBonds', dl.veber.rotatableBonds],
+                    ]));
+                blocks.push(lines.join('\n'));
+            }
+            // Classification
+            if (c.classification) {
+                const cls = c.classification;
+                lines.length = 0;
+                lines.push('\n**Classification:**');
+                if (cls.fdaClasses.length > 0)
+                    lines.push(`  FDA: ${cls.fdaClasses.join(', ')}`);
+                if (cls.fdaMechanisms.length > 0)
+                    lines.push(`  MoA: ${cls.fdaMechanisms.join(', ')}`);
+                if (cls.meshClasses.length > 0) {
+                    const meshDisplay = cls.meshClasses.length > 3
+                        ? `${cls.meshClasses.slice(0, 3).join('; ')} (+${cls.meshClasses.length - 3} more)`
+                        : cls.meshClasses.join('; ');
+                    lines.push(`  MeSH: ${meshDisplay}`);
+                }
+                if (cls.atcCodes.length > 0) {
+                    const atcDisplay = cls.atcCodes
+                        .map((a) => (a.description ? `${a.code} (${a.description})` : a.code))
+                        .join(', ');
+                    lines.push(`  ATC: ${atcDisplay}`);
+                }
+                blocks.push(lines.join('\n'));
+            }
             // Description
             if (c.description) {
                 blocks.push(`\n> ${c.description.replace(/\n/g, '\n> ')}`);
             }
             // Synonyms
             if (c.synonyms && c.synonyms.length > 0) {
-                const shown = c.synonyms.slice(0, 20);
+                const synShown = c.synonyms.slice(0, 20);
                 const more = c.synonyms.length > 20 ? ` (+${c.synonyms.length - 20} more)` : '';
-                blocks.push(`\n**Synonyms:** ${shown.join(', ')}${more}`);
+                blocks.push(`\n**Synonyms:** ${synShown.join(', ')}${more}`);
             }
             blocks.push('');
         }
         return [{ type: 'text', text: blocks.join('\n') }];
     },
 });
+function formatRules(rules) {
+    return rules
+        .map(([label, r]) => {
+        if (r.pass === null)
+            return `${label}: N/A`;
+        const icon = r.pass ? 'ok' : 'FAIL';
+        return `${label}: ${r.value}/${r.limit} ${icon}`;
+    })
+        .join(' | ');
+}
 //# sourceMappingURL=get-compound-details.tool.js.map

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

@@ -34,12 +34,16 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
     }>>>;
     includeDescription: import("zod").ZodDefault<import("zod").ZodBoolean>;
     includeSynonyms: import("zod").ZodDefault<import("zod").ZodBoolean>;
+    includeDrugLikeness: import("zod").ZodDefault<import("zod").ZodBoolean>;
+    includeClassification: import("zod").ZodDefault<import("zod").ZodBoolean>;
 }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
     compounds: import("zod").ZodArray<import("zod").ZodObject<{
         cid: import("zod").ZodNumber;
         properties: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
         description: import("zod").ZodOptional<import("zod").ZodString>;
         synonyms: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
+        drugLikeness: import("zod").ZodOptional<import("zod").ZodCustom<import("../../../services/pubchem/types.js").DrugLikenessAssessment, import("../../../services/pubchem/types.js").DrugLikenessAssessment>>;
+        classification: import("zod").ZodOptional<import("zod").ZodCustom<import("../../../services/pubchem/types.js").CompoundClassification, import("../../../services/pubchem/types.js").CompoundClassification>>;
     }, import("zod/v4/core").$strip>>;
 }, import("zod/v4/core").$strip>> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     cid: import("zod").ZodNumber;

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

@@ -1 +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"}
+{"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/services/pubchem/pubchem-client.d.ts

@@ -3,7 +3,7 @@
  * Wraps both PUG REST and PUG View APIs behind a shared rate limiter.
  * @module services/pubchem/pubchem-client
  */
-import type { BioactivityRow, GHSClassification } from './types.js';
+import type { BioactivityRow, CompoundClassification, GHSClassification } from './types.js';
 export declare class PubChemClient {
     private readonly pugBase;
     private readonly viewBase;
@@ -27,6 +27,7 @@ export declare class PubChemClient {
     getXrefs(cid: number, xrefType: string): Promise<(string | number)[]>;
     getDescription(cid: number): Promise<string | null>;
     getSafetyData(cid: number): Promise<GHSClassification | null>;
+    getClassification(cid: number): Promise<CompoundClassification | null>;
     getAssaySummary(cid: number): Promise<BioactivityRow[]>;
     private parseAssayTable;
     searchAssaysByTarget(targetType: string, query: string): Promise<number[]>;

package/dist/services/pubchem/pubchem-client.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"pubchem-client.d.ts","sourceRoot":"","sources":["../../../src/services/pubchem/pubchem-client.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAGV,cAAc,EAEd,iBAAiB,EAQlB,MAAM,YAAY,CAAC;AAuJpB,qBAAa,aAAa;IACxB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAA+C;IACvE,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAoD;IAC7E,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAsB;YAIpC,SAAS;YAgDT,WAAW;IAwBzB,wEAAwE;YAC1D,SAAS;IAWvB,qDAAqD;YACvC,WAAW;IAgBzB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAI7C,cAAc,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAQjD,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAMrD,eAAe,CAAC,OAAO,EAAE,MAAM,EAAE,UAAU,UAAQ,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAOvE,iBAAiB,CACf,IAAI,EAAE,cAAc,GAAG,gBAAgB,GAAG,YAAY,EACtD,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,QAAQ,GAAG,KAAK,EAC3B,SAAS,CAAC,EAAE,MAAM,GACjB,OAAO,CAAC,MAAM,EAAE,CAAC;IA2Bd,aAAa,CACjB,IAAI,EAAE,MAAM,EAAE,EACd,UAAU,EAAE,MAAM,EAAE,GACnB,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG;QAAE,GAAG,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IA+BtD,WAAW,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAYjD,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,GAAE,OAAO,GAAG,OAAiB,GAAG,OAAO,CAAC,WAAW,CAAC;IAKxE,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,CAAC,MAAM,GAAG,MAAM,CAAC,EAAE,CAAC;IAiBrE,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC;IAoBnD,aAAa,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,GAAG,IAAI,CAAC;IA4E7D,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,EAAE,CAAC;IAY7D,OAAO,CAAC,eAAe;IA+DjB,oBAAoB,CAAC,UAAU,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAgB1E,gBAAgB,CACpB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,GAAG,MAAM,GAC1B,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC;CA6B3C;AAMD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC;AAED,wBAAgB,gBAAgB,IAAI,aAAa,CAIhD"}
+{"version":3,"file":"pubchem-client.d.ts","sourceRoot":"","sources":["../../../src/services/pubchem/pubchem-client.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAGV,cAAc,EAEd,sBAAsB,EACtB,iBAAiB,EAQlB,MAAM,YAAY,CAAC;AAgKpB,qBAAa,aAAa;IACxB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAA+C;IACvE,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAoD;IAC7E,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAsB;YAIpC,SAAS;YAgDT,WAAW;IAwBzB,wEAAwE;YAC1D,SAAS;IAWvB,qDAAqD;YACvC,WAAW;IAgBzB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAI7C,cAAc,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAQjD,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAMrD,eAAe,CAAC,OAAO,EAAE,MAAM,EAAE,UAAU,UAAQ,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAOvE,iBAAiB,CACf,IAAI,EAAE,cAAc,GAAG,gBAAgB,GAAG,YAAY,EACtD,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,QAAQ,GAAG,KAAK,EAC3B,SAAS,CAAC,EAAE,MAAM,GACjB,OAAO,CAAC,MAAM,EAAE,CAAC;IA2Bd,aAAa,CACjB,IAAI,EAAE,MAAM,EAAE,EACd,UAAU,EAAE,MAAM,EAAE,GACnB,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG;QAAE,GAAG,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IA+BtD,WAAW,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAYjD,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,GAAE,OAAO,GAAG,OAAiB,GAAG,OAAO,CAAC,WAAW,CAAC;IAKxE,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,CAAC,MAAM,GAAG,MAAM,CAAC,EAAE,CAAC;IAiBrE,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC;IAoBnD,aAAa,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,GAAG,IAAI,CAAC;IA0E7D,iBAAiB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,sBAAsB,GAAG,IAAI,CAAC;IA8EtE,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,EAAE,CAAC;IAY7D,OAAO,CAAC,eAAe;IA+DjB,oBAAoB,CAAC,UAAU,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAgB1E,gBAAgB,CACpB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,GAAG,MAAM,GAC1B,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC;CA+B3C;AAMD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC;AAED,wBAAgB,gBAAgB,IAAI,aAAa,CAIhD"}

package/dist/services/pubchem/pubchem-client.js

@@ -44,10 +44,12 @@ class RateLimiter {
 }
 // ── Helpers ──────────────────────────────────────────────────────────
 const sleep = (ms) => new Promise((r) => setTimeout(r, ms));
-/** PubChem returns different field names than the request parameter names for some properties */
+/** PubChem returns different field names than the request parameter names for some properties.
+ * Request IsomericSMILES → response key "SMILES" (includes stereochemistry).
+ * Request CanonicalSMILES → response key "ConnectivitySMILES" (connectivity only). */
 const PROPERTY_NAME_MAP = {
-    SMILES: 'CanonicalSMILES',
-    ConnectivitySMILES: 'IsomericSMILES',
+    SMILES: 'IsomericSMILES',
+    ConnectivitySMILES: 'CanonicalSMILES',
 };
 function normalizePropertyNames(row) {
     const result = {};
@@ -57,6 +59,7 @@ function normalizePropertyNames(row) {
     return result;
 }
 function parseFaultMessage(text) {
+    // JSON fault response (most endpoints)
     try {
         const data = JSON.parse(text);
         if (data.Fault?.Message) {
@@ -64,8 +67,13 @@ function parseFaultMessage(text) {
         }
     }
     catch {
-        /* not JSON */
+        /* not JSON — try plain-text format below */
     }
+    // Plain-text fault response (image endpoint): "Status: 400\nCode: X\nMessage: Y"
+    const code = text.match(/^Code:\s*(.+)$/m)?.[1];
+    const message = text.match(/^Message:\s*(.+)$/m)?.[1];
+    if (code && message)
+        return `${code}: ${message}`;
     return;
 }
 // ── PUG View Parsing ─────────────────────────────────────────────────
@@ -423,6 +431,81 @@ export class PubChemClient {
             throw error;
         }
     }
+    async getClassification(cid) {
+        try {
+            const data = await this.fetchJson(`${this.viewBase}/data/compound/${cid}/JSON?heading=Pharmacology+and+Biochemistry`);
+            const sections = data.Record.Section;
+            if (!sections)
+                return null;
+            const result = {
+                atcCodes: [],
+                fdaClasses: [],
+                fdaMechanisms: [],
+                meshClasses: [],
+            };
+            // FDA Pharmacological Classification
+            const fdaSection = findSection(sections, 'FDA Pharmacological Classification');
+            if (fdaSection) {
+                const strings = extractStrings(fdaSection);
+                for (const s of strings) {
+                    if (!s.startsWith('Pharmacological Classes:'))
+                        continue;
+                    const classes = s.slice('Pharmacological Classes:'.length).trim();
+                    for (const entry of classes.split(';')) {
+                        const trimmed = entry.trim();
+                        const tagMatch = trimmed.match(/^(.+?)\s*\[(\w+)\]$/);
+                        if (!tagMatch)
+                            continue;
+                        const [, name, tag] = tagMatch;
+                        if (!name)
+                            continue;
+                        if (tag === 'EPC' || tag === 'CS')
+                            result.fdaClasses.push(name.trim());
+                        else if (tag === 'MoA')
+                            result.fdaMechanisms.push(name.trim());
+                    }
+                }
+                result.fdaClasses = [...new Set(result.fdaClasses)];
+                result.fdaMechanisms = [...new Set(result.fdaMechanisms)];
+            }
+            // MeSH Pharmacological Classification
+            const meshSection = findSection(sections, 'MeSH Pharmacological Classification');
+            if (meshSection) {
+                result.meshClasses = extractStrings(meshSection);
+            }
+            // ATC Code
+            const atcSection = findSection(sections, 'ATC Code');
+            if (atcSection) {
+                const strings = extractStrings(atcSection);
+                for (const s of strings) {
+                    // Match leaf codes like "N02BA01 - Acetylsalicylic acid" or bare "N02BA01"
+                    const match = s.match(/^([A-Z]\d{2}[A-Z]{2}\d{2})\b/);
+                    if (match) {
+                        const desc = s.includes(' - ') ? s.split(' - ').slice(1).join(' - ').trim() : '';
+                        result.atcCodes.push({ code: match[1] ?? '', description: desc });
+                    }
+                }
+                // Deduplicate by code
+                const seen = new Set();
+                result.atcCodes = result.atcCodes.filter((a) => {
+                    if (seen.has(a.code))
+                        return false;
+                    seen.add(a.code);
+                    return true;
+                });
+            }
+            const hasData = result.fdaClasses.length > 0 ||
+                result.fdaMechanisms.length > 0 ||
+                result.meshClasses.length > 0 ||
+                result.atcCodes.length > 0;
+            return hasData ? result : null;
+        }
+        catch (error) {
+            if (error instanceof PubChemNotFoundError)
+                return null;
+            throw error;
+        }
+    }
     // ── Bioactivity ─────────────────────────────────────────────────
     async getAssaySummary(cid) {
         try {
@@ -529,6 +612,9 @@ export class PubChemClient {
         catch (error) {
             if (error instanceof PubChemNotFoundError)
                 return null;
+            // PubChem returns HTTP 400 (not 404) for nonexistent entity IDs in some endpoints
+            if (error instanceof Error && /PubChem HTTP 400/.test(error.message))
+                return null;
             throw error;
         }
     }

package/dist/services/pubchem/pubchem-client.js.map

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package/dist/services/pubchem/types.d.ts

@@ -120,6 +120,42 @@ export interface BioactivityRow {
     targetAccession?: string;
     targetGeneId?: number;
 }
+/** Pharmacological classification from PUG View */
+export interface CompoundClassification {
+    /** ATC codes with hierarchical descriptions */
+    atcCodes: Array<{
+        code: string;
+        description: string;
+    }>;
+    /** FDA Established Pharmacologic Classes (e.g. "Nonsteroidal Anti-inflammatory Drug") */
+    fdaClasses: string[];
+    /** FDA Mechanisms of Action (e.g. "Cyclooxygenase Inhibitors") */
+    fdaMechanisms: string[];
+    /** MeSH pharmacological class descriptions */
+    meshClasses: string[];
+}
+/** Drug-likeness rule evaluation */
+export interface DrugLikenessRule {
+    limit: number;
+    pass: boolean | null;
+    value: number | null;
+}
+/** Computed drug-likeness assessment (Lipinski + Veber) */
+export interface DrugLikenessAssessment {
+    lipinski: {
+        hba: DrugLikenessRule;
+        hbd: DrugLikenessRule;
+        mw: DrugLikenessRule;
+        violations: number;
+        xLogP: DrugLikenessRule;
+    };
+    pass: boolean;
+    veber: {
+        rotatableBonds: DrugLikenessRule;
+        tpsa: DrugLikenessRule;
+        violations: number;
+    };
+}
 /** Structured error from PubChem API */
 export declare class PubChemNotFoundError extends Error {
     name: "PubChemNotFoundError";

package/dist/services/pubchem/types.d.ts.map

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package/dist/services/pubchem/types.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubchem-mcp-server",
-  "version": "0.1.1",
+  "version": "0.1.2",
   "description": "MCP server for the PubChem chemical database. Search compounds, fetch properties, safety data, bioactivity, cross-references, and entity summaries.",
   "mcpName": "io.github.cyanheads/pubchem-mcp-server",
   "type": "module",
@@ -9,7 +9,7 @@
   "bin": {
     "pubchem-mcp-server": "dist/index.js"
   },
-  "files": ["dist/"],
+  "files": ["dist/", "README.md", "LICENSE", "server.json", "Dockerfile"],
   "scripts": {
     "build": "bun scripts/build.ts",
     "rebuild": "bun scripts/clean.ts && bun scripts/build.ts",
@@ -32,7 +32,7 @@
   "bugs": {
     "url": "https://github.com/cyanheads/pubchem-mcp-server/issues"
   },
-  "author": "Casey Hand <casey@cyanheads.dev> (https://github.com/cyanheads)",
+  "author": "Casey Hand <casey@caseyjhand.com> (https://github.com/cyanheads)",
   "keywords": [
     "mcp",
     "mcp-server",
@@ -52,7 +52,7 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.1.18",
+    "@cyanheads/mcp-ts-core": "^0.1.20",
     "pino-pretty": "^13.1.3"
   },
   "devDependencies": {

package/server.json

@@ -0,0 +1,87 @@
+{
+  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
+  "name": "io.github.cyanheads/pubchem-mcp-server",
+  "description": "MCP server for the PubChem chemical database. Search compounds, fetch properties, safety data, bioactivity, cross-references, and entity summaries.",
+  "repository": {
+    "url": "https://github.com/cyanheads/pubchem-mcp-server",
+    "source": "github"
+  },
+  "version": "0.1.2",
+  "packages": [
+    {
+      "registryType": "npm",
+      "registryBaseUrl": "https://registry.npmjs.org",
+      "identifier": "@cyanheads/pubchem-mcp-server",
+      "runtimeHint": "bun",
+      "version": "0.1.2",
+      "packageArguments": [
+        { "type": "positional", "value": "run" },
+        { "type": "positional", "value": "start:stdio" }
+      ],
+      "environmentVariables": [
+        {
+          "name": "MCP_LOG_LEVEL",
+          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').",
+          "format": "string",
+          "isRequired": false,
+          "default": "info"
+        }
+      ],
+      "transport": {
+        "type": "stdio"
+      }
+    },
+    {
+      "registryType": "npm",
+      "registryBaseUrl": "https://registry.npmjs.org",
+      "identifier": "@cyanheads/pubchem-mcp-server",
+      "runtimeHint": "bun",
+      "version": "0.1.2",
+      "packageArguments": [
+        { "type": "positional", "value": "run" },
+        { "type": "positional", "value": "start:http" }
+      ],
+      "environmentVariables": [
+        {
+          "name": "MCP_HTTP_HOST",
+          "description": "The hostname for the HTTP server.",
+          "format": "string",
+          "isRequired": false,
+          "default": "127.0.0.1"
+        },
+        {
+          "name": "MCP_HTTP_PORT",
+          "description": "The port to run the HTTP server on.",
+          "format": "string",
+          "isRequired": false,
+          "default": "3010"
+        },
+        {
+          "name": "MCP_HTTP_ENDPOINT_PATH",
+          "description": "The endpoint path for the MCP server.",
+          "format": "string",
+          "isRequired": false,
+          "default": "/mcp"
+        },
+        {
+          "name": "MCP_AUTH_MODE",
+          "description": "Authentication mode to use: 'none', 'jwt', or 'oauth'.",
+          "format": "string",
+          "isRequired": false,
+          "default": "none"
+        },
+        {
+          "name": "MCP_LOG_LEVEL",
+          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').",
+          "format": "string",
+          "isRequired": false,
+          "default": "info"
+        }
+      ],
+      "transport": {
+        "type": "streamable-http",
+        "url": "http://localhost:3010/mcp"
+      }
+    }
+  ]
+}