@cyanheads/pubchem-mcp-server 0.1.1

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

@@ -0,0 +1,133 @@
+/**
+ * @fileoverview PubChem API response types and shared constants.
+ * @module services/pubchem/types
+ */
+/** CID list from identifier/formula/structure searches */
+export interface CidListResponse {
+    IdentifierList: {
+        CID: number[];
+    };
+}
+/** Async search response — PubChem returns a ListKey when results aren't ready yet */
+export interface ListKeyResponse {
+    Waiting: {
+        ListKey: string;
+    };
+}
+/** AID list from assay target searches */
+export interface AidListResponse {
+    IdentifierList: {
+        AID: number[];
+    };
+}
+/** Compound property table */
+export interface PropertyTableResponse {
+    PropertyTable: {
+        Properties: Array<Record<string, unknown> & {
+            CID: number;
+        }>;
+    };
+}
+/** Synonym list for a compound */
+export interface SynonymResponse {
+    InformationList: {
+        Information: Array<{
+            CID: number;
+            Synonym: string[];
+        }>;
+    };
+}
+/** Cross-reference list for a compound */
+export interface XrefResponse {
+    InformationList: {
+        Information: Array<Record<string, unknown> & {
+            CID: number;
+        }>;
+    };
+}
+/** Bioassay summary table (column-oriented) */
+export interface AssaySummaryTableResponse {
+    Table: {
+        Columns: {
+            Column: string[];
+        };
+        Row: Array<{
+            Cell: (string | number | null)[];
+        }>;
+    };
+}
+export interface PugViewResponse {
+    Record: {
+        RecordType: string;
+        RecordNumber: number;
+        Section?: PugViewSection[];
+        Reference?: Array<{
+            ReferenceNumber: number;
+            SourceName: string;
+            SourceID?: string;
+        }>;
+    };
+}
+export interface PugViewSection {
+    Description?: string;
+    Information?: PugViewInformation[];
+    Section?: PugViewSection[];
+    TOCHeading: string;
+}
+export interface PugViewInformation {
+    Description?: string;
+    Name?: string;
+    ReferenceNumber?: number;
+    Value: {
+        StringWithMarkup?: Array<{
+            String: string;
+            Markup?: Array<{
+                Start: number;
+                Length: number;
+                URL?: string;
+                Type?: string;
+                Extra?: string;
+            }>;
+        }>;
+        Number?: number[];
+        Boolean?: boolean[];
+    };
+}
+/** Parsed GHS hazard classification */
+export interface GHSClassification {
+    hazardStatements: Array<{
+        code: string;
+        statement: string;
+    }>;
+    pictograms: string[];
+    precautionaryStatements: Array<{
+        code: string;
+        statement: string;
+    }>;
+    signalWord?: string;
+    source?: string;
+}
+/** Parsed bioactivity row from assay summary table */
+export interface BioactivityRow {
+    activityValues: Array<{
+        name: string;
+        value: number;
+        unit: string;
+    }>;
+    aid: number;
+    assayName: string;
+    outcome: string;
+    targetAccession?: string;
+    targetGeneId?: number;
+}
+/** Structured error from PubChem API */
+export declare class PubChemNotFoundError extends Error {
+    name: "PubChemNotFoundError";
+}
+/** All valid PubChem compound property names */
+export declare const COMPOUND_PROPERTIES: readonly ["MolecularFormula", "MolecularWeight", "CanonicalSMILES", "IsomericSMILES", "InChI", "InChIKey", "IUPACName", "Title", "XLogP", "ExactMass", "MonoisotopicMass", "TPSA", "Complexity", "Charge", "HBondDonorCount", "HBondAcceptorCount", "RotatableBondCount", "HeavyAtomCount", "IsotopeAtomCount", "AtomStereoCount", "DefinedAtomStereoCount", "UndefinedAtomStereoCount", "BondStereoCount", "DefinedBondStereoCount", "UndefinedBondStereoCount", "CovalentUnitCount", "Volume3D"];
+/** Default properties when none specified */
+export declare const DEFAULT_PROPERTIES: readonly ["MolecularFormula", "MolecularWeight", "IUPACName", "CanonicalSMILES", "IsomericSMILES", "InChIKey", "XLogP", "TPSA", "HBondDonorCount", "HBondAcceptorCount", "RotatableBondCount", "HeavyAtomCount", "Charge", "Complexity"];
+/** Supported cross-reference types */
+export declare const XREF_TYPES: readonly ["RegistryID", "RN", "PubMedID", "PatentID", "GeneID", "ProteinGI", "TaxonomyID"];
+//# sourceMappingURL=types.d.ts.map

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

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package/dist/services/pubchem/types.js

@@ -0,0 +1,68 @@
+/**
+ * @fileoverview PubChem API response types and shared constants.
+ * @module services/pubchem/types
+ */
+// ── PubChem error ────────────────────────────────────────────────────
+/** Structured error from PubChem API */
+export class PubChemNotFoundError extends Error {
+    name = 'PubChemNotFoundError';
+}
+// ── Constants ────────────────────────────────────────────────────────
+/** All valid PubChem compound property names */
+export const COMPOUND_PROPERTIES = [
+    'MolecularFormula',
+    'MolecularWeight',
+    'CanonicalSMILES',
+    'IsomericSMILES',
+    'InChI',
+    'InChIKey',
+    'IUPACName',
+    'Title',
+    'XLogP',
+    'ExactMass',
+    'MonoisotopicMass',
+    'TPSA',
+    'Complexity',
+    'Charge',
+    'HBondDonorCount',
+    'HBondAcceptorCount',
+    'RotatableBondCount',
+    'HeavyAtomCount',
+    'IsotopeAtomCount',
+    'AtomStereoCount',
+    'DefinedAtomStereoCount',
+    'UndefinedAtomStereoCount',
+    'BondStereoCount',
+    'DefinedBondStereoCount',
+    'UndefinedBondStereoCount',
+    'CovalentUnitCount',
+    'Volume3D',
+];
+/** Default properties when none specified */
+export const DEFAULT_PROPERTIES = [
+    'MolecularFormula',
+    'MolecularWeight',
+    'IUPACName',
+    'CanonicalSMILES',
+    'IsomericSMILES',
+    'InChIKey',
+    'XLogP',
+    'TPSA',
+    'HBondDonorCount',
+    'HBondAcceptorCount',
+    'RotatableBondCount',
+    'HeavyAtomCount',
+    'Charge',
+    'Complexity',
+];
+/** Supported cross-reference types */
+export const XREF_TYPES = [
+    'RegistryID',
+    'RN',
+    'PubMedID',
+    'PatentID',
+    'GeneID',
+    'ProteinGI',
+    'TaxonomyID',
+];
+//# sourceMappingURL=types.js.map

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

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package/package.json

@@ -0,0 +1,67 @@
+{
+  "name": "@cyanheads/pubchem-mcp-server",
+  "version": "0.1.1",
+  "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",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "bin": {
+    "pubchem-mcp-server": "dist/index.js"
+  },
+  "files": ["dist/"],
+  "scripts": {
+    "build": "bun scripts/build.ts",
+    "rebuild": "bun scripts/clean.ts && bun scripts/build.ts",
+    "clean": "bun scripts/clean.ts",
+    "devcheck": "bun scripts/devcheck.ts",
+    "tree": "bun scripts/tree.ts",
+    "format": "biome check --write --unsafe .",
+    "lint:mcp": "bun scripts/lint-mcp.ts",
+    "test": "vitest run",
+    "dev:stdio": "bun --watch src/index.ts",
+    "dev:http": "MCP_TRANSPORT_TYPE=http bun --watch src/index.ts",
+    "start:stdio": "node dist/index.js",
+    "start:http": "MCP_TRANSPORT_TYPE=http node dist/index.js"
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/cyanheads/pubchem-mcp-server.git"
+  },
+  "homepage": "https://github.com/cyanheads/pubchem-mcp-server#readme",
+  "bugs": {
+    "url": "https://github.com/cyanheads/pubchem-mcp-server/issues"
+  },
+  "author": "Casey Hand <casey@cyanheads.dev> (https://github.com/cyanheads)",
+  "keywords": [
+    "mcp",
+    "mcp-server",
+    "model-context-protocol",
+    "pubchem",
+    "chemistry",
+    "compounds",
+    "bioactivity"
+  ],
+  "license": "Apache-2.0",
+  "engines": {
+    "node": ">=22.0.0",
+    "bun": ">=1.2.0"
+  },
+  "packageManager": "bun@1.3.2",
+  "publishConfig": {
+    "access": "public"
+  },
+  "dependencies": {
+    "@cyanheads/mcp-ts-core": "^0.1.18",
+    "pino-pretty": "^13.1.3"
+  },
+  "devDependencies": {
+    "@biomejs/biome": "^2.4.8",
+    "@types/node": "^25.5.0",
+    "depcheck": "^1.4.7",
+    "ignore": "^7.0.5",
+    "tsc-alias": "^1.8.16",
+    "typescript": "^5.9.3",
+    "vitest": "^4.1.0"
+  }
+}