PubChem MCP Server

/** * @fileoverview Handles the registration of the `pubchem_search_compounds_by_similarity` tool. * @module src/mcp-server/tools/searchCompoundsBySimilarity/registration */ import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js"; import type { CallToolResult } from "@modelcontextprotocol/sdk/types.js"; import { BaseErrorCode, McpError } from "../../../types-global/errors.js"; import { ErrorHandler, logger, requestContextService, } from "../../../utils/index.js"; import { PubchemSearchCompoundsBySimilarityInput, PubchemSearchCompoundsBySimilarityInputSchema, pubchemSearchCompoundsBySimilarityLogic, } from "./logic.js"; /** * Registers the 'pubchem_search_compounds_by_similarity' tool with the MCP server. * This tool finds compounds with a 2D structure similar to a query compound. * * @param {McpServer} server - The MCP server instance to register the tool with. */ export const registerPubchemSearchCompoundsBySimilarityTool = async ( server: McpServer, ): Promise<void> => { const toolName = "pubchem_search_compounds_by_similarity"; const toolDescription = "Finds compounds with a similar 2D structure to a query compound (provided as SMILES or CID), based on a Tanimoto similarity score."; server.tool( toolName, toolDescription, PubchemSearchCompoundsBySimilarityInputSchema.shape, async ( params: PubchemSearchCompoundsBySimilarityInput, mcpContext: any, ): Promise<CallToolResult> => { const handlerContext = requestContextService.createRequestContext({ operation: "HandleToolRequest", toolName, mcpToolContext: mcpContext, input: params, }); try { logger.info( `Initiating tool request for ${toolName} for query: '${params.query}'`, handlerContext, ); const result = await pubchemSearchCompoundsBySimilarityLogic( params, handlerContext, ); return { content: [{ type: "text", text: JSON.stringify(result, null, 2) }], isError: false, }; } catch (error) { const handledError = ErrorHandler.handleError(error, { operation: "pubchemSearchCompoundsBySimilarityToolHandler", context: handlerContext, input: params, }); const mcpError = handledError instanceof McpError ? handledError : new McpError( BaseErrorCode.INTERNAL_ERROR, "An unexpected error occurred while searching for similar compounds.", { originalErrorName: handledError.name }, ); logger.error(`Error in ${toolName} handler`, { ...handlerContext, error: mcpError, }); return { content: [ { type: "text", text: JSON.stringify({ error: { code: mcpError.code, message: mcpError.message, details: mcpError.details, }, }), }, ], isError: true, }; } }, ); };