analyze_stereochemistry
Analyze stereochemistry, chirality, and isomer information for chemical compounds using PubChem data to identify structural variations and molecular configurations.
Instructions
Analyze stereochemistry, chirality, and isomer information
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| cid | Yes | PubChem Compound ID (CID) |
Implementation Reference
- src/index.ts:1048-1073 (handler)The handler function that implements the core logic of the 'analyze_stereochemistry' tool. It validates the input CID, queries the PubChem API for stereochemistry properties (AtomStereoCount, DefinedAtomStereoCount, BondStereoCount, DefinedBondStereoCount, IsomericSMILES), and returns the results as formatted JSON.
private async handleAnalyzeStereochemistry(args: any) { if (!isValidCidArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid stereochemistry arguments'); } try { const response = await this.apiClient.get(`/compound/cid/${args.cid}/property/AtomStereoCount,DefinedAtomStereoCount,BondStereoCount,DefinedBondStereoCount,IsomericSMILES/JSON`); return { content: [ { type: 'text', text: JSON.stringify({ cid: args.cid, stereochemistry: response.data, }, null, 2), }, ], }; } catch (error) { throw new McpError( ErrorCode.InternalError, `Failed to analyze stereochemistry: ${error instanceof Error ? error.message : 'Unknown error'}` ); } } - src/index.ts:493-499 (schema)The JSON schema defining the input parameters for the tool, requiring a 'cid' (PubChem Compound ID) as number or string.
inputSchema: { type: 'object', properties: { cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' }, }, required: ['cid'], }, - src/index.ts:490-500 (registration)The tool registration entry in the list of available tools returned by ListToolsRequestSchema, including name, description, and input schema.
{ name: 'analyze_stereochemistry', description: 'Analyze stereochemistry, chirality, and isomer information', inputSchema: { type: 'object', properties: { cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' }, }, required: ['cid'], }, }, - src/index.ts:762-763 (registration)The dispatch case in the CallToolRequestSchema handler's switch statement that routes tool calls to the specific handler function.
case 'analyze_stereochemistry': return await this.handleAnalyzeStereochemistry(args); - src/index.ts:65-74 (helper)Helper validation function used by the handler to check if arguments contain a valid CID (number or string), shared across multiple tools.
const isValidCidArgs = ( args: any ): args is { cid: number | string; format?: string } => { return ( typeof args === 'object' && args !== null && (typeof args.cid === 'number' || typeof args.cid === 'string') && (args.format === undefined || ['json', 'sdf', 'xml', 'asnt', 'asnb'].includes(args.format)) ); };