get_3d_conformers
Retrieve 3D molecular conformer data and structural information from PubChem using compound IDs to support chemical analysis and visualization.
Instructions
Get 3D conformer data and structural information
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| cid | Yes | PubChem Compound ID (CID) | |
| conformer_type | No | Type of conformer data (default: 3d) |
Implementation Reference
- src/index.ts:1020-1046 (handler)The core handler function for the 'get_3d_conformers' tool. Validates input using isValidConformerArgs, fetches 3D conformer properties (Volume3D, ConformerCount3D) from PubChem API via axios, and returns formatted JSON response or throws MCP errors.
private async handleGet3dConformers(args: any) { if (!isValidConformerArgs(args)) { throw new McpError(ErrorCode.InvalidParams, 'Invalid 3D conformer arguments'); } try { const response = await this.apiClient.get(`/compound/cid/${args.cid}/property/Volume3D,ConformerCount3D/JSON`); return { content: [ { type: 'text', text: JSON.stringify({ cid: args.cid, conformer_type: args.conformer_type || '3d', properties: response.data, }, null, 2), }, ], }; } catch (error) { throw new McpError( ErrorCode.InternalError, `Failed to get 3D conformers: ${error instanceof Error ? error.message : 'Unknown error'}` ); } } - src/index.ts:481-488 (schema)The input schema definition for the 'get_3d_conformers' tool, specifying parameters cid (required, number or string) and optional conformer_type (enum '3d' or '2d'). Used in tool listing.
inputSchema: { type: 'object', properties: { cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' }, conformer_type: { type: 'string', enum: ['3d', '2d'], description: 'Type of conformer data (default: 3d)' }, }, required: ['cid'], }, - src/index.ts:478-490 (registration)Registration of the 'get_3d_conformers' tool in the ListToolsRequestSchema response, including name, description, and input schema.
{ name: 'get_3d_conformers', description: 'Get 3D conformer data and structural information', inputSchema: { type: 'object', properties: { cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' }, conformer_type: { type: 'string', enum: ['3d', '2d'], description: 'Type of conformer data (default: 3d)' }, }, required: ['cid'], }, }, { - src/index.ts:760-761 (registration)Dispatch/registration case in the CallToolRequestSchema switch statement that routes calls to the handleGet3dConformers handler.
case 'get_3d_conformers': return await this.handleGet3dConformers(args); - src/index.ts:103-112 (helper)Type guard helper function for validating arguments to the get_3d_conformers tool, checking cid and conformer_type types.
const isValidConformerArgs = ( args: any ): args is { cid: number | string; conformer_type?: string } => { return ( typeof args === 'object' && args !== null && (typeof args.cid === 'number' || typeof args.cid === 'string') && (args.conformer_type === undefined || ['3d', '2d'].includes(args.conformer_type)) ); };