get_pharmacophore_features
Extract pharmacophore features and binding site data for PubChem compounds to support drug discovery and molecular interaction analysis.
Instructions
Get pharmacophore features and binding site information
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| cid | Yes | PubChem Compound ID (CID) |
Implementation Reference
- src/index.ts:1121-1123 (handler)The handler function that executes the core logic of the 'get_pharmacophore_features' tool. It currently returns a placeholder response indicating the feature is not yet implemented.
private async handleGetPharmacophoreFeatures(args: any) { return { content: [{ type: 'text', text: JSON.stringify({ message: 'Pharmacophore features not yet implemented', args }, null, 2) }] }; } - src/index.ts:563-572 (schema)The input schema definition for the tool, specifying the required 'cid' parameter as number or string.
name: 'get_pharmacophore_features', description: 'Get pharmacophore features and binding site information', inputSchema: { type: 'object', properties: { cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' }, }, required: ['cid'], }, }, - src/index.ts:776-777 (registration)Registration in the switch statement of the request handler, dispatching calls to the specific handler method.
case 'get_pharmacophore_features': return await this.handleGetPharmacophoreFeatures(args); - src/index.ts:562-732 (registration)The tool is registered as part of the comprehensive tools list provided to the MCP server.
{ name: 'get_pharmacophore_features', description: 'Get pharmacophore features and binding site information', inputSchema: { type: 'object', properties: { cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' }, }, required: ['cid'], }, }, // Bioassay & Activity Data (5 tools) { name: 'search_bioassays', description: 'Search for biological assays by target, description, or source', inputSchema: { type: 'object', properties: { query: { type: 'string', description: 'General search query' }, target: { type: 'string', description: 'Target protein or gene name' }, source: { type: 'string', description: 'Data source (e.g., ChEMBL, NCGC)' }, max_records: { type: 'number', description: 'Maximum number of results (1-1000, default: 100)', minimum: 1, maximum: 1000 }, }, required: [], }, }, { name: 'get_assay_info', description: 'Get detailed information for a specific bioassay by AID', inputSchema: { type: 'object', properties: { aid: { type: 'number', description: 'PubChem Assay ID (AID)' }, }, required: ['aid'], }, }, { name: 'get_compound_bioactivities', description: 'Get all bioassay results and activities for a compound', inputSchema: { type: 'object', properties: { cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' }, activity_outcome: { type: 'string', enum: ['active', 'inactive', 'inconclusive', 'all'], description: 'Filter by activity outcome (default: all)' }, }, required: ['cid'], }, }, { name: 'search_by_target', description: 'Find compounds tested against a specific biological target', inputSchema: { type: 'object', properties: { target: { type: 'string', description: 'Target name (gene, protein, or pathway)' }, activity_type: { type: 'string', description: 'Type of activity (e.g., IC50, EC50, Ki)' }, max_records: { type: 'number', description: 'Maximum number of results (1-1000, default: 100)', minimum: 1, maximum: 1000 }, }, required: ['target'], }, }, { name: 'compare_activity_profiles', description: 'Compare bioactivity profiles across multiple compounds', inputSchema: { type: 'object', properties: { cids: { type: 'array', items: { type: 'number' }, description: 'Array of PubChem CIDs (2-50)', minItems: 2, maxItems: 50 }, activity_type: { type: 'string', description: 'Specific activity type for comparison (optional)' }, }, required: ['cids'], }, }, // Safety & Toxicity (4 tools) { name: 'get_safety_data', description: 'Get GHS hazard classifications and safety information', inputSchema: { type: 'object', properties: { cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' }, }, required: ['cid'], }, }, { name: 'get_toxicity_info', description: 'Get toxicity data including LD50, carcinogenicity, and mutagenicity', inputSchema: { type: 'object', properties: { cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' }, }, required: ['cid'], }, }, { name: 'assess_environmental_fate', description: 'Assess environmental fate including biodegradation and bioaccumulation', inputSchema: { type: 'object', properties: { cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' }, }, required: ['cid'], }, }, { name: 'get_regulatory_info', description: 'Get regulatory information from FDA, EPA, and international agencies', inputSchema: { type: 'object', properties: { cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' }, }, required: ['cid'], }, }, // Cross-References & Integration (4 tools) { name: 'get_external_references', description: 'Get links to external databases (ChEMBL, DrugBank, KEGG, etc.)', inputSchema: { type: 'object', properties: { cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' }, }, required: ['cid'], }, }, { name: 'search_patents', description: 'Search for chemical patents and intellectual property information', inputSchema: { type: 'object', properties: { cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' }, query: { type: 'string', description: 'Patent search query (alternative to CID)' }, }, required: [], }, }, { name: 'get_literature_references', description: 'Get PubMed citations and scientific literature references', inputSchema: { type: 'object', properties: { cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' }, }, required: ['cid'], }, }, { name: 'batch_compound_lookup', description: 'Process multiple compound IDs efficiently', inputSchema: { type: 'object', properties: { cids: { type: 'array', items: { type: 'number' }, description: 'Array of PubChem CIDs (1-200)', minItems: 1, maxItems: 200 }, operation: { type: 'string', enum: ['property', 'synonyms', 'classification', 'description'], description: 'Operation to perform (default: property)' }, }, required: ['cids'], }, }, ], }));