PubChem MCP Server

get_pharmacophore_features

Extract pharmacophore features and binding site data for PubChem compounds to analyze molecular interactions and drug design potential.

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 implements the core logic for the 'get_pharmacophore_features' tool. Currently a placeholder indicating 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:562-572 (registration)

Tool registration in the ListToolsRequestSchema response, including name, description, and input schema definition.

{
  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)
Dispatcher case in the CallToolRequestSchema handler that routes calls to the tool's handler function.
```
case 'get_pharmacophore_features':
  return await this.handleGetPharmacophoreFeatures(args);
```

src/index.ts:565-571 (schema)

Input schema definition for validating tool arguments (CID required).

inputSchema: {
  type: 'object',
  properties: {
    cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
  },
  required: ['cid'],
},

Schema Changelog

Changes observed during successful MCP inspections.

First observedSep 29, 2025

TDQS

C2.9/5.0

Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

No annotations are provided, so the description carries the full burden of behavioral disclosure. It states what is retrieved but doesn't mention any behavioral traits such as data format, potential errors, rate limits, or authentication needs. For a tool with no annotations, this is a significant gap in transparency.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is a single, efficient sentence with zero waste. It front-loads the key action and resources, making it easy to parse quickly without unnecessary details.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the lack of annotations and output schema, the description is incomplete. It doesn't explain what 'pharmacophore features and binding site information' entails in terms of return values or format, leaving the agent uncertain about the tool's output. For a tool with no structured output documentation, this is inadequate.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, with the parameter 'cid' clearly documented as 'PubChem Compound ID (CID)'. The description doesn't add any meaning beyond this, such as examples or constraints, but the schema provides adequate baseline information, justifying a score of 3.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the verb 'Get' and the resources 'pharmacophore features and binding site information', making the purpose specific. However, it doesn't distinguish this tool from potential siblings like 'get_compound_info' or 'get_3d_conformers' that might provide overlapping or related data, which prevents a perfect score.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

No guidance is provided on when to use this tool versus alternatives. Given the many sibling tools for compound analysis (e.g., 'get_compound_info', 'get_3d_conformers'), the description lacks context on prerequisites, typical use cases, or exclusions, leaving the agent with minimal direction.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.