Unofficial PubChem MCP Server

analyze_molecular_complexity

Analyze molecular complexity and synthetic accessibility for chemical compounds using PubChem CID to assess synthesis feasibility and structural complexity.

Instructions

Analyze molecular complexity and synthetic accessibility

Input Schema

TableJSON Schema

Name	Required	Description	Default
`cid`	Yes	PubChem Compound ID (CID)

Implementation Reference

src/index.ts:1117-1119 (handler)

The main handler function that executes the analyze_molecular_complexity tool logic. Currently implemented as a placeholder returning a 'not yet implemented' message.

private async handleAnalyzeMolecularComplexity(args: any) {
  return { content: [{ type: 'text', text: JSON.stringify({ message: 'Molecular complexity analysis not yet implemented', args }, null, 2) }] };
}

src/index.ts:551-561 (schema)

The input schema and metadata definition for the analyze_molecular_complexity tool, registered in the list of available tools.

{
  name: 'analyze_molecular_complexity',
  description: 'Analyze molecular complexity and synthetic accessibility',
  inputSchema: {
    type: 'object',
    properties: {
      cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
    },
    required: ['cid'],
  },
},

src/index.ts:774-775 (registration)
The dispatch case in the tool request handler that routes calls to analyze_molecular_complexity to its handler function.
```
case 'analyze_molecular_complexity':
  return await this.handleAnalyzeMolecularComplexity(args);
```

Schema Changelog

Changes observed during successful MCP inspections.

First observedAug 15, 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 the tool analyzes molecular complexity and synthetic accessibility but does not describe how it behaves—e.g., whether it returns scores, reports, or predictions; if it requires specific permissions or has rate limits; or what the output format is. This is a significant gap for a tool with no annotation coverage.

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 that directly states the tool's purpose without unnecessary words. It is front-loaded with the core functionality and appropriately sized for the context, making it easy to parse quickly.

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 complexity of molecular analysis, no annotations, and no output schema, the description is incomplete. It does not explain what the analysis entails, the format or content of results, or any behavioral traits. This leaves significant gaps for an AI agent to understand how to use the tool effectively, especially compared to more detailed siblings.

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

Parameters4/5

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

The input schema has 100% description coverage, with the 'cid' parameter clearly documented as a PubChem Compound ID. The description does not add any parameter-specific information beyond the schema, but with only one parameter and high schema coverage, the baseline is strong. No additional semantics are needed, so a score of 4 reflects adequate parameter understanding from the schema alone.

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

Purpose3/5

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

The description states the tool's purpose as analyzing molecular complexity and synthetic accessibility, which is clear but vague. It specifies the action ('analyze') and domain ('molecular complexity and synthetic accessibility'), but lacks specificity on what 'analyze' entails (e.g., scoring, classification, or detailed breakdown) and does not differentiate from siblings like 'calculate_descriptors' or 'assess_drug_likeness', which might overlap in assessing compound properties.

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?

The description provides no guidance on when to use this tool versus alternatives. It does not mention prerequisites, context (e.g., for drug discovery or chemical synthesis), or exclusions. With siblings like 'calculate_descriptors' and 'assess_drug_likeness' that might relate to molecular analysis, the lack of differentiation leaves usage ambiguous.

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