Skip to main content
Glama
Augmented-Nature

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
NameRequiredDescriptionDefault
cidYesPubChem Compound ID (CID)

Implementation Reference

  • 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) }] };
    }
  • 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);
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. The description mentions analyzing complexity and synthetic accessibility but doesn't explain what the tool actually does behaviorally—e.g., whether it performs calculations, returns scores, provides recommendations, or has limitations like computational intensity or data availability. It lacks details on output format, error conditions, or any operational constraints.

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

Conciseness4/5

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

The description is concise with a single phrase, making it front-loaded and easy to parse. However, it may be overly brief, potentially under-specifying the tool's functionality. There is no wasted text, but the brevity could compromise clarity given the lack of additional context.

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 implied by analyzing molecular complexity and synthetic accessibility, the description is incomplete. No output schema is provided, and the description doesn't explain what the tool returns (e.g., scores, reports, or structured data). With no annotations and a vague purpose, the description fails to provide enough context for an agent to understand how to interpret results or handle this tool effectively.

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?

The input schema has 100% description coverage, with the single parameter 'cid' clearly documented as a PubChem Compound ID. The description doesn't add any parameter-specific information beyond what the schema provides, such as examples or constraints on CID values. Since schema coverage is high, the baseline score of 3 is appropriate, as the description doesn't compensate but also doesn't detract.

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 general domain (molecular analysis) but doesn't distinguish it from sibling tools like 'calculate_descriptors' or 'predict_admet_properties' that also perform molecular analysis. The description lacks specific details about what 'complexity' and 'synthetic accessibility' mean in this context.

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. With many sibling tools focused on molecular analysis (e.g., 'calculate_descriptors', 'assess_drug_likeness'), there is no indication of what makes this tool unique or when it should be preferred. No exclusions, prerequisites, or alternative tools are mentioned.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/Augmented-Nature/Augmented-Nature-PubChem-MCP-Server'

If you have feedback or need assistance with the MCP directory API, please join our Discord server