Skip to main content
Glama
Augmented-Nature

PubChem MCP Server

search_by_inchi

Find chemical compounds in PubChem by entering an InChI string or InChI key for precise and targeted search results.

Instructions

Search for compounds by InChI or InChI key

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
inchiYesInChI string or InChI key

Implementation Reference

  • The main handler function that executes the 'search_by_inchi' tool logic. It currently returns a placeholder response indicating the feature is not yet implemented.
    private async handleSearchByInchi(args: any) {
      return { content: [{ type: 'text', text: JSON.stringify({ message: 'InChI search not yet implemented', args }, null, 2) }] };
    }
  • The input schema definition for the 'search_by_inchi' tool, specifying the expected 'inchi' parameter.
    inputSchema: {
      type: 'object',
      properties: {
        inchi: { type: 'string', description: 'InChI string or InChI key' },
      },
      required: ['inchi'],
    },
  • src/index.ts:746-747 (registration)
    The dispatch registration in the switch statement that routes calls to the 'search_by_inchi' handler method.
    case 'search_by_inchi':
      return await this.handleSearchByInchi(args);
  • src/index.ts:406-416 (registration)
    The tool registration object in the tools array passed to the MCP server, defining name, description, and input schema.
    {
      name: 'search_by_inchi',
      description: 'Search for compounds by InChI or InChI key',
      inputSchema: {
        type: 'object',
        properties: {
          inchi: { type: 'string', description: 'InChI string or InChI key' },
        },
        required: ['inchi'],
      },
    },
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 performs a search, implying a read-only operation, but doesn't clarify aspects like whether it returns exact matches only, handles partial keys, supports pagination, or has rate limits. For a search tool with zero annotation coverage, this leaves significant gaps in understanding its behavior.

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 front-loads the core functionality. There is no wasted verbiage or redundancy, making it easy to parse quickly. It earns its place by succinctly conveying the tool's purpose.

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

Completeness3/5

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

Given the tool's low complexity (one parameter, no output schema, no annotations), the description is adequate but incomplete. It covers the basic purpose but lacks details on usage context, behavioral traits, and output expectations. For a search tool among many siblings, more guidance would improve completeness.

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 description adds minimal value beyond the input schema, which has 100% coverage. It mentions 'InChI or InChI key', aligning with the schema's description of 'InChI string or InChI key'. No additional semantics, such as format examples or validation rules, are provided. With high schema coverage, the baseline score of 3 is appropriate.

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 tool's purpose: 'Search for compounds by InChI or InChI key'. It specifies the verb ('search'), resource ('compounds'), and input type ('InChI or InChI key'), which is specific and unambiguous. However, it doesn't explicitly differentiate from siblings like 'search_by_smiles' or 'search_by_cas_number', which perform similar searches with different input formats.

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 doesn't mention sibling tools like 'search_by_smiles' or 'search_by_cas_number', nor does it specify scenarios where InChI-based searching is preferred over other methods. The agent must infer usage from the tool name alone.

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

Related 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/PubChem-MCP-Server'

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