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Augmented-Nature

Unofficial PubChem MCP Server

search_by_inchi

Find chemical compounds in PubChem using InChI or InChI key identifiers to retrieve molecular data and properties.

Instructions

Search for compounds by InChI or InChI key

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
inchiYesInChI string or InChI key

Implementation Reference

  • The main execution handler for the 'search_by_inchi' tool. This is a placeholder implementation that returns a message 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) }] };
    }
  • src/index.ts:406-416 (registration)
    Tool registration in the listTools response, defining the name, description, and input JSON schema for validation.
    {
      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'],
      },
    },
  • Switch case in the CallToolRequest handler that dispatches to the specific tool handler.
    case 'search_by_inchi':
      return await this.handleSearchByInchi(args);
Behavior2/5

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

With no annotations provided, the description carries the full burden of behavioral disclosure. It only states the basic function without detailing aspects like whether it's a read-only operation, what the search scope is (e.g., exact match, partial), performance expectations, or error handling. This leaves significant gaps for a tool that likely queries a database.

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 with zero wasted words. It is front-loaded and appropriately sized for a simple search tool, making it easy for an agent 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 a search tool with no annotations and no output schema, the description is incomplete. It lacks details on behavioral traits, return values, or error conditions, which are crucial for an agent to use it effectively in a chemistry context with many sibling alternatives.

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 schema description coverage is 100%, with the 'inchi' parameter fully documented in the schema as 'InChI string or InChI key'. The description adds no additional meaning beyond this, such as format examples or validation rules, so it meets the baseline for high schema coverage without compensating value.

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 action ('Search for compounds') and the resource ('by InChI or InChI key'), which is specific and unambiguous. However, it doesn't explicitly differentiate from sibling tools like 'search_by_smiles' or 'search_by_cas_number', which perform similar searches using different identifiers.

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_compounds', nor does it specify scenarios where InChI searching is preferred over other methods, leaving the agent without contextual usage cues.

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

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