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Augmented-Nature

PubChem MCP Server

get_compound_properties

Retrieve molecular properties such as MW, logP, and TPSA by specifying a PubChem Compound ID (CID) and optional desired properties via the PubChem MCP Server.

Instructions

Get molecular properties (MW, logP, TPSA, etc.)

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidYesPubChem Compound ID (CID)
propertiesNoSpecific properties to retrieve (optional)
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 retrieves properties but does not cover critical aspects such as data source, rate limits, error handling, or response format. This leaves significant gaps for an agent to understand how the tool behaves in practice.

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 extremely concise—a single sentence that efficiently conveys the core functionality without any wasted words. It is front-loaded with the main action and includes helpful examples, 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 lack of annotations and output schema, the description is incomplete for effective tool use. It does not explain what the return values look like (e.g., format, units), potential limitations, or how it integrates with other tools in the server, leaving the agent with insufficient context.

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, clearly documenting both parameters (cid and properties). The description adds minimal value by implying the types of properties (e.g., MW, logP, TPSA) but does not provide additional syntax, constraints, or examples beyond what the schema already specifies.

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 with a specific verb ('Get') and resource ('molecular properties'), and lists examples of properties (MW, logP, TPSA). However, it does not explicitly distinguish this tool from similar siblings like 'calculate_descriptors' or 'get_compound_info', which might also retrieve property-related data.

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 available (e.g., 'calculate_descriptors', 'get_compound_info'), there is no mention of specific contexts, prerequisites, or exclusions to help an agent choose appropriately.

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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