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kmaneesh

BioPython MCP Server

by kmaneesh

find_active_site

Extract detailed information about specific residues, such as active site, from a PDB file by providing residue numbers and an optional chain identifier.

Instructions

Extract information about specific residues (e.g., active site).

Args: pdb_file: Path to PDB file residue_numbers: List of residue numbers to analyze chain_id: Chain identifier (default: 'A')

Returns: Dictionary containing active site residue information

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pdb_fileYes
residue_numbersYes
chain_idNoA

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior2/5

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

With no annotations, the description must disclose behavioral traits. It implies a read-only operation but does not mention file requirements, error handling, performance, or side effects. The return type is noted but not detailed.

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 concise with a clear one-line purpose, structured Args/Returns sections. Every sentence adds value without redundancy.

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

Completeness4/5

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

Given the tool's complexity (3 params, output schema exists), the description covers purpose, parameters, and return type. It lacks error handling and usage context, but is sufficient for basic understanding.

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 'Args' section adds meaning beyond the schema, explaining each parameter (e.g., 'Path to PDB file', 'List of residue numbers'). Given 0% schema coverage, this provides necessary semantics, though constraints like valid ranges are missing.

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 verb 'Extract' and the resource 'information about specific residues', with an example 'active site'. It distinguishes from sibling tools like 'find_motif' implicitly by focusing on residue-level data, but lacks explicit differentiation.

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?

No guidance on when to use this tool versus alternatives like 'find_motif' or other structure analysis tools. There is no mention of prerequisites, exclusions, or context, leaving the agent to infer usage.

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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