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huangjianhuster

Biomolecule Modeling MCP Server

set_working_directory

Set the base directory for all subsequent file operations, allowing relative paths to resolve correctly for PDB structures in one folder.

Instructions

Set the working directory for all subsequent file I/O.

WHEN TO USE

Call this first when the user's PDB files are in a specific directory and you want to avoid writing absolute paths in every subsequent call. After this call, relative paths in all other tools resolve against path.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pathYesAbsolute path to the desired working directory.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

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

With no annotations provided, the description carries the full burden. It discloses a key behavioral trait: the working directory affects all subsequent file I/O and that relative paths resolve against the set path. This is essential context, though it doesn't mention error handling or how to reset the directory, which would make it more complete.

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 and front-loaded with the core purpose. It uses two sentences plus a brief usage note, with no redundancy or filler. Every sentence contributes actionable information, making it highly efficient.

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

Completeness5/5

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

For a simple tool with one parameter, the description adequately covers purpose, usage, and behavioral impact. The presence of an output schema means return values need not be explained. It is complete for an agent to select and invoke the tool successfully.

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 schema already describes 'path' as an absolute path, but the description adds meaning by explaining that relative paths in other tools resolve against this path. This clarifies the practical role of the parameter beyond the schema's basic type description, enhancing understanding.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's function: 'Set the working directory for all subsequent file I/O.' It uses a specific verb ('set') and resource ('working directory'), and it distinguishes itself from sibling tools by focusing on a configuration action rather than PDB structure operations.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The 'WHEN TO USE' section explicitly instructs when to call the tool: when a user's PDB files are in a specific directory and to avoid writing absolute paths in every call. It also states the consequence (relative paths resolve against `path`), which provides clear guidance on 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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