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wjgoarxiv

vmd-hydrate-mcp

by wjgoarxiv

measure_geometry

Calculate distance (2 atoms), angle (3), or dihedral (4) measurements from molecular coordinates at a given frame.

Instructions

Measure a distance (2 atom indices), angle (3), or dihedral (4) at a frame. Distances are in Angstrom, angles in degrees.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pathYes
frameNo
indicesYes
topologyNo
Behavior2/5

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

No annotations are provided, so the description carries full behavioral disclosure burden. It mentions units and number of indices for different measurement types, but lacks details on return format, error handling (e.g., invalid indices), side effects, or whether it modifies state.

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 sentence that immediately conveys the core purpose, measurement types, and units. No redundant information.

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?

With no output schema and 0% parameter description coverage, the tool is underspecified. The description omits return value structure, error behavior, and prerequisites for use (e.g., needs a loaded trajectory).

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description must compensate. It only explains indices implicitly and mentions frame ('at a frame'), but does not explain the 'path' or 'topology' parameters, nor the expected format of indices (e.g., 0-indexed, atom serial numbers).

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 that the tool measures distances, angles, or dihedrals using atom indices, and specifies units (Angstrom for distance, degrees for angle/dihedral). It distinguishes itself from sibling tools like radius_of_gyration which measures a different property.

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

Usage Guidelines3/5

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

The description implies usage for molecular geometry measurements in a trajectory, but does not provide explicit when-to-use or when-not-to-use guidance, nor does it mention prerequisites like having a structure loaded or topology available.

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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