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wjgoarxiv

vmd-hydrate-mcp

by wjgoarxiv

load_structure

Load a structure or trajectory into a VMD session for visualization. Supports PDB, GROMACS, LAMMPS, DCD; coordinate-only formats require a topology. Returns the molid.

Instructions

Load a structure/trajectory into the persistent VMD session for visualization. Supports PDB, GROMACS (.gro/.xtc/.trr), LAMMPS (.data/dump), DCD. Coordinate-only formats (.xtc/.trr/.dcd) require a topology. Returns the molid used to reference this molecule in later calls.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
pathYes
filetypeNoauto
topologyNo
Behavior4/5

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

No annotations provided, so the description carries the full burden. It discloses that the session is persistent, the return value (molid) for later references, and supported formats. Lacks details on error handling or side effects, but covers essential behavioral aspects.

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 paragraph that efficiently conveys the main action, supported formats, and return value without unnecessary words. It is well-organized and front-loaded.

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?

For a tool with three parameters and no output schema, the description covers the return value (molid), persistence of the session, and supported formats. It does not address error cases or session lifecycle, but provides adequate context for most use cases.

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?

Schema description coverage is 0%, so the description must compensate. It adds context for the 'topology' parameter (needed for coordinate-only formats) and implies 'path' is the file to load. However, it does not explicitly describe each parameter beyond what the schema provides, leaving the 'filetype' parameter ambiguous.

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 loads a structure/trajectory into a persistent VMD session for visualization. It lists supported formats and distinguishes from sibling tools like list_molecules or set_representation.

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

Usage Guidelines4/5

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

Provides explicit context for when to use the tool and mentions the need for a topology with coordinate-only formats. Could be improved by stating when not to use it or mentioning alternatives, but it is clear enough given the sibling tools are distinct operations.

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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