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convert_structure

Convert molecular structure files between common formats like mae, sdf, pdb, mol2, and cif, with input format inferred from file extension.

Instructions

Convert a structure file between formats (mae, maegz, sdf, pdb, mol2, smi, cif). Schrödinger infers the input format from its extension. Returns the output path.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
input_pathYes
output_formatYes
output_pathNo
Behavior3/5

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 that input format is inferred from extension and that the output path is returned, but lacks details on error handling, default behavior for optional output_path, or whether the tool is destructive.

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 two sentences long, directly relevant, and contains no unnecessary words. It front-loads the main action and then adds key details.

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

Completeness3/5

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

Given the absence of output schema and 0% parameter coverage, the description minimally covers the conversion action and return value but omits important behavior like handling of unsupported formats or the effect of a null output_path.

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 coverage is 0%, so the description must compensate. It lists supported formats but does not explain each parameter individually, such as that output_format must be one of the listed formats or that output_path is optional and defaults to a generated path.

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 verb 'convert' and the resource 'structure file', lists supported formats explicitly, and distinguishes from sibling tools like merge_structures or split_structures by focusing on format conversion.

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 converting structure file formats but does not explicitly state when to use this tool versus alternatives, nor does it mention when not to use it.

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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