generate_molecule_def

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

With no annotations, the description discloses important behaviors such as coordinate origin (centre of mass), units (Å), and file path. However, it omits behavior of key parameters like return_only, rigid, n_groups, and doesn't state overwrite behavior or return value.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is well-structured, with a clear purpose line, representative code blocks for array formats, and a usage note. No redundant sentences.

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

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

For a 13-parameter tool with no output schema or annotations, the description covers the main file content and path but leaves several parameters undocumented. It provides a good foundation but not enough for fully independent use, especially regarding return_only and thermodynamic parameters.

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

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

Schema has zero description coverage for parameters. The description explains the structure of atoms/bonds/bends/torsions arrays and the path template implicitly covers work_dir, subdirectory, molecule_name. But critical properties, rigid, n_groups, and return_only remain unexplained, so coverage is partial.

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

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

The description clearly states the tool's function: 'Generate a per-molecule .def file' with a specific path pattern. This distinguishes it from sibling tools like generate_force_field_def and get_molecule_definition.

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

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

Provides clear context on how to use the generated file ('Set MoleculeDefinition <subdirectory> in simulation.input') and a specific warning against 'MoleculeDefinition local'. However, it doesn't explicitly compare against alternative tools for retrieving or generating molecule definitions.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.