pharmacophore_view

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

With no annotations, the description carries the full burden of behavioral disclosure. It thoroughly describes the visual output: color-coded atoms, H-bond dashes, residue sidechains, pocket surface, and backbone cartoon. However, it does not mention potential side effects (e.g., overriding existing representations) or prerequisites like a loaded protein structure, which would provide fuller transparency.

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 and front-loaded with the core purpose in the first sentence. It then systematically details the color legend and additional visual elements. Every sentence contributes meaningful information with no redundancy or fluff.

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?

The description is remarkably detailed for a visualization tool, covering all visual elements comprehensively. It implies interaction with a protein-ligand complex but does not explicitly state prerequisites or limitations (e.g., requirement for a protein chain). Given the output schema is likely trivial (success/failure), the description is nearly complete.

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 description coverage is 100%, so both parameters (resn, obj_name) are already documented in the input schema. The description adds no additional parameter-specific context beyond the schema, so the baseline score of 3 is appropriate.

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: 'Colors a ligand by pharmacophore feature type.' It provides a specific verb, resource, and distinct visualization details (color mappings, H-bonds, sidechains, pocket surface) that differentiate it from sibling view tools like ligand_view or bfactor_view.

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?

The description implies the tool is for visualizing pharmacophore features but provides no explicit when-to-use guidance or comparison to alternative view tools. It does not name specific alternatives or state exclusions, leaving usage inference to the reader.

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