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ligand_interaction_diagram

Generate a 2D diagram of a protein-ligand complex highlighting hydrogen bonds, salt bridges, pi-pi, and pi-cation interactions with a legend mapping to protein residues.

Instructions

Render a 2D ligand-interaction diagram (PNG, shown inline) for a protein-ligand complex or Glide pose-viewer file: the ligand drawn in 2D with the atoms that make interactions highlighted by type (blue=H-bond, red=salt bridge, green=pi-pi, orange=pi-cation) and a legend mapping them to protein residues. Also writes the PNG.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
input_pathYes
ligand_aslNo
ligand_indexNo
output_pathNo
Behavior3/5

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

No annotations are provided, so the description bears full responsibility. It discloses the inline display of PNG and file writing, but does not explicitly state that the operation is non-destructive or mention error conditions. However, as a rendering tool, non-destructiveness is implied.

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

Conciseness4/5

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

The description is a single sentence that efficiently conveys the core functionality and output details, though it could be slightly reorganized for readability. No wasted words.

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 lack of output schema and the complexity of four parameters (one required), the description is incomplete. It does not clarify the return format (whether it returns image data or just writes to file) or handle error cases, though the essential function is covered.

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%, and the description adds no explanation for the four parameters (input_path, ligand_asl, ligand_index, output_path). It only mentions input and output in general terms, failing to help an agent understand parameter usage.

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 it renders a 2D ligand-interaction diagram as a PNG, specifies the input type (protein-ligand complex or Glide pose-viewer file), and distinguishes from siblings like render_2d_structure and analyze_interactions by focusing on interaction visualization.

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?

The description implicitly tells when to use this tool (to obtain a visual diagram of interactions with color-coded highlights and legend), but does not explicitly state when not to use it or list alternatives. Sibling tools provide context for differentiation.

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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