Skip to main content
Glama

identify_cages

Detect clathrate cages via TRACE ring perception, assemble them, and classify by face counts to return cage-type counts and overall hydrate structure (sI/sII/sH).

Instructions

Identify clathrate cages (TRACE): ring perception -> cage assembly -> face-count typing.

Returns per-type cage counts (5^12, 5^12 6^2, 5^12 6^4, ...) and the overall structure (sI / sII / sH). Validated: sII -> 128x 5^12 + 64x 5^12 6^4; sI -> 16x 5^12 + 48x 5^12 6^2.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
boxNoPeriodic box in nm (3/6/9 values); else from get_symmetry.
rcut_nmNoH-bond O-O cutoff in nm.
angle_degNoH-bond donor angle cutoff in degrees.
selectionNoSelection of the water system.all
object_nameNoObject whose box to use.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior3/5

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

No annotations are provided, so the description carries full transparency responsibility. It discloses the algorithmic pipeline and includes validation examples (e.g., 'sII -> 128x 5^12 + 64x 5^12 6^4'), which adds useful behavioral context. However, it does not mention side effects, error handling, or what happens on empty selections, leaving gaps.

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 compact and well-structured, with a single paragraph that front-loads the purpose, describes the pipeline, and gives essential validation details. Every sentence earns its place and no unnecessary words are present.

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?

The description covers the full workflow, output types, and validation results, making it fairly complete for a computational tool. Since an output schema exists, additional return formatting details are unnecessary, though usage guidance gaps slightly reduce completeness.

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?

The input schema covers all five parameters with descriptions and defaults (100% coverage), so the baseline is 3. The description does not add extra parameter-level details beyond what the schema already provides, so it neither raises nor lowers the score.

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 identifies the tool's purpose with a specific verb and resource: 'Identify clathrate cages'. It also outlines the pipeline ('ring perception -> cage assembly -> face-count typing') and explicitly lists the return outputs (per-type cage counts and sI/sII/sH structure). This distinguishes it from related siblings like cage_occupancy or mark_cages.

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

Usage Guidelines2/5

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

The description does not provide explicit guidance on when to use this tool versus alternatives such as cage_occupancy or mark_cages. It implies usage by the phrase 'Identify clathrate cages', but lacks exclusions, prerequisites, or comparative direction, leaving the agent to infer the appropriate context.

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

Install Server

Other Tools

Latest Blog Posts

MCP directory API

We provide all the information about MCP servers via our MCP API.

curl -X GET 'https://glama.ai/api/mcp/v1/servers/wjgoarxiv/pymol-mcp'

If you have feedback or need assistance with the MCP directory API, please join our Discord server