Clarity Research

Search protein folding research data from Clarity Protocol. Use when the user asks to search variants, query protein research, find fold results, or explore...

Security Scan

The skill's code and instructions align with its stated purpose (querying Clarity Protocol's protein variant API); issues are limited to minor metadata and dependency omissions rather than malicious behavior.

Purpose & Capability

Name/description match the code and endpoints. The scripts call https://clarityprotocol.io/api/v1 and implement queries, filtering, pagination, and optional API-key usage consistent with the stated capabilities.

Instruction Scope

SKILL.md and the scripts limit actions to querying the Clarity Protocol API and printing results. The only environment access is reading an optional CLARITY_API_KEY and there are no instructions to read unrelated files or transmit data to other endpoints.

Install Mechanism

There is no install spec (lower risk). However, the Python scripts import the third-party 'requests' library and assume python is available; the skill PACKAGE/registry metadata does not declare this dependency. Users should ensure a Python runtime with 'requests' is available.

Credentials

The code and SKILL.md reference an optional CLARITY_API_KEY environment variable for higher rate limits, but the registry metadata lists no required env vars. The skill reads CLARITY_API_KEY at runtime (optional) — this is proportionate to the API purpose but should have been declared in the skill metadata.

Persistence & Privilege

The skill does not request elevated or persistent platform privileges (always:false). It does not modify other skills or system-wide configuration and only runs when invoked.

Assessment

This skill appears to do what it says: query Clarity Protocol's API for protein variant information. Before installing, note two minor issues: (1) the scripts expect a Python runtime and the 'requests' package but the skill metadata doesn't declare that dependency — run in an environment with Python and requests installed or add that dependency; (2) the code reads an optional CLARITY_API_KEY environment variable for higher rate limits but the registry metadata doesn't list it — if you provide an API key, only use a key you control. Otherwise the code only contacts clarityprotocol.io and has no hidden endpoints or extra credential requests. If you want extra caution, run the scripts in an isolated environment or review/execute the included Python files locally.

Clarity Research Skill

Search protein folding research data from Clarity Protocol, a community-driven platform for protein mutation analysis using AlphaFold2 via ColabFold.

Quick Start

List all available variants:

python scripts/query_variants.py

Filter by disease:

python scripts/query_variants.py --disease Alzheimer

Filter by protein name:

python scripts/query_variants.py --protein-name MAPT

Output Fields

Each variant result includes:

• id: Unique fold identifier
• protein_name: Protein name (e.g., "tau", "APP")
• variant: Mutation notation (e.g., "P301L", "A246E")
• disease: Associated disease
• uniprot_id: UniProt database identifier
• average_confidence: AlphaFold confidence score (0-100)
• created_at: When the fold was created

Rate Limits

• Anonymous (no API key): 10 requests/minute
• With API key: 100 requests/minute

To use an API key, set the CLARITY_API_KEY environment variable:

export CLARITY_API_KEY=your_key_here
python scripts/query_variants.py

Get your API key at https://clarityprotocol.io

Error Handling

404 Not Found: The endpoint or resource does not exist.

429 Rate Limit: You've exceeded the rate limit. The script will display how long to wait before retrying.

500 Server Error: The API server encountered an error. Try again later.

Timeout: The request took longer than 30 seconds. The server may be under heavy load.

Pagination

Results are paginated. The API returns a next_cursor field if more results are available. The script automatically handles pagination for typical queries.

Use Cases

• Explore available protein variants for a specific disease
• Find all folded mutations for a particular protein
• Get an overview of research data available in Clarity Protocol
• Identify fold IDs for detailed analysis with other skills