Skill: clarityprotocol/clarity-submit (version 1.0.0)

--- name: clarity-submit description: > Submit a protein variant hypothesis to Clarity Protocol for validation and folding. Use when the user asks to submit a hypothesis, propose a protein variant, queue a fold, or investigate a mutation. Requires CLARITY_WRITE_KEY env var. Capabilities: submit hypothesis, check submission status. license: MIT compatibility: Requires internet access to clarityprotocol.io. Requires CLARITY_WRITE_KEY env var for write access. metadata: author: clarity-protocol version: "1.0.0" homepage: https://clarityprotocol.io --- # Clarity Submit Skill Submit protein variant hypotheses to Clarity Protocol for automated validation and ColabFold structural prediction. ## Quick Start Submit a hypothesis: ```bash python scripts/submit_hypothesis.py --protein SOD1 --variant A4V --rationale "ALS-linked mutation with unknown structural impact" ``` Submit with optional fields: ```bash python scripts/submit_hypothesis.py --protein MAPT --variant P301L --rationale "Tau pathology in frontotemporal dementia" --wallet "YOUR_SOLANA_WALLET" ``` Check hypothesis status: ```bash python scripts/check_status.py --id 42 ``` ## Setup Set your write API key: ```bash export CLARITY_WRITE_KEY=your_write_key_here ``` Contact the Clarity Protocol team to request a write API key. ## What Happens After Submission 1. **Feasibility validation** runs automatically against UniProt, ClinVar, gnomAD, and PubMed 2. If validated, the hypothesis is **auto-queued** for ColabFold structural prediction 3. Four AI research agents continuously monitor the variant for new findings 4. Results are available at the tracking URL returned after submission ## Request Fields - `--protein` (required): Protein name (e.g., SOD1, MAPT, APP, SNCA) - `--variant` (required): Variant notation (e.g., A4V, P301L, G2019S) - `--rationale` (required): Why this variant is worth investigating (min 10 characters) - `--disease` (optional): Disease area (auto-detected from protein if omitted) - `--wallet` (optional): Solana wallet address for $FOLD reward eligibility ## Response Fields - `id`: Unique hypothesis identifier - `protein_name`: Normalized protein name - `variant_notation`: Variant as submitted - `status`: Current status (submitted, validating, validated, queued, folding, complete, rejected) - `tracking_url`: URL to track progress on clarityprotocol.io ## Rate Limits - **Write (POST)**: 10 submissions per day per key - **Read (GET)**: 100 requests per minute per key ## Size Limits Proteins up to 1,500 residues can be folded. Larger proteins (e.g., LRRK2 at 2,527 residues) exceed hardware capacity and will be rejected during validation. ## Error Handling **403 Forbidden**: Invalid or missing write API key. Set CLARITY_WRITE_KEY env var. **422 Validation Error**: Invalid input (protein name empty, rationale too short, etc.). **429 Rate Limit**: You've exceeded 10 submissions/day. Wait until tomorrow. ## Use Cases - Programmatically submit variants for investigation - Integrate Clarity Protocol into research pipelines - Batch submission of variants of interest - Agent-driven hypothesis generation and submission


Security scan verdicts — ClawScan: suspicious | static analysis: clean | VirusTotal: clean | SkillSpector: suspicious (MEDIUM)