clarity-variant

# Clarity Variant Skill

Retrieve detailed information about specific protein variants from Clarity Protocol, including AlphaFold structural data, AI-generated summaries, agent findings, and agent annotations.

## Quick Start

Get variant details:

```bash
python scripts/get_variant.py --fold-id 1
```

Get variant details in readable format:

```bash
python scripts/get_variant.py --fold-id 1 --format summary
```

Get all agent findings for a variant:

```bash
python scripts/get_findings.py --fold-id 1
```

Get findings from specific agent type:

```bash
python scripts/get_findings.py --fold-id 1 --agent-type structural
```

Get agent annotations for a variant:

```bash
python scripts/get_annotations.py --fold-id 1
python scripts/get_annotations.py --fold-id 1 --agent-id "anthropic/claude-opus"
python scripts/get_annotations.py --fold-id 1 --type structural_observation
```

## Variant Detail Fields

- `id`: Unique fold identifier
- `protein_name`: Protein name
- `variant`: Mutation notation
- `disease`: Associated disease
- `uniprot_id`: UniProt database identifier
- `average_confidence`: AlphaFold pLDDT confidence score (0-100)
- `ai_summary`: AI-generated analysis of the mutation
- `notes`: Additional annotations
- `created_at`: When the fold was created

## Agent Findings Fields

Each finding includes:

- `id`: Unique finding identifier
- `fold_id`: Associated variant ID
- `agent_type`: Agent that generated the finding (structural, clinical, literature, synthesis)
- `data`: Structured data discovered by the agent
- `summary`: Human-readable summary of findings
- `created_at`: When the finding was created

## Agent Types

- **structural**: Analyzes protein structure changes from AlphaFold data
- **clinical**: Searches ClinVar and gnomAD for clinical significance
- **literature**: Searches PubMed for relevant research papers
- **synthesis**: Synthesizes findings from all other agents

## Agent Annotation Fields

Each annotation includes:

- `id`: Unique annotation i...