# Amina CLI

Command-line interface for the [AminoAnalytica](https://aminoanalytica.com) protein engineering platform.

Run protein structure prediction, sequence design, and analysis tools directly from your terminal.

## Installation

```bash
pip install amina-cli
```

## Quick Start

```bash
# Set your API key (get one at https://app.aminoanalytica.com/settings/api)
amina auth set-key "ami_your_api_key"

# List available tools
amina tools

# Run ESMFold structure prediction
amina run esmfold --sequence "MKFLILLFNILCLFPVLAADNH" -o ./results/

# Run ProteinMPNN sequence design
amina run proteinmpnn --pdb ./structure.pdb --num-sequences 10 -o ./results/
```

## Available Tools

### Folding
- `esmfold` - Predict protein structure from sequence
- `boltz2` - Structure prediction with Boltz-2
- `openfold3` - OpenFold3 structure prediction

### Design
- `proteinmpnn` - Design sequences for a backbone structure
- `rfdiffusion` - Generate novel protein backbones
- `esm-if1` - Inverse folding with ESM-IF1

### Analysis
- `simple-rmsd` - Calculate RMSD between structures
- `hydrophobicity` - Analyze hydrophobic properties
- `surface-charge` - Electrostatic surface analysis

### Utilities
- `pdb-cleaner` - Clean and prepare PDB files
- `pdb-to-fasta` - Extract sequences from structures

Run `amina tools` for the complete list.

## Usage

```bash
# Get help
amina --help
amina run --help
amina run esmfold --help

# Check tool parameters
amina tools esmfold

# Run with custom job name
amina run esmfold --sequence "MKTV..." --job-name my_protein -o ./output/
```

## Authentication

Get an API key from your [account settings](https://app.aminoanalytica.com/settings/api).

```bash
# Set API key
amina auth set-key "ami_your_api_key"

# Check auth status
amina auth status

# Remove stored key
amina auth logout
```

## Output

Results are downloaded to your specified output directory:

```
./results/
├── esmfold_XXXX_structure.pdb      # Predicted structure
├── esmfold_XXXX_plddt_scores.csv   # Per-residue confidence
└── esmfold_XXXX_plddt_plot.png     # Confidence visualization
```

## Requirements

- Python 3.11+
- API key from [AminoAnalytica](https://app.aminoanalytica.com)

## Links

- [Website](https://aminoanalytica.com)
- [Documentation](https://docs.aminoanalytica.com)
- [Get API Key](https://app.aminoanalytica.com/settings/api)

## License

Apache 2.0
