amina-cli 0.1.0

CLI for AminoAnalytica protein engineering platform

Amina CLI

Command-line interface for the AminoAnalytica protein engineering platform.

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

Installation

pip install amina-cli

Quick Start

# 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

# 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.

# 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

Links

• Website
• Documentation
• Get API Key

License

Apache 2.0