amina-cli 0.2.9

CLI for AminoAnalytica protein engineering platform

Amina CLI

Command-line interface for AminoAnalytica protein engineering tools.

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

Installation

pip install amina-cli

Requires Python 3.11+

Quick Start

# 1. Set your API key
amina auth set-key "ami_your_api_key"

# 2. List available tools
amina tools

# 3. Run a tool
amina run esmfold --sequence "MKFLILLFNILCLFPVLAADNH" -o ./results/

Get an API key at app.aminoanalytica.com/settings/api

Commands Overview

Command	Description
amina auth	Manage API key authentication
amina init	Initialize project resources (Claude Code skills)
amina tools	List available tools and view parameters
amina run <tool>	Run a computational biology tool
amina jobs	Manage background jobs
amina version	Show CLI version

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Authentication

# Set API key (required before running tools)
amina auth set-key "ami_your_api_key"

# Check authentication status
amina auth status

# Link CLI outputs to a web conversation
amina auth session <conversation_id>

# Unlink session
amina auth session --unlink

# Remove stored credentials
amina auth logout

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Claude Code Integration

Install Amina skills to help Claude Code assist with protein engineering tasks.

# Install skills to .claude/skills/ in your project directory
amina init claude-skills

After installing, run /amina-init in Claude Code to get started.

The skills teach Claude Code how to:

• Use the Amina CLI effectively
• Run structure prediction, sequence design, and docking tools
• Interpret results and suggest next steps

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Discovering Tools

# List all available tools
amina tools

# Filter by category
amina tools --category folding
amina tools --category design
amina tools --category interactions
amina tools --category analysis
amina tools --category properties
amina tools --category utilities

# Search for tools
amina tools --search dock
amina tools --search glyco

# View tool parameters and usage
amina tools esmfold
amina tools proteinmpnn

# List all categories
amina tools categories

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Running Tools

# Basic usage
amina run <tool> [OPTIONS] -o ./output/

# Run in background (returns immediately)
amina run esmfold --sequence "MKTV..." -o ./output/ --background

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

# Get help for any tool
amina run esmfold --help
amina run proteinmpnn --help

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Managing Jobs

Background jobs continue running on the server while you work locally.

# List recent jobs
amina jobs list
amina jobs list --limit 50
amina jobs list --json

# Check job status
amina jobs status <job_id>
amina jobs status job1 job2 job3
amina jobs status <job_id> --json

# Wait for jobs to complete
amina jobs wait <job_id>
amina jobs wait job1 job2 --timeout 7200

# Download results from a completed job
amina jobs download <job_id> -o ./results/

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Available Tools

Folding

Predict 3D protein structures from sequences.

Tool	Command	Description
ESMFold	amina run esmfold	Fast structure prediction from sequence
Boltz-2	amina run boltz2	Predict protein/ligand/nucleic acid complexes
OpenFold3	amina run openfold3	Predict structures of proteins, RNA, DNA, ligands
Protenix	amina run protenix	AlphaFold3 structure prediction

Examples:

# ESMFold from sequence
amina run esmfold --sequence "MKFLILLFNILCLFPVLAADNH" -o ./results/

# ESMFold from FASTA file
amina run esmfold --fasta ./protein.fasta -o ./results/

# Boltz-2 with ligand
amina run boltz2 --sequence "MKTV..." --ligand "CCO" -o ./results/

# Boltz-2 multi-chain complex
amina run boltz2 --sequence "CHAIN_A_SEQ" --sequence "CHAIN_B_SEQ" -o ./results/

# OpenFold3 protein-DNA complex
amina run openfold3 --sequence "MKTV..." --dna "ATCGATCG" -o ./results/

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Design

Generate and optimize protein sequences.

Tool	Command	Description
ProteinMPNN	amina run proteinmpnn	Design sequences for a backbone structure
RFDiffusion	amina run rfdiffusion	Generate novel protein backbones
ESM-IF1	amina run esm-if1	Inverse folding - sequences from structure
Protein-MC	amina run protein-mc	Monte Carlo sequence optimization

Examples:

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

# ProteinMPNN with fixed positions
amina run proteinmpnn --pdb ./structure.pdb --fixed "A10,A15,A20" -o ./results/

# RFDiffusion unconditional generation
amina run rfdiffusion --mode unconditional --length 100 --num-designs 5 -o ./results/

# RFDiffusion binder design
amina run rfdiffusion --mode binder-design --input ./target.pdb --hotspots "A30,A35" -o ./results/

# ESM-IF1 inverse folding
amina run esm-if1 --pdb ./structure.pdb --chain A --num-samples 5 -o ./results/

# Protein-MC optimization
amina run protein-mc --sequence "MKTV..." --temperature 0.01 --num-steps 100 -o ./results/

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Interactions

Molecular docking, binding site prediction, and glycosylation analysis.

Tool	Command	Description
DiffDock	amina run diffdock	Diffusion-based molecular docking
AutoDock Vina	amina run autodock-vina	Classical molecular docking
DockQ	amina run dockq	Assess docked complex quality
P2Rank	amina run p2rank	Predict ligand-binding sites
Interface Identifier	amina run interface-identifier	Identify interface residues between chains
PeSTo	amina run pesto	Predict protein-protein/DNA/RNA/ligand interactions
LMNgly	amina run lmngly	N-linked glycosylation prediction
EMNGly	amina run emngly	ESM-1b based N-glycosylation prediction
ISOGlyP	amina run isoglyp	O-linked glycosylation prediction
Glycosylation Ensemble	amina run glycosylation-ensemble	Combined N/O-glycosylation prediction

Examples:

# DiffDock with SMILES ligand
amina run diffdock --protein-pdb ./protein.pdb --ligand-smiles "CCO" --samples 10 -o ./results/

# DiffDock with SDF ligand file
amina run diffdock --protein-pdb ./protein.pdb --ligand-sdf ./ligand.sdf -o ./results/

# AutoDock Vina docking
amina run autodock-vina --protein-pdb ./protein.pdb --ligand-smiles "CCO" --exhaustiveness 16 -o ./results/

# P2Rank binding site prediction
amina run p2rank --pdb ./protein.pdb -o ./results/

# DockQ quality assessment
amina run dockq --model-pdb ./model.pdb --reference-pdb ./reference.pdb -o ./results/

# Glycosylation prediction
amina run glycosylation-ensemble --fasta ./protein.fasta -o ./results/

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Analysis

Structural comparison and property analysis.

Tool	Command	Description
RMSD Analysis	amina run rmsd-analysis	Calculate RMSD with active site support
Simple RMSD	amina run simple-rmsd	Quick backbone RMSD calculation
US-Align	amina run usalign	TM-score structural alignment
SASA	amina run sasa	Solvent accessible surface area
Hydrophobicity	amina run hydrophobicity	Hydrophobic residue distribution
Surface Charge	amina run surface-charge	Electrostatic surface analysis
MMseqs2 Cluster	amina run mmseqs2-cluster	Sequence clustering

Examples:

# Simple RMSD calculation
amina run simple-rmsd --mobile ./model.pdb --target ./reference.pdb -o ./results/

# RMSD with active site focus
amina run rmsd-analysis --main ./model.pdb --reference ./reference.pdb --active-main "A:50,A:55,A:60" -o ./results/

# US-Align TM-score
amina run usalign --structure1 ./model.pdb --structure2 ./reference.pdb -o ./results/

# SASA calculation
amina run sasa --pdb ./protein.pdb -o ./results/

# Surface charge analysis
amina run surface-charge --pdb ./protein.pdb -o ./results/

# Sequence clustering
amina run mmseqs2-cluster --fasta ./sequences.fasta --identity 0.5 -o ./results/

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Properties

Sequence-based property prediction.

Tool	Command	Description
AminoSol	amina run aminosol	Predict E. coli solubility
ESM2 Embedding	amina run esm2-embedding	Extract protein embeddings

Examples:

# Solubility prediction from FASTA
amina run aminosol --fasta ./proteins.fasta -o ./results/

# Solubility for individual sequences (comma-separated)
amina run aminosol --sequences "MKTVGQW...,MGSSHHH..." -o ./results/

# ESM2 embeddings
amina run esm2-embedding --fasta ./proteins.fasta -o ./results/

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Utilities

File preparation and conversion tools.

Tool	Command	Description
PDB Cleaner	amina run pdb-cleaner	Clean and prepare PDB files
PDB to FASTA	amina run pdb-to-fasta	Extract sequences from structures
PDB Quality Assessment	amina run pdb-quality-assessment	Ramachandran and geometry analysis
PDB Distance Calculator	amina run pdb-distance-calculator	Calculate inter-residue distances
PDB Chain Selector	amina run pdb-chain-select	Extract or remove specific chains
PDB B-factor Overwrite	amina run pdb-bfactor-overwrite	Replace B-factors with custom scores
Active Site Verifier	amina run activesite-verifier	Verify active-site residue presence
Protein Relaxer	amina run protein-relaxer	Energy minimization for steric clashes
MAXIT Converter	amina run maxit-convert	Convert between PDB and mmCIF
Open Babel Converter	amina run obabel-convert	Multi-format molecule conversion
Molecule Size Calculator	amina run mol-size-calculator	Calculate molecule dimensions

Examples:

# Clean PDB file
amina run pdb-cleaner --pdb ./messy.pdb -o ./results/

# Clean PDB preserving B-factors
amina run pdb-cleaner --pdb ./messy.pdb --preserve-bfactors -o ./results/

# Extract FASTA from PDB
amina run pdb-to-fasta --pdb ./structure.pdb -o ./results/

# Keep specific chains
amina run pdb-chain-select --pdb ./complex.pdb --chains "A,B" -o ./results/

# Remove chains (invert selection)
amina run pdb-chain-select --pdb ./complex.pdb --chains "C" --invert -o ./results/

# Calculate distance between residues
amina run pdb-distance-calculator --pdb ./protein.pdb --chain1 A --resnum1 50 --chain2 A --resnum2 100 -o ./results/

# Convert PDB to mmCIF
amina run maxit-convert --input ./structure.pdb --format cif -o ./results/

# Relax structure (energy minimize)
amina run protein-relaxer --pdb ./clashing.pdb -o ./results/ --background

# Convert molecule formats
amina run obabel-convert --input ./molecule.mol2 --output-format sdf -o ./results/

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Output Files

Results are downloaded to your specified output directory. File names include the tool name and job ID:

./results/
├── esmfold_abc123_structure.pdb
├── esmfold_abc123_plddt_scores.csv
└── esmfold_abc123_plddt_plot.png

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Common Options

Most tools support these options:

Option	Description
-o, --output	Output directory (required)
-j, --job-name	Custom name for the job
-b, --background	Submit job and return immediately
--help	Show tool parameters and usage

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Links

• Website
• Documentation
• Get API Key

License

Apache 2.0