agentic-proteins 0.1.0

Deterministic, artifact-first protein design runtime and CLI

Agentic Proteins

Deterministic, artifact-first protein design runtime and CLI for traceable runs, human review, and reproducible decision trails.

At a glance: Deterministic runs • artifact-first output • human-in-the-loop gating • stable JSON contracts
Audience: Computational biology teams and lab workflows that require auditability and reproducibility.

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Table of Contents

• Why Agentic Proteins?
• Try It in 30 Seconds
• Installation
• Quick Start
• What This Does
• What This Does Not Do
• Stable Public Surface
• Docs & Resources
• Contributing
• License

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Why Agentic Proteins?

Protein design workflows need traceable decisions, stable artifacts, and reproducible execution paths. Agentic Proteins provides a deterministic loop that separates planning, execution, evaluation, and human decision points so that labs can audit and reproduce runs without digging into internal code.

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Try It in 30 Seconds

pipx install agentic-proteins  # Or: pip install agentic-proteins
agentic-proteins run --sequence "ACDEFGHIKLMNPQRSTVWY"
agentic-proteins inspect-candidate --latest

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Installation

Requires Python 3.11+.

# Isolated install (recommended)

pipx install agentic-proteins

# Standard

pip install agentic-proteins

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Quick Start

# Run a deterministic loop

agentic-proteins run --sequence "ACDEFGHIKLMNPQRSTVWY"

# Resume a run by ID

agentic-proteins resume --run-id <run_id>

# Compare two runs

agentic-proteins compare --left <run_id> --right <run_id>

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What This Does

• Runs a deterministic agentic loop with traceable artifacts and telemetry.
• Produces proxy structure-quality signals from sequence heuristics by default.
• Requires explicit opt-in to run real structure predictors via --provider.

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What This Does Not Do

• It does not run real structure prediction unless --provider esmfold|rosettafold|openprotein is specified and requirements are met.
• It does not finalize candidate selection without a signed human decision artifact.
• It does not expose internal modules as stable APIs.

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Stable Public Surface

• Supported CLI commands: run, resume, compare, inspect-candidate, export-report.
• Stable artifacts: artifacts/<run_id>/ layout and JSON payloads.
• Stable CLI JSON output schema (see docs).

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Docs & Resources

Start here:

• Getting Started: https://bijux.github.io/agentic-proteins/overview/

• CLI Reference: https://bijux.github.io/agentic-proteins/cli/cli/

• Architecture: https://bijux.github.io/agentic-proteins/architecture/architecture/

• Concepts: https://bijux.github.io/agentic-proteins/concepts/terminology/

• Site: https://bijux.github.io/agentic-proteins/

• Changelog: https://github.com/bijux/agentic-proteins/blob/main/CHANGELOG.md

• Repository: https://github.com/bijux/agentic-proteins

• Issues: https://github.com/bijux/agentic-proteins/issues

• Security: https://github.com/bijux/agentic-proteins/security/advisories/new

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Contributing

See CONTRIBUTING.md for setup, style, and tests.

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License

Apache-2.0 — see LICENSE. © 2025 Bijan Mousavi.

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