hedgehog 1.1.13

Hierarchical Evaluation of Drug GEnerators tHrOugh riGorous filtration

HEDGEHOG: Hierarchical Evaluation of Drug GEnerators tHrOugh riGorous filtration.

Quick Start

HEDGEHOG is a benchmark pipeline for evaluating generated molecules. It applies a staged filtering workflow (standardization, descriptors, structural filters, synthesis checks, docking, and post-docking validation) and generates an interactive HTML report.

Install from PyPI

pip install hedgehog
hedgehog --help

Install from source

git clone https://github.com/LigandPro/hedgehog.git
cd hedgehog
uv sync

First run

uv run hedgehog

# Optional: auto-install missing optional tools without prompts
uv run hedgehog --auto-install

Common Commands

# Full pipeline
uv run hedgehog

# Run with your own molecules
uv run hedgehog --mols input/my_molecules.csv

# Run a single stage
uv run hedgehog --stage descriptors

# Run docking with a live progress bar
uv run hedgehog --stage docking --progress

# Run docking without progress bar (default)
uv run hedgehog --stage docking

# Regenerate report for an existing run
uv run hedgehog report results/run_10

# Show stages / version
uv run hedgehog info
uv run hedgehog version

# Launch terminal UI
uv run hedgehog tui

Progress bar behavior in CLI runs:

• Enabled: add --progress
• Disabled: omit --progress (default)

Documentation

For full details, use the documentation instead of this README:

• Introduction
• Getting Started
• CLI Reference
• Pipeline Stages
• Configuration
• Reporting
• Advanced Topics
• TUI README

To run the docs site locally:

cd docs
pnpm install
pnpm dev

License

MIT