hedgehog 1.1.25

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.

Recommended install: source checkout

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

This is the recommended way to run HEDGEHOG end to end. The repository checkout contains the editable configs, bundled examples, TUI sources, and the modules/ workspace used by setup commands.

PyPI install

python -m pip install hedgehog
hedgehog --help

Use the PyPI package only if you already manage your own config files and input paths. The default quick start, hedgehog setup ... workflows, and TUI usage are designed around a source checkout.

First run (from a source checkout)

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 multiple selected stages
uv run hedgehog --stage descriptors --stage struct_filters

# 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
• TUI
• Pipeline Stages
• Configuration
• Reporting
• Advanced Topics
• TUI README

To run the docs site locally:

cd docs
pnpm install
pnpm dev

License

MIT