Getting Started

Welcome! This guide helps you install PepKit and run a quick sanity check.

What is PepKit?

PepKit is a small toolbox for peptide-centric computational workflows, covering representation conversion, dataset preparation, structure post-processing, and complex-quality evaluation.

It supports:

• Conversion between peptide representations (FASTA / sequence ⇄ SMILES)

• Standardization and filtering of peptide datasets

• Computation of peptide properties and descriptors for machine learning

• Querying protein–peptide complexes from the Protein Data Bank using user-defined constraints (e.g. release date)

• Post-processing of AlphaFold-Multimer outputs

• External rescoring of predicted complexes (pDockQ, pDockQ2, MPDockQ)

• Computation of ``DockQ`` when a native (experimental) complex is available

TL;DR install

pip install pepkit

Verify installation

python -c "import pepkit; print(pepkit.__version__)"

If that prints a version string, you’re good.

Recommended: use a virtual environment

Creating an isolated environment prevents dependency conflicts.

Option A — venv (cross-platform)

python3 -m venv pepkit-env
source pepkit-env/bin/activate    # Linux/macOS
pepkit-env\Scripts\activate       # Windows PowerShell

Option B — conda

conda create -n pepkit-env python=3.11
conda activate pepkit-env

Support

If you hit an issue:

• Report bugs and feature requests on GitHub: PepKit Issues

• Check the API Reference section for complete function/class references.