Getting Started

This page covers how to install QuantumPDB and its dependencies.

Prerequisites

  • Python 3.8+

  • Conda (recommended for managing the environment and installing Modeller)

  • Internet access (required for Protoss protonation via the ProteinsPlus web server)

Installation

  1. Clone the repository:

    git clone https://github.com/davidkastner/quantumPDB.git
cd quantumPDB

  2. Create the conda environment:

    The provided environment.yml installs all required dependencies, including Modeller from the salilab channel:

    conda env create -f environment.yml
conda activate qp

  3. Install the package:

    pip install -e .

    This performs a development install so that the qp command is available on your path.

Modeller Setup

Modeller is used for modeling missing atoms, residues, and loops (Stage 1). It is installed automatically via the conda environment, but requires a free academic license key.

  1. Register at https://salilab.org/modeller/ to obtain a license key.

  2. Set the key as an environment variable:

    export KEY_MODELLER="XXXX"

    Replace XXXX with your key. Add this line to your ~/.bashrc or ~/.zshrc so it persists across sessions.

Protoss

Protoss assigns protonation states and resolves alternate conformations (Stage 2). QuantumPDB accesses Protoss through the ProteinsPlus web API, so no local installation is needed — just an internet connection.

Note

The Protoss web server may throttle users who submit too many requests in a short period. If you are processing a large batch, expect some requests to be rate-limited. QuantumPDB handles retries automatically, but very large batches may require patience.

Optional Dependencies

These are only needed for specific pipeline stages and are not required to generate cluster models.

TeraChem (Stage 4 — QM calculations)

TeraChem is the primary GPU-accelerated quantum chemistry code supported by QuantumPDB. A license is required. See https://www.petachem.com/.

ORCA (Stage 4 — QM calculations)

ORCA is supported as a CPU-based alternative. See https://orcaforum.kofo.mpg.de/.

Multiwfn (Stage 5 — post-processing)

Multiwfn is required only for charge scheme analysis and dipole moment calculations in the analyze stage. Install it separately and ensure the Multiwfn executable is on your PATH, or set the multiwfn_path parameter in your config file.

Verifying the Installation

After installation, verify that the qp command is available:

qp --help

This should display the three available commands: run, submit, and analyze.