Installation

Setting up Pose Rescorer with AmberTools via conda

Requirements

Rescore requires the following dependencies:

• AmberTools 24.8 or later (provides MMPBSA.py, antechamber, tleap, sander, pdb4amber)
• Python 3.10 or later
• BioPython 1.86+
• Typer 0.21.1+ (CLI framework)
• Rich 13.7.1+ (colored terminal output)
• Loguru 0.7.3+ (logging)

Installation via Conda

The recommended installation method uses conda to manage AmberTools and Python dependencies.

Step 1: Clone Repository

git clone https://github.com/Amirtesh/Pose-Rescorer
cd Pose-Rescorer

Step 2: Create Conda Environment

The repository includes an environment.yml file with all dependencies:

conda env create -f environment.yml
conda activate pose-rescorer

This creates an environment called pose-rescorer with:

• AmberTools from conda-forge
• Python 3.10
• All required Python packages

Step 3: Install Pose Rescorer

Make sure you're in the Pose-Rescorer directory, then install the package in development mode:

pip install -e .

Step 4: Verify Installation

Test that the installation succeeded:

rescore --version

You should see:

rescore version 1.1

Verify that AmberTools commands are available:

which MMPBSA.py
which antechamber
which sander

Manual Installation

If you prefer not to use the provided environment file, you can install dependencies manually. Ensure AmberTools is installed and available in your PATH, then install Python dependencies:

pip install biopython typer rich loguru

System Requirements

• OS: Linux or macOS (Windows via WSL2)
• RAM: 4 GB minimum, 8+ GB recommended for larger systems
• Disk: 5 GB for AmberTools + conda environment
• CPU: Multi-core recommended (AmberTools parallelizes GB calculations)

Testing the Installation

Run a quick validation to ensure everything works:

rescore validate --help
rescore integrate --help

Both commands should display help text without errors.

Troubleshooting

Command not found: rescore

Ensure the conda environment is activated:

conda activate pose-rescorer

MMPBSA.py not found

Verify AmberTools installation:

conda list ambertools

If not installed, add it manually:

conda install -c conda-forge ambertools

Import errors for Python packages

Reinstall dependencies:

pip install --upgrade biopython typer rich loguru