SwiftTCR

Overview

SwiftTCR is a powerful tool designed to predict bindings between T-cell receptors (TCR) and peptide-MHC complexes.

Features

Predict binding interactions between TCRs and peptide-MHC.
User-friendly command-line interface.
Efficient clustering algorithms for data analysis.

Getting Started

To get started with SwiftTCR, follow these steps:

Clone or Download this repository.
Navigate into the SwiftTCR folder.

Installation

To quickly install all the necessary packages, you can use the provided swifttcr_install.yml file. Run the following commands:

conda env create -f swifttcr_install.yml
conda activate swifttcr

Running SwiftTCR

Use the following command to execute SwiftTCR:

python3 scripts/swift_tcr.py -r /your/input/peptide-mhc -l /your/input/tcr -o output_directory -op output_prefix -c number_of_cores -t clustering_threshold (default=9)

Example command:

python3 scripts/swift_tcr.py -r example/input/benchmark_dataset/3w0w/3w0w_pmhc_renumbered.pdb -l example/input/benchmark_dataset/3w0w/3w0w_tcr.pdb -o example/output/ -op first_test -c 6 -t 9

Dependencies:

Output Structure Naming Convention initial placement

Peptide-MHC Chains

A = MHC (Not IMGT numbered)
B = β2m (Not IMGT numbered)
C = Peptide (Not IMGT numbered)

TCR Chains

D = TCR Alpha Chain (IMGT numbered)
E = TCR Beta Chain (IMGT numbered)

Output Structure Naming Convetion SwiftTCR

TCR-Peptide-MHC

A = The ABC Chains of original Peptide-MHC combined
D = The Alpha and Beta chains of TCR combined

Installing Python 2.7 and Python 3.12.9 in a Conda Environment

Because of prepare.py, this program requires both Python 2.7 and Python 3.12.9. Follow these steps to install and configure both versions.

Step-by-Step Installation Guide

1. Install Conda (if not already installed)

If you don't have Conda installed, you can download and install Miniconda or Anaconda.

2. Create a Conda Environment for Python 3.12.9

Run the following command to create a new Conda environment named swifttcr with Python 3.12.9:

conda create -n swifttcr python=3.12.9

3. Activate the Conda Environment

Activate the newly created environment:

conda activate swifttcr

4. Install Required Packages

Install any required packages for your project within this environment. For example, if you need numpy and pandas, you can do so with:

conda install numpy pandas

5. Install Python 2.7

To install Python 2.7, you can use the following commands:

5.1. Download Python 2.7

Run this command to download the Python 2.7 source code:

wget https://www.python.org/ftp/python/2.7.18/Python-2.7.18.tgz

5.2. Extract the Source Code

Extract the downloaded tarball:

tar -xvf Python-2.7.18.tgz

5.3. Move to the Python Directory

Change into the newly created Python directory:

cd Python-2.7.18

5.4. Configure the Installation

Run the configure script with the --prefix option to specify the installation directory:

./configure --prefix=$HOME/.local

5.5. Build and Install Python 2.7

Compile and install Python 2.7 with:

make
make install

6. Add Python 2.7 to Your PATH

To make Python 2.7 accessible from the command line, add it to your PATH by running:

echo 'export PATH=$HOME/.local/bin:$PATH' >> ~/.bashrc

7. Reload Your Profile

Apply the changes to your current session:

source ~/.bashrc

8. Check Installations

Verify the installations by checking the versions:

python2.7 --version
python3 --version  # This will point to Python 3.12.9 in the active Conda environment.

Additional Notes

The .local directory is used as an example; you can choose a different directory if preferred.
To switch between Python versions, activate the Conda environment using conda activate swifttcr for Python 3.12.9 and use python2.7 for Python 2.
Ensure you deactivate your Conda environment when you're done working by running:

conda deactivate

rhinowarrior / swifttcr

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