ZMPY: accelerating protein structure volume analysis through vectorized 3D Zernike Moments and Python-based GPU Integration

This repository is a Tensorflow implementation.

For GPU support with CuPy, please refer to the other repository: ZMPY_CP supports CuPy (https://github.com/tawssie/ZMPY_CP)

For CPU support only, please refer to the other repository: ZMPY supports NumPy (https://github.com/tawssie/ZMPY)

Here presents a Python-based software package, ZMPY, to accelerate the moments computation by vectorizing the mathematical formulae, enabling their computation in graphical processing units (GPUs). The package offers popular GPU-supported libraries such as CuPy and TensorFlow along with NumPy implementations, aiming to improve computational efficiency, adaptability, and flexibility in future algorithmic development.

Prerequisites:

• ZMPY : Python >=3.9.16, NumPy >=1.23.5
• ZMPY_CP: Python >=3.9.16, NumPy, CuPy >=12.2.0
• ZMPY_TF: Python >=3.9.16, NumPy >=1.23.5, Tensorflow >=2.12.0, Tensorflow-Probability >=0.20.1

1. Open the terminal
2. Using pip to install the package through PyPI
3. Run pip install ZMPY_TF for the installation

• 3D Zernike moments: [access Colab notebook demo here]
• Shape similarity: [access Colab notebook demo here]
• Structure superposition: [access Colab notebook demo here]

A voxel cube with dimensions of 100x100x100 was applied to perform 10,000 3D Zernike moment calculations, using 2 different maximum orders 20 and 40. Execution times for different hardware configurations using TensorFlow, CuPy, and NumPy libraries:

Note: m = minutes, s = seconds.

Due to GitHub's file size limitations, follow these steps to download the cache data for order 40 (1.3G) in the ZMPY_TF package:

• Open your terminal and execute the following command to find the folder of the ZMPY_TF package:
• python -c "import ZMPY_TF; print(ZMPY_TF.__file__)"
• Note the path, which ends with /User/path/ptyhon/site-packages/ZMPY_TF/__init__.py.

• Go to the cache_data folder at the same level as __init__.py file, i.e., /User/path/ptyhon/site-packages/ZMPY_TF/cache_data.

• Download the 1.3 GB max order 40 .pkl file to the cache_data folder from the link below. https://drive.google.com/uc?id=1RR1rF_5YJqaxNC5AK0Ie_8MswGb0Tttw

Feel free to submit pull requests for improvements or bug fixes.

Lai, J. S., Burley, S. K., & Duarte, J. M. (2024). ZMPY: Accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration. (Submitted)

This project is licensed under the GNU General Public License v3.0. You can view the full license here.