ZMPY NumPy version
Project description
ZMPY
ZMPY: accelerating protein structure volume analysis through vectorized 3D Zernike Moments and Python-based GPU Integration
This repository is a NumPy implementation without GPU support. For GPU support with TensorFlow and CuPy, please refer to the other two repositories:
ZMPY_TF
supports Tensorflow
(https://github.com/tawssie/ZMPY_TF)
ZMPY_CP
supports CuPy
(https://github.com/tawssie/ZMPY_CP)
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.
Installation
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
- Open the terminal
- Using pip to install the package through PyPI
- Run
pip install ZMPY
for the installation
Usage (Google Colab notebooks)
- 3D Zernike moments: [access Colab notebook demo here]
- Shape similarity: [access Colab notebook demo here]
- Structure superposition: [access Colab notebook demo here]
Performances
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:
NumPy
Order | CPU1 | CPU2 |
---|---|---|
20 | 33m20s | 14m1s |
40 | 951m40s | 338m20s |
TensorFlow
Order | T4 | RX3070Ti | V100 | L4 |
---|---|---|---|---|
20 | 1m1s | 0m36s | 0m31s | 0m39s |
40 | 24m40s | 9m3s | 10m54s | 11m13s |
CuPy
Order | T4 | RX3070Ti | V100 | L4 |
---|---|---|---|---|
20 | 4m45s | 2m30s | 1m42s | 2m50s |
40 | 35m20s | 19m19s | 14m45s | 18m40s |
Note: m = minutes, s = seconds.
Cache data for order 40
Due to GitHub's file size limitations, follow these steps to download the cache data for order 40 (1.3G) in the ZMPY package:
1. Locate Package Folder
- Open your terminal and execute the following command to find the folder of the ZMPY package:
python -c "import ZMPY; print(ZMPY.__file__)"
- Note the path, which ends with
/User/path/ptyhon/site-packages/ZMPY/__init__.py
.
2. Navigate to Cache Data Folder
- Go to the
cache_data
folder at the same level as__init__.py
file, i.e.,/User/path/ptyhon/site-packages/ZMPY/cache_data
.
3. Download the Cache File:
- Download the 1.3 GB max order 40
.pkl
file to thecache_data
folder from the link below. https://drive.google.com/uc?id=1RR1rF_5YJqaxNC5AK0Ie_8MswGb0Tttw
Contributing
Feel free to submit pull requests for improvements or bug fixes.
Citation
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)
License
This project is licensed under the GNU General Public License v3.0. You can view the full license here.
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