Metadata-Version: 2.1
Name: ProtY
Version: 1.3
Summary: The project is about using a pretrained protein transformer architecture to create embeddings of various proteins, and then performing nonlinear dimensionality reduction on those embeddings to see which kinds of similarities in protein function/structure we can restore
Home-page: https://github.com/uhlarbrigi/PEPTIDE-SEQUENCE-EMBEDDING-AND-CLUSTERING-VISUALIZATION.git
Author: Csapó Bence, Galló Dominik, Uhlár Brigitta
Author-email: uhlarbrigi@gmail.com
Maintainer-email: "Csapó Bence, Galló Dominik, Uhlár Brigitta" <uhlarbrigi@gmail.com>
License: GPL-3.0-only
Project-URL: Homepage, http://your-git.com
Project-URL: Documentation, https://peptide-sequence-embedding-and-clustering-visualization.readthedocs.io/en/latest/
Project-URL: Repository, https://github.com/uhlarbrigi/PEPTIDE-SEQUENCE-EMBEDDING-AND-CLUSTERING-VISUALIZATION.git
Project-URL: Issues, http://your-git.com/issues
Classifier: Development Status :: 1 - Planning
Classifier: Programming Language :: Python :: 3.10
Classifier: Operating System :: OS Independent
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=1.25.2
Requires-Dist: matplotlib>=3.6.2
Requires-Dist: scikit-learn>=1.1.3
Requires-Dist: scipy>=1.9.3
Requires-Dist: PyWavelets>=1.5.0
Requires-Dist: pandas>=2.0.0
Requires-Dist: emd>=0.6.2
Requires-Dist: nolds>=0.5.2
Requires-Dist: tqdm>=4.64.1
Requires-Dist: pyQt5>=5.15.7
Requires-Dist: fair-esm>=0.1.0
Requires-Dist: sphinx_rtd_theme>=3.0.2
Provides-Extra: docs
Requires-Dist: sphinx; extra == "docs"
Requires-Dist: sphinx_rtd_theme; extra == "docs"

# Peptide sequence embedding and clustering/visualization
The project is about using a pretrained protein transformer architecture to create embeddings of various proteins, and then performing nonlinear dimensionality reduction on those embeddings to see which kinds of similarities in protein function/structure we can restore.

## Installation
Install `ProtY` using pip

```
pip install ProtY
```

Clone the git repository
```
git clone https://github.com/uhlarbrigi/PEPTIDE-SEQUENCE-EMBEDDING-AND-CLUSTERING-VISUALIZATION.git
```

Change directory to the cloned repository
```
cd pyPCG-tooblox
```
Install with pip
```
pip install .
```

## Building the documentation
Install required packages
```
pip install -r docs/requirements.txt
```
Call Sphinx build command
```
sphinx-build -M html docs/source docs/build
```
On Windows you can also run the `make.bat` file
```
.\docs\make.bat html
```

## Correspondence
Brigitta Uhlár 
Dominik Galló 
Bence Csapó
