Metadata-Version: 2.1
Name: rational_protein_design
Version: 0.1.0
Summary: A package for rational protein binder design using Biopython
Home-page: https://github.com/rohitium/rational_protein_design
Author: Rohit Satija
Author-email: rohitsatija0092@gmail.com
License: MIT
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Operating System :: OS Independent
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: biopython>=1.79
Requires-Dist: numpy>=1.21.0
Requires-Dist: setuptools>=49.6.0

# Rational Protein Design

This package is designed for rational protein binder design using Biopython data structures. It allows for efficient identification and extraction of protein sequences based on proximity to target residues in a protein structure.

## Features

- Parse PDB files and extract chains
- Identify neighboring residues based on distance thresholds
- Extract protein sequences and generate rational binders
- Support for randomization and multiple design attempts

## Installation

You can install the package from PyPI:

```bash
pip install rational_protein_design
```

## Usage

```python
from rational_protein_design import BinderDesigner

designer = BinderDesigner(
    pdb_file="path/to/pdb/file.pdb",
    chain_id="A",
    target_residues_range=(100, 120),
    neighbor_chain_id="B",
    N=50,
    num_seq=10
)
designer.design_binder("output_fasta_file.fasta")
```

## License

This project is licensed under the MIT License.

