semvec/pypi-packages huggingface dataset:
rational-protein-design 0.1.0
A package for rational protein binder design using Biopython
License: MIT
Requires Python: >=3.7

# 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.
ypm 0.0.1
Yoda Package Manager
License: MIT
Requires Python: <4.0,>=3.9

# ypm
Yoda Plugin Manager (or Yoda Padawan Manager, if you will)

## What you can do with `ypm`
- Generate boilerplate for a new yoda plugin
- Install yoda plugins from a variety of sources (GitHub repos, code, etc)
- Enable/Disable plugins
- List locally available plugins
- List globally available plugins (plugins can have a github tag that can make it searchable)
- Validate plugins
- Get information about a plugin