# Protein Matcher

Protein Matcher is a tool designed to find the closest matches a new pdb in the opm database. This README provides an overview of the project, instructions for installation, and guidelines for usage.

## Table of Contents

- [Introduction](#introduction)
- [Installation](#installation)
- [Usage](#usage)
- [Contributing](#contributing)
- [License](#license)

## Introduction

Protein Matcher utilizes [ncbi-blast-2.15.0+](https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html) to efficiently search through a local database of protein sequences and identify the closest matches in terms of their primary sequence. 

## Installation

To install and set up Protein Matcher, follow these steps:

1. Clone the repository to your local machine:
git clone: [email protected]:oreoqke/opm_align.git

2. Install the ncbi balst and choose the appropriate version for your system:
https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html
Don't forget to add to the path.

For blastp documentation, visit https://www.ncbi.nlm.nih.gov/books/NBK279684/table/appendices.T.options_common_to_all_blast/


3. Install USalign:
https://zhanggroup.org/US-align/help/

4. create a virtual environment, activate it, and install requirements.txt:
python3 -m venv env
source env/bin/activate
pip install -r requirements.txt

5. Specify the right name for database in get_all_pdbid.py and user information if needed