exia 0.1.0

A tool for preparing protein structures for simulation studies

exia - PDB preparation tool

exia is a command-line tool for preparing protein structure data in the PDB format for use in structural bioinformatics analyses.

Features

• Downloads PDB files from the RCSB PDB database
• Selects and saves specific chains from the PDB file
• Calculates the coordinates for adding an additional oxygen atom
• Adds an oxygen atom to the PDB file in order to make the Compound I (CpdI)
• Cleans the PDB file by removing unnecessary ligands or residues and adding missing atoms
• Removes extra hydrogen atom on cysteine axial ligand of CpdI

Installation

exia requires Python 3.8 or higher and the following dependencies:

• argparse
• sys

To install exia, use pip: pip install exia

Usage

To prepare a PDB file, use the exia command followed by the PDB ID and a list of chain IDs: exia 6DWN A

This will download the PDB file for the protein structure with PDB ID 1abc, select the chains with IDs A, B, and C, and perform the necessary preparation steps. The resulting PDB file will be saved in a directory with the same name as the PDB ID.

Contributing

If you encounter any bugs or have a feature request, please open an issue on the exia GitHub repository.

To contribute code to exia, please follow these guidelines:

• Fork the repository and create a new branch for your changes.
• Write tests for any new functionality.
• Follow the existing code style.
• Run the tests and ensure that they pass before submitting a pull request.

License

exia is released under the MIT License. See the LICENSE file for details.

Copyright (c) 2021 John Doe