sea-cli 0.1.6

A command-line utility for Structured Entropy Analysis (SEA)

SEA CLI: Structured Entropy Analysis Command-Line Utility

Overview

The sea-cli is a command-line utility designed to perform Structured Entropy Analysis (SEA). It processes data from various molecular dynamics simulations and analysis files, providing a streamlined way to perform complex calculations directly from your terminal. The utility is configured via a simple YAML file, making it easy to integrate into existing workflows.

Structured Entropy Analysis (SEA) is a Python framework for revealing hidden structural dynamics in molecular systems by going beyond traditional descriptors like RMSD, Rg, and RMSF. By converting molecular dynamics features into entropy-based signatures, SEA quantifies complexity, evaluates randomness, and highlights non-random patterns tied to underlying physical properties. With built-in visualization and statistical tools, the framework provides a fresh perspective on biomolecular behavior and is extensible to other dynamical systems in materials science, nanotechnology, and beyond.

Features

• Simple Interface: A clean and intuitive command-line interface powered by click.

• Configuration-Driven: All inputs and parameters are managed through a single YAML configuration file, ensuring reproducibility and easy sharing of settings.

• Flexible Inputs: Supports multiple input files, including rmsd.txt, rg.txt, and rmsf.txt.

• Structured Output: Generates processed data into a specified export folder, with a clear output format.

Installation

The sea-cli can be easily installed from PyPI using pip.

    pip install sea-cli

Usage

The primary command to run the analysis is sea run. You must provide the path to your configuration file using the --config or -c option.

    sea run --config /path/to/your/config.yaml

If you need to see all available options, you can use the built-in help command:

    sea --help
    sea run --help

Configuration File (config.yaml)

The sea-cli is configured using a YAML file. The file must contain a top-level config key with the following structure. Pay close attention to the indentation, as it is critical in YAML.

    input:
      rmsd: rmsd.txt
      rg: rg.txt
      rmsf: rmsf.txt
    bits: 8
    export_folder: Exported_Data

• input: A nested dictionary specifying the paths to your input data files. All files listed are relative to the directory where the command is executed.

• bits: An integer value used for the analysis.

• export_folder: The name of the folder where the processed data will be saved.

Alternatively, you can pass the input files directly to the run command:

    sea run --rmsd rmsd.txt --rg rg.txt --rmsf rmsf.txt --bits 8 --export-folder Exported_Data

This allows you to override or specify inputs without needing a config file.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Contact

If you have any questions or issues, please open an issue on the project's GitHub repository.

Author	Email
Ezekiel Edward Nettey-Oppong	[e-mail]
Per Badasu	[e-mail]
Emmanuel Essel Mensah	[e-mail]