Metadata-Version: 2.4
Name: COBY
Version: 1.0.6
Summary: Build coarse-grained molecular systems
Project-URL: Repository, https://github.com/MikkelDA/COBY
Author-email: "Andreasen, M.D." <mdahlandreasen@hotmail.com>
License-File: LICENSE
Keywords: building,dynamics,martini,molecular,system
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Python: >=3.9
Requires-Dist: alphashape>=1.3.1
Requires-Dist: shapely>=2.0.0
Description-Content-Type: text/markdown

# Coarse-grained System Builder (COBY)

The publication is available open-source at [https://doi.org/10.1021/acs.jcim.5c00069](https://doi.org/10.1021/acs.jcim.5c00069).

The source code, documentation, and tutorials are avialable on [GitHub](https://github.com/MikkelDA/COBY).

COBY is a Python-based software tool for building flat membranes at a coarse-grained resolution. It supports asymmetric membranes, phase-separated systems, multiple bilayers, protein insertion, solvation, and flooding with one or multiple solute molecules of choice.

COBY is versatile, fast, easy to use and offers a high degree of customisation. It can be used either as a **Python package** or directly from the **terminal command line**. It efficiently manages multiple parameter libraries (even within the same system), making it developer-friendly. 

COBY is continuously under development, and we welcome suggestions for new features, which should be submitted under [Issues](https://github.com/MikkelDA/COBY/issues). 

![](https://github.com/MikkelDA/COBY/raw/master/figures/COBY_Logo.png)

## Citation (JCIM)
```
@article{Andreasen2025,
	author = {Andreasen, Mikkel D. and Souza, Paulo C. T. and Schiøtt, Birgit and Zuzic, Lorena},
	title = {Creating Coarse-Grained Systems with COBY: Toward Higher Accuracy of Complex Biological Systems},
	journal = {Journal of Chemical Information and Modeling},
	volume = {0},
	number = {0},
	pages = {null},
	year = {0},
	doi = {10.1021/acs.jcim.5c00069},
	URL = {https://doi.org/10.1021/acs.jcim.5c00069},
	eprint = {https://doi.org/10.1021/acs.jcim.5c00069}
}
```

## Installation 

**Using pip (requires python>=3.9)**

    conda create --name COBY python==3.9 ipykernel

    conda activate COBY

    pip install COBY

    python -m ipykernel install --user --name=COBY

Ipykernel allows the user to use COBY environment within the Jupyter notebook.

## OS compatability

COBY has been developed and thoroughly tested on Ubuntu Linux. It has also been tested to a lesser extent on Windows 11 and macOS, with all tutorial systems running without issue.

## Testing

Installation can be tested using the tutorial notebooks, which cover the majority of the functions available in COBY.

## Basic usage 

For a detailed introduction to the software, please refer to the [COBY Documentation](https://github.com/MikkelDA/COBY/blob/master/COBY_Documentation.pdf).

For a quick reminder of available commands, you can use the [Cheat Sheet](https://github.com/MikkelDA/COBY/blob/master/COBY_CHEAT_SHEET.pdf).

Three [tutorials](https://github.com/MikkelDA/COBY/tree/master/Tutorial) are available as Jupyter Notebooks: one covering the basics, another focusing on more advanced functionalities, and the final tutorial showcasing the systems from the manuscript.

## Licence

COBY is preserved under the [Apache License 2.0](https://github.com/MikkelDA/COBY/blob/main/LICENSE).

![](https://github.com/MikkelDA/COBY/raw/master/figures/membrane_protein.png)
