| Name | COBY JSON |
| Version |
1.0.6
JSON |
| download |
| home_page | None |
| Summary | Build coarse-grained molecular systems |
| upload_time | 2025-07-17 07:32:41 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.9 |
| license | None |
| keywords |
building
dynamics
martini
molecular
system
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# 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).
## 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).
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