| Name | COBY JSON |
| Version |
0.2.5
JSON |
| download |
| home_page | None |
| Summary | Build coarse-grained molecular systems |
| upload_time | 2025-02-05 12:19:15 |
| 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 paper is currently in pre-print at [bioRxiv](https://www.biorxiv.org/content/10.1101/2024.07.23.604601v1).
The program as well as documentation and a tutorial is avialable on the [GitHub](https://github.com/MikkelDA/COBY).
COBY is a Python-based software for building flat membranes in coarse-grained resolution. It handles 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 it also allows for high-level of customisation. It can be used either as a **Python package** or directly from the **terminal command line**. It neatly handles multiple parameter libraries (even within the same system), making it developer-friendly.
COBY is continuously under development and we welcome suggestions for new features.
## Citation (bioRxiv)
```
@article {Andreasen2024COBY,
author = {Andreasen, Mikkel D. and Souza, Paulo C. T. and Schi{\o}tt, Birgit and Zuzic, Lorena},
title = {Creating Coarse-Grained Systems with COBY: Towards Higher Accuracy in Membrane Complexity},
elocation-id = {2024.07.23.604601},
year = {2024},
doi = {10.1101/2024.07.23.604601},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2024/07/23/2024.07.23.604601},
eprint = {https://www.biorxiv.org/content/early/2024/07/23/2024.07.23.604601.full.pdf},
journal = {bioRxiv}
}
```
## 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.
## Basic usage
For a detailed introduction to the software, please consult [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 covering more advanced functionalities and the final covering the systems shown in our soon-to-be released paper.
The tutorials includes (amongst other systems):
* **Simple membrane with protein**: A simple POPC membrane with a protein in solvent (water + 0.15 M NaCl) which explains the various arguments in COBY
* **Asymmetric membrane**: An asymmetric complex membrane (POPC, POPE and CHOL) in solvent with different area per lipid values for each membrane
* **Phase separated Membrane**: A phase separated membrane
* **Monolayers**: Two monolayers with solvent between them and vacuum over the pbc
* **Nanodisc**: A nanodisc with DMPC lipid contained within and with solvent surrounding it
* **Holes**: A membrane with multiple manually defined holes
* **Patches**: Multiple manually shaped membrane patches
* **Matryoshka membrane**: A matryoshka membrane with a protein in the center
* **Stacked membranes**: Three vertically stacked membranes
* **Mixed solvent**: A symmetric membrane solvated with regular and small water beads in specified ratios
* **Phase separated solvent**: A symmetric membrane solvated with two solvent volumes containing different salt concentrations
* **Flooding of imported solutes**: A membrane system that has been flooded with imported solute molecules, followed by solvation
* **COBY logo**: Our logo
## Licence
COBY is preserved under the [Apache License 2.0](https://github.com/MikkelDA/COBY/blob/main/LICENSE).
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