mdonatello 0.0.1

2D small molecule visualization for MDAnalysis

MDonatello

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2D small molecule visualization for MDAnalysis

This Repository is part of the Google Summer of Code 2024 for the following project: 2D Visualization for small molecules

The following Release is the submission for the GSoC 2024 Evaluation: GSoC 2024: 2D visualization for small molecules Release

Here is the final report for the GSoC2024 Project: GSoC 2024 - 2D visualization for small molecules

MDonatello is bound by a Code of Conduct.

Installation

To build MDonatello from source, First clone the repository:

git clone https://github.com/talagayev/MDonatello

Create a virtual environment and activate it:

conda create --name mdonatello
conda activate mdonatello

Then go into the MDonatello folder:

cd MDonatello

Finally this package from source:

pip install -e .

Running MDonatello

To use the mdonatello package you need to run a jupyter notebook, thus run the command:

jupyter notebook

Now that you started a jupyter notebook create a notebook file and enter the following command to use mdonatello:

import MDAnalysis as mda
import mdonatello
from mdonatello import MoleculeVisualizer

u = mda.Universe("input.pdb")
ag = u.select_atoms("resname UNK")
visualizer = MoleculeVisualizer(ag, show_atom_indices=False, width=-1, height=-1)

For a more detailed use of MDonatello and an example of the output follow the instructions in this section:

Running MDonatello

Copyright

The MDonatello source code is hosted at https://github.com/talagayev/mdonatello and is available under the GNU General Public License, version 2 (see the file LICENSE).

Copyright (c) 2024, Valerij Talagayev

Acknowledgements

Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using MDonatello in published work.