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2D small molecule visualization for MDAnalysis
MDonatello is bound by a Code of Conduct.
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 .
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:
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
Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using MDonatello in published work.