twod-analysis-kit 1.0.0

Project created to study lipid membranes in a 2D fashion.

2Danalysis

Latest release
Status
Community

Toolkit created to map biophysical properties of biopolymers (proteins, nucleic acids, glycans) onto surfaces, and those of lipid bilayers onto the membrane plane to track local and global changes in molecular dynamics and correlations in 2D. This kit is built following the format of MDAKits.

2Danalysis is bound by a Code of Conduct.

Installation

To build twodanalysis from source, We strongly recommend that you use virtual environments and Anaconda as your package manager. Below we provide instructions both for conda and pip.

With conda

Ensure that you have conda installed.

Create a virtual environment and activate it:

conda create --name twod
conda activate twod

Install the development and documentation dependencies:

git clone https://github.com/monjegroup/twod-analysis-kit.git
cd twod-analysis-kit
conda env update --name twod-analysis-kit --file devtools/conda-envs/test_env.yaml
conda env update --name twod-analysis-kit --file docs/requirements.yaml

Build this package from source:

pip install -e .

If you want to update your dependencies (which can be risky!), run:

conda update --all

And when you are finished, you can exit the virtual environment with:

conda deactivate

With pip

To build the package from source, run:

pip install .

If you want to create a development environment, install the dependencies required for tests and docs with:

pip install ".[test,doc]"

Tutorials!

The toolkit offers tutorials with a detailed explanation of the routines included in 2Danalysis, follow the tutorials step by step in this repo pyF4all

git clone https://github.com/pyF4all/2DanalysisTutorials.git

Copyright

The 2D Analysis source code is hosted at https://github.com/monjegroup/twod-analysis-kit and is available under the GNU General Public License, version 2 (see the file LICENSE).

Copyright (c) 2025, Ricardo Ramirez, Antonio Bosch, Ruben Perez, Horacio V Guzman, and Viviana Monje

Acknowledgements

Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using 2D Analysis in published work.

Funding

H.V.G. acknowledges financial support from the Ramón y Cajal grant No. RYC2022-038082-I and Spanish Ministry of Science and Innovation, through project PID2023-150536NA-I00, and the “Severo Ochoa” Grant No. CEX2023-001263-S for Centers of Excellence; and thanks the Red Española de Supercomputación (RES) for the computing time and technical support at the Finisterrae III supercomputer project FI-2024-3-0033.