Collection of tutorials and examples of the novel 2Danalysis toolbox, for the analysis of lipid membranes and biopolymers.
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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.
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.
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 --file devtools/conda-envs/test_env.yaml
conda env update --name twod --file docs/requirements.yaml
Build this package from source:
pip install -e .
If you want to update your dependencies (which could be risky!), run:
conda update --all
And when you are finished, you can exit the virtual environment with:
conda deactivate
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]"
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
Project based on the MDAnalysis Cookiecutter version 0.1. Please cite MDAnalysis when using 2D Analysis in published work.
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.