Welcome to MembraneCurvature’s Documentation
Minimum MDAnalysis version: 1.1.1
Last updated: Aug 30, 2022
The MDAnalysis MembraneCurvature tool module calculates the Gaussian and mean curvature from Molecular Dynamics (MD) simulations.
MembraneCurvature derives 2D curvature profiles of a surface of reference. To suit the needs of your system, we offer flexible atom selection that will enable you to use the most convenient AtomGroup to extract curvature from your MD simulations!
This is an example on how to use MembraneCurvature:
import MDAnalysis as mda from membrane_curvature.base import MembraneCurvature u = mda.Universe(coordinates, trajectory) mc = MembraneCurvature(u).run() surface = mc.results.average_z_surface mean_curvature = mc.results.average_mean_curvature gaussian_curvature = mc.results.average_gaussian_curvature
You can find more details on how to use MembraneCurvature in the Usage page.
MembraneCurvature calculates mean and Gaussian curvature from MD simulations in:
MembraneCurvature is a user-friendly, actively-maintained, well-documented tool in Python 3 to derive 2D maps of membrane curvature from MD Simulations, using the most recent version of MDAnalysis Are you interested in calculating mean and Gaussian curvature from MD simulations? This tool is for you!
MembraneCurvature is available via pip:
pip install membrane-curvature
To install from source:
git clone https://github.com/MDAnalysis/membrane-curvature.git cd membrane-curvature conda env create -f devtools/conda-envs/environment.yaml conda activate membrane-curvature python setup.py install
Some of the examples included in the MembraneCurvature documentation use test cases from MDAnalysis Tests. To install the unit tests via conda:
conda install -c conda-forge MDAnalysisTests
or via pip:
pip install --upgrade MDAnalysisTests
- Getting Started
- MembraneCurvature’s API Documentation