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Curvature\n==============================\n[![Powered by MDAnalysis](https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16\u0026logo=data:image/x-icon;base64,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)](https://www.mdanalysis.org)\n[![GitHub Actions Status](https://github.com/MDAnalysis/membrane-curvature/workflows/CI/badge.svg)](https://github.com/MDAnalysis/membrane-curvature/actions?query=workflow%3ACI)\n[![codecov](https://codecov.io/gh/MDAnalysis/membrane-curvature/branch/main/graph/badge.svg)](https://codecov.io/gh/MDAnalysis/membrane-curvature/branch/main)\n[![docs](https://readthedocs.org/projects/membrane-curvature/badge/?version=latest)](https://membrane-curvature.readthedocs.io/en/latest/)\n![PyPI](https://img.shields.io/pypi/v/membrane-curvature?color=lightgray)\n\n![](https://github.com/MDAnalysis/membrane-curvature/blob/main/docs/source/_static/PM_Membrane_EBO.png?raw=true)\n\nMembraneCurvature is an [MDAnalysis] tool to calculate membrane curvature from \nMolecular Dynamics simulations. \n\n\u003e **Interested in becoming a maintainer?** We welcome your passion and expertise to help shape and grow this open-source project! Please contact estefania@ojeda-e.com for more details.\n\nFeatures\n--------------\n\nWith MembraneCurvature you can:\n\n- Calculate mean and Gaussian curvature from MD simulations.\n- Derive 2D curvature profiles.\n- Live a happier life.\n\n\nInstallation\n--------------\n\nThe main dependency in MembraneCurvature is [MDAnalysis]. You can find\ninstructions to install the latest stable version of MDAnalysis via `conda` in the [UserGuide].\n\nMembraneCurvature is available via `pip`:\n\n```\npip install membrane-curvature\n```\n\nTo install from source:\n\n```\ngit clone https://github.com/MDAnalysis/membrane-curvature.git\ncd membrane-curvature\nconda env create -f devtools/conda-envs/environment.yaml\nconda activate membrane-curvature\npython setup.py install\n```\n\nSome of the examples included in the MembraneCurvature documentation use test\ncases from [MDAnalysisTests]. To install the unit tests via `conda`:\n\n```\nconda install -c conda-forge MDAnalysisTests\n```\n\nor via `pip`:\n\n```\npip install --upgrade MDAnalysisTests\n```\n\n\nUsage\n--------------\n\nThis is a quick example on how to run MembraneCurvature:\n\n```Python\nimport MDAnalysis as mda\nfrom membrane_curvature.base import MembraneCurvature\nfrom MDAnalysis.tests.datafiles import Martini_membrane_gro\n\nuniverse = mda.Universe(Martini_membrane_gro)\n\ncurvature_upper_leaflet = MembraneCurvature(universe,\n                                            select='resid 1-225 and name PO4',\n                                            n_x_bins=8,\n                                            n_y_bins=8,\n                                            wrap=True).run()\n\n# extract mean curvature\nmean_upper_leaflet = curvature_upper_leaflet.results.z_surface\n\n# extract mean curvature\nmean_upper_leaflet = curvature_upper_leaflet.results.mean\n\n# extract Gaussian\ngaussian_upper_leaflet = curvature_upper_leaflet.results.gaussian\n```\n\nIn this example, we use the PO4 beads in the upper leaflet as reference to\nderive a surface and calculate its respective mean and Gaussian curvature.\n\nYou can find more examples on how to run MembraneCurvature in the [Usage] page.\nTo plot results from MembraneCurvature please check the [Visualization] page.\n\nDocumentation\n---------------\n\nTo help you get the most out MembraneCurvature, we have [documentation] available \nwhere you can find:\n\n- The standard [API] documentation.\n- Quick examples of how to run Membrane Curvature in the [Usage] page.\n- Detailed explanation of the [Algorithm] implemented in MembraneCurvature.\n- Examples on how to plot the results obtained from MembraneCurvature in the [Visualization] page.\n\n\nLicense\n---------------\n\nSource code included in this project is available in the GitHub repository\nhttps://github.com/MDAnalysis/membrane-curvature under the GNU Public License\nv3 , version 3 (see [LICENSE]).\n\nMembraneCurvature was developed as a [Google Summer of Code 2021][GSoC] \nproject with [MDAnalysis] and it is linked to a [Code of Conduct][code_of_conduct].\n\n\n[GSoC]: https://summerofcode.withgoogle.com/\n[MDAnalysis]: https://www.mdanalysis.org\n[NumPy]: https://numpy.org\n[SciPy]: https://www.scipy.org\n[code_of_conduct]: https://www.mdanalysis.org/conduct/\n[Usage]: https://membrane-curvature.readthedocs.io/en/latest/source/pages/Usage.html\n[License]: https://github.com/MDAnalysis/membrane-curvature/blob/main/LICENSE\n[documentation]: https://membrane-curvature.readthedocs.io/en/latest/index.html#\n[Visualization]: https://membrane-curvature.readthedocs.io/en/latest/source/pages/Visualization.html\n[Algorithm]: https://membrane-curvature.readthedocs.io/en/latest/source/pages/Algorithm.html\n[API]: https://membrane-curvature.readthedocs.io/en/latest/api/membrane_curvature.html\n[MDAnalysisTests]: https://github.com/MDAnalysis/mdanalysis/wiki/UnitTests\n[UserGuide]: https://userguide.mdanalysis.org/2.0.0-dev0/installation.html\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmdanalysis%2Fmembrane-curvature","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmdanalysis%2Fmembrane-curvature","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmdanalysis%2Fmembrane-curvature/lists"}