Metadata-Version: 2.1
Name: membrane-curvature
Version: 0.0.1
Summary: UNKNOWN
Home-page: UNKNOWN
Author: Estefania Barreto-Ojeda
Author-email: estefania.b.ojeda@gmail.com
License: GNU General Public License v3 (GPLv3)
Description: Membrane Curvature
        ==============================
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        <img src="docs/source/_static/PM_Membrane_EBO.png" alt="solution_posres"
        width="650"/>
        
        MembraneCurvature is an [MDAnalysis] tool to calculate membrane curvature from 
        Molecular Dynamics simulations. 
        
        Features
        --------------
        
        With MembraneCurvature you can:
        
        - Calculate mean and Gaussian curvature from MD simulations.
        - Derive 2D curvature profiles.
        - Live a happier life.
        
        
        Installation
        --------------
        
        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 MembraneCurvatre documentation use test
        cases from `MDAnalysisTests`. To install the unit tests:
        
        ```
        conda install MDAnalysisTests
        ```
        
        Usage
        --------------
        
        This is a quick example on how to run MembraneCurvature:
        
        ```
        import MDAnalysis as mda
        from membrane_curvature.base import MembraneCurvature
        from MDAnalysis.tests.datafiles import Martini_membrane_gro
        
        universe = mda.Universe(Martini_membrane_gro)
        
        curvature_upper_leaflet = MembraneCurvature(universe,
                                                    select='resid 1-225 and name PO4',
                                                    n_x_bins=8,
                                                    n_y_bins=8,
                                                    wrap=True).run()
        
        # extract mean curvature
        mean_upper_leaflet = curvature_upper_leaflet.results.z_surface
        
        # extract mean curvature
        mean_upper_leaflet = curvature_upper_leaflet.results.mean
        
        # extract Gaussian
        gaussian_upper_leaflet = curvature_upper_leaflet.results.gaussian
        ```
        
        In this example, we use the PO4 beads in the upper leaflet as reference to
        derive a surface and calculate its respective mean and Gaussian curvature.
        
        You can find more examples on how to run MembraneCurvature in the [Usage] page.
        
        Documentation
        ---------------
        
        To help you get the most out MembraneCurvature, we have [documentation] available 
        where you can find:
        
        - The standard [API] documentation.
        - Quick examples of how to run Membrane Curvature in the [Usage] page.
        - Detailed explanation of the [Algorithm] implemented in MembraneCurvature.
        - Examples on how to plot the results obtained from MembraneCurvature in the [Visualization] page.
        
        
        License
        ---------------
        
        Source code included in this project is available in the GitHub repository
        https://github.com/MDAnalysis/membrane-curvature under the GNU Public License
        v3 , version 3 (see [LICENSE]).
        
        MembraneCurvature was developed as a [Google Summer of Code 2021][GSoC] 
        project with [MDAnalysis] and it is linked to a [Code of Conduct][code_of_conduct].
        
        Copyright (c) 2021, Estefania Barreto-Ojeda
        
        
        [GSoC]: https://summerofcode.withgoogle.com/
        [MDAnalysis]: https://www.mdanalysis.org
        [NumPy]: https://numpy.org
        [SciPy]: https://www.scipy.org
        [code_of_conduct]: https://www.mdanalysis.org/pages/conduct/
        [Usage]: https://membrane-curvature.readthedocs.io/en/latest/source/pages/Usage.html
        [License]: https://github.com/MDAnalysis/membrane-curvature/blob/main/LICENSE
        [documentation]: https://membrane-curvature.readthedocs.io/en/latest/index.html#
        [Visualization]: https://membrane-curvature.readthedocs.io/en/latest/source/pages/Visualization.html
        [Algorithm]: https://membrane-curvature.readthedocs.io/en/latest/source/pages/Algorithm.html
        [API]: https://membrane-curvature.readthedocs.io/en/latest/api/membrane_curvature.html
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Description-Content-Type: text/markdown
