Metadata-Version: 2.1
Name: nmrformd
Version: 0.1.0
Summary: Calculate NMR relaxation time from                    molecular dynamics trajectory file
Home-page: https://github.com/simongravelle/nmrformd
Author: Simon Gravelle
Author-email: simon.gravelle@live.fr
License: GNU GENERAL PUBLIC LICENSE
Download-URL: https://github.com/simongravelle/nmrformd/archive/refs/tags/v0.0.9.tar.gz
Description: .. image:: https://readthedocs.org/projects/nmrformd/badge/?version=latest
        
        .. image:: https://raw.githubusercontent.com/simongravelle/nmrformd/main/docs/source/images/NMRforMD_READMEc.png
        
        .. inclusion-readme-intro-start
        
        NMRforMD is a python toolkit to calculate NMR relaxation times
        from molecular dynamics trajectory files. Used in combination
        with `MDAnalysis`_, it allows for the analysis of trajectory
        files from `LAMMPS`_ and `GROMACS`_ simulation package.
        
        ..
        	This documentation is separated in four parts: tutorials, how-to scripts,
        	description, and theory.
        
        .. _`MDAnalysis`: https://www.mdanalysis.org/
        .. _`LAMMPS`: https://www.lammps.org/
        .. _`GROMACS`: https://www.gromacs.org/
        .. _`Github`: https://github.com/simongravelle/nmrformd
        
        Notes :
            - NMRforMD is still in development, please raise an issue on `Github`_ if you encounter a problem
            - the code has mostly been tested with GROMACS and LAMMPS trajectory files, but should work with other molecular dynamics packages, as long as they are compatible with MDAnalysis
            - NMRforMD does not work with triclinic box, use MDAnalysis to convert your trajectory to orthorhombic
            
            
        .. image:: https://raw.githubusercontent.com/simongravelle/nmrformd/main/docs/source/images/main_image.png
        
        Example of systems that can be analysed using NMRforMD, from left to right: a 
        bulk water reservoir, a PEG molecule, and water in a slit silica pore. 
            
        .. inclusion-readme-intro-end
        
        For details and instructions for beginners,
        have a look at the `documentation`_.
        
        Installation
        ------------
        
        .. inclusion-readme-installation-start
        
        Using pip, type in a terminal:
        
        .. code-block:: bash
        
        	pip3 install nmrformd
        
        .. inclusion-readme-installation-end
        
        To get the last version, clone this repository on your computer
        and use pip3 from the main directory:
        
        .. code-block:: bash
        
        	git clone https://github.com/simongravelle/nmrformd.git
        	
        	cd nmrformd/
        
        	pip install .
        	
        You can run the tests using pytest:
        	
        .. code-block:: bash	
        	
        	cd tests
        	pytest .
        
        .. inclusion-basic-intro-start
        
        Basic example
        -------------
        
        This is an example showing how to use NMRforMD to measure NMR signal from 
        a molecular dynamics simulations. See the `tutorial`_ for more information.
        
        .. _`tutorial`: https://nmrformd.readthedocs.io/en/latest/documentation_pages/tutorial1.html
        
        .. code-block:: python3
        
        	import MDAnalysis as mda
        	import nmrformd
        	u = mda.Universe("topology.tpr", "trajectory.xtc")
        	nmr_result = nmrformd.NMR(u, "type H", "type H")
        
        The NMR relaxation time T1 is given by ``nmr_result.T1``.
        
        .. inclusion-basic-intro-end
        
        Known issues
        ------------
        
        - for very large trajectory file, the code requires a lot of memory
        - the code has only beed tested with hydrogen atoms
        
        .. _`documentation`: https://nmrformd.readthedocs.io/en/latest/
        
        
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