Metadata-Version: 2.1
Name: nmrformd
Version: 0.0.8
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/v0.0.8.tar.gz
Description: .. image:: https://raw.githubusercontent.com/simongravelle/nmrformd/main/docs/source/images/NMRforMD_READMEc.png
        
        .. inclusion-readme-intro-start
        
        NMRforMD is a python script 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, GROMACS, or AMBER simulation package.
        
        Information
        -----------
        
        NMRforMD is in development and likely to return errors. Please raise an issue here if you find one.
        
        .. _`MDAnalysis`: https://www.mdanalysis.org/
        .. inclusion-readme-intro-end
        
        For details and a tutorial, have a look at the `documentation`_.
        	
        Installation
        ------------
        
        .. inclusion-readme-installation-start
        
        Using pip, type in a terminal:
        
        .. code-block:: bash
        
        	pip install nmrformd
        
        Or, clone this repository on your computer and use pip from the main directory:
        
        .. code-block:: bash
        
        	git clone git@github.com:simongravelle/nmrformd.git
        	
        	cd nmrformd/
        
        	pip install .
        	
        You can run the test using pytest:
        	
        .. code-block:: bash	
        	
        	cd tests
        	pytest mytest.py
        
        .. inclusion-readme-installation-end
        .. 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", "full", 0, "m0")
        
        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
        - currently only residues have been tested
        - the code has mostly been tested with GROMACS trajectory file
        
        .. _`documentation`: https://nmrformd.readthedocs.io/en/latest/
        
        
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