Metadata-Version: 2.1
Name: GromacsWrapper
Version: 0.8.3
Summary: A Python wrapper around the Gromacs tools.
Home-page: https://github.com/Becksteinlab/GromacsWrapper
Author: Oliver Beckstein
Author-email: orbeckst@gmail.com
License: GPLv3
Download-URL: https://github.com/Becksteinlab/GromacsWrapper/downloads
Description: .. -*- mode: rst, coding: utf-8 -*-
        .. The whole GromacsWrapper package is Copyright (c) 2009-2018 Oliver
        .. Beckstein and AUTHORS except where noted otherwise.
        
        
        ========================
         README: GromacsWrapper
        ========================
        
        |build| |cov| |docs| |zenodo| |PRsWelcome| |anaconda| |install-conda|
        
        A primitive Python wrapper around the Gromacs_ tools. The library is
        tested with GROMACS 4.6.5, 2018.x, 2019.x, 2020.x, and 2021.x (and 5.x
        and 2016.x should also work). It supports Python 2.7 and
        3.6--3.9 on Linux and macOS.
        
        GromacsWrapper also provides a small library (cook book) of often-used
        recipes and helper functions to set up MD simulations.
        
        `Documentation`_ is mostly provided through the python doc strings and
        available at https://gromacswrapper.readthedocs.org for recent releases.
        
        The source code is available in the `GromacsWrapper git repository`_.
        
        Please be aware that this is **beta** software that most definitely
        contains bugs. It is *your* responsibility to ensure that you are
        running simulations with sensible parameters.
        
        .. _Gromacs: http://www.gromacs.org
        .. _Documentation: 
           https://gromacswrapper.readthedocs.org/en/latest/
        .. _GromacsWrapper git repository:
           https://github.com/Becksteinlab/GromacsWrapper
        .. |build| image:: https://github.com/Becksteinlab/GromacsWrapper/actions/workflows/ci.yaml/badge.svg?branch=master
           :target: https://github.com/Becksteinlab/GromacsWrapper/actions/workflows/ci.yaml
           :alt: Build Status	     
        .. |cov| image:: https://codecov.io/gh/Becksteinlab/GromacsWrapper/badge.svg
           :target: https://codecov.io/gh/Becksteinlab/GromacsWrapper
           :alt: Code Coverage
           :scale: 100%
        .. |zenodo| image:: https://zenodo.org/badge/13219/Becksteinlab/GromacsWrapper.svg
           :target: https://zenodo.org/badge/latestdoi/13219/Becksteinlab/GromacsWrapper
           :alt: Latest release on zenodo (with DOI)
        .. |docs| image:: https://readthedocs.org/projects/gromacswrapper/badge/?version=latest
           :target: https://gromacswrapper.readthedocs.org/en/latest/?badge=latest
           :alt: Documentation
        .. |PRsWelcome| image:: https://img.shields.io/badge/PRs-welcome-brightgreen.svg
           :target: http://makeapullrequest.com
           :alt: PRs Welcome!
        .. |anaconda| image:: https://anaconda.org/bioconda/gromacswrapper/badges/version.svg
           :target: https://anaconda.org/bioconda/gromacswrapper
           :alt: Anaconda.org package
        .. |install-conda| image:: https://anaconda.org/bioconda/gromacswrapper/badges/installer/conda.svg
           :target: https://conda.anaconda.org/bioconda
           :alt: install with conda	    
        	 
        	 
        Quick Start
        ===========
        
        Given a PDB file ``1iee.pdb``, set up and run a simple simulation (assuming
        you have all other input files at hand such as the MDP files)::
        
          >>> import gromacs
          >>> print(gromacs.release)
          2018.2
          >>> help(gromacs.pdb2gmx)
          DESCRIPTION
        
          gmx pdb2gmx reads a .pdb (or .gro) file, reads some database files,
          adds hydrogens to the molecules and generates coordinates in GROMACS
          ...
          ...
          OPTIONS
        
          Options to specify input files:
        
          -f      [<.gro/.g96/...>]  (eiwit.pdb)
                    Structure file: gro g96 pdb brk ent esp tpr
          ...
          ...
          >>> gromacs.pdb2gmx(f="1iee.pdb", o="protein.gro", p="topol.top",
          ...                 ff="oplsaa", water="tip4p")
          >>> gromacs.editconf(f="protein.gro", o="boxed.gro",
          ...                  bt="dodecahedron", d=1.5, princ=True,
          ...                  input="Protein")
          >>> gromacs.solvate(cp="boxed.gro", cs="tip4p", p="topol.top",
          ...                 o="solvated.gro")
          >>> gromacs.grompp(f="emin.mdp", c="solvated.gro", p="topol.top",
          ...                o="emin.tpr")
          >>> gromacs.mdrun(v=True, deffnm="emin")
          >>> gromacs.grompp(f="md.mdp", c="emin.gro", p="topol.top", o="md.tpr")
          >>> gromacs.mdrun(v=True, deffnm="md")
        
        
        	 
        License
        =======
        
        The **GromacsWrapper** package is made available under the terms of
        the `GNU Public License v3`_ (or any higher version at your choice)
        except as noted below. See the file COPYING for the licensing terms
        for all modules.
        
        .. _GNU Public License v3: http://www.gnu.org/licenses/gpl.html
        
        
        Installation
        ============
        
        Releases
        --------
        
        The `latest version of GromacsWrapper from PyPi`_ can be installed
        with ::
        
          pip install GromacsWrapper
        
        
        or as a `bioconda package`_ with ``conda`` from the *bioconda* channel ::
        
           conda install -c conda-forge -c bioconda gromacswrapper
            
        
        .. _`latest version of GromacsWrapper from PyPi`:
           https://pypi.org/project/GromacsWrapper/
        
        .. _`bioconda package`:
           https://anaconda.org/bioconda/GromacsWrapper
           
        Development version
        -------------------
        
        The *master* branch in the GitHub source repository generally
        contains useful code but nevertheless, things can break in weird and
        wonderful ways. Please report issues through the `Issue Tracker`_ and
        mention that you used the *develop branch*.
        
        To use the *development code base*:  checkout the ``master`` branch::
        
           git clone https://github.com/Becksteinlab/GromacsWrapper.git
           cd GromacsWrapper
        
        and install ::
        
           python setup.py install
        
        
        
        
        Download and Availability
        =========================
        
        The GromacsWrapper home page is
        http://github.com/Becksteinlab/GromacsWrapper.  The latest release of the
        package is being made available from https://github.com/Becksteinlab/GromacsWrapper/releases
        
        You can also clone the `GromacsWrapper git repository`_ or fork for
        your own development::
        
          git clone git://github.com/Becksteinlab/GromacsWrapper.git
        
        Questions
        =========
        
        Please ask questions in the `Issue Tracker`_ (instead of private email).
        
        
        Reporting Bugs and Contributing to GromacsWrapper
        =================================================
        
        Please use the `Issue Tracker`_ to report bugs, installation problems,
        and feature requests.
        
        **Pull requests** for bug fixes and enhancements are very welcome. See http://makeapullrequest.com for a 
        general introduction on how make a pull request and contribute to open source projects.
        
        .. _Issue Tracker: http://github.com/Becksteinlab/GromacsWrapper/issues
        
        
        Building Documentation
        ======================
        
        Install Sphinx::
        
           pip install sphinx
        
        and compile::
        
          cd GromacsWrapper
          python setup.py build_sphinx
          
        
        Citing
        ======
        
        |zenodo|
        
        GromacsWrapper was written by Oliver Beckstein with contributions from
        many other people. Please see the file AUTHORS_ for all the names.
        
        If you find this package useful and use it in published work I'd be
        grateful if it was acknowledged in text as
        
          "... used GromacsWrapper (Oliver Beckstein et al,
          https://github.com/Becksteinlab/GromacsWrapper doi: 10.5281/zenodo.17901)"
        
        or in the Acknowledgements section.
        
        Thank you.
        
        .. _AUTHORS:
           https://raw.githubusercontent.com/Becksteinlab/GromacsWrapper/master/AUTHORS
        
        
Keywords: science Gromacs analysis 'molecular dynamics'
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows 
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Description-Content-Type: text/x-rst
