Metadata-Version: 1.2
Name: taurenmd
Version: 0.5.0
Summary: Command-line and library interface for analysis routines in Molecular Dynamics
Home-page: https://github.com/joaomcteixeira/taurenmd
Author: Joao MC Teixeira
Author-email: joaomcteixeira@gmail.com
License: GNU GPLv2
Project-URL: Documentation, https://taurenmd.readthedocs.io/
Project-URL: Changelog, https://taurenmd.readthedocs.io/en/latest/changelog.html
Project-URL: Issue Tracker, https://github.com/joaomcteixeira/taurenmd/issues
Description: taurenmd
        ========
        
        **Command-line and library interface for analysis routines in Molecular Dynamics.**
        *This is an experimental project.*
        
        .. start-badges
        
        Stable version
        --------------
        
        .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3551990.svg
            :target: https://doi.org/10.5281/zenodo.3551990
            :alt: Zenodo
        
        .. image:: https://img.shields.io/travis/joaomcteixeira/taurenmd/master?label=TravisCI
            :target: https://travis-ci.org/joaomcteixeira/taurenmd
            :alt: Travis master branch
        
        .. image:: https://ci.appveyor.com/api/projects/status/v9r2032bry817tjh/branch/master?svg=true 
            :target: https://ci.appveyor.com/project/joaomcteixeira/taurenmd
            :alt: Appveyor master branch
        
        .. image:: https://codecov.io/gh/joaomcteixeira/taurenmd/branch/master/graph/badge.svg
            :target: https://codecov.io/gh/joaomcteixeira/taurenmd
            :alt: Codecov master branch
        
        .. image:: https://img.shields.io/coveralls/github/joaomcteixeira/taurenmd/master?label=COVERALLS&logo=COVERALLS
            :target: https://coveralls.io/github/joaomcteixeira/taurenmd
            :alt: Coveralls master
        
        .. image:: https://img.shields.io/codacy/grade/147029f2635e4e62bf670efdef728c28/master?label=Codacy
            :target: https://app.codacy.com/manual/joaomcteixeira/taurenmd/dashboard
            :alt: Codacy master branch
        
        .. image:: https://img.shields.io/readthedocs/taurenmd/stable?label=Read%20the%20Docs
            :target: https://taurenmd.readthedocs.io/en/stable/index.html
            :alt: Read the Docs (stable)
        
        .. image:: https://img.shields.io/pypi/v/taurenmd.svg
            :alt: PyPI Package latest release
            :target: https://pypi.org/project/taurenmd
        
        .. image:: https://img.shields.io/pypi/wheel/taurenmd.svg
            :alt: PyPI Wheel
            :target: https://pypi.org/project/taurenmd
        
        .. image:: https://img.shields.io/pypi/pyversions/taurenmd.svg
            :alt: Supported versions
            :target: https://pypi.org/project/taurenmd
        
        .. image:: https://img.shields.io/pypi/implementation/taurenmd.svg
            :alt: Supported implementations
            :target: https://pypi.org/project/taurenmd
        
        The stable version is hosted at the `master branch`_.
        
        Notes
        ~~~~~
        
        - AppVeyor builds only for py36; see `#1`_
        - Travis is not yet configured for OSX; see `#2`_ 
        
        Development Branch
        ------------------
        
        *where new features are tested and code maybe broken :)*
        
        .. image:: https://img.shields.io/travis/joaomcteixeira/taurenmd/develop?label=TravisCI
            :target: https://travis-ci.org/joaomcteixeira/taurenmd
            :alt: Travis-CI latest branch
        
        .. image:: https://ci.appveyor.com/api/projects/status/v9r2032bry817tjh?svg=true
            :target: https://ci.appveyor.com/project/joaomcteixeira/taurenmd
            :alt: Appveyor-CI latest branch
        
        .. image:: https://codecov.io/gh/joaomcteixeira/taurenmd/branch/develop/graph/badge.svg
            :target: https://codecov.io/gh/joaomcteixeira/taurenmd
            :alt: Codecov latest branch
        
        .. image:: https://img.shields.io/coveralls/github/joaomcteixeira/taurenmd/develop?label=COVERALLS&logo=COVERALLS
            :target: https://coveralls.io/github/joaomcteixeira/taurenmd
            :alt: Coveralls latest
        
        .. image:: https://img.shields.io/codacy/grade/147029f2635e4e62bf670efdef728c28/develop?label=Codacy
            :target: https://app.codacy.com/manual/joaomcteixeira/taurenmd/dashboard
            :alt: Codacy latest grade
        
        .. image:: https://api.codeclimate.com/v1/badges/d69e2e9866338d88955c/maintainability
           :target: https://codeclimate.com/github/joaomcteixeira/taurenmd
           :alt: Code Climate
        
        .. image:: https://img.shields.io/codeclimate/tech-debt/joaomcteixeira/taurenmd?label=Code%20Climate%20tech%20debt
            :target: https://codeclimate.com/github/joaomcteixeira/taurenmd
            :alt: Code Climate technical debt
        
        .. image:: https://img.shields.io/readthedocs/taurenmd/latest?label=Read%20the%20Docs
            :target: https://taurenmd.readthedocs.io/en/latest/index.html
            :alt: Read the Docs (latest)
        
        .. image:: https://img.shields.io/github/commits-since/joaomcteixeira/taurenmd/v0.5.0/develop
            :alt: Commits since latest release
            :target: https://github.com/joaomcteixeira/taurenmd/compare/v0.5.0...develop
        
        The latest development is hosted at the `develop branch`_.
        
        Motivation
        ==========
        
        Provide an easy interface for the most common (and not so common) routines of analysis and data representation for Molecular Dynamics.
        
        Documentation
        =============
        
        Read the documentation: https://taurenmd.readthedocs.io
        
        Dependencies
        ============
        
        :code:`taurenmd` wraps around high performance Molecular Dynamics analysis libraries, such as: `MDAnalysis`_, `MDTraj`_, `OpenMM`_ (and implementing others...); and it contains its own routines for data representation and export, such as curated plotting templates through `matplotlib`_ and `bioplottemplates`_.
        
        
        Citing
        ======
        
        When using and citing :code:`taurenmd`, you **SHOULD** by all means cite the Molecular Dynamics (MD) analysis libraries upon which :code:`taurenmd` wraps. Please read through each project's documentation to understand how to cite them; these projects are linked in the `Dependencies` header.
        
        Acknowledges
        ============
        
        The concept of this project is largely inspired in the `pdb-tools`_ *one script one action* idea.
        Thanks to `JoaoRodrigues`_ for all the mentoring on MD! CI in this repository provided by `cookiecutter-pylibrary`_ with final setup by me.
        
        .. _pdb-tools: https://github.com/haddocking/pdb-tools
        .. _JoaoRodrigues: https://github.com/JoaoRodrigues
        .. _MDTraj: https://github.com/mdtraj/mdtraj
        .. _MDAnalysis: https://www.mdanalysis.org/
        .. _OpenMM: https://github.com/openmm/openmm
        .. _matplotlib: https://matplotlib.org/
        .. _bioplottemplates: https://github.com/joaomcteixeira/python-bioplottemplates
        .. _cookiecutter-pylibrary: https://github.com/ionelmc/cookiecutter-pylibrary
        .. _master branch: https://github.com/joaomcteixeira/taurenmd/tree/master
        .. _develop branch: https://github.com/joaomcteixeira/taurenmd/tree/develop
        .. _#1: https://github.com/joaomcteixeira/taurenmd/issues/1
        .. _#2: https://github.com/joaomcteixeira/taurenmd/issues/2
        
        Changelog
        =========
        
        0.5.0 (2019-11-24)
        ------------------
        
        * created ``cli_angle``. Calculates angles between a plane along the trajectory. Plane is given by the three centre_of_geometries of three selections.
        * args to plot passed as list are transformed to tuple
        * added distance calc and plot interface ``cli_distances``
        * ``trajedit`` now saves topology unwrapped
        
        0.4.1 (2019-11-21)
        ------------------
        
        * renumbered version to 0.4.1. from 0.3.1
        * RMSD Cli now calculates for several selections
        * Parse plot vars now registers floats
        * corrected fext cli entry point
        * added align option to trajedit
        * topology model writen from first frame of time slicing
        * added unwrap() molecule method from MDAnalysis in ``trajedit`` with respective options
        * topology output now defaults to traj name + ``frame0.pdb``
        * added .myparents() to Path in ``__init__``
        
        0.3.0 (2019-11-06)
        ------------------
        
        * Created *develop* branch
        * Created client for frame extraction: ``cli_fext``
        * Added option to disable export of frame0 topology in trajedit
        
        0.2.1 (2019-10-26)
        ------------------
        
        * dropped py35
        * separated lib MDAnalysis from MDTraj
        * ``libio`` concerns only general functions
        * improved ``imagemol`` I/O
        
        0.2.0 (2019-10-26)
        ------------------
        
        * added ``cli_report``
        
        0.1.1 (2019-10-26)
        ------------------
        
        * corrected libio
        * trajectory loads based on MDAnalysis now read and concatenate multiple trajectories.
        
        0.1.0 (2019-10-26)
        ------------------
        
        * added interfaces:
          * ``trajedit``
          * ``noSol``
          * ``imagemol``
          * ``rmsd``
          * ``cli template``
        
        0.0.0 (2019-10-15)
        ------------------
        
        * First release on PyPI.
        
Platform: UNKNOWN
Classifier: Development Status :: 1 - Planning
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: License :: OSI Approved :: GNU General Public License v2 (GPLv2)
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX
Classifier: Operating System :: Microsoft :: Windows
Classifier: Environment :: Console
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Utilities
Requires-Python: >=3, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*
