Metadata-Version: 1.2
Name: taurenmd
Version: 0.7.2
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
        ========
        
        .. start-description
        
        .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3551990.svg
            :target: https://doi.org/10.5281/zenodo.3551990
            :alt: Zenodo
        
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            :target: https://taurenmd.readthedocs.io/en/latest/index.html
            :alt: Read the Docs (latest)
        
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            :target: https://travis-ci.org/joaomcteixeira/taurenmd
            :alt: Travis master branch
        
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            :target: https://codecov.io/gh/joaomcteixeira/taurenmd
            :alt: Codecov master branch
        
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            :alt: Codacy
        
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           :target: https://codeclimate.com/github/joaomcteixeira/taurenmd
           :alt: Code Climate
        
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            :alt: Code Climate technical debt
        
        .. image:: https://img.shields.io/pypi/v/taurenmd.svg
            :alt: PyPI Package latest release
            :target: https://pypi.org/project/taurenmd
        
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            :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/github/commits-since/joaomcteixeira/taurenmd/v0.7.2/master
            :alt: Commits since latest release
            :target: https://github.com/joaomcteixeira/taurenmd/compare/v0.7.2...master
        
        
        **A command-line interface for analysis routines in Molecular Dynamics.**
        
        **Taurenmd** provides an easy, flexible and extensible, interface for the most common (and not so common) routines of analysis and representation of Molecular Dynamics (MD) data.
        
        It bridges the gap between the highly complex (and powerful) Python libraries available for analysis of MD data and the *non-developer* users that lack the programming skills to use those libraries thoroughly. But not only, **taurenmd** also facilitates high throughput operations, even to those proficient *devs*, because complex executions are reduced to a single argument-rich command line.
        
        **Taurenmd** wraps around feature-rich and powerful MD analysis libraries such as `MDAnalysis <https://www.mdanalysis.org/>`_ and `MDTraj <http://mdtraj.org>`_ (but not only), combining them to extract the best of *those worlds*. We use these libraries to access and extract MD data and calculate observables, and we have also added our own routines of analysis when needed.
        
        With this said, **taurenmd** aims to be a flexible and extensible peace of software, built as simple and modular as we can think of, to *agile* the incorporation of new functionalities as needed.
        
        **taurenmd** aims to be a command-line user-directed interface, but its core functions are openly available and distributed in the library architecture. Currently, there are already several *commands* available, some that perform only single tasks, while others allow complex setups, all are *one-liners*.
        
        .. end-description
        
        Documentation
        =============
        
        **taurenmd** full documentation is available at: https://taurenmd.readthedocs.io, read there:
        
        #. how to install
        #. usage
        #. citing
        #. *etc...*
        
        
        Changelog
        =========
        
        0.7.2 (2019-12-25)
        ------------------
        
        * bridged from 0.7.1
        * Dropped Appveyor and EXPLICIT Windows support because of #1.
        * restructured project GitHub layout. Deprecated develop branch.
        * Readthedocs documentation improvements in structure and content.
        
        0.7.0 (2019-12-23)
        ------------------
        
        * implemented ``cli_rotations``, calculates roll, pitch and yaw
            rotation angles of selection.
        
        0.6.0 (2019-12-15)
        ------------------
        
        * implemented ``cli_rmsf`` to calculate RMSFs.
        
        0.5.1 (skipped to 0.6.0)
        ------------------------
        
        * added sort numbered trajs to ``cli_trajedit``
        * added sort numbered trajectory paths in lib
        * improved ``cli_imagemol`` readability
        * added selection in ``cli_noSol``
        
        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.*
