Metadata-Version: 1.2
Name: taurenmd
Version: 0.8.2
Summary: A command-line interface for analysis routines in Molecular Dynamics data.
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://img.shields.io/pypi/v/taurenmd.svg
            :alt: PyPI Package latest release
            :target: https://pypi.org/project/taurenmd
        
        .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3551990.svg
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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
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            :target: https://codecov.io/gh/joaomcteixeira/taurenmd
            :alt: Codecov master branch
        
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           :target: https://codeclimate.com/github/joaomcteixeira/taurenmd/test_coverage
           :alt: Test Coverage
        
        .. image:: https://api.codeclimate.com/v1/badges/d69e2e9866338d88955c/maintainability
           :target: https://codeclimate.com/github/joaomcteixeira/taurenmd
           :alt: Code Climate
        
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            :target: https://codeclimate.com/github/joaomcteixeira/taurenmd
            :alt: Code Climate technical debt
        
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            :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/github/commits-since/joaomcteixeira/taurenmd/v0.8.2/master
            :alt: Commits since latest release
            :target: https://github.com/joaomcteixeira/taurenmd/compare/v0.8.2...master
        
        
        **A command-line interface for analysis routines of Molecular Dynamics data.**
        
        **Taurenmd** provides an easy, flexible and extensible, **command-line** 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 perform a thorough and proficient use those libraries. *But not only*, **taurenmd** also facilitates high throughput operations, even to those proficient *devs*, because complex executions are reduced to single argument-rich command-lines that can be concatenated or aliased.
        
        **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. When using this software, you **should** cite **taurenmd** together with the dependencies used, please read our **Citing** page on the documentation for a detailed explanation.
        
        Though designed to perform as a command-line user-directed interface, all **taurenmd**'s core functions are openly, distributed and documented. Currently, there are already several *commands* available, some that perform only single tasks, while others allow complex setups, all are *one-liners*. The complete list of command line clients implemented is detailed in our `documentation page <https://taurenmd.readthedocs.io/en/latest/reference/clients.html>`_.
        
        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.
        
        .. end-description
        
        Documentation
        =============
        
        **taurenmd** full documentation is available at: https://taurenmd.readthedocs.io, read there:
        
        #. how to install
        #. usage
        #. citing
        #. *etc...*
        
        
        Versioning
        ==========
        
        This project follows strictly `Semantic Versioning 2.0 <https://semver.org/#semantic-versioning-200>`_ for version control. 
        
        Upon release of version 1.0.0, all additions to the ``master`` branch are done by PR followed by its respective version increment and release on `PyPI <https://pypi.org/project/taurenmd/>`_.
        
        Upon version 0.8, and before version 1, SV2 major version increments are reflected in the *minor* version number, and minor and patch increments are reflected together in the *patch* version number. Everything else follows SV2 rules, in this way users can track backwards incompatibilities if they happen.
        
        Changelog
        =========
        
        0.8.2 (2020-01-17)
        ------------------
        
        * Improved CI workflow
          * Dropped COVERALLS
          * Dropped Codacy
          * Setup test-coverage in CodeClimate
          * created `.codeclimate.yml` with explicit configuration
        * updated badges
        
        0.8.1 (2020-01-15)
        ------------------
        
        * PR #14
        * Corrected version display in documentation
        
        0.8.0 (2020-01-15)
        ------------------
        
        * PR #13
        * Code architecture improvements
        * Complete project main documentation
        * Complete library documentation
        * command line documented
        * Code clean
        
        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.
        
Keywords: Molecular Dynamics,Proteins,DNA,RNA,Structural Biology,Molecular Biology,Biochemistry
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
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: 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: >=3.6, <3.8
