Metadata-Version: 2.1
Name: taurenmd
Version: 0.11.2
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
        ========
        
        .. image:: https://raw.githubusercontent.com/joaomcteixeira/taurenmd/master/docs/img/taurenmd_logo_black_readme.png
        
        .. start-description
        
        .. image:: https://img.shields.io/pypi/v/taurenmd.svg
            :alt: PyPI Package latest release
            :target: https://pypi.org/project/taurenmd
        
        .. image:: https://joss.theoj.org/papers/10.21105/joss.02175/status.svg
            :target: https://doi.org/10.21105/joss.02175
            :alt: joss
        
        .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.3551990.svg
            :target: https://doi.org/10.5281/zenodo.3551990
            :alt: Zenodo
        
        .. image:: https://github.com/joaomcteixeira/taurenmd/workflows/tests/badge.svg?branch=master
            :target: https://github.com/joaomcteixeira/taurenmd/actions?workflow=tests
            :alt: Test Status
        
        .. 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://codecov.io/gh/joaomcteixeira/taurenmd/branch/master/graph/badge.svg
            :target: https://codecov.io/gh/joaomcteixeira/taurenmd
            :alt: Codecov master branch
        
        .. 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/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/dm/taurenmd?label=PyPI%20Downloads
            :alt: PyPI - Downloads
            :target: https://pypistats.org/packages/taurenmd
        
        **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 <https://taurenmd.readthedocs.io/en/latest/citing.html>`_ page 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 command-line interfaces available <https://taurenmd.readthedocs.io/en/latest/reference/clients.html>`_, some that perform only single tasks, while others allow complex setups, all are *one-liners*.
        
        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**'s full documentation is available at: https://taurenmd.readthedocs.io, read there:
        
        #. how to install
        #. usage examples
        #. 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
        =========
        
        v0.11.2 (2022-07-14)
        ------------------------------------------------------------
        
        * Add output dir option to `fext` #66
        
        v0.11.1 (2022-07-14)
        ------------------------------------------------------------
        
        * Update badges after 0.11 #65
        
        v0.11.0 (2022-07-13)
        ------------------------------------------------------------
        
        * Dropped `python-bioplottemplates`
        * updated export statements
        * Added plots to `taurenmd rotations`
        * Added plots to `taurenmd dist`
        * Added plots to `taurenmd rmsf`
        * Added plots to `taurenmd rmsd`
        * `taurenmd dist` now can take multiple `--sel2`, and all are plotted
        * `ParamsToDict` now uses `ast.literal_eval`
        * trajectory slice now accepts timesteps (10ns, for example)
        
        v0.10.4 (2022-01-14)
        ------------------------------------------------------------
        
        * update logo link in README #63
        
        v0.10.3 (2021-12-11)
        ------------------------------------------------------------
        
        * Improved documentation for `cli_rotations`
        * Added illustration explaining the roll, pitch, and yaw angles
        
        v0.10.2 (2021-12-03)
        ------------------------------------------------------------
        
        * Add frame timestep and whole trajectory duration to `report` (#61)
        
        v0.10.1 (2021-11-24)
        ------------------------------------------------------------
        
        * Add support for CIF topologies in libmda using openmm.app.pdbxfile
        * removes the install*.yml gitactions
        
        v0.10.0 (2021-11-24)
        ------------------------------------------------------------
        
        * Updates MDAnalysis to version 2.0.0
        * Defines versions for all other dependencies
        * Updates CI
        
        v0.9.9 (2021-11-22)
        ------------------------------------------------------------
        
        * Corrects taking/passing of `insort` argument in some clients.
        
        v0.9.8 (2021-11-22)
        ------------------------------------------------------------
        
        * Upgraded roll, pitch, and yaw angle calculations with torsion angle strategy
        * Removed usage of PyQuaternion
        
        v0.9.7 (2021-11-20)
        ------------------------------------------------------------
        
        * improved trajectory report (#54)
        
        v0.9.6 (2021-02-22)
        ------------------------------------------------------------
        
        * Remove README badge for build: not needed.
        * Added some comments in the workflow files.
        * no changes in code, only CI.
        
        v0.9.5 (2021-02-17)
        ------------------------------------------------------------
        
        * Upgraded CI to Github Actions according to: https://github.com/joaomcteixeira/python-project-skeleton
        * Updated README badges
        
        0.9.4 (2020-06-02)
        ------------------
        
        * Updates documentation with JOSS citation (PR #49)
        
        0.9.3 (2020-05-25)
        ------------------
        
        * Improves CONTRIBUTION.rst guidelines (PR #46)
        
        0.9.2 (2020-05-17)
        ------------------
        
        * Client progression is now represented by a progress bar (PR #44)
        
        0.9.1 (2020-05-15)
        ------------------
        
        * Improves log in `.taurenmd.cmd` (PR #43)
        
        0.9.0 (2020-05-15)
        ------------------
        
        * Adds `-i` to every `CLI` interface (PR #42)
        * `major` version change because `cli_imagemol` lost backwards compatibility
        
        0.8.14 (2020-05-12)
        -------------------
        
        * Updates `tox.ini` file for Continuous Integration (PR #40)
        
        0.8.13 (2020-05-12)
        -------------------
        
        * Added support for sequence of trajectories in CLIs that use `MDTraj` (PR #39)
        
        0.8.12 (2020-05-04)
        -------------------
        
        * PR: #37
        * Installs taurenmd directly with Conda env
        
        0.8.11 (2020-04-03)
        -------------------
        
        * PR: #33
        * Corrected command representation in .taurenmd.cwd adding quotes when needed
        
        0.8.10 (2020-04-02)
        -------------------
        
        * PR: #32
        * Corrects incorrect usage of MDAnalysis.analysis.alignto function in ``trajedit``.
        
        0.8.9 (2020-03-03)
        ------------------
        
        * Changed logos, PR #28
        
        0.8.8 (2020-02-03)
        ------------------
        
        * PRs: #25 #26 #27
        * Added taurenmd logo for readthedocs
        * Added tauranmd logo in README
        * Added taurenmd repository banner
        * Improved details in the documentation
        * Removed ``.ci`` folder, unnecessary
        
        0.8.7 (2020-02-02)
        ------------------
        
        * PR #24
        * Added PyPI downloads badge
        * Improved installation instructions
        * Improved and clarified contributing instructions
        
        0.8.6 (2020-01-20)
        ------------------
        
        * Restructured pip deps: install_requires only takes bioplottemplates and pyquaternion
        * two extras_require: `sup` and `md` and `all` which consider both
        
        0.8.5 (2020-01-20)
        ------------------
        
        * PR #22
        * organized dependencies for PyPI
        * PyPI only dependencies are referred as install_requires
        * MDAnalysis and MDTraj referred in extras_require
        * OpenMM left out from pip, only available in Anaconda
        
        0.8.4 (2020-01-19)
        ------------------
        
        * PR #15
        * Added simtk lib import check for controlled failure 
        * added error message output for user
        
        0.8.3 (2020-01-19)
        ------------------
        
        * PR #16 and #19
        * corrected argparse autodoc in ReadTheDocs (mock strategy)
        * improved tox configuration with better env separation
        * #19 reports a communication error between TravisCI and coverage servers
        
        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 :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Topic :: Utilities
Requires-Python: >=3.8, <3.11
Provides-Extra: all
Provides-Extra: md
Provides-Extra: sup
