Metadata-Version: 2.1
Name: taurenmd
Version: 0.11.1
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
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
Requires-Dist: MDAnalysis (==2) ; extra == 'all'
Requires-Dist: mdtraj (<2,>=1.9) ; extra == 'all'
Requires-Dist: matplotlib (<4,>=3) ; extra == 'all'
Requires-Dist: numpy (<2,>=1) ; extra == 'all'
Provides-Extra: md
Requires-Dist: MDAnalysis (==2) ; extra == 'md'
Requires-Dist: mdtraj (<2,>=1.9) ; extra == 'md'
Provides-Extra: sup
Requires-Dist: matplotlib (<4,>=3) ; extra == 'sup'
Requires-Dist: numpy (<2,>=1) ; extra == 'sup'

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
=========

v0.11.1 (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.


