mdciao 0.0.1b3

mdciao: Analysis of Molecular Dynamics Simulations Using Residue Neighborhoods

mdciao: Analysis of Molecular Dynamics Simulations Using Residue Neighborhoods
==============================================================================

|Python Package| |Coverage| |License|

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``mdciao`` is a Python module that provides quick, "one-shot" command-line tools to analyze molecular simulation data using residue-residue distances. ``mdciao`` tries to automate as much as possible for non-experienced users while remaining highly customizable for advanced users, by exposing an API to construct your own analysis workflow.

Under the hood, the module `mdtraj <https://mdtraj.org/>`_ is doing most of the computation and handling of molecular information, using `BioPython <https://biopython.org/>`_ for sequence alignment, `pandas <pandas.pydata.org/>`_ for many table and IO related operations, and `matplotlib <https://matplotlib.org.org>`_ for visualizaton. It tries to automatically use the

* `Ballesteros-Weinstein-Numbering (BW) <https://www.sciencedirect.com/science/article/pii/S1043947105800497>`_
* `Common G-alpha Numbering (CGN) <https://www.mrc-lmb.cam.ac.uk/CGN/faq.html>`_

consensus-nomenclature schemes by either using local files or on-the-fly lookups of the `GPCRdb <https://gpcrdb.org/>`_
and/or `<https://www.mrc-lmb.cam.ac.uk/CGN/>`_

Licenses
========
* ``mdciao`` is licensed under the `GNU Lesser General Public License v3.0 or later <https://www.gnu.org/licenses/lgpl-3.0-standalone.html>`_ (``LGPL-3.0-or-later``, see the LICENSE.txt).

* ``mdciao`` uses a modified version of the method `mdtraj.compute_contacts <https://github.com/mdtraj/mdtraj/blob/70a94ff87a6c4223ca1be78c752ef3ef452d3d44/mdtraj/geometry/contact.py#L42>`_ of `mdtraj <https://mdtraj.org/>`_. This modified version is published along with ``mdciao`` and can be found in `contacts/_md_compute_contacts.py <mdciao/contacts/_md_compute_contacts.py>`_. Please see that file for details on the modifications.

* Modules used by ``mdciao`` have different licenses. You can check any module's license in your Python environment using `pip-licenses <https://github.com/raimon49/pip-licenses>`_:

>>> pip-licenses | grep module_name

Status
======
``mdciao`` is in its initial development, with versions 0.Y.Z. Anything MAY change at any time.
`The public API SHOULD NOT be considered stable <https://semver.org/#spec-item-4>`_.

Documentation
=============
Currently, docs are hosted at `<http://proteinformatics.org/mdciao/>`_, but this can change in the future.

TODOs
=====
This is an informal list of known issues and TODOs:
* overhaul the "printing" system with proper warnings (perhaps use `loguru <https://github.com/Delgan/loguru>`_
* progressbar not very informative for one chunked trajectory or parallel runs
* the "consensus" fragmentation sometimes breaks automatic flareplot labelling #should no longer be the case after https://github.com/gph82/mdciao/pull/21 (check)
* Building the docs with sphinx v>2.4.4 doesn't autogen a class' method's linked doc
* improve sequence alignment choices
* the affiliation of a residue to a fragment is done as "res@frag" on the string output and res^frag in figures, this implementation is simply using replace("@","^"), could be better
* heuristics for proper font-sizing of flareplots could be optimized
* parallel execution with memory mdtraj.Trajectory objects should be better
* harmonize documentation API cli methods (mdciao.cli) and the CLI scripts (mdc_*)
* The interface between API methods and cli scripts could be better, using sth like `click <https://click.palletsprojects.com/en/7.x/>`_
* The API-cli methods (interface, neighborhoods, sites, etc) have very similar flows but a lot of code repetition, I am sure `some patterns/boilerplate could be outsourced/refactored even more <https://en.wikipedia.org/wiki/Technical_debt>`_.
* color handling of the flare-plots is buggy because it tries to guess too many things. Undecided about best decision.
* Most of the tests were written against a very rigid API that mimicked the CLI closely. Now the API is more flexible
and many `tests could be re-written or deleted <https://en.wikipedia.org/wiki/Technical_debt>`_ , like those needing
mock-input or writing to tempdirs because writing figures or files could not be avoided.
* There's some inconsistencies in private vs public attributes of classes. An attribute might've "started" as private and is exceptionally used somewhere else until the number of exceptions is enough for it to make sense to be public, documented and well tested. I'm working on it.
* neighborlists could be computed much more efficiently
* There's many other TODOs spread throughout the code
* Use `violing plots <https://matplotlib.org/stable/api/_as_gen/matplotlib.axes.Axes.violinplot.html>`_ instead of bars to inform about spread


System Requirements
===================
At the moment, ``mdciao`` is CI-tested only for GNU/Linux and Python versions
3.6, 3.7, 3.8, 3.9. MacOS CI-tests are failing currently because of a segmentation error (139 and 11) when `calling mdtraj.dsssp <https://github.com/gph82/mdciao/runs/2415051993?check_suite_focus=true>`_.

Authors
=======
``mdciao`` is written and maintained by Guillermo Pérez-Hernández (`ORCID <http://orcid.org/0000-0002-9287-8704>`_) currently at the `Institute of Medical Physics and Biophysics <https://biophysik.charite.de/ueber_das_institut/team/>`_ in the
`Charité Universitäsmedizin Berlin <https://www.charite.de/>`_.

Please cite "mdciao, G. Pérez-Hernández and P.W. Hildebrand, 2021 (in preparation)"


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