Metadata-Version: 2.0
Name: dockerasmus
Version: 0.1.1
Summary: An easy to use docking library.
Home-page: https://gitlab.com/althonos/dockerasmus
Author: Martin Larralde
Author-email: martin.larralde@ens-cachan.fr
License: GPLv3
Keywords: bioinformatics,docking,protein,PDB,structural,biology
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Operating System :: OS Independent
Requires-Dist: numpy
Requires-Dist: six
Provides-Extra: docs
Requires-Dist: numpy; extra == 'docs'
Requires-Dist: six; extra == 'docs'
Requires-Dist: sphinx; extra == 'docs'
Requires-Dist: sphinxjp.themes.basicstrap; extra == 'docs'

dockerasmus
=======================================
*docking itself through university*

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Introduction
------------

``dockerasmus`` is a version-agnostic Python module that was created
to quickly solve docking problems, as part of a Python assignment from
the M1 BIBS of the Université Paris-Saclay.

``dockerasmus`` provides a generic implementation of a scoring function,
which can be used with several *components* to compute the score of
a docking conformation involving two proteins. It is backend agnostic, and
every scoring component can be rewritten with any library supporting
``numpy`` arrays.



Example
-------

Use ``dockerasmus`` to compute the score of the barnase-barstar complex
using the scoring function defined by `Cornell et al
<http://dx.doi.org/10.1021/ja00124a002>`_:

.. code:: python

    from dockerasmus.pdb import Protein
    from dockerasmus.score import ScoringFunction, components

    # Import the pdb files (supports gzipped files or plain .pdb)
    barnase = Protein.from_pdb_file("tests/data/barnase.native.pdb.gz")
    barstar = Protein.from_pdb_file("tests/data/barstar.native.pdb.gz")

    # Create a scoring function with two components
    scoring_function = ScoringFunction(components.LennardJones,
                                       components.Coulomb)

    # Call the scoring function on the barnase (receptor)
    # and the barstar (ligand)
    scoring_function(barnase, barstar)  # -84.94...


API
---

``dockerasmus`` provides several submodules:

* a parser & object model for the Protein Data Bank (``dockerasmus.pdb``)
* a scoring library (``dockerasmus.score``)
* a soft 3D engine for spatial transformations (``dockerasmus.spatial``)

See the `API reference <http://dockerasmus.readthedocs.io/en/latest/api/>`_
from the online documentation to get more details.


License
-------

``dockerasmus`` is fully open-source and is released under the GPLv3.


