Metadata-Version: 1.1
Name: contact-map
Version: 0.3.3
Summary: Contact maps based on MDTraj
Home-page: http://github.com/dwhswenson/contact_map
Author: David W.H. Swenson
Author-email: dwhs@hyperblazer.net
License: LGPL-2.1+
Description: |Documentation Status| |Linux Build Status| |Windows Build status|
        |Coverage Status| |PyPI| |conda-forge|
        
        |Codacy Badge| |Maintainability|
        
        Contact Maps
        ============
        
        This package provides tools for analyzing and exploring contacts
        (residue-residue and atom-atom) from a trajectory generated by molecular
        dynamics. It builds on the excellent tools provided by
        `MDTraj <http://mdtraj.org>`__.
        
        Contacts can be an important tool for defining (meta)stable states in
        processes involving biomolecules. For example, an analysis of contacts
        can be particularly useful when defining bound states during a binding
        processes between proteins, DNA, and small molecules (such as potential
        drugs).
        
        The contacts analyzed by ``contact_map`` can be either intermolecular or
        intramolecular, and can be analyzed on a residue-residue basis or an
        atom-atom basis.
        
        This package makes it very easy to answer questions like:
        
        -  What contacts are present in a trajectory?
        -  Which contacts are most common in a trajectory?
        -  What is the difference between the frequency of contacts in one
           trajectory and another? (Or with a specific frame, such as a PDB
           entry.)
        -  For a particular residue-residue contact pair of interest, which
           atoms are most frequently in contact?
        
        It also facilitates visualization of the contact matrix, with colors
        representing the fraction of trajectory time that the contact was
        present.
        
        Full documentation is at http://contact-map.readthedocs.io/.
        
        Installation
        ------------
        
        The easiest way to install is with ``conda``. Conda is a powerful
        package and environment management system. If you do not already have a
        highly customized Python environment, we recommend starting by
        installing ``conda``, either in the `full anaconda
        distribution <https://www.anaconda.com/download/>`__ or the
        `smaller-footprint miniconda <https://conda.io/miniconda.html>`__. This
        package is distributed through the
        `conda-forge <http://conda-forge.org>`__ channel; install it with:
        
        .. code:: bash
        
            conda install -c conda-forge contact_map
        
        If you don't want to use ``conda``, you can also use ``pip`` (via a more
        complicated process) or do a developer install. See the `installation
        documentation <http://contact-map.readthedocs.io/en/latest/installing.html>`__
        for details.
        
        Support and development
        -----------------------
        
        ``contact_map`` is an open source project, released under the GNU LGPL,
        version 2.1 or (at your option) any later version. Development takes
        place in public at https://github.com/dwhswenson/contact\_map; your
        contributions would be welcome!
        
        If you have suggestions or bug reports, please `raise an issue on our
        GitHub issue page <https://github.com/dwhswenson/contact_map/issues>`__.
        
        .. |Documentation Status| image:: https://readthedocs.org/projects/contact-map/badge/?version=latest
           :target: http://contact-map.readthedocs.io/en/latest/?badge=latest
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           :target: https://travis-ci.org/dwhswenson/contact_map
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           :target: https://ci.appveyor.com/project/dwhswenson/contact-map/branch/master
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           :target: https://coveralls.io/github/dwhswenson/contact_map?branch=master
        .. |PyPI| image:: https://img.shields.io/pypi/v/contact-map.svg
           :target: https://pypi.python.org/pypi/contact-map/
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           :target: https://github.com/conda-forge/contact_map-feedstock
        .. |Codacy Badge| image:: https://api.codacy.com/project/badge/Grade/f7f3cf53698e4655ac8895f13fa5dea6
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        .. |Maintainability| image:: https://api.codeclimate.com/v1/badges/84768756d594176d8da6/maintainability
           :target: https://codeclimate.com/github/dwhswenson/contact_map/maintainability
        
Platform: Linux
Platform: Mac OS X
Platform: Unix
Platform: Windows
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v2 or later (GPLv2+)
Classifier: Operating System :: POSIX
Classifier: Operating System :: Microsoft :: Windows
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Requires: future
Requires: numpy
Requires: mdtraj
Requires: scipy
Requires: pandas
