Metadata-Version: 2.1
Name: bcforms
Version: 0.0.9
Summary: Toolkit for concretely describing macromolecular complexes
Home-page: https://github.com/KarrLab/bcforms
Author: Karr Lab
Author-email: info@karrlab.org
License: MIT
Download-URL: https://github.com/KarrLab/bcforms
Description: |Documentation| |Test results| |Test coverage| |Code analysis| |License|
        |Analytics|
        
        ``BcForms``: toolkit for concretely describing macromolecular complexes
        =======================================================================
        
        ``BcForms`` is a toolkit for concretely describing the molecular
        structure (atoms and bonds) of macromolecular complexes, including
        non-canonical monomeric forms, circular topologies, and crosslinks.
        
        ``BcForms`` encompasses five tools: \* A grammar for concretely
        describing subunit composition and interchain crosslinks of
        biocomplexes. See the
        `documentation <https://docs.karrlab.org/bcforms/>`__ for more
        information. For example, the following text represents a homodimer
        complex with a disulfide bond between the first monomer in the first
        subunit and the first monomer in the second subunit.
        ``complex: 2 * sub_c | x-link: [         l-bond-atom: sub_c(1)-1S11 |         l-displaced-atom: sub_c(1)-1H11 |         r-bond-atom: sub_c(2)-1S11 |         r-displaced-atom: sub_c(2)-1H11       ]``
        
        ::
        
            This concrete representation enables the `BcForms` software tools to calculate properties of biocomplexes when the subunits are concretely defined.
        
        -  Tools for calculating properties of biocomplexes including their
           structure, chemical formulae, molecular weights, and charges.
        -  A web app: https://bcforms.org
        -  A JSON REST API: https://bcforms.org/api
        -  A command line interface. See the
           `documentation <https://docs.karrlab.org/bcforms/master/0.0.1/>`__
           for more information.
        -  A Python API. See the
           `documentation <https://docs.karrlab.org/bcforms/master/0.0.1/>`__
           for more information.
        
        Installation
        ------------
        
        The following is a brief guide to installing ``BcForms``. The
        `Dockerfile <https://github.com/KarrLab/bpforms/blob/master/Dockerfile>`__
        in the ``BpForms`` repository contains detailed instructions for how to
        install ``BcForms`` in Ubuntu Linux.
        
        1. Install dependencies
        
        -  `ChemAxon Marvin <https://chemaxon.com/products/marvin>`__: optional
           to calculate major protonation and tautomerization states and draw
           molecules
        
           -  `Java <https://www.java.com>`__ >= 1.8
        
        -  `Open Babel <http://openbabel.org>`__
        -  `Pip <https://pip.pypa.io>`__ >= 19.0
        -  `Python <https://www.python.org>`__ >= 3.6
        
        2. Install this package
        
           -  Install the latest release from PyPI ``pip install bcforms[all]``
        
           -  Install the latest revision from GitHub
              ``pip install git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils   pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils[chem, protonation]   pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms   pip install git+https://github.com/KarrLab/bcforms.git#egg=bcforms[all]``
        
           -  To draw molecules, ``BcForms`` must be installed with the
              ``[draw]`` option:
              ``pip install bcforms[draw]   pip install git+https://github.com/KarrLab/bcforms.git#egg=bcforms[draw]``
        
           -  To install the REST API, ``BcForms`` must be installed with the
              ``[rest_api option]``:
              ``pip install bcforms[rest_api]   pip install git+https://github.com/KarrLab/bcforms.git#egg=bcforms[rest_api]``
        
        Documentation
        -------------
        
        Please see the `API documentation <https://docs.karrlab.org/bcforms>`__.
        
        License
        -------
        
        The package is released under the `MIT license <LICENSE>`__.
        
        Development team
        ----------------
        
        This package was developed by the `Karr Lab <https://www.karrlab.org>`__
        at the Icahn School of Medicine at Mount Sinai in New York, USA.
        
        -  `Jonathan Karr <https://www.karrlab.org>`__
        -  `Xiaoyue Zheng <https://www.linkedin.com/in/xiaoyue-zheng/>`__
        
        Questions and comments
        ----------------------
        
        Please contact the `Karr Lab <mailto:info@karrlab.org>`__ with any
        questions or comments.
        
        .. |Documentation| image:: https://readthedocs.org/projects/bcforms/badge/?version=latest
           :target: https://docs.karrlab.org/bcforms
        .. |Test results| image:: https://circleci.com/gh/KarrLab/bcforms.svg?style=shield
           :target: https://circleci.com/gh/KarrLab/bcforms
        .. |Test coverage| image:: https://coveralls.io/repos/github/KarrLab/bcforms/badge.svg
           :target: https://coveralls.io/github/KarrLab/bcforms
        .. |Code analysis| image:: https://api.codeclimate.com/v1/badges/c8f15ac1e50c27ca44cc/maintainability
           :target: https://codeclimate.com/github/KarrLab/bcforms
        .. |License| image:: https://img.shields.io/github/license/KarrLab/bcforms.svg
           :target: LICENSE
        .. |Analytics| image:: https://ga-beacon.appspot.com/UA-86759801-1/bcforms/README.md?pixel
        
        
Keywords: complex post-translational modification crosslinks systems biology
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Provides-Extra: draw
Provides-Extra: rest_api
Provides-Extra: tests
Provides-Extra: docs
Provides-Extra: all
