bcforms 0.0.9
Toolkit for concretely describing macromolecular complexes
License: MIT
Keywords: complex post-translational modification crosslinks systems biology

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``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.

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