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bcforms-0.0.9
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مشاهده بیشترتوضیحات
Toolkit for concretely describing macromolecular complexes
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | bcforms-0.0.9 |
| نام | bcforms |
| نسخه کتابخانه | 0.0.9 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Karr Lab |
| ایمیل نویسنده | info@karrlab.org |
| آدرس صفحه اصلی | https://github.com/KarrLab/bcforms |
| آدرس اینترنتی | https://pypi.org/project/bcforms/ |
| مجوز | MIT |
|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
نیازمندی
| مقدار | نام |
|---|---|
| >=0.0.15 | bpforms |
| >=3.0.0 | cement |
| >=0.6.6 | lark-parser |
| <3 | openbabel |
| - | setuptools |
| >=0.0.14 | wc-utils[chem] |
| - | capturer |
| - | flask |
| - | flask-restplus |
| - | mock |
| >=1.8 | sphinx |
| - | sphinx-fontawesome |
| >=0.4.2 | sphinx-rtd-theme |
| >=0.1.1 | sphinxcontrib-addmetahtml |
| - | sphinxcontrib-bibtex |
| >=0.1.1 | sphinxcontrib-googleanalytics |
| - | sphinxcontrib-spelling |
| - | sphinxprettysearchresults |
| >=0.0.15 | wc-utils[protonation] |
| >=1.8 | sphinx |
| - | sphinx-fontawesome |
| >=0.4.2 | sphinx-rtd-theme |
| >=0.1.1 | sphinxcontrib-addmetahtml |
| - | sphinxcontrib-bibtex |
| >=0.1.1 | sphinxcontrib-googleanalytics |
| - | sphinxcontrib-spelling |
| - | sphinxprettysearchresults |
| >=0.0.15 | wc-utils[protonation] |
| - | flask |
| - | flask-restplus |
| - | capturer |
| - | mock |
نحوه نصب
نصب پکیج whl bcforms-0.0.9:
pip install bcforms-0.0.9.whl
نصب پکیج tar.gz bcforms-0.0.9:
pip install bcforms-0.0.9.tar.gz