bcforms

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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.

• 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

• 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:[e-mail]>__ with any questions or comments.

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