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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 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 for more information.
  • A Python API. See the documentation for more information.

Installation

The following is a brief guide to installing BcForms. The Dockerfile in the BpForms repository contains detailed instructions for how to install BcForms in Ubuntu Linux.

1. Install dependencies

   • ChemAxon Marvin: optional to calculate major protonation and tautomerization states and draw molecules
     • Java >= 1.8
   • Open Babel
   • Pip >= 19.0
   • Python >= 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.

License

The package is released under the MIT license.

Development team

This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York, USA.

• Jonathan Karr
• Xiaoyue Zheng

Questions and comments

Please contact the Karr Lab with any questions or comments.