Toolkit for concretely describing macromolecular complexes
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.
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.
- Install dependencies
- ChemAxon Marvin: optional
to calculate major protonation and tautomerization states and draw
- Java >= 1.8
- Open Babel
- Pip >= 19.0
- Python >= 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]
Please see the API documentation.
The package is released under the MIT license.
This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York, USA.
Questions and comments
Please contact the Karr Lab with any questions or comments.
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