https://github.com/karrlab/bcforms
Toolkit for concretely describing macromolecular complexes
https://github.com/karrlab/bcforms
Last synced: 8 months ago
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Toolkit for concretely describing macromolecular complexes
- Host: GitHub
- URL: https://github.com/karrlab/bcforms
- Owner: KarrLab
- License: mit
- Created: 2019-06-25T20:55:41.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2020-07-09T13:56:06.000Z (over 5 years ago)
- Last Synced: 2025-06-17T03:26:02.023Z (8 months ago)
- Language: Python
- Size: 545 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
[//]: # ( [](https://pypi.python.org/pypi/bcforms) )
[](https://docs.karrlab.org/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](https://bcforms.org)
* A JSON REST API: [https://bcforms.org/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.