{"id":29016270,"url":"https://github.com/karrlab/bcforms","last_synced_at":"2025-06-25T22:07:54.197Z","repository":{"id":57414295,"uuid":"193782185","full_name":"KarrLab/bcforms","owner":"KarrLab","description":"Toolkit for concretely describing macromolecular complexes","archived":false,"fork":false,"pushed_at":"2020-07-09T13:56:06.000Z","size":558,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-06-17T03:26:02.023Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/KarrLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-06-25T20:55:41.000Z","updated_at":"2020-07-09T13:56:05.000Z","dependencies_parsed_at":"2022-08-26T20:34:41.759Z","dependency_job_id":null,"html_url":"https://github.com/KarrLab/bcforms","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"purl":"pkg:github/KarrLab/bcforms","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarrLab%2Fbcforms","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarrLab%2Fbcforms/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarrLab%2Fbcforms/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarrLab%2Fbcforms/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/KarrLab","download_url":"https://codeload.github.com/KarrLab/bcforms/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/KarrLab%2Fbcforms/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":261960463,"owners_count":23236575,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-06-25T22:07:53.467Z","updated_at":"2025-06-25T22:07:54.181Z","avatar_url":"https://github.com/KarrLab.png","language":"Python","readme":"[//]: # ( [![PyPI package](https://img.shields.io/pypi/v/bcforms.svg)](https://pypi.python.org/pypi/bcforms) )\n[![Documentation](https://readthedocs.org/projects/bcforms/badge/?version=latest)](https://docs.karrlab.org/bcforms)\n[![Test results](https://circleci.com/gh/KarrLab/bcforms.svg?style=shield)](https://circleci.com/gh/KarrLab/bcforms)\n[![Test coverage](https://coveralls.io/repos/github/KarrLab/bcforms/badge.svg)](https://coveralls.io/github/KarrLab/bcforms)\n[![Code analysis](https://api.codeclimate.com/v1/badges/c8f15ac1e50c27ca44cc/maintainability)](https://codeclimate.com/github/KarrLab/bcforms)\n[![License](https://img.shields.io/github/license/KarrLab/bcforms.svg)](LICENSE)\n![Analytics](https://ga-beacon.appspot.com/UA-86759801-1/bcforms/README.md?pixel)\n\n# `BcForms`: toolkit for concretely describing macromolecular complexes\n\n`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.\n\n`BcForms` encompasses five tools:\n* 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.\n    ```\n    complex: 2 * sub_c | x-link: [\n        l-bond-atom: sub_c(1)-1S11 |\n        l-displaced-atom: sub_c(1)-1H11 |\n        r-bond-atom: sub_c(2)-1S11 |\n        r-displaced-atom: sub_c(2)-1H11\n      ]\n    ```\n\n    This concrete representation enables the `BcForms` software tools to calculate properties of biocomplexes when the subunits are concretely defined.\n\n* Tools for calculating properties of biocomplexes including their structure, chemical formulae, molecular weights, and charges.\n  * A web app: [https://bcforms.org](https://bcforms.org)\n  * A JSON REST API: [https://bcforms.org/api](https://bcforms.org/api)\n  * A command line interface. See the [documentation](https://docs.karrlab.org/bcforms/master/0.0.1/) for more information.\n  * A Python API. See the [documentation](https://docs.karrlab.org/bcforms/master/0.0.1/) for more information.\n\n## Installation\nThe 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.\n\n1. Install dependencies\n\n   * [ChemAxon Marvin](https://chemaxon.com/products/marvin): optional to calculate major protonation and tautomerization states and draw molecules\n     * [Java](https://www.java.com) \u003e= 1.8\n   * [Open Babel](http://openbabel.org)\n   * [Pip](https://pip.pypa.io) \u003e= 19.0\n   * [Python](https://www.python.org) \u003e= 3.6\n\n2. Install this package\n\n    * Install the latest release from PyPI\n      ```\n      pip install bcforms[all]\n      ```\n\n    * Install the latest revision from GitHub\n      ```\n      pip install git+https://github.com/KarrLab/pkg_utils.git#egg=pkg_utils\n      pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils[chem, protonation]\n      pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms\n      pip install git+https://github.com/KarrLab/bcforms.git#egg=bcforms[all]\n      ```\n\n    * To draw molecules, `BcForms` must be installed with the `[draw]` option:\n      ```\n      pip install bcforms[draw]\n      pip install git+https://github.com/KarrLab/bcforms.git#egg=bcforms[draw]\n      ```\n\n    * To install the REST API, `BcForms` must be installed with the `[rest_api option]`:\n      ```\n      pip install bcforms[rest_api]\n      pip install git+https://github.com/KarrLab/bcforms.git#egg=bcforms[rest_api]\n      ```\n\n## Documentation\nPlease see the [API documentation](https://docs.karrlab.org/bcforms).\n\n## License\nThe package is released under the [MIT license](LICENSE).\n\n## Development team\nThis package was developed by the [Karr Lab](https://www.karrlab.org) at the Icahn School of Medicine at Mount Sinai in New York, USA.\n\n* [Jonathan Karr](https://www.karrlab.org)\n* [Xiaoyue Zheng](https://www.linkedin.com/in/xiaoyue-zheng/)\n\n## Questions and comments\nPlease contact the [Karr Lab](mailto:info@karrlab.org) with any questions or comments.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkarrlab%2Fbcforms","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkarrlab%2Fbcforms","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkarrlab%2Fbcforms/lists"}