{
"info": {
"author": "Karr Lab",
"author_email": "info@karrlab.org",
"bugtrack_url": null,
"classifiers": [
"Development Status :: 3 - Alpha",
"License :: OSI Approved :: MIT License",
"Natural Language :: English",
"Operating System :: OS Independent",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Topic :: Scientific/Engineering :: Bio-Informatics"
],
"description": "|PyPI package| |Documentation| |Test results| |Test coverage| |Code\nanalysis| |License| |Analytics|\n\n``BpForms``: toolkit for concretely describing non-canonical DNA, RNA, and proteins\n===================================================================================\n\n``BpForms`` is a set of tools for concretely representing the primary\nstructures of non-canonical forms of biopolymers, such as oxidized DNA,\nmethylated RNA, and acetylated proteins, and calculating properties of\nnon-canonical biopolymers.\n\n``BpForms`` encompasses five tools:\n\n- A grammar for concretely describing the primary structures of\n non-canonical biopolymers. See the\n `documentation `__ for more\n information. For example, the following text represents a modified\n DNA molecule that contains a deoxyinosine monomeric form at the\n fourth position.\n ``ACG[id: \"dI\" | structure: \"[H][C@]1(O)C[C@@]([H])(O[C@]1([H])CO)N1C=NC2=C1N=CN=C2O\"]T``\n\nThis concrete representation enables the ``BpForms`` software tools to\ncalculate properties of non-canonical biopolymers.\n\n- Tools for calculating properties of non-canonical biopolymers\n including their chemical formulae, molecular weights, charges, and\n major protonation and tautomerization states.\n- A web app: https://bpforms.org\n- A JSON REST API: https://bpforms.org/api\n- A command line interface. See the\n `documentation `__\n for more information.\n- A Python API. See the\n `documentation `__\n for more information.\n\n``BpForms`` was motivated by the need to concretely represent the\nbiochemistry of DNA modification, DNA repair, post-transcriptional\nprocessing, and post-translational processing in `whole-cell\ncomputational models `__. ``BpForms`` is also\na valuable tool for experimental proteomics and synthetic biology. In\nparticular, we developed ``BpForms`` because there were no notations,\nschemas, data models, or file formats for concretely representing\nnon-canonical forms of biopolymers, despite the existence of several\ndatabases and ontologies of DNA, RNA, and protein modifications, the\n`ProForma Proteoform\nNotation `__, and\nthe `MOMODICS `__ codes for modified RNA\nbases.\n\n*BpForms* can be combined with `*BcForms* `__\nto concretely describe the primary structure of complexes.\n\nInstallation\n------------\n\n1. Install the third-party dependencies listed below. Detailed\n installation instructions are available in `An Introduction to\n Whole-Cell\n Modeling `__.\n\n - `ChemAxon Marvin `__:\n optional to calculate major protonation and tautomerization states\n - `Java `__ >= 1.8\n - `Open Babel `__\n - `Pip `__ >= 19.0\n - `Python `__ >= 3.6\n\n2. To use Marvin to calculate major protonation and tautomerization\n states, set ``JAVA_HOME`` to the path to your Java virtual machine\n (JVM) ``export JAVA_HOME=/usr/lib/jvm/default-java``\n\n3. To use Marvin to calculate major protonation and tautomerization\n states, add Marvin to the Java class path\n ``export CLASSPATH=$CLASSPATH:/opt/chemaxon/marvinsuite/lib/MarvinBeans.jar``\n\n4. Install this package\n\n - Install the latest release from PyPI: ``pip install bpforms``\n\n - Install the latest revision from GitHub:\n ``pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils[all] pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms``\n\n - To install the rest API, ``BpForms`` must be installed with the\n ``[all]`` option:\n ``pip install bpforms[all] pip install git+https://github.com/KarrLab/bpforms.git#egg=bpforms[all]``\n\nExamples, tutorial, and documentation\n-------------------------------------\n\nPlease see the `documentation `__. An\n`interactive\ntutorial `__\nis also available in the whole-cell modeling sandbox.\n\nLicense\n-------\n\nThe package is released under the `MIT license `__.\n\nCiting ``BpForms``\n------------------\n\nLang PF, Chebaro Y & Jonathan R. Karr. BpForms: a toolkit for concretely\ndescribing modified DNA, RNA and proteins. arXiv:1903.10042.\n`:link: `__\n\nDevelopment team\n----------------\n\nThis package was developed by the `Karr Lab `__\nat the Icahn School of Medicine at Mount Sinai in New York, USA.\n\n- `Jonathan Karr `__\n- `Yassmine\n Chebaro `__\n- `Paul Lang `__\n\nQuestions and comments\n----------------------\n\nPlease contact the `Karr Lab `__ with any\nquestions or comments.\n\n.. |PyPI package| image:: https://img.shields.io/pypi/v/bpforms.svg\n :target: https://pypi.python.org/pypi/bpforms\n.. |Documentation| image:: https://readthedocs.org/projects/bpforms/badge/?version=latest\n :target: https://docs.karrlab.org/bpforms\n.. |Test results| image:: https://circleci.com/gh/KarrLab/bpforms.svg?style=shield\n :target: https://circleci.com/gh/KarrLab/bpforms\n.. |Test coverage| image:: https://coveralls.io/repos/github/KarrLab/bpforms/badge.svg\n :target: https://coveralls.io/github/KarrLab/bpforms\n.. |Code analysis| image:: https://api.codeclimate.com/v1/badges/e35081f676dfbb5ac46f/maintainability\n :target: https://codeclimate.com/github/KarrLab/bpforms\n.. |License| image:: https://img.shields.io/github/license/KarrLab/bpforms.svg\n :target: LICENSE\n.. |Analytics| image:: https://ga-beacon.appspot.com/UA-86759801-1/bpforms/README.md?pixel\n\n\n\n",
"description_content_type": "",
"docs_url": null,
"download_url": "https://github.com/KarrLab/bpforms",
"downloads": {
"last_day": -1,
"last_month": -1,
"last_week": -1
},
"home_page": "https://www.bpforms.org",
"keywords": "DNA,RNA,protein,post-transcriptional modification,post-translational modification,proteoform,phosphorylation,methylation",
"license": "MIT",
"maintainer": "",
"maintainer_email": "",
"name": "bpforms",
"package_url": "https://pypi.org/project/bpforms/",
"platform": "",
"project_url": "https://pypi.org/project/bpforms/",
"project_urls": {
"Download": "https://github.com/KarrLab/bpforms",
"Homepage": "https://www.bpforms.org"
},
"release_url": "https://pypi.org/project/bpforms/0.0.10/",
"requires_dist": [
"attrdict",
"beautifulsoup4",
"biopython",
"cement (>=3.0.0)",
"configobj",
"jinja2",
"lark-parser (>=0.6.6)",
"mendeleev",
"openbabel",
"pandas",
"requests",
"requests-cache",
"ruamel.yaml (>=0.15)",
"setuptools",
"sqlalchemy",
"wc-utils (>=0.0.9)",
"capturer; extra == 'all'",
"flask; extra == 'all'",
"flask-restplus; extra == 'all'",
"hurry.filesize; extra == 'all'",
"jupyter; extra == 'all'",
"lxml; extra == 'all'",
"matplotlib; extra == 'all'",
"mock; extra == 'all'",
"numpy; extra == 'all'",
"plyplus; extra == 'all'",
"pronto; extra == 'all'",
"psutil; extra == 'all'",
"sphinx (>=1.8); extra == 'all'",
"sphinx-fontawesome; extra == 'all'",
"sphinx-rtd-theme (>=0.4.2); extra == 'all'",
"sphinxcontrib-addmetahtml (>=0.1.1); extra == 'all'",
"sphinxcontrib-bibtex; extra == 'all'",
"sphinxcontrib-googleanalytics (>=0.1.1); extra == 'all'",
"sphinxcontrib-spelling; extra == 'all'",
"sphinxprettysearchresults; extra == 'all'",
"sphinx (>=1.8); extra == 'docs'",
"sphinx-fontawesome; extra == 'docs'",
"sphinx-rtd-theme (>=0.4.2); extra == 'docs'",
"sphinxcontrib-addmetahtml (>=0.1.1); extra == 'docs'",
"sphinxcontrib-bibtex; extra == 'docs'",
"sphinxcontrib-googleanalytics (>=0.1.1); extra == 'docs'",
"sphinxcontrib-spelling; extra == 'docs'",
"sphinxprettysearchresults; extra == 'docs'",
"pronto; extra == 'onto_export'",
"flask; extra == 'rest_api'",
"flask-restplus; extra == 'rest_api'",
"capturer; extra == 'tests'",
"hurry.filesize; extra == 'tests'",
"jupyter; extra == 'tests'",
"lxml; extra == 'tests'",
"matplotlib; extra == 'tests'",
"mock; extra == 'tests'",
"numpy; extra == 'tests'",
"plyplus; extra == 'tests'",
"psutil; extra == 'tests'"
],
"requires_python": "",
"summary": "Unambiguous representation of modified DNA, RNA, and proteins",
"version": "0.0.10"
},
"last_serial": 5933414,
"releases": {
"0.0.10": [
{
"comment_text": "",
"digests": {
"md5": "0eeb2997d9b27420a5d87a7adc4d9497",
"sha256": "5bda0899501771f95c2265d7fec3714adee6908d2d546409ea02529c0a2edc67"
},
"downloads": -1,
"filename": "bpforms-0.0.10-py2.py3-none-any.whl",
"has_sig": false,
"md5_digest": "0eeb2997d9b27420a5d87a7adc4d9497",
"packagetype": "bdist_wheel",
"python_version": "py2.py3",
"requires_python": null,
"size": 343956,
"upload_time": "2019-10-06T01:10:27",
"url": "https://files.pythonhosted.org/packages/83/19/55fab4819c8c50332b03cf2e3f4109e79f77dfdce616e709358114b8d469/bpforms-0.0.10-py2.py3-none-any.whl"
},
{
"comment_text": "",
"digests": {
"md5": "b674254f1834c017e2adf0a61f4005f4",
"sha256": "f724c1132ec544187d805a0c4fdb780041834a6d247cc9189efbaa604580ee91"
},
"downloads": -1,
"filename": "bpforms-0.0.10.tar.gz",
"has_sig": false,
"md5_digest": "b674254f1834c017e2adf0a61f4005f4",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 2390914,
"upload_time": "2019-10-06T01:10:30",
"url": "https://files.pythonhosted.org/packages/18/dd/42783a32c391683aa3dca8c24ede5f1f86bcd3fd0a01c27bbac0d26a7e52/bpforms-0.0.10.tar.gz"
}
],
"0.0.2": [
{
"comment_text": "",
"digests": {
"md5": "8daaa23c6328b8205f009bab405a5395",
"sha256": "9e4520371cf5dcaec317f1d6558356bb5cf83cda34fc881f8d334fc7ff896c74"
},
"downloads": -1,
"filename": "bpforms-0.0.2-py2.py3-none-any.whl",
"has_sig": false,
"md5_digest": "8daaa23c6328b8205f009bab405a5395",
"packagetype": "bdist_wheel",
"python_version": "py2.py3",
"requires_python": null,
"size": 2585582,
"upload_time": "2019-03-11T17:06:19",
"url": "https://files.pythonhosted.org/packages/06/ea/6cb8f50b87cf13a2f824d9225271300a7cdd24630673c7002e82a592bcc6/bpforms-0.0.2-py2.py3-none-any.whl"
},
{
"comment_text": "",
"digests": {
"md5": "0049c043ac250253badf78285a44a5f1",
"sha256": "943d5492c886e779f31ce9e78c9f519abff2e41d4249b449ad099034fe910ea4"
},
"downloads": -1,
"filename": "bpforms-0.0.2.tar.gz",
"has_sig": false,
"md5_digest": "0049c043ac250253badf78285a44a5f1",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 2545976,
"upload_time": "2019-03-11T17:06:22",
"url": "https://files.pythonhosted.org/packages/b2/80/41a0c1a894a0bd3b5caf2262fd375378e83fe77ceb6b144362f69f1a53c7/bpforms-0.0.2.tar.gz"
}
],
"0.0.3": [
{
"comment_text": "",
"digests": {
"md5": "2177359248ff6dafe82ffd653d4f3687",
"sha256": "018cc1075314762d58cd1fa05dbd19c9dad22cb46d2a863b23c85d1beca1fcac"
},
"downloads": -1,
"filename": "bpforms-0.0.3-py2.py3-none-any.whl",
"has_sig": false,
"md5_digest": "2177359248ff6dafe82ffd653d4f3687",
"packagetype": "bdist_wheel",
"python_version": "py2.py3",
"requires_python": null,
"size": 2586322,
"upload_time": "2019-03-13T03:40:26",
"url": "https://files.pythonhosted.org/packages/75/8e/22f166d82b94b0b8a5c4803adedfede71ea842ce56176df016722d090bd2/bpforms-0.0.3-py2.py3-none-any.whl"
},
{
"comment_text": "",
"digests": {
"md5": "c5c14f7ecb3cb0dd3ea9a6e80dd8cd1b",
"sha256": "c415c481e6a6663d71e7fbf285afdad309013816cdb56b332ce2ec6c2da383f6"
},
"downloads": -1,
"filename": "bpforms-0.0.3.tar.gz",
"has_sig": false,
"md5_digest": "c5c14f7ecb3cb0dd3ea9a6e80dd8cd1b",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 2547041,
"upload_time": "2019-03-13T03:40:29",
"url": "https://files.pythonhosted.org/packages/51/1b/18060233686c3fa22389711956c6c6abb87a5e3cd9ae164b9aa2298ca694/bpforms-0.0.3.tar.gz"
}
],
"0.0.4": [
{
"comment_text": "",
"digests": {
"md5": "1233366188e19f4726be560a0baa72e6",
"sha256": "f09830273ec740651b3f2def716d4e8c5f66d0cc897619c1b111a34931df0b1a"
},
"downloads": -1,
"filename": "bpforms-0.0.4-py2.py3-none-any.whl",
"has_sig": false,
"md5_digest": "1233366188e19f4726be560a0baa72e6",
"packagetype": "bdist_wheel",
"python_version": "py2.py3",
"requires_python": null,
"size": 2586521,
"upload_time": "2019-03-15T23:13:09",
"url": "https://files.pythonhosted.org/packages/27/c0/f9c3714ab20590af6ea6fb12d88c0aa4f42aa61a369258fb34a1456db013/bpforms-0.0.4-py2.py3-none-any.whl"
},
{
"comment_text": "",
"digests": {
"md5": "3eeaf5dd331532962a6c80ee259ed715",
"sha256": "aede293edb70b281dcdee80dbd69d90a9bacfc9a7d716330c913b3ef5eca753b"
},
"downloads": -1,
"filename": "bpforms-0.0.4.tar.gz",
"has_sig": false,
"md5_digest": "3eeaf5dd331532962a6c80ee259ed715",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 2547203,
"upload_time": "2019-03-15T23:13:12",
"url": "https://files.pythonhosted.org/packages/ea/b8/ffa529b8c2e3874dca9e1f5ffdeb1abd552a9b349906eb7f267d0aed9d28/bpforms-0.0.4.tar.gz"
}
],
"0.0.5": [
{
"comment_text": "",
"digests": {
"md5": "08ef01e7cc5876755e3ff08ec76d2418",
"sha256": "04a80cf86b9b00f34bc8e8e8ee60329e0224dbfeef3ee5a1a553683e1151dc7f"
},
"downloads": -1,
"filename": "bpforms-0.0.5-py2.py3-none-any.whl",
"has_sig": false,
"md5_digest": "08ef01e7cc5876755e3ff08ec76d2418",
"packagetype": "bdist_wheel",
"python_version": "py2.py3",
"requires_python": null,
"size": 2587770,
"upload_time": "2019-04-02T16:41:08",
"url": "https://files.pythonhosted.org/packages/24/d5/b9fb4fae6bc28cc286c562dd9934b399258adee622f5cb330c3f9722f458/bpforms-0.0.5-py2.py3-none-any.whl"
},
{
"comment_text": "",
"digests": {
"md5": "36e1db7245c175421a5664bd91d9be23",
"sha256": "e04f809fd0a1d47292ab8e64f9ad46e0d4054b276c88217583c3e880639d8f05"
},
"downloads": -1,
"filename": "bpforms-0.0.5.tar.gz",
"has_sig": false,
"md5_digest": "36e1db7245c175421a5664bd91d9be23",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 2548124,
"upload_time": "2019-04-02T16:41:11",
"url": "https://files.pythonhosted.org/packages/80/19/e9e54900823c5e16c1b27a50a81e17ec637a2805adf603f629c117c72537/bpforms-0.0.5.tar.gz"
}
],
"0.0.9": [
{
"comment_text": "",
"digests": {
"md5": "561dcf10b59d698aee99b5e19a2b9a36",
"sha256": "3cc075ad9ccbb76188a080d20c019a886b02d38c2aae19a95d8dfc051c9d507d"
},
"downloads": -1,
"filename": "bpforms-0.0.9-py2.py3-none-any.whl",
"has_sig": false,
"md5_digest": "561dcf10b59d698aee99b5e19a2b9a36",
"packagetype": "bdist_wheel",
"python_version": "py2.py3",
"requires_python": null,
"size": 280209,
"upload_time": "2019-08-01T02:54:13",
"url": "https://files.pythonhosted.org/packages/21/f2/e32c8e3a2ff5ebe84c15f610039a031fd596b748bc3d434ab480796ab2e4/bpforms-0.0.9-py2.py3-none-any.whl"
},
{
"comment_text": "",
"digests": {
"md5": "ba1da982b1045e267f6c7ab5343c1cb1",
"sha256": "f531302e0332f41b5bc467a2310facff3d2a5dc1951c41bb49c8202392b10c75"
},
"downloads": -1,
"filename": "bpforms-0.0.9.tar.gz",
"has_sig": false,
"md5_digest": "ba1da982b1045e267f6c7ab5343c1cb1",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 2329003,
"upload_time": "2019-08-01T02:54:16",
"url": "https://files.pythonhosted.org/packages/17/22/52a37a614279b53b070f9e03b53627100b69e7e3d5361596f86f21807368/bpforms-0.0.9.tar.gz"
}
]
},
"urls": [
{
"comment_text": "",
"digests": {
"md5": "0eeb2997d9b27420a5d87a7adc4d9497",
"sha256": "5bda0899501771f95c2265d7fec3714adee6908d2d546409ea02529c0a2edc67"
},
"downloads": -1,
"filename": "bpforms-0.0.10-py2.py3-none-any.whl",
"has_sig": false,
"md5_digest": "0eeb2997d9b27420a5d87a7adc4d9497",
"packagetype": "bdist_wheel",
"python_version": "py2.py3",
"requires_python": null,
"size": 343956,
"upload_time": "2019-10-06T01:10:27",
"url": "https://files.pythonhosted.org/packages/83/19/55fab4819c8c50332b03cf2e3f4109e79f77dfdce616e709358114b8d469/bpforms-0.0.10-py2.py3-none-any.whl"
},
{
"comment_text": "",
"digests": {
"md5": "b674254f1834c017e2adf0a61f4005f4",
"sha256": "f724c1132ec544187d805a0c4fdb780041834a6d247cc9189efbaa604580ee91"
},
"downloads": -1,
"filename": "bpforms-0.0.10.tar.gz",
"has_sig": false,
"md5_digest": "b674254f1834c017e2adf0a61f4005f4",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 2390914,
"upload_time": "2019-10-06T01:10:30",
"url": "https://files.pythonhosted.org/packages/18/dd/42783a32c391683aa3dca8c24ede5f1f86bcd3fd0a01c27bbac0d26a7e52/bpforms-0.0.10.tar.gz"
}
]
}