{ "info": { "author": "Andrey Smelter", "author_email": "andrey.smelter@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "Environment :: Console", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Operating System :: OS Independent", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Software Development :: Libraries :: Python Modules" ], "description": "nmrstarlib\n==========\n\n.. image:: https://img.shields.io/pypi/l/nmrstarlib.svg\n :target: https://choosealicense.com/licenses/mit/\n :alt: License information\n\n.. image:: https://img.shields.io/pypi/v/nmrstarlib.svg\n :target: https://pypi.org/project/nmrstarlib/\n :alt: Current library version\n\n.. image:: https://img.shields.io/pypi/pyversions/nmrstarlib.svg\n :target: https://pypi.org/project/nmrstarlib/\n :alt: Supported Python versions\n\n.. image:: https://readthedocs.org/projects/nmrstarlib/badge/?version=latest\n :target: http://nmrstarlib.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation status\n\n.. image:: https://api.travis-ci.org/MoseleyBioinformaticsLab/nmrstarlib.svg?branch=master\n :target: https://travis-ci.org/MoseleyBioinformaticsLab/nmrstarlib\n :alt: Travis CI status\n\n.. image:: https://codecov.io/gh/MoseleyBioinformaticsLab/nmrstarlib/branch/master/graphs/badge.svg?branch=master\n :target: https://codecov.io/gh/MoseleyBioinformaticsLab/nmrstarlib\n :alt: Code coverage information\n\n.. image:: https://img.shields.io/badge/DOI-10.1186%2Fs12859--017--1580--5-blue.svg\n :target: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1580-5\n :alt: Citation link\n\n|\n\n.. image:: https://raw.githubusercontent.com/MoseleyBioinformaticsLab/nmrstarlib/master/docs/_static/images/nmrstarlib_logo.png\n :width: 50%\n :align: center\n :target: http://nmrstarlib.readthedocs.io/\n\nThe `nmrstarlib` package is a Python library that facilitates reading and writing\nNMR-STAR formatted files used by the Biological Magnetic Resonance Data Bank (BMRB_)\nfor archival of Nuclear Magnetic Resonance (NMR) data and CIF formatted files used\nby Protein Data Bank (PDB_).\n\nThe `nmrstarlib` package provides facilities to convert NMR-STAR and CIF formatted\nfiles into their equivalent JSONized representation and vice versa. JSON stands\nfor JavaScript Object Notation, an open-standard format that uses human-readable\ntext to transmit data objects consisting of attribute-value pairs.\n\nThe `nmrstarlib` package also provides facilities to create simulated peak lists for\ndifferent types of standard solution and solid-state NMR experiments from chemical\nshifts and assignment information deposited in NMR-STAR files.\n\nIn addition, the `nmrstarlib` package provides methods to visualize chemical shift data.\n\nThe `nmrstarlib` package can be used in several ways:\n\n * As a library for accessing and manipulating data stored in NMR-STAR and CIF formatted files.\n * As a command-line tool to convert between NMR-STAR/CIF format and its equivalent JSONized\n NMR-STAR/CIF format, to create a large number of simulated peak lists,\n and also to visualize chemical shift data from NMR-STAR formatted files.\n\nCitation\n~~~~~~~~\n\nWhen using `nmrstarlib` in published work, please cite the following paper:\n\n * Smelter, Andrey, Morgan Astra, and Hunter NB Moseley. \"A fast and efficient python\n library for interfacing with the Biological Magnetic Resonance Data Bank.\"\n *BMC Bioinformatics* 18.1 (2017): 175. doi: `10.1186/s12859-017-1580-5`_.\n\n\nLinks\n~~~~~\n\n * nmrstarlib @ GitHub_\n * nmrstarlib @ PyPI_\n * Documentation @ ReadTheDocs_\n\nInstallation\n~~~~~~~~~~~~\n\nThe `nmrstarlib` package runs under Python 2.7 and Python 3.4+. Use pip_ to install.\nStarting with Python 3.4, pip_ is included by default.\n\n\nInstall on Linux, Mac OS X\n--------------------------\n\n.. code:: bash\n\n python3 -m pip install nmrstarlib\n\nInstall on Windows\n------------------\n\n.. code:: bash\n\n py -3 -m pip install nmrstarlib\n\nQuickstart\n~~~~~~~~~~\n\nImport `nmrstarlib` library and create generator function that will yield\n`StarFile` instance(s):\n\n.. code:: python\n\n >>> import nmrstarlib\n >>>\n >>> # \"path\": path_to_file / path_to_dir / path_to_archive / bmrb_id / pdb_id / file_url\n >>> for file in nmrstarlib.read_files(\"path\"):\n ... print(file.id) # print BMRB/PDB id of a file\n ... print(file.source) # print source of a file\n ... print(file.keys()) # print top-level keys\n >>>\n\n.. image:: https://raw.githubusercontent.com/MoseleyBioinformaticsLab/nmrstarlib/master/docs/_static/images/nmrstarlib_demo.gif\n :align: center\n\n\n.. note:: Read the `User Guide`_ and `The nmrstarlib Tutorial`_ on ReadTheDocs_\n to learn more and to see code examples on using the `nmrstarlib` as a\n library and as a command-line tool.\n\nLicense\n~~~~~~~\n\nThis package is distributed under the MIT_ `license`.\n\n.. _pip: https://pip.pypa.io\n.. _docopt: http://docopt.readthedocs.io\n.. _graphviz: http://graphviz.readthedocs.io\n.. _BMRB: http://www.bmrb.wisc.edu\n.. _PDB: https://www.rcsb.org\n.. _Graphviz download page: http://www.graphviz.org/Download.php\n\n.. _GitHub: https://github.com/MoseleyBioinformaticsLab/nmrstarlib\n.. _ReadTheDocs: http://nmrstarlib.readthedocs.io\n.. _User Guide: http://nmrstarlib.readthedocs.io/en/latest/guide.html\n.. _The nmrstarlib Tutorial: http://nmrstarlib.readthedocs.io/en/latest/tutorial.html\n.. _PyPI: https://pypi.org/project/nmrstarlib\n\n.. _MIT: https://choosealicense.com/licenses/mit\n\n.. _10.1186/s12859-017-1580-5: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1580-5", "description_content_type": "", "docs_url": null, 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