{
    "info": {
        "author": "Michal Mrozek",
        "author_email": "michau.mrozek@student.uj.edu.pl",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "Intended Audience :: End Users/Desktop",
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 3.0",
            "Programming Language :: Python :: 3.1",
            "Programming Language :: Python :: 3.2",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3 :: Only",
            "Topic :: Database",
            "Topic :: Internet",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Scientific/Engineering :: Chemistry",
            "Topic :: Software Development :: Libraries :: Python Modules"
        ],
        "description": "Adapter for `Nucleic Acid Database <http://ndbserver.rutgers.edu/>`_\r\n====================================================================\r\n\r\n.. image:: https://img.shields.io/pypi/status/ndb_adapter.svg\r\n    :target: https://pypi.python.org/pypi/ndb_adapter\r\n\r\n.. image:: https://img.shields.io/pypi/v/ndb_adapter.svg\r\n    :target: https://pypi.python.org/pypi/ndb_adapter\r\n\r\n.. image:: https://img.shields.io/pypi/dm/ndb_adapter.svg\r\n        :target: https://pypi.python.org/pypi/ndb_adapter\r\n\r\n.. image:: https://img.shields.io/pypi/l/ndb_adapter.svg\r\n        :target: https://pypi.python.org/pypi/ndb_adapter\r\n\r\n.. image:: https://img.shields.io/pypi/pyversions/ndb_adapter.svg\r\n    :target: https://pypi.python.org/pypi/ndb_adapter\r\n\r\nAdapter for easy access to NDB resources directly from python (3.*).\r\n\r\nUsage\r\n-----\r\n\r\nAdapter offers 4 types of search: summary, advanced, dna and rna.\r\n\r\nSummary\r\n~~~~~~~\r\n\r\nTo get summary of structure, type:\r\n\r\n.. code-block:: python\r\n\r\n    >>> from ndb_adapter import NDB\r\n    >>> res = NDB.summary('4Z4B')\r\n    >>> res.ndb_id\r\n    '4Z4B'\r\n    >>> res.title\r\n    '2-PYRIDYL HOECHST - A NEW GENERATION DNA-BINDING RADIOPROTECTOR'\r\n    >>> res.description\r\n    \"DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')\"\r\n    >>> res.get_dict()\r\n    {'Molecular Description': \"DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')\", ...}\r\n\r\nAs you see some properties are available for summary result. Full list of them is\r\n`here <http://michsior14.github.io/ndb_adapter/ndb_adapter.html#module-ndb_adapter.summary_result>`_.\r\n\r\nAdvanced search\r\n~~~~~~~~~~~~~~~\r\n\r\nTo perform advanced search you should use `AdvancedOptions\r\n<http://michsior14.github.io/ndb_adapter/ndb_adapter.html#module-ndb_adapter.advanced_search_options>`_\r\nobject and pass it as argument to `advanced_search\r\n<http://michsior14.github.io/ndb_adapter/ndb_adapter.html#ndb_adapter.ndb.NDB.advanced_search>`_ function from NDB,\r\nhowever it's not required. That object has a lot of `setters\r\n<http://michsior14.github.io/ndb_adapter/ndb_adapter.html#ndb_adapter.advanced_search_options.AdvancedSearchOptions.set_author>`_\r\nfor modify search query. Look at them to search what you want. It's also possible to\r\nchange result `report type <http://michsior14.github.io/ndb_adapter/ndb_adapter.html#ndb_adapter.enums.ReportType>`_,\r\njust pass wanted type into constructor.\r\n\r\n.. code-block:: python\r\n\r\n    >>> from ndb_adapter import *\r\n    # options preparation\r\n    >>> opt = AdvancedSearchOptions()   # default report type NDBStatus\r\n    >>> opt.set_crystal_structure(yes_no_ignore=YesNoIgnore.Yes)    # default and_or=AndOr.And\r\n    >>> opt.set_dna(and_or=AndOr.Or, yes_no_ignore=YesNoIgnore.Yes)\r\n\r\n    # search\r\n    >>> res = NDB.advanced_search(opt)\r\n    >>> print(res.count)\r\n    4695\r\n    >>> print(res.report)\r\n    [<ndb_adapter.search_report.NDBStatusReport object at 0x00000248F9E02128>, ...]\r\n\r\n    # working on result\r\n    >>> first = res.report[0] # first structure from search\r\n    # if you want have annotations in IDE (i.e. Pycharm) do something like this:\r\n    >>> first = res.report[0] # type: ReportType.NDBStatus\r\n    >>> print(first.title)\r\n    \"2-Pyridyl Hoechst - a New Generation DNA-Binding Radioprotector\"\r\n\r\nEvery report type result is different - you can examine theirs `properties\r\n<http://michsior14.github.io/ndb_adapter/ndb_adapter.html#module-ndb_adapter.search_report>`_ or use typing.\r\n\r\nSome of them has `statistics <http://michsior14.github.io/ndb_adapter/ndb_adapter.html#module-ndb_adapter.statistics>`_\r\nalso, for example:\r\n\r\n.. code-block:: python\r\n\r\n    >>> from ndb_adapter import *\r\n\r\n    >>> opt = AdvancedSearchOptions(ReportType.RNABasePairRelFreq)\r\n    >>> opt.set_hybrid(yes_no_ignore=YesNoIgnore.Yes)\r\n\r\n    >>> res = NDB.advanced_search(opt)\r\n    >>> print(res.statistics)\r\n    Min: {'Relative cWW': 0.5, 'Relative tWW': 0.0, 'Relative cHS': 0.0, 'Relative tWS': 0.0, ...}\r\n    Max: {'Relative cWW': 1.0, 'Relative tWW': 0.05, 'Relative cHS': 0.06, 'Relative tWS': 0.06, ...}\r\n    Mean: {'Relative cWW': 0.8, 'Relative tWW': 0.01, 'Relative cHS': 0.01, 'Relative tWS': 0.01, ...}\r\n    Standard Deviation: {'Relative cWW': 0.12, 'Relative tWW': 0.01, 'Relative cHS': 0.02, 'Relative tWS': 0.02, ...}\r\n    >> print(res.statistics.min)\r\n    {'Relative tWS': 0.0, 'Relative tWW': 0.0, 'Relative cHH': 0.0, 'Relative cWW': 0.5, ...}\r\n\r\nDna search\r\n~~~~~~~~~~\r\n\r\n`Dna search <http://michsior14.github.io/ndb_adapter/ndb_adapter.html#ndb_adapter.ndb.NDB.dna_search>`_\r\nis very similar to advanced search, but with `DnaSearchOptions\r\n<http://michsior14.github.io/ndb_adapter/ndb_adapter.html#module-ndb_adapter.dna_search_options>`_ and smaller\r\namount of setters.\r\n\r\n.. code-block:: python\r\n\r\n    >>> from ndb_adapter import *\r\n    # options preparation\r\n    >>> opt = DnaSearchOptions()\r\n    >>> opt.set_structural_features(StructuralFeatures.A_DNA)\r\n\r\n    # search\r\n    >>> result = NDB.dna_search(opt)\r\n    >>> print(result.count)\r\n    393\r\n    >>> str(result.report)\r\n    [<ndb_adapter.search_report.SimpleReport object at 0x00000152D0FCB438>, ...]\r\n\r\n    # working on result\r\n    >>> first = result.report[0]   # type: SimpleReport\r\n    >>> print(first.title)\r\n    \"Crystal structure of 60-mer BFDV Capsid Protein ...\"\r\n\r\nRna search\r\n~~~~~~~~~~\r\n\r\n`Rna search <http://michsior14.github.io/ndb_adapter/ndb_adapter.html#ndb_adapter.ndb.NDB.rna_search>`_\r\nis just like dna search. Options: `RnaSearchOptions\r\n<http://michsior14.github.io/ndb_adapter/ndb_adapter.html#ndb-adapter-rna-search-options-module>`_.\r\n\r\n.. code-block:: python\r\n\r\n    >>> from ndb_adapter import *\r\n    # search\r\n    >>> result = NDB.rna_search()   # default is empty RnaSearchOptions object\r\n    >>> print(result.count)\r\n    3014\r\n    >>> str(result.report)\r\n    [<ndb_adapter.search_report.SimpleReport object at 0x0000018B3C877E48>, ...]\r\n\r\n    # working on result\r\n    >>> first = result.report[0]   # type: SimpleReport\r\n    >>> print(first.title)\r\n    \"Crystal structure of the bacterial A1408C-mutant ...\"\r\n\r\nStructure Download\r\n~~~~~~~~~~~~~~~~~~\r\n\r\nAlmost on every result of search you can download related files `(.pdb, .cif, .xml etc.)\r\n<http://michsior14.github.io/ndb_adapter/ndb_adapter.html#ndb_adapter.ndb_download.DownloadType>`_\r\nto buffer or save.\r\n\r\n.. code-block:: python\r\n\r\n    >>> from ndb_adapter import NDB\r\n    >>> res = NDB.summary('4Z4B')\r\n    >>> res.download()  # .pdb is default\r\n    \"HEADER DNA 01-APR-15 4Z4B ...\"\r\n\r\n    >>> from ndb_adapter import DownloadType\r\n    >>> res.download(download_type=DownloadType.Cif)\r\n    'data_4Z4B\\n# \\n_entry.id   4Z4B ...'\r\n\r\n    >>> res = NDB.advanced_search()\r\n    >>> res.download(save=True) # saves n files in current directory\r\n    >>> res.download(save=True, target_dir='/home/user/Downloads/')  # saves n files in ~/Downloads/\r\n\r\n    >>> res.report[0].download(save=True) # saves first structure file in current directory\r\n\r\nYou can also search and download in one line:\r\n\r\n.. code-block:: python\r\n\r\n    >>> from ndb_adapter import NDB\r\n    >>> res = NDB.download('4Z4B')   # like above .pdb is default\r\n    \"HEADER DNA 01-APR-15 4Z4B ...\"\r\n    # save and target dir is also available\r\n\r\nRequirements\r\n------------\r\n\r\n- python 3.*\r\n- `requests <https://pypi.python.org/pypi/requests>`_\r\n- `xlrd <https://pypi.python.org/pypi/xlrd>`_\r\n\r\nInstallation\r\n------------\r\n\r\nTo install, simply:\r\n\r\n.. code-block:: bash\r\n\r\n    $ pip install ndb_adapter\r\n\r\nDocumentation\r\n-------------\r\n\r\nDocumentation is available at https://michsior14.github.io/ndb_adapter/.\r\n\r\nLicence\r\n-------\r\n\r\nSoftware is distributed under the MIT Licence.",
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