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        "author": "Christopher Bevan Barnett",
        "author_email": "chrisbarnettster@gmail.com",
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            "Development Status :: 2 - Pre-Alpha",
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            "License :: OSI Approved :: Apache Software License",
            "Natural Language :: English",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.3",
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        "description": "==========\nTessellate\n==========\n\n\n.. image:: https://img.shields.io/pypi/v/tessellate.svg\n        :target: https://pypi.python.org/pypi/tessellate\n\n.. image:: https://readthedocs.org/projects/tessellate/badge/?version=latest\n        :target: https://tessellate.readthedocs.io/en/latest/?badge=latest\n        :alt: Documentation Status\n\n.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1068656.svg\n   :target: https://doi.org/10.5281/zenodo.1068656\n\nA package for quantifying cyclic molecule conformations.\n\n\n* Free software: Apache Software License 2.0\n* Documentation: https://tessellate.readthedocs.io.\n\nUsing\n-----\n\n.. code:: bash\n\n    make install; tessellate  data/example-builtin --input-format=builtin --output-format=json\n    make install; tessellate  data/*DNA --input-format=pdblist --output-format=json\n\nInstalling\n----------\n- Use Python3. For example, Anaconda Python https://www.anaconda.com/download/ https://repo.continuum.io/archive/Anaconda3-5.0.1-Linux-x86_64.sh\n- Use a virtual environment or conda environment.\n- Install with pip or compile the source code\n\n.. code:: bash\n\n    # installing with pip\n    pip install tessellate\n\n    # Alternatively: compile from source\n    make install\n\n\nUsecase 1 - timeseries data\n---------------------------\n\n.. code:: bash\n\n    tessellate  data/usecase-timeseries --input-format=builtin --output-format=json --output-dir=output-usecase-timeseries\n\nThis data is from an in vacuo ribose simulation stored in data/timeseries-from-VMD\nTo recreate data use the run.sh script. This calls VMD and runs pucker-bigdcd.tcl.\n\nUsecase 2 - RNA and DNA\n-----------------------\n\n.. code:: bash\n\n    tessellate  data/usecase-*DNA --input-format=pdblist --output-format=json --output-dir=output-usecase-rnadna\n\nUsecase 3 - Alpha Cyclodextrin\n------------------------------\n\n.. code:: bash\n\n    tessellate  data/usecase-*CD --input-format=pdblist --output-format=json --output-dir=output-usecase-cyclodextrin\n\nRun All Usecases\n----------------\n\n.. code:: bash\n\n    tessellate  data/usecase-timeseries --input-format=builtin --output-format=json --output-dir=output-usecase-timeseries\n    tessellate  data/usecase-*DNA --input-format=pdblist --output-format=json --output-dir=output-usecase-rnadna\n    tessellate  data/usecase-*CD --input-format=pdblist --output-format=json --output-dir=output-usecase-cyclodextrin\n\nAdditional UseCases\n-------------------\n\n- `Pandas Dataframes`_  Supported with --output-format=pandas\n- `Using Tessellate as a library`_\n\n\nViewing Data\n------------\n\nTry out Montage to create reports for these datasets.\nFor example:\n\n.. code:: bash\n    USECASE_DATA=output-usecase-cyclodextrin\n    multiqc $USECASE_DATA -m comp_tessellate -f  # -f to overwrite existing reports\n    google-chrome multiqc_report.html\n\nCompare all outputs:\n\n.. code:: bash\n    multiqc output* -m comp_tessellate -f  # -f to overwrite existing reports\n    google-chrome multiqc_report.html\n\n\nDevelopment\n-----------\nBump version numbers using bumpversion\nX=thecurrentversion\n`bumpversion  --current-version X minor`\n\nTo bump from x.y.z to x.y.a use patch as the part:\n`bumpversion  --current-version X patch`\n\nFeatures to include:\n--------------------\n\n* Improve testing and documentation. Port existing tests over. \n* Tables\n* include more RAD functionality\n\nUploading to PyPi\n-----------------\nUse twine\n\n.. code:: bash\n    conda install -c conda-forge twine\n    make install\n    make dist\n    twine upload dist/*\n\nIssues\n------\nReport Issues at https://github.com/scientificomputing/tessellate/issues \nKnown issue - only relative paths supported\n\n\n\nRead the Docs\n-------------\nDocs are here. RTD is authorised to access GitHub repos. The RTD service hook builds doc on push.\n\n\nPandas Dataframes\n-----------------\n.. code:: bash\n\n    tessellate  data/usecase-timeseries --input-format=builtin --output-format=pandas --output-dir=output-usecase-timeseries\n\n.. code:: python \n    python\n    import pandas as pd\n    df = pd.read_json('output-usecase-timeseries/tessellate_report_usecase-timeseries.pandas.json')\n    df.head()\n    df.groupby('conformer').count()\n    df.groupby(['ringsize','conformer']).count()\n\nUsing Tessellate as a library\n-----------------------------\n\n.. code:: python\n    import tessellate as t\n    import tessellate.utils.pucker as p\n    import collections\n    ordered_ringatoms=['C3','C4','C5','O5','C1','C2']\n    frame={'C1': (-5.799, -5.308, 4.847), 'C2': (-5.383, -5.328, 3.394), 'C3': (-3.904, -4.906, 3.181),'C4': (-3.576, -3.54, 3.944), 'C5': (-4.115, -3.556, 5.339), 'O5': (-5.551, -3.941, 5.38)}\n    def return_pucker(atomids,frame):\n     import tessellate as t\n     import tessellate.utils.pucker as p\n     import itertools\n     a=[frame[i] for i in atomids]\n     pobj=p.Pucker(tuple(itertools.chain.from_iterable(a)))\n     return pobj.calculate_triangular_tessellation(), pobj.deduce_canonical_conformation()[0],pobj.deduce_canonical_conformation()[-1],pobj.deduce_canonical_conformation(nextguess=True)[0]\n\n    result=collections.OrderedDict()\n    result[\"pucker\"],result[\"pucker_conformer\"],result[\"pucker_distance_to_canonical\"],result[\"pucker_next_guess\"] = return_pucker(ordered_ringatoms, frame)\n    import pprint\n    pprint.pprint(result)\n\nCredits\n---------\n\nThis package incorporates work from existing packages (all originally developed by Chris B. Barnett.)\n* https://bitbucket.org/scientificomputing/triangular-tessellation-class http://git.cem.uct.ac.za/analysis-pucker/triangular-tessellation-class\n* https://bitbucket.org/scientificomputing/ring-analytics-webserver https://bitbucket.org/rxncor/rad-dev http://git.cem.uct.ac.za/analysis-pucker/ring-analytics-dash\n* https://bitbucket.org/scientificomputing/triangular-tessellation-in-vmd http://git.cem.uct.ac.za/analysis-pucker/triangular-decomposition-timeseries-in-VMD\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n\n\n\n=======\nHistory\n=======\n\n0.3.7 (2018-03-29)\n------------------\n* Pandas! \n* Pandas dataframe output in json and csv is the default\n* make Pandas default\n* how to use a library example in the README\n* biopython and pytest have different signatures beneath a certain version. Fixed this in setup.py\n* removed hardcoded python interpreter, in some cases machine point to python2.7 with python3 pointing to 3. Remove in *.py files. Removed in Makefile. To use another python in the make file, modify the pythonexe variable\n* Tested with --user flag. --user flag seems to work for me - e.g. pip3 install --user tessellate\n\n0.3.6 (2017-12-18)\n------------------\n* Zenodo DOI\n* empty list bug resolved \n* feature order json output\n\n0.3.5 (2017-11-30)\n------------------\n* Includes tcl script for VMD and example data\n\n0.3.4 (2017-11-29)\n------------------\n* Documentation update. Ring finder update\n\n0.3.1 0.3.2 0.3.3  (2017-11-24)\n------------------\n* Usecase, documentation update. 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