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    "info": {
        "author": "Justin Chan",
        "author_email": "capslockwizard@gmail.com",
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            "Development Status :: 5 - Production/Stable",
            "Environment :: Console",
            "Environment :: Plugins",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Operating System :: MacOS",
            "Operating System :: POSIX :: Linux",
            "Programming Language :: Python :: 2.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# DR-SIP: Distance Restraints- and Cyclic Symmetry-Imposed Packing\nDR-SIP contains tools and molecular docking protocols for predicting the quaternary structures of homo-oligomeric transmembrane proteins (HoTPs) by assuming the complex is cyclic (C<sub>n</sub>) symmetric and filtering docking poses with experimentally measured distance restraints between the monomers in the complex.\n\nThe DR-SIP package contains 4 Python modules:\n1. drsip: Implements the molecular docking protocols. Current implementation accepts ZDOCK output files.\n2. zdock-parser: Parses ZDOCK output files, generates and returns the coordinates of poses without first writing to PDB files.\n3. docking-eval: Implements the CAPRI criteria to evaluate docking results with respect to a reference structure. \n4. drsip-common: Common functions used by the other modules.\n\nIf you're using any of our packages please [cite us](#how-to-cite-us)\n\n# How to Install DR-SIP?\nThere are 2 ways to install the DR-SIP, using conda (recommended) or pip.\n\n## Conda Installation\nWe recommend that you install the [Anaconda distribution](https://www.anaconda.com/download/) for Python 2.7.\n\nTo install DR-SIP:\n```\nconda config --append channels conda-forge\nconda config --append channels drsip\nconda install drsip\n```\n\n## Pip Installation\nFor pip:\n```\npip install drsip\n```\n\n# How to Use?\n## Membrane Protein Docking Protocol\n```\ndrsip membrane static-pdb-file mobile-pdb-file trans-helix zdock-output-file -d distance-restraints-file -o DRSIP-results.csv -p top20/\n```\nThe trans-helix argument is a string containing comma separated resids of each transmembrane helix. Example: \"17-46, 69-93\", where the first transmembrane helix is from resid 17 to 46 and the second is from resid 69 to 93. Transmembrane helix assignments can be obtained from the [Orientations of Proteins in Membranes database](https://opm.phar.umich.edu/).\n\nWhile the -o argument is for writing the results of top 20 poses to an CSV file and -p is the folder to write out the PDB files of the top 20 complexes generated from the top 20 poses.\n\nThe distance restraints file is optional, the filter will not be applied if there are no distance restraints. Each line in the distance restraints file contains a residue pair formatted as:\n```\nchainID1 resID1 chainID2 resID2 distance\n```\nNOTE: The columns are separated by tabs (tab-delimited).\n\n## Soluble Protein Protocol\n```\ndrsip soluble static-pdb-file mobile-pdb-file zdock-output-file distance-restraints-file -o DRSIP-results.csv -p top20/\n```\nSimilar to running the membrane protein docking protocol except that the distance restraints file is required and there is no trans-helix argument.\n\n## Examples:\nDownload the examples [here](https://github.com/capslockwizard/drsip/raw/master/examples.zip) and extract the zip file.\n\nFirst, change the current working directory to the examples folder:\n```\ncd examples\n```\n\nThen for the HoTP system, MscL:\n```\ndrsip membrane 2oar_static_marked.pdb 2oar_mobile_marked.pdb \"17-46, 69-93\" MscL_54000_ZDOCK.out -d MscL_FRET_Data.txt -o MscL/DRSIP_results.csv -p MscL/\n```\nwhere \"17-46, 69-93\" are the 2 transmembrane helices assigned by [OPM](https://opm.phar.umich.edu/proteins/35). The results table and top 20 complexes will be written into the MscL folder.\n\nWhile, MscL_FRET_Data.txt contains:\n```\nA\t40\tB\t40\t5.033146272\nB\t25\tA\t25\t4.528073406\n...\n```\n\nFor more details run \"drsip membrane -h\" or see the [documentation](http://drsip.readthedocs.io/).\n\nAs for the soluble system, Syt1-SNARE:\n```\ndrsip soluble 5ccg_SNARE_marked.pdb 2r83_aligned_domains_marked.pdb Syt1-SNARE_ZDOCK_54000.out Syt1-SNARE_FRET_Data.txt -o Syt1_SNARE/DRSIP_results.csv -p Syt1_SNARE/\n```\nThe results table and the top 20 poses will be written into the Syt1_SNARE folder.\n\nFor more details run \"drsip soluble -h\" or see the [documentation](http://drsip.readthedocs.io/).\n\nSee the MscL_ref and Syt1_SNARE_ref folders for the pre-computed results.\n\n# Documentation\nFull documentation available [here](http://drsip.readthedocs.io/)\n\n# How to Cite Us?\nIf you use any part of the DR-SIP package please cite us:\n```\nChan Justin, Chien Chi-Hong Chang, Zou Jinhao, Pan Rong-Long, Yang Lee-Wei.\n(2019) DR-SIP: Protocols for Higher Order Structure Modeling with Distance\nRestraints- and Cyclic Symmetry-Imposed Packing. BioRxiv [Preprint].\nAvailable at: https://doi.org/10.1101/500397.\n```\n\nManuscript is available on the preprint site [BioRxiv](https://doi.org/10.1101/500397).\n\n# References\nThe DR-SIP package uses the following packages:\n1. [MDAnalysis](https://www.mdanalysis.org/pages/citations/)\n2. [BioPython](https://biopython.org/wiki/Documentation#papers)\n3. [NumPy](https://www.scipy.org/citing.html)\n4. [SciPy](https://www.scipy.org/citing.html)\n5. [Numba](https://numba.pydata.org/numba-doc/dev/user/faq.html#how-do-i-reference-cite-acknowledge-numba-in-other-work)\n6. [Pandas](https://www.scipy.org/citing.html)\n7. [u-msgpack-python](https://github.com/vsergeev/u-msgpack-python).\n\n",
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